Input: Claim: Examples of genetic memory include migration patterns in birds and seasonal changes in fur thickness in mammals. [SEP] Text: Birds are often treated as important indicators that reflect the state of ecosystem functioning, because they are widely distributed, easy to detect and sensitive to environmental changes [4, 5]. They have played an important role in the mountain ecosystem, serving as arthropods predator, seeds consumer and disperser [6–8]. Their mobility has profoundly influenced many other aspects of their ecology and evolution, such as strong dispersal facilitates colonisation of new regions, thereby driving range expansion [9]. When on islands, speciation is most likely to occur when dispersal is relatively high [10], while on the mainland there is evidence that low dispersal promotes bird diversification [11]. Previous studies of avian movements have mostly focused on their migration (i. e. predictable, annually return movements between breeding and non-breeding ranges [12], and most species of avian migrants are partial migrants rather than complete migrants [13]. Such type of migratory behavior involves movements over altitudinal gradients. Most birds conduct seasonal migrations over altitudinal gradients [12], including short-distance upslope movement from low-altitude breeding areas to high-altitude non-breeding areas and downslope movement from high-altitude breeding areas to low-altitude non-breeding areas [5, 12, 14, 15]. Compared with latitudinal migrations, altitudinal migration is characterized with shorter distances such that individuals consume less energy. Asia is home to the greatest number of altitudinal migrants of the world and it is estimated that up to 65% of the Himalayan and 58% of Taiwanese high-elevation breeding species are involved in this activity [12, 16]. However, this behaviour remains poorly understood, especially for montane and temperate avifaunas. Studying the seasonal altitudinal migration patterns of birds is essential to understanding their distributional responses to seasonal changes in climate (energy), which has important conservation implication for avian biodiversity [6, 15]. According to previous research, birds can reduce risk of predation [17], avoid the harsh climatic conditions [18, 19] and track the food resources by vertical migration [20–24].

Output: corroborate


Input: Claim: Desert agriculture can fully solve global food shortages regardless of other conditions. [SEP] Text: They are highly solitary and often thrive in warm and sunny ecosystems5,6. Consecutive droughts, accompanied by moderate and humid winters, create the conditions for the proliferation of this insect, and changes in soil temperature cause variations in the hatching time of this insect's larvae from eggs7–10. However, population outbreaks occur in some species of Locusts with short antennae from the Acrididae family. After hatching, locusts are in the form of larvae and cannot fly, mate, or lay eggs, but they can hop. After reaching maturity, they gain the ability to fly, mate, and lay eggs. Vinylanisole, Phenol, Guaiacol, and Veratrole are gases produced by the locusts' digestive system, serving as cohesive pheromones that transform them into social beings, forming large groups11–13. Increased tactile stimulation of their hind legs results in an elevation of serotonin levels14. Under the influence of heightened serotonin levels, their color changes, they engage in more feeding, their reproductive processes accelerate, and they exhibit more collective behavior. After several generations, their population surges, transforming them into the most significant and destructive plant pests15. Locust attacks have occurred frequently throughout history and have caused significant damage16–18. Reports of grassland areas being infested by locusts date back to 19744. A typical swarm of locusts can cover and infest an area of 150 square kilometers and travel up to 150 kilometers per day. The massive locust outbreak in the in 1875 has been documented, with the dimensions of the swarm measuring 180x2900 kilometers and an estimated population of around 3. 5 trillion locusts19. Even the migratory journey of desert locusts from Africa to the between 1987 and 1989 has been documented20–23. Planting vegetation in distant rangelands, removing plant cover from lands, concentrating damages in specific regions of pastures, deliberately and systematically igniting fires, establishing green belts, and employing D4-2 and Carbaryl pesticides have been common approaches for combating locusts15,24–31. At various stages of their life cycle, locusts are influenced by parasites, fungi, bacteria, and natural predators15,32–39. Even alterations in their dietary habits40 or feeding on certain plants like Nerium oleander can contribute to population control41–43.

Output: contrast


Input: Claim: Fossilized plants provide insights into ancient climates and ecosystems. [SEP] Text: 4a), and the pathways “Glycosphingolipid biosynthesis − globo series” and “Limonene and pinene degradation” were significantly enriched (Additional file 1: Fig. S4c). Additionally, a total of 1122 DEGs, including 593 upregulated and 529 downregulated DEGs, were specifically expressed in QQ-vs-LYQQ (Fig. 4a), but only the “Plant-pathogen interaction” pathway was significantly enriched (Additional file 1: Fig. S4d). Moreover, a total of 2175 DEGs, including 1177 downregulated and 998 upregulated DEGs, overlapped between MZ-vs-LYQQ and MZ-vs-QQ specifically, indicating that these DEGs might be associated with zigzag-shaped stem formation in both QQ and LYQQ. KEGG analysis showed that these DEGs were mainly involved in the “Plant-pathogen interaction”, “Phenylpropanoid biosynthesis”, “Flavonoid biosynthesis” and “Linoleic acid metabolism” pathways (Fig. 4b). GO enrichment analysis showed that these DEGs were significantly enriched in 59 GO terms, of which the most highly enriched components were categorized as catalytic activity (465), metabolic process (381), binding (323), cellular process (322), single-organism process (285) and membrane (274) (Fig. 4c). Identification of key DEGs regulating zigzag-shaped stem formation Based on the changes in expression in the comparisons MZ-vs-QQ and MZ-vs-LYQQ, 76 DEGs potentially involved in zigzag-shaped stem formation were identified (Fig. 5). Among these DEGs, 19 were associated with cell wall synthesis and cell expansion, of which seven, namely, cellulose synthase (TEA032164. 1, TEA030545. 1), expansin (TEA027164. 1), leucine-rich repeat extensin-like protein 1 (XLOC_003301), chitinase-like protein (TEA022978. 1) and pectinesterase (XLOC_003301, and TEA004581.

Output: pass


Input: Claim: Examples of genetic memory include migration patterns in birds and seasonal changes in fur thickness in mammals. [SEP] Text: Species with different life-history and ecological traits also show different migration patterns in response to climate change and several related ecological traits such as territoriality [25], nest height [17, 26], diet [27] and body mass [28] that could influence species’ ability to shift their altitudinal ranges [28, 29]. Most studies on altitudinal migration have focused on the food-limitation hypothesis, which proposes that food availability varies seasonally over altitudinal gradients in response to fluctuations in temperature and precipitation throughout the year [15]. Animals may move up and down in altitudes in response to these variations. Consequently, species with different diets may respond differently to seasonality. For example, in some regions, frugivores and nectarivores are more likely to exhibit altitudinal migration than omnivores and invertivores [16, 20, 21, 23]. Similarly, avian territorial behaviors may also influence their distributional responses to climate change because species with stronger territoriality may guard the territory year-round [25, 30]. In addition, birds may actively adopt strategies to avoid or reduce nest predation. A probably more noticeable strategy is nest-site selection, which often determines the safety of the nest [26, 31]. It can be expected that species with lower nest sites have greater probability of altitudinal migration than species with higher ones. However, while many possible drivers of seasonal altitude migration have been proposed, they have only been empirically examined in few cases and their generalizability is mostly unknown [12, 32]. The causes of altitudinal migration have only been studied in a few systems and species. Most studies have been conducted in America, with few studies located in Asia [15]. Boyle found that altitudinal migration was prevalent, occurring in > 20% of continental and nearly 30% of Hawaiian species [12]. In addition, majority of birds that undergo altitudinal migration are frugivores or nectarivores in the Neotropics [17, 33, 34]. In China, Taiwanese scholars modeled the behavior based on occurrence records collected by citizen scientists and suggested that seasonal variations in climates and food availability could be major drivers of the behavior [16]. Studies in the have found that species' seasonal distribution shifts were mainly associated with breeding altitudes and diet [23]. Relative to long-distance latitudinal migration, altitudinal migration has been poorly studied in Asia.

Output: corroborate


Input: Claim: Desert agriculture can fully solve global food shortages regardless of other conditions. [SEP] Text: Mechanical mechanisms lack sufficient power to effectively combat their extensive onslaught. In chemical confrontation, weaknesses such as lack of durability, development of resistance, high economic costs, and adverse environmental impacts are evident5. Furthermore, the persistence of toxic effects has been reported to range from 10 days to several months44,45 and a study conducted in the demonstrated the expenditure of 25 million dollars for controlling 3 million hectares of pastures through the use of 5 million liters of malathion46. The proactive biological control of the Locust population constitutes a scientific strategy. However, the allocation of budgetary resources by governments is contingent upon their political inclinations rather than the scientific discoveries of researchers. Preventing the emergence of crises through the application of integrated pest management (IPM) approach is a strategy grounded in a comprehensive understanding of the behavior and ecology of locusts47. This research aimed to explore the feasibility of hunting Locusts to determine the potential changes in agricultural field yields resulting from their capture, as an alternative to chemical spraying. Additionally, a discussion will take place regarding the comparison of damages caused by Locust invasions with the damages resulting from the use of pesticides. Considering the predictions of the Ministry of Agriculture and the Agency regarding the Locust invasions, necessary planning was conducted to study their behavior about the proposed hypothesis of capturing them. Materials and Two similar parcels of land (each approximately 5000 m2 − 111x45 and 120x42) were selected at a distance of 1723 meters from each other in the agricultural fields of Nahand village (27. 201035, 54. 197782) located in the Kohij county of Hormozgan province. These parcels were monitored in the field from April 24th to April 29th, 2020. Both parcels were in their second year of fall alfalfa cultivation. Planting 13. 5 kg of Nikshahri seeds per 5000 m2, with rows spaced 20 to 25 cm apart, had been carried out. The planting and harvesting of both parcels were done using mechanized methods, and they were irrigated through traditional fixed rain irrigation systems. Twenty metal barrels, each with a capacity of 220 liters, along with woven sacks made of 40 kg nylon fibers, as well as twenty 200-watt filament lamps with 450 meters of electrical wire, were utilized. Iron materials were employed as supportive bases for holding the lamps.

Output: contrast


Input: Claim: Fossilized plants provide insights into ancient climates and ecosystems. [SEP] Text: 1), were upregulated, whereas 12, especially xyloglucan endotransglucosylase/hydrolase (XLOC_007313, TEA019643. 1, TEA031643. 1), pectinesterase (TEA026842. 1), reduced wall acetylation 2 (XLOC_021264), expansin (TEA012391. 1), UDP-glycosyltransferase 74B5 (TEA020219. 1) and isoamylase 3 (XLOC_040461), were downregulated in both QQ and LYQQ (Fig. 5a and Additional file 3: Table S3). Eighteen transcription factor genes, including the 13 downregulated genes floral homeotic protein 1 (TEA017728. 1), TIFY (TEA012041. 1), NAC transcription factor 010 (TEA026168. 1), transcription factor 2 (XLOC_053049), -related homeobox 2 (TEA032867. 1), ethylene-responsive transcription factor TINY (TEA027175. 1), transcription factor MYB1R1 (TEA026206. 1), squamosa promoter-binding-like protein (TEA003577. 1), transcription factor HEC1 (TEA030941. 1), transcription factor bHLH18 (TEA000681. 1), transcription factor (TEA006216. 1), growth-regulating factor 1 (TEA022970. 1), and Scarecrow-like protein (TEA030046. 1) and the five upregulated genes transcription factor bHLH041 (TEA031877. 1), transcription factor IBH1-like (TEA009726. 1), WRKY transcription factor 28 (TEA023233. 1), transcription factor (TEA031729. 1) and transcription factor 1 (TEA022287. 1), were identified (Fig. 5b and Additional file 3: Table S3). In addition, 10 DEGs involved in auxin, jasmonic acid, and salicylic acid metabolism and transport were also identified in the list of key DEGs; interestingly, except for jasmonic acid-amido synthetase (TEA020186.

Output: pass


Input: Claim: Examples of genetic memory include migration patterns in birds and seasonal changes in fur thickness in mammals. [SEP] Text: Among them, the altitudinal difference of 14 species were below zero, indicating downhill migration from breeding to non-breeding season, while the other 6 species were above zero, indicating uphill migration. There were three altitudinal shift patterns among the studied species (Fig. 3). First, most species (11) breeded at a higher altitude in breeding season, while migrated downward in non-breeding season. Second, some species (2) tended to move higher in non-breeding seasons, as both their abundance-weighted range centres and upper-altitude limits showed upward movements (Fig. 3). At last, the altitudinal ranges of seven species did not change significantly between seasons, and the altitudes during the breeding and non-breeding seasons were mostly the same (the abundance-weighted range center altitudechange < 50m), suggesting that the partial migration might be prevalent among the migrants (Fig. 2). Effects of species’ traits on shift patterns The PGLS models indicated that HWI, nest height, annualtemp and temprange (Table 1) were important in explaining the elevational shifts from breeding to non-breeding seasons (Fig. 2). In the uphill-altitude model, annualtemp was positively correlated with upslope shift, while temprange was negatively correlated with upslope shift. Temperature changes were closely related to seasonal altitude shifts, as confirmed by our model results. Both the lower- altitude limit and the abundance-weighted range center shift model indicated that the species nesting in scrub were more likely to present a downhill movement in the non-breeding season. Moreover, we found that seasonal shifts were associated with flight efficiency, for the range of both uphill movement and abundance-weighted range center changes were positively correlated with HWI. Phylogenetic paired t-test showed that territoriality, nest height and diet were significantly correlated with altitudinal shifts (Table 2). Specifically, territorially weaker species migrated more widely and had even diverse patterns than stronger species. For species with different diets, omnivores showed apparent downslope shifts in weighted mean altitude in the non-breeding season. For nest height, shown by the PGLS results, scrub-nesting species had a broader range of migration and presented a downward shift in the non-breeding season. No correlation was found between other traits in our models. Table 1 SE Z value Pr(> z) Lower-altitude limit shift HWI 32. 825 13. 043 2.

Output: corroborate


Input: Claim: Desert agriculture can fully solve global food shortages regardless of other conditions. [SEP] Text: 6% higher than the number of locusts in the experimental field. Table 3 Number of counted locusts per square meter of the field. (Source: Current study). Control field 92 108 141 136 104 116 Experimental field 67 92 78 85 103 85 Trap 3652 3829 3531 3762 3648 3684 The average weight of Locusts present in 1 square meter of the control field was 283 grams, 220 grams on the experimental field, and 10328 grams in the traps. Comparing the weight of Locusts in 1 square meter of the control field to the experimental field indicates that 22. 5% fewer Locusts accumulated in the experimental field. Furthermore, the average weight of Locusts within the traps was 3644. 5% higher compared to the control field and 4705. 1% higher compared to the experimental field. 4. Table 4 Weight of Locusts per square meter of the field (g) (Source: Current study). Control field 225 263 344 332 254 283 Experimental field 172 238 202 220 267 220 Trap 10270 10300 10192 10558 10332 10328 *- The unit of measurement for weight was grams (gr). It is worth mentioning that the total amount of crops gathered from the standard plot after the fifth day of the research reached 2635 kilos, while the amount harvested from the unique plot was indicated as 6045 kilos. ConclusionOne could argue that the reduction in the number of locusts on the ground in the experiment was a result of the presence of traps, and the significant difference between the number of trapped locusts and the locusts on the experimental ground was due to the attraction of locusts from neighboring areas to the traps on the experimental ground. Considering the spatial distance and physical barriers between the two areas (such as walls, etc. ), it becomes evident that the number of locusts on the ground in the natural conditions was the control, and the light pollution caused by the traps present on the experimental ground did not have a direct impact on attracting locusts from the control area to the experimental area. The rank correlation coefficient (r = -0. 666) indicates that 44. 4% of the variance in the number of locusts is attributed to the presence of traps. The significant and notable increase in the number of trapped locusts suggests that the experimental area has attracted a substantial number of specimens. The rank correlation coefficient (r = -0.

Output: contrast


Input: Claim: Fossilized plants provide insights into ancient climates and ecosystems. [SEP] Text: 1), the remaining genes, especially PIN3 (TEA019069. 1), were downregulated in both QQ and LYQQ (Fig. 5c and Additional file 3: Table S3). Furthermore, seven DEGs involved in protein processing and transportation on the endoplasmic reticulum and vesicles, namely, vesicle-associated membrane protein 714 (XLOC_031693), SEC1 family transport protein, signal peptidase complex catalytic subunit SEC11A (TEA001395. 1), SEC13B (XLOC_004426), SECA2 (XLOC_057225), SEC6 (TEA030236. 1), SEC11A (TEA001395. 1), and SEC22 (XLOC_037235); the three vacuolar protein sorting-related proteins VPS18 (TEA007337. 1), VPS41 (TEA031089. 1) and VSR6 (TEA021222. 1); and the vacuole membrane protein KMS1 (XLOC_036914) were identified from the MZ-vs-QQ and MZ-vs-LYQQ comparisons (Fig. 5d and Additional file 3: Table S3). Among these 18, VPS41, SEC11A and SEC1 were significantly repressed in both QQ and LYQQ. Genes that regulate cell division (cell division cycle 20. 1 and cell division control protein 6 B) and plant development, such as shaggy-related protein kinase, 3 (XLOC_028596), -3 (XLOC_032980), -like (XLOC_028345), -related protein (TEA008751. 1), LAZY protein (TEA031847. 1) and LAZY 1-like (TEA001744. 1), were also identified, and all of these genes were downregulated in both QQ and LYQQ (Fig. 5e and Additional file 3: Table S3). Moreover, the 2 protein (VLN2) and actin-depolymerizing factor 2 (ADF2) were suppressed in both QQ and LYQQ (Fig. 5e and Additional file 3: Table S3).

Output: pass


Input: Claim: Examples of genetic memory include migration patterns in birds and seasonal changes in fur thickness in mammals. [SEP] Text: In mountainous areas, invertebrate abundance normally decreases from birds’ breeding to non-breeding season, [58–60], and this decline is particularly obvious at high altitudes. In breeding season the invertebrate resources at the altitude inhabited by insectivores are sufficient to meet their needs, but harsh climates and reduced food supplies over non-breeding season may drive them to move downhill [19, 23, 27]. The demand for various food types at different periods in a year may also drive altitudinal movements. A more diverse diet spectrum allows omnivores to use habitats at different altitudes and thus perform altitudinal migrations to obtain food resources, thus presenting varying migration patterns. Our results show that the weakly territorial species had more diverse migration patterns, and strong territoriality species tended to move uphill (Table 2). Researchers generally accepted the idea that strong territorial species would expend more time defending their territories [25, 30], so that they are less likely to go through rapid distribution changes but may be constrained to move upwards by interactions with closely related species [61, 62], whereas species with weak territoriality would continuously move to seek access to food resources [25, 63]. Changes in temperature have great impact on bird’s behaviour, as we found that species with a narrower temprange (< 30°) migrate predominantly uphill during the breeding season, and species with a wider temprange (> 30°) and lower annualtemp (< 10°) tend to migrate downhill during the non-breeding season (Table 2). This is consistent with the results of another research carried out in Taiwan [16]. Species with wider range of temperature tolerance and cold endurance will have greater opportunities to broaden their ecological niches in competition as predicted. Meanwhile, relying on the rich food resource in Gongga and better cold endurance allow them to breed at higher altitudes, to avoid the more intense resource competitions at lower altitudes [16]. In addition, nearly all 8 species with wider temprange (> 30°) and lower annualtemp (< 10°) are weakly territorial species except Trochalopteron elliotii, verifing our conjecture that species with weak territoriality will put more effort in foraging resources. If temperature changes intensify interspecific competition, those species would be forced to migrate at altitudes for an 'exploration', and adjust to colder and harsher conditions for breeding season.

Output: corroborate


Input: Claim: Desert agriculture can fully solve global food shortages regardless of other conditions. [SEP] Text: 866) further demonstrates that 75% of the variance in the number of locusts has been influenced by the traps. The total yield obtained from the experimental field, despite the Locusts' attack, was 2. 3 times higher than the control field (229. 4%). This indicates that the use of traps has effectively mitigated significant losses in yield. Both fields experienced an onslaught of the same insect species, yet due to the lesser proximity and contact between the products of the experimental field and the Locusts, lesser damage has been inflicted upon the yield of the experimental field. The research findings indicate that the traps have managed to reduce the movement of Locusts and prevent damage caused by them. The utilization of these traps not only reduces harm to the crops but also has a positive impact on generating income for farmers and insurance claims. Under normal circumstances, there shouldn't be a significant difference between the two agricultural fields (during the Locusts' attack). However, considering the differences in the number and weight of Locusts between the two fields, while all conditions were equal (crop type, planting method, irrigation method, field dimensions, weather conditions, geographical location, pest type, pesticide type, timing of pesticide application, simultaneous monitoring of both fields, etc. ), it can be deduced that the sole determining factor for the difference between these two fields was the presence of traps on the experimental field. The presence of strip lights in the experimental field attracted Locusts and ultimately aided in reducing damages and pest control. DiscussionGiven the increasing human demand for food, ensuring food supply has become a challenge, and maintaining food security is a necessity that, in its absence, can jeopardize national security48. Therefore, any threat to food resources must be taken seriously. On the other hand, combating threats should not lead to secondary problems. While pest control is essential, it's important to recognize that the use of pesticides can have unintended biological effects49. While pesticide spraying may eliminate large locust populations, it can lead to the development of biological resistance in smaller populations, allowing them to rebound and pose new threats50–53. Due to the developed biological resistance, pesticides might not have a sufficient impact. Observations of the feeding habits of Geladas, wolves, and ravens on locusts in the located in Ethiopia in 2009 revealed the extent to which these insects can integrate into an ecosystem's food chain54.

Output: contrast


Input: Claim: Fossilized plants provide insights into ancient climates and ecosystems. [SEP] Text: Metabolic analysis and key metabolite identification To investigate the metabolic pathways involved in zigzag-shaped stem formation, the metabolites in the stems of and MZ were detected using UPLC-ESI-TOF-MS/MS. In total, 752 metabolites clustered into 97 KEGG pathways were identified from and MZ, and among these metabolites, 75, 84 and 86 metabolites showed significantly different levels in the MZ-vs-QQ, MZ-vs-LYQQ and QQ-vs-LYQQ comparisons, respectively (Additional file 1: Fig. S5). diagram analysis showed that 13 metabolites overlapped between MZ-vs-QQ and MZ-vs-LYQQ, which were our metabolites of interest (Fig. 6a), and the results indicated that these differential metabolites might be associated with zigzag-shaped stem formation in tea plants. Based on their log2 fold change values, these differential metabolites were visualized as a heat map in Fig. 6b. Quercetin O-acetylhexoside, methyl gallate, D-pantothenic acid and L-glutamic acid were upregulated in both QQ and LYQQ, whereas the remaining metabolites, including fustin, 10-formyl-THF, skimmin, LysoPC 20:4, LysoPC 18:1 (2n isomer), LysoPC 18:3 (2n isomer), 2-methylsuccinic acid, 2-isopropylmalate, and caffeine, were significantly downregulated in tea plants with zigzag-shaped shoots. DiscussionPlants are sessile and cannot move freely from their habitat, even if they encounter adverse environments. Generally, plant shoots grow upward, whereas roots grow downward; therefore, shoot architecture is a determinant of plant morphology. In tea plants, the shoots play a substantial role in determining the horticultural characteristics and tea yield, and almost all tea plant cultivars exhibit straight stems. The two tea plants QQ and LYQQ, with zigzag-shaped shoots, were identified and planted previously; however, with advances in research, there is increasing interest in the mechanism by which QQ and LYQQ develop their zigzag-shaped shoots.

Output: pass


Input: Claim: Examples of genetic memory include migration patterns in birds and seasonal changes in fur thickness in mammals. [SEP] Text: Migration patterns and seasonal forest use by birds in the Published online by Press: 18 May 2017 JOÃÔandÂauthor details JOÃ* Affiliation: Núcleo de Estudos Ecológicos do Pantanal (NEPA)/Instituto de Biociências, de Mato Grosso, 78060-900, Cuiabá - MT, Brazil; and de Ciência e Tecnologia em Áreas Úmidas (INAU). MÔ: Instituto de Engenharias - de Mato Grosso, 78060-900, Cuiabá - MT, Brazil; Núcleo de Estudos Ecológicos do Pantanal (NEPA)/Instituto de Biociências, de Mato Grosso, 78060-900, Cuiabá - MT, Brazil; and de Ciência e Tecnologia em Áreas Úmidas (INAU). : Núcleo de Estudos Ecológicos do Pantanal (NEPA)/Instituto de Biociências, de Mato Grosso, 78060-900, Cuiabá - MT, Brazil. Â: Departamento de Zoologia, IB, Universidade de Brasília, 70910-900, Brasília, DF, Brazil. * *Author for correspondence; e-mail: pinhoufmt@gmail. com 0. 56 mb) View PDF [Opens in a new window] Save to to Save to & Permissions [Opens in a new window] use of forest habitats and migratory patterns are still unclear for tropical birds. Some are described herein for the Pantanal wetlands of Brazil. Thus, our aim was to describe different patterns of forest habitat use by birds and classify the birds’ migration patterns for the northern Pantanal region, Brazil. 1999 to December 2003, we sampled four forest types, during which we collected standardised data with mist-net captures and point counts, with additional ad lib. observations. We recorded 214 bird species: 113 (52. 8%) were total habitat generalists; 41 (19. 2%) were forest generalists; 19 (8. 9%) were flooded habitat specialists; and 28 (13.

Output: corroborate


Input: Claim: Desert agriculture can fully solve global food shortages regardless of other conditions. [SEP] Text: Many countries are grappling with the impact of the Locusts' invasion. Most of the outbreaks and damages are witnessed in Africa and Asia, while the territories of European countries bordering the are also among the destinations for Locusts. The scarcity of food resources and environmental preservation can be considered reasons behind the pursuit of Locusts. One behavioral characteristic of Locusts is their attraction to light, which leads to their entrapment55. Research conducted in the Mauritanian desert has shown that they are drawn to light during the night and gather on elevated vegetation56. Researchers from the of have observed that Locusts are attracted to visible light rays, displaying a positive phototactic response57. On the other hand, a positive response of their visual system to 610 nm orange light has been reported58,59. Moreover, reports indicate an increase in phototaxis at a temperature of 65°C60. Consuming bugs, or entomophagy, is highly suggested by the Food and (FAO) of the as a strategy to combat poverty and starvation61–64. Numerous countries have adopted the habit of eating insects for sustenance, with a plethora of choices on offer such as worms, ants, beetles, grasshoppers, crickets, tree bugs, water beetles, honeybees, wild bees, silkworms, aquatic insect larvae, and a multitude of other insect species being relished as meals or snacks. Due to their high nutritional value65, Locusts are used as appetizers or even complete meals in restaurants in certain countries66. countries, African countries, countries, and others have embraced insect farming, including Locusts. Some of them consume these edible insects due to food scarcity among consumers67. Creating livestock, chicken, and fish farming hubs is a method to guarantee food availability, however, the reproduction rate of mammals, birds, and marine creatures can't rival that of Locusts68. Thus, besides human consumption, Locusts can be utilized to nourish a variety of animals like livestock, poultry, and fish48,68–74. Considering that the majority of feed for farmed birds is composed of corn and soybeans (Table 5), Locusts can be considered the best alternative due to their high protein content75,76.

Output: contrast


Input: Claim: Fossilized plants provide insights into ancient climates and ecosystems. [SEP] Text: Zigzag-shaped shoots, which occasionally appear in garden plants, are an unusual trait in woody plants, but there is relatively little information regarding this feature. Similarly, in Arabidopsis, zig mutant stems elongate in a zigzag fashion, curve upward at the internodes and, interestingly, exhibit abnormal gravitropism in hypocotyls and shoots [8-11]. To understand the cause of this anomalous zigzag-shaped morphology, we observed stem sections using optical microscopy. There were no aberrations in the main tissue structures (Fig. 1). However, differences in cell arrangement and shape were observed between the zigzag-shaped stems of QQ and LYQQ and the MZ stems, including the arrangement of cortex cells, which were disordered and loosely arranged, and the cells in the cortex and pith exhibited aberrant shapes (Fig. 1). Consistent with our findings, similar cell shapes and arrangements were found in the zig-1 mutant stems of Arabidopsis [8]; however, different cell shapes and arrangements were observed in the epidermal layer and pith of Arabidopsis than in the cortex and pith of tea plants; this may represent a difference between woody plants and Arabidopsis. Thus, zigzag-shaped stems might be caused by the anomalous shape, arrangement and expansion of cells in tea plants. To investigate the molecular mechanism of zigzag-shaped stem formation in tea plants, shoots were collected, and transcriptome sequence analysis was performed. In total, 46. 06 million clean reads were generated, and 6232, 7212 and 6930 DEGs were identified from MZ-vs-QQ, MZ-vs-LYQQ and QQ-vs-LYQQ, respectively (Additional file 2: Table S1 and Fig. 3b). These DEGs were mainly enriched in several pathways, such as ‘Biosynthesis of secondary metabolites’, ‘Plant-pathogen interaction’, and ‘Stilbenoid, diarylheptanoid and gingerol biosynthesis’, indicating that these pathways might be associated with differences among cultivars (Fig. 3b).

Output: pass


Input: Claim: Examples of genetic memory include migration patterns in birds and seasonal changes in fur thickness in mammals. [SEP] Text: 1%) were not classified due to the low number of records; three other categories of habitat use divide the remaining 6% of records. About half of the species showed some migratory behaviour, these were classified by us according to the season they spent in the area: 121 species (56. 5%) as residents, 28 (13. 1%) as run-off and dry migrants, 11 (5. 1%) as run-off (winter) migrants, eight (3. 7%) as dry (breeding) migrants, eight (3. 7%) as dry and flooding (summer) migrants, eight (3. 7%) as flooding migrants, three (1. 4%) as flooding and run-off migrants, and 27 (12. 6%) as uncommon. We constructed community occupancy models with six of the eight patterns of migration described; flooding migrants and run-off migrants were not modelled since the few species recorded also had very few detections. As expected, the model confirmed that species from all six tested migration patterns arrive and depart from the Pantanal across the seasons. Contrary to most Neotropical forests, there was a high percentage (43. 5%) of non-resident species. The results show the need of investing heavily in preserving different landscape units within the Pantanal, but also in the surrounding Cerrado region, in order to conserve resident and short distance intra-tropical migrants. 10. 1017/S0959270916000290 [Opens in a new window] © Bird2017 bird communities are the result of stable and variable habitat components. While some species are resident in an area throughout the year, others may migrate and change the community composition at temporal and spatial scales (Loiselle and Loiselle and Blake1992). The simultaneous use of different habitats by both migratory and resident birds reflects the complexity, interconnection, flexibility of interactions, and trophic webs that can be established in a mosaic system (Blake and Blake and Loiselle2002, Figueira et al. Reference Figueira, Cintra, Viana and Yamashita2006). Thus, each patch of the habitat is important if it is able to supply seasonal needs of a species (Law and Law and Dickman1998), and this reinforces the well-established importance of preserving extensive areas of habitat mosaic within a landscape. Many thousands of birds make seasonal movements between North and (Sick1983).

Output: corroborate


Input: Claim: Desert agriculture can fully solve global food shortages regardless of other conditions. [SEP] Text: Research on the possibility of raising poultry in areas affected by Locusts' invasion in the grasslands of Huángchēng, China, indicates that birds feed well on them, leading to an increase in both the quantity and quality of their meat77. Table 5 Resources needed to produce 1 kg of protein78,79 Amount of feed needed to produce 1 kg of protein (kg) Amount of water needed to produce 1 kg of protein (Li) Cow 20 1500 Pig 6. 7 600 Chicken 3. 3 360 Locust 1. 7 1 Research indicates that Locusts have a high nutritional value (Table 6). Protein constitutes 46–56% of the dry weight of Locusts. The fat content is estimated to be 31–35%, which is lower than the protein content. Chitin makes up 6–13%, and the share of saturated and unsaturated fatty acids is reported as 44% and 54%, respectively. Locust has a cholesterol level of approximately 286 mg/100g, surpassing that of beef or chicken by a significant margin80,81. Additionally, Locust meat is rich in iodine, phosphorus, iron, thiamine, riboflavin, niacin, calcium, magnesium, selenium, and vitamin B82,83. The carbohydrate content in Locusts is minimal, making it a favored choice in certain dietary plans in nations. Edible insects, in terms of energy content, are a more suitable source compared to soybeans, corn, lentils, meat, and legumes. The quality of Locust’s meat improves with a diet rich in nitrogenous plant leaves40,84,85. Table 6 Nutritional value of locust meat (100gr)78,86,87 Water - 57. 98 (g) 58. 6 (g) < 65 (g) Protein 3. 14 (g) 25. 93 (g) 18 (g) 18. 7 (g) Fat 3. 3 (g) 15. 41 (g) 18 (g) 0. 8 (g) Carbohydrate 2. 2 (g) - - - Calcium 5. 27 (ml/g) 18 (ml/g) 9 (ml/g) - Iron 0. 3 (ml/g) 2. 6 (ml/g) 2. 3 (ml/g) < 0.

Output: contrast


Input: Claim: Fossilized plants provide insights into ancient climates and ecosystems. [SEP] Text: To gain insights into the DEGs that specifically regulate zigzag-shaped stem development, we made a Venn diagram of cultivar comparisons and identified 2175 overlapping DEGs between MZ-vs-QQ and MZ-vs-LYQQ, which were mainly enriched in the “Plant-pathogen interaction”, “Phenylpropanoid biosynthesis”, “Flavonoid biosynthesis” and “Linoleic acid metabolism” pathways (Fig. 4). Among these pathways, the “Phenylpropanoid biosynthesis” pathway serves as a source of metabolites in plants, is involved in the biosynthesis of lignin, flavonoids, coumarins and lignans, and plays a fundamental role in plant structural support [29, 30]. It has been found that, in Arabidopsis, mutation of the genes encoding cinnamate 4-hydroxylase (C4H) and hydroxycinnamoyl-coenzyme A shikimate:quinate hydroxycinnamoyl-transferase (HCT) involved in this pathway resulted in changes in the structural, developmental, and reproductive phenotypes of Arabidopsis plants [31-33]. Interestingly, the flavonols quercetin and kaempferol have been shown to inhibit polar auxin transport and to enhance consequent localized auxin accumulation [34-36]. Recently, Kuhn, et al. [34] suggested that flavonols could modulate auxin transport by modifying the antagonistic kinase/phosphatase equilibrium. Therefore, flavonols could affect auxin transport in zigzag-shaped shoots. On the other hand, Ramos, et al. [37] found that the concentration of quercetin in the upper half of longitudinally dissected 45-degree-inclined radiata pine seedlings was higher than that in the lower half and than that in non-inclined seedlings when seedlings were inclined for one month, indicating that quercetin can accumulate in inclined shoots such as the internodes of zigzag-shaped shoots. Consistently, we observed that a C4H gene (TEA016772.

Output: pass


Input: Claim: Examples of genetic memory include migration patterns in birds and seasonal changes in fur thickness in mammals. [SEP] Text: Those recorded for three or four months in the same season were categorised as either: 1) flooding migrant, present between January and April; 2) run-off (= winter) migrant, present between May and August; or 3) dry (= breeding) migrant, present between September and December. Those recorded for three to eight months in two seasons were categorised as either: 4) flooding and run-off migrant, absent between September and December; 5) run-off and dry migrant, absent between January and April; or 6) dry and flood (= summer) migrant, absent between May and August. For each season, we calculated birds’ frequency of occurrence (FO), following Vielliard and Silva (Reference Vielliard, Silva and Azevedo1990). of (IPA) for each species was calculated for each forest type and season using point count and mist net data (Vielliard and Vielliard, Silva and Azevedo1990, Aleixo and Aleixo and Vielliard1995). For bird records made with point counts, we grouped all sampling points from each trail as one event. Similarly, for mist net data we considered each day (10 mist nets times 06h00 to 11h00 period per site) as one event. To ensure that the variation of detectability over the year did not itself create the migratory patterns found through FO analysis, we constructed community occupancy models that corrected for the detection effect (MacKenzie et al. and Hines2006, with 3. 1 programme created by Hines2006). This approach estimates the fraction of species present, defines if the composition of species changed between seasons, and estimates the increase or decrease in species number. Together, it estimates how the variation of detectability affected the above estimators. Community models were constructed for migratory pattern. For these analyses, we defined each forested habitat as the site, which was surveyed for 90 minutes at nine points per month (with exception of D-D that were surveyed for 80 minutes, at eight points). This is the survey data from 2000 and 2001 of the study, but we randomly excluded some survey points to equalise sampling effort over the sites. Each month was considered a temporal re-sampling. Because the dry season had more re-samplings (n = 6), we had to insert some “missed observations” on the data of the other seasons until it reached six samples per season.

Output: corroborate


Input: Claim: Desert agriculture can fully solve global food shortages regardless of other conditions. [SEP] Text: 2 (ml/g) It should be recognized as a necessity that diversifying food sources contributes to food security88. The challenges associated with food production in farms, poultry houses, and livestock farms are driving the world towards increased utilization of insects in the not-so-distant future68. is feasible and can be done at a low cost49,89,90. Through taking this action, we can not only reduce the spread of Locusts but also create job prospects. Refraining from using chemicals results in cost savings and stops the influx of harmful substances into ecosystems and food webs. In conclusion, based on the findings of this study and other referenced research above, it can be stated that: Large-scale harvesting of Locusts is feasible. as a natural and environmentally-friendly control method can aid in maintaining ecosystem balance without causing environmental pollution and unintended side effects associated with pesticide use. Locust hunting can contribute to reducing agricultural damage and preserving product quality, potentially reducing the need for chemical pesticides. is more cost-effective compared to spraying them with chemicals. Earnings obtained from vending Locusts may assist in offsetting monetary setbacks caused by pest-ridden farm goods. is a more cost-effective and more eco-friendly alternative to raising different kinds of animals, birds, and aquatic creatures. Feeding various types of livestock, poultry, and fish with Locusts can enhance the quality of meat and derived products. Entomophagy as a necessity for food security should be given more attention than ever before. Locusts, as rich sources of protein and nutrients, can partially address nutritional deficiencies in communities facing food scarcity. The use of Locusts in nutrition can help reduce reliance on traditional food sources. in the diet of other animals can contribute to water-saving in food production. In light of these points, considering the potential benefits of Locust utilization, it is evident that exploring and implementing strategies for their sustainable harvesting and integration into various food systems can have multifaceted positive impacts on food security, environmental preservation, and economic development. Declarations10. 5281/zenodo. 8251060 for access to the dataset file, please. (Conflict of Interest): The author declares no conflicts of interest.

Output: contrast


Input: Claim: Fossilized plants provide insights into ancient climates and ecosystems. [SEP] Text: 1) was significantly differentially expressed between MZ-vs-QQ and MZ-vs-LYQQ; moreover, we found that skimmin (pmf0295) expression was reduced in the MZ-vs-QQ (log2 FC: -0. 995) and MZ-vs-LYQQ (log2 FC: -3. 52) comparisons. Therefore, the zigzag-shaped stems of tea plants might be partially related to flavonoids, especially flavonol-mediated auxin transport. It is well recognized that a zigzag-shaped inflorescence stem results from the mutation of zig (zigzag)/sgr4, which encodes VPS10 interacting 11 (VTI11), a Qb-SNARE involved in vesicle transport between the trans-Golgi network and vacuole that causes abnormal gravitropism in Arabidopsis when mutated [8, 10, 11, 38, 39]. SNAREs play an important role in membrane fusion at the vacuole and are involved in the regulation of amyloplast sedimentation in response to gravity and in cell shape development [11, 39]. ZIG can form a complex with other types of SNARE proteins, including SYP22/SGR3/VAM3, SYP5, and VAMP727, most likely at the prevacuolar compartment and vacuole [11, 40-42]. Although ZIG and the other SGR genes were not significantly expressed, 11 genes mainly involved in vesicular trafficking were identified (Fig. 5d and Additional file 3: Table S3). Among these genes, both vacuolar protein sorting-associated protein genes (VPS18 and VPS41) were repressed in QQ and LYQQ, whereas the expression levels of vesicle-associated membrane protein 714 (VAMP714) and vacuolar-sorting receptor 6 (VSR6) were increased in QQ and LYQQ. It has been established that the phenotype of zig-1 could be partially suppressed by mutations in the zig suppressor1 (ZIP1), ZIP2, ZIP3 and ZIP4 genes in Arabidopsis [38, 43, 44]. Niihama, et al.

Output: pass


Input: Claim: Epigenetics explores how certain environmental factors can influence gene expression across generations. [SEP] Text: Javascript is disabled in your browser. Please enable Javascript to view PeerJ. Related research -of the experimental design of gene expression studies on the inference of gene regulatory networks: environmental factors View 10. 7717/peerj. 10 Published 2013-02-12 Accepted 2012-12-31 Received 2012-11-13 regulatory networks, Statistical network inference, Gene expression data, Experimental design, Interventional data Copyright © 2013 Emmert-This is an open access 2013. Influence of the experimental design of gene expression studies on the inference of gene regulatory networks: environmental factors. PeerJ 1:e10 inference of gene regulatory networks gained within recent years a considerable interest in the biology and biomedical community. The purpose of this paper is to investigate the influence that environmental conditions can exhibit on the inference performance of network inference algorithms. Specifically, we study five network inference methods, Aracne, BC33NET and MRNET, and compare the results for three different conditions: (I) observational gene expression data: normal environmental condition, (II) interventional gene expression data: growth in rich media, (III) interventional gene expression data: normal environmental condition interrupted by a positive spike-in stimulation. Overall, we find that different statistical inference methods lead to comparable, but condition-specific results. Further, our results suggest that non-steady-state data enhance the inferability of regulatory networks. than ten years after the completion of the Project (Consortium, 2004; Lander et al. , 2001; Venter et al. , 2001) it is nowadays generally acknowledged that in order to obtain a functional understanding of organisms and the emergence of their phenotypes it is not sufficient to study sequence data alone. Instead, within recent years there are increasing attempts to infer genome-scale molecular interactions from high-throughput data to tackle this problem. Depending on the applied technology, this resulted in the construction of protein–protein interaction networks, metabolic networks or transcription regulatory networks (Blais & Dynlacht, 2005; Förster et al. , 2003; Lee et al. , 2002; Ma et al. , 2004; Palsson, 2006; Yu et al. , 2008). These networks can be considered as phenomenological networks because each interaction within these networks is based on the measurement of the corresponding biochemical binding between genes or gene products.

Output: corroborate


Input: Claim: Most desert farming methods can be used without environmental impact. [SEP] Text: Brief communicationMarch 20, 2024Sciences and Sustainability; Issue 1addShow moreremoveShow lessReceivedDecember 21, 2023AcceptedMarch 08, 2024PublishedMarch 20, 2024Academic editorsDr. 912Views2,485Sciences and Sustainability; Issue 1 21, 2023AcceptedMarch 08, 2024PublishedMarch 20, 2024Academic editorsDr. this 2024. H. , & Rappleye, J. (2024). Exploring inconsistencies in environmental impact assessments of organic farming, 1(1). Hikaru, and Jeremy Rappleye. “in Assessments of Organic Farming” 1, no. 1 (2024). doi:10. 20935/AcadEnvSci6192. VancouverKomatsu H, Rappleye J. Exploring inconsistencies in environmental impact assessments of organic farming. 2024;1(1). H. and Rappleye, J. (2024) “Exploring inconsistencies in environmental impact assessments of organic farming. ” Sciences and Sustainability, 1(1). doi: 10. 20935/AcadEnvSci6192. Publication dates & DOIReceivedDecember 21, 2023AcceptedMarch 08, 2024PublishedMarch 20, 2024DOI Related 4. 0/ the growing popularity of organic farming, persistent questions surround its environmental effects. A 2017 meta-analysis suggested elevated acidification and eutrophication potentials per unit of agricultural production for organic farming relative to conventional farming. However, a recent 2023 meta-analysis contradicted these findings. This brief communication 1. global expansion of organic farming over the past two decades has been remarkable, with organic farmland areas increasing by approximately 500% [1, 2]. This growth trend remains steadfast, as many countries, both high-income nations like the [3] and middle-income countries such as Argentina, India, and Mexico, have implemented policies to encourage organic farming [2]. This policy shift reflects a prevailing academic and public perception that organic farming aligns with pro-environmental values and contributes to sustainability [4–6]. However, the pro-environmental stance of organic farming is a subject of scientific scrutiny. Although organic farming generally exhibits lower environmental impacts per unit of land area, it requires more land to produce equivalent quantities of agricultural products compared to conventional farming [7–9].

Output: contrast


Input: Claim: Fossilized plants provide insights into ancient climates and ecosystems. [SEP] Text: [44] reported that ZIP2, which encodes an AtVPS41/AtVAM2 protein, is involved in protein sorting to the vacuole in Arabidopsis, and the zip2 mutation is a missense mutation. These results indicate that zigzag-shaped stem formation is mainly related to abnormal gravitropism responses mediated by membrane trafficking. Additionally, we also found that six SEC family genes were significantly expressed in the MZ-vs-QQ and MZ-vs-LYQQ comparisons (Fig. 5d and Additional file 3: Table S3); these genes are crucial for SNARE complex assembly and preprotein translocation [45, 46]. Interestingly, we found that both LAZY genes (TEA031847. 1, TEA001744. 1) were markedly repressed in QQ and LYQQ (Fig. 5d and Additional file 3: Table S3). It is well known that loss-of-function mutation of LAZY1 enhances polar indole-3-acetic acid (IAA) transport and reduces shoot gravitropism and therefore regulates the growth angle of lateral branches in rice, Arabidopsis and maize [17-19, 21, 47]; however, the function of LAZY in woody plants remains to be elucidated. Therefore, we propose that the development of zigzag-shaped stems in tea plants might be associated with a change in the shoot gravitropism response, especially one affecting the disruption of membrane trafficking to vacuoles, although the ZIG/SGR4 gene did not exhibit a significant change in expression. The plant hormone auxin is important for organ growth and cell morphogenesis. In this study, seven DEGs involved in auxin metabolism, transport and signalling were identified by comparison of the MZ-vs-QQ and MZ-vs-LYQQ sets, and all of the genes were downregulated in QQ and LYQQ (Fig. 5c and Additional file 3: Table S3). Numerous studies have suggested that polar auxin transport, which is primarily determined by polar localization of PIN auxin efflux carriers, controls plant tropism in roots and shoots and plays essential roles in plant growth [13, 48, 49]. Gerttula, et al.

Output: pass


Input: Claim: Epigenetics explores how certain environmental factors can influence gene expression across generations. [SEP] Text: In this paper, we study an aspect of the experimental design of gene expression data in the particular context of inferring gene regulatory networks from such data. Specifically, we investigate the influence of environmental conditions on the inference performance of five popular network estimation algorithms, namely, Aracne (Margolin et al. , 2006), BC3NET (de & Emmert-Streib, 2012), CLR (Faith et al. , 2007), C3NET (Altay & Emmert-Streib, 2011; Altay & Emmert-Streib, 2010) and MRNET (Meyer, Kontos & Bontempi, 2007; Meyer, Lafitte & Bontempi, 2008). The rational behind our study is the fact that the information stored in the DNA is not sufficient to explain the phenotypic characteristics of an organism. Instead, there are genotype-environment interactions that have an important influence on this (Falconer & Mackay, 1996; Lynch & Walsh, 1998). For similar reasons studying the expression of genes without considering the environmental conditions of the cells under investigation is fragmented. In order to study the influence of environmental conditions on the gene expression, and ultimately on the inference performance of network inference algorithms, we focus on two important, biologically relevant conditions. The first environmental condition we study corresponds to the placement of cells into a rich media. This leads to an increased proliferation of the cells due to the surplus of nutrition. The second environmental condition corresponds to a positive spike-in stimulation of cells as induced, e. g. , by the administration of drugs. Here by spike-in stimulation we mean that the influence of a drug starts abruptly and lasts only for a short period of time. In addition to these two environmental conditions, we contrast the inference performance for data generated under these two conditions with results for data that correspond to a normal condition, where we do not assume an environment influence. For conducting these investigations we simulate gene expression data because this allows us controlling the corresponding conditions and simultaneously guarantees the availability of sufficiently large sample sizes to enable robust statistical findings that can be utilized to advance the experimental design of future gene expression studies aiming to infer gene regulatory networks. Specifically, for our study we generate 6600 different data sets and infer a total of 33,000 different regulatory networks.

Output: corroborate


Input: Claim: Most desert farming methods can be used without environmental impact. [SEP] Text: As a result, researchers have increasingly turned their attention to measuring environmental impacts per unit of agricultural production. This shift in focus has unearthed conflicting findings across various cases. Organic farming had lower environmental impacts for some cases, whereas the opposite was true for other cases [10]. These findings have cast doubt on the efficacy of policies aimed at promoting organic farming. Meta-analysis provides a valuable means to distill general conclusions from the diverse results of individual case studies. One pivotal contribution to this ongoing discourse is Clark and Tilman’s meta-analysis [7]. This meta-analysis was far more comprehensive than previous ones [11, 12], scrutinizing 164 publications to examine multiple environmental impacts of organic farming. Their findings, including a 13% higher acidification and a 37% higher eutrophication potential compared to conventional farming, have been widely disseminated in academia. Just after the publication of Clark and Tilman’s paper [7], prominent academic journals such as the Health [13] introduced Clark and Tilman’s findings [7], highlighting the limitations of organic farming in reducing environmental impacts. Subsequent academic review papers often relied on Clark and Tilman’s findings [7] regarding the effectiveness and limitations of organic farming in reducing environmental impacts [14, 15]. However, a recent meta-analysis by Boschiero et al. [16] has presented findings that contradict those of Clark and Tilman [7]. Analyzing 77 previous publications, Boschiero et al. [16] report comparable or reduced environmental impacts for organic farming compared to conventional farming for acidification and eutrophication. The same was the case for most environmental other impact indicators except land use and ionizing radiation. et al. [16] acknowledge the disparities between their results and those of Clark and Tilman [7], they refrain from delving into the origins of these distinctions. Boschiero et al. [16] merely suggest that the discrepancy might be partly explained by the difference in the considered agricultural products. Boschiero et al. [16] considered only plant-based agricultural products, whereas Clark and Tilman [7] considered both plant-based and animal agricultural products. These discrepant findings have generated a pressing need for a comprehensive understanding of the underlying causes and implications. This study seeks to unravel the source of these disparities and eventually suggests that researchers should incorporate Boschiero et al.

Output: contrast


Input: Claim: Fossilized plants provide insights into ancient climates and ecosystems. [SEP] Text: [50] proposed that PIN expression in different cambium cells results in auxin transport towards the cambium in the top and bottom of the stem to trigger wood formation in response to gravity in woody stems. Consistent with this finding, we found that the expression of was repressed in QQ and LYQQ (Fig. 5c and Additional file 3: Table S3); these changes in expression in QQ and LYQQ might alter the polar transport of auxin and then affect the auxin gradients between stem sides; therefore, the shoots exhibit bending. Wu, et al. [51] reported that rice VLN2, a type of actin-binding protein involved in microfilament regulation, affects the recycling of PIN2 and polar auxin transport, and vln2-defective mutant plants exhibited a hypersensitive gravitropic response and twisted roots and shoots at the seedling stage. In this study, we also found that VLN2 (TEA030753. 1) was markedly repressed in QQ and LYQQ (Fig. 5e and Additional file 3: Table S3), suggesting that zigzag-shaped stems in tea plants might be related to polar auxin transport and the gravitropism response. Moreover, cell expansion might exert a compressive force, leading to bending of the stem. Our results showed that genes involved in cell expansion and cell wall synthesis, such as expansin, and xyloglucan endotransglucosylase/hydrolase protein, were differentially expressed (Fig. 5a and Additional file 3: Table S3), resulting in alteration of cell expansion and elongation. In addition, wall-associated kinase (WAK) genes were also differentially expressed in MZ-vs-QQ and MZ-vs-LYQQ, suggesting that WAK-mediated cell expansion and signalling pathways might be required for zigzag-shaped stem formation in tea plants. It is possible that cell expansion in the stems can produce a force that can lead to zigzag-shaped shoots. Importantly, cell expansion and differentiation predominantly rely on auxin [12, 52, 53]; thus, the mechanism of auxin regulation in zigzag-shaped shoot development needs to be studied precisely in the different tissue sides of zigzag-shaped stems.

Output: pass


Input: Claim: Epigenetics explores how certain environmental factors can influence gene expression across generations. [SEP] Text: For the subnetwork of the transcriptional regulatory network of S. cerevisiae (Fig. 4B) we find a surprising result because these results are qualitatively similar to the results for the normal condition (shown in Fig. 2B). This means that the underlying topology of the regulatory network is capable of compensating the dynamical modifications, as induced by the spike-in stimulation. Further, this behavior is method-independent because for all five inference methods, we observe qualitatively similar results. this paper we investigated the influence that environmental conditions can have on the inference performance of network inference algorithms. Specifically, we studied and compared the results for three different conditions: (I) observational gene expression data: normal environmental condition, (II) interventional gene expression data: growth in rich media, (III) interventional gene expression data: normal environmental condition interrupted by a positive spike-in stimulation. We found that different statistical inference methods lead to comparable but condition-specific results. That means, qualitatively, the five network inference methods (Aracne (Margolin et al. , 2006), BC3NET (de & Emmert-Streib, 2012), CLR (Faith et al. , 2007), C3NET (Altay & Emmert-Streib, 2011; Altay & Emmert-Streib, 2010) and MRNET (Meyer, Kontos & Bontempi, 2007; Meyer, Lafitte & Bontempi, 2008)) we used for our study showed a similar behavior in their inference performance, for each condition. The only exception we found is for (III) interventional gene expression data (normal environmental condition interrupted by a positive spike-in stimulation) and Erdös–Réyni networks, because for this condition MRNET and Aracne assume a significantly larger variation in the estimated F-scores than the other three inference methods (see Fig. 4). However, even for this condition the observed median F-scores are for all five methods comparable. Overall, we can draw the following conclusions from our numerical results. (1) The problem to infer gene regulatory networks from expression data is very challenging and depends on (A) the time point when data are measured, (B) the kind of the external stimulation and (C) the interconnectedness of the genes respectively their molecular interactions.

Output: corroborate


Input: Claim: Most desert farming methods can be used without environmental impact. [SEP] Text: It is thus crucial to the critical importance of reassessing the potential of organic farming for mitigating environmental impacts based on Boschiero et al. ’s [16] updated data and findings, although we acknowledge that organic farming is not always an effective solution. authors declare no financial support for the research, authorship, or publication of this 5221. doi: 10. 1038/nplants. 2015. 221 2 Willer H, Schlatter B, Tráníček J. The world of organic agriculture: statistics & emerging trends 2023. Frick and Bonn: FiBL & IFOAM; 2023. Available from: 3 European Commission. Organic farming in the EU: a decade of organic growth. European Union. 2023. Available from: 4 Eyhorn F, et al. Sustainability in global agriculture driven by organic farming. Nat Sustain. 2019;2:253–55. doi: 10. 1038/s41893-019-0266-6 5 Food and of the United Nations. Organic agriculture. Food and of the United Nations. 2023. Available from: 6 Gamage A, et al. Role of organic farming for achieving sustainability in agriculture. Farming Syst. 2023;1(1):100005. doi: 10. 1016/j. farsys. 2023. 100005 7 Clark M, Tilman D. Comparative analysis of environmental impacts of agricultural production systems, agricultural input efficiency, and food choice. Lett. 2017;12:064016. doi: 10. 1088/1748-9326/aa6cd5 8 Jouzi Z, et al. Organic farming and small-scale farmers: main opportunities and challenges. Ecol Econ. 2017;132:144–54. doi: 10. 1016/j. ecolecon. 2016. 10. 016 9 Seufert V, Ramakutty N. Many shades of gray—the context-dependent performance of organic agriculture. Sci Adv. 2017;3:e1602638. doi: 10. 1126/sciadv. 1602638 10 Meier MS, et al. Environmental impacts of organic and conventional agricultural products - are the differences captured by life cycle assessment? J Environ Manage. 2015;149:193–208. doi: 10. 1016/j. jenvman. 2014. 10.

Output: contrast


Input: Claim: Fossilized plants provide insights into ancient climates and ecosystems. [SEP] Text: In this study, 20 transcription factors (TFs) belonging to different TF families, including two ARFs, were differentially expressed in MZ-vs-QQ and MZ-vs-LYQQ, and most of these TFs were significantly repressed in QQ and LYQQ (Fig. 5b and Additional file 3: Table S3). Almost all of these genes had homologues associated with plant growth and developmental regulation in other plants. For instance, (TEA031729. 1), a MYB-type TF, could interact with WOX to control wood formation in poplar [54]; overexpression of IBH1 causes erect leaves in rice and dwarfism in Arabidopsis [55]; and HEC1 coordinates with WUS to promote stem cell proliferation in the shoot meristem [56, 57]. kawakamii, antisense suppression of PkMADS1, a regulator of shoot morphogenesis, resulted in zigzag-shaped shoots [58]. Interestingly, in some transformants of antisense PkMADS1, the main shoot apex appeared to be used up early during leaf formation, and then, the axillary bud of the youngest leaf took over the function of the apical meristem, resulting in the formation of one leaf per node and the zigzag-shaped growth habit for the stem, indicating that central and lateral meristem fates regulated by a variety of TFs may relate to zigzag-shaped shoot formation. Recently, several genes that regulate architectural phenotypes in woody plants, such as 2 (ARK2) in Populus [50] and 1C (GID1C), Control 1 (TAC1) and WEEP in peach [23, 59, 60], have been isolated; however, most of these genes are related to the plant gravitropic response, and none of these genes encode TFs. Additionally, among the nine SGR genes, SGR1 and SGR7 encode scarecrow (SCR) and GRAS family TFs, respectively. We found that the SCR gene (TEA030046. 1) was markedly repressed in QQ and LYQQ (Fig. 5b and Additional file 3: Table S3).

Output: pass


Input: Claim: Epigenetics explores how certain environmental factors can influence gene expression across generations. [SEP] Text: AbstractThrough epigenetic modifications, specific long-term phenotypic consequences can arise from environmental influence on slowly evolving genomic DNA. Heritable epigenetic information regulates nucleosomal arrangement around DNA and determines patterns of gene silencing or active transcription. One of the greatest challenges in the study of epigenetics as it relates to disease is the enormous diversity of proteins, histone modifications and DNA methylation patterns associated with each unique maladaptive phenotype. This is further complicated by a limitless combination of environmental cues that could alter the epigenome of specific cell types, tissues, organs and systems. In addition, complexities arise from the interpretation of studies describing analogous but not identical processes in flies, plants, worms, yeast, ciliated protozoans, tumor cells and mammals. This review integrates fundamental basic concepts of epigenetics with specific focus on how the epigenetic machinery interacts and operates in continuity to silence or activate gene expression. Topics covered include the connection between DNA methylation, methyl-CpG-binding proteins, transcriptional repression complexes, histone residues, histone modifications that mediate gene repression or relaxation, histone core variant stability, H1 histone linker flexibility, FACT complex, nucleosomal remodeling complexes, HP1 and nuclear lamins. Keywords: : DNA methyltransferasesH2A. ZMethyl-CpG-binding proteinsSWI-SNFepigeneticsheterochromatin proteinshigh mobility group proteinsnucleosomal remodeling complexes IntroductionThe human genome is composed of billions of sequence arrangements containing a bioinformatics code that controls how genes are expressed. This code is further dependent upon heritable non-static epigenetic arrangement of histone scaffolding that surrounds the DNA and comprises the “epigenome. ” The historical transitional evolution of the human genome is believed to have occurred through a number of processes, one being the altered sequence and re-arrangement of transposable elements located at segments of non-coding DNA. It is believed that the greater the complexity of an organism, the greater amount of non-coding DNA. In humans, protein-coding regions of DNA account for <1. 6% of the genome.

Output: corroborate


Input: Claim: Desert agriculture yields the same crop productivity as traditional farming everywhere. [SEP] Text: – : SOCIO-online by Press: 31 May 2016 A. C. . . . . andK. E. author details A. C. * Affiliation: 430, 6700AK Wageningen, the Netherlands Soil, Crop and Climate Sciences, University of the. : of (IITA), Dar es Salaam, Tanzania S. : of (IITA), Kigali, Rwanda M. : 430, 6700AK Wageningen, the of Systems, for Research (ZALF), Muencheberg, Germany B. : of (IITA), Nairobi, Kenya K. E. : 430, 6700AK Wageningen, the Netherlands * §§Corresponding author. Email: FrankeAC@ufs. ac. za 0. 46 mb) View PDF [Opens in a new window] Save to to Save to & Permissions [Opens in a new window] bean is the key staple legume crop in the highlands of East and Central Africa. We assessed the impact of interactions between soil fertility characteristics, crop management and socio-economic factors, such as household resource endowment and gender of the farmer, on climbing bean productivity and yield responses to basal P fertiliser in northern Rwanda. Through a combination of detailed characterisations of 12 farms and on-farm demonstration trials at 110 sites, we evaluated variability in grain yields and responses to fertiliser. Grain yields varied between 0. 14 and 6. 9 t ha−1 with an overall average of 1. 69 t ha−1. Household resource endowment and gender of the farmer was strongly associated with climbing bean yield, even though these were partly confounded with Sector. Poorer households and women farmers achieved lower yields than wealthier households and male farmers. Household resource endowment and gender were likely to act as proxies for a range of agronomic and crop management factors that determine crop productivity, such as soil fertility, current and past access to organic manure and mineral fertiliser, access to sufficient quality staking material, ability to conduct crop management operation on time, but we found evidence for only some of these relationships. Poorer households and female farmers grew beans on soils with poorer soil fertility. Moreover, poorer households had a lower density of stakes, while stake density was strongly correlated with yield.

Output: contrast


Input: Claim: Fossilized plants provide insights into ancient climates and ecosystems. [SEP] Text: Plant growth and development are directed by a TF-mediated complex network integrated with plant hormones, enzymes and other cellular components; therefore, as-yet-unknown TFs may be involved in the regulation of plant architectural phenotypes. ConclusionIn the current study, we investigated the mechanism of zigzag-shaped shoot formation in tea plants using comparative transcriptomics and metabolomic analysis. The results showed that zigzag-shaped stem development in tea plants might be regulated by a complex network involving vesicular trafficking, phytohormones, cell expansion, secondary metabolism, and diverse transcription factors. Importantly, zigzag-shaped shoot formation might be closely related to alterations in the gravitropic response and polar auxin transport in tea plants. Our findings provide insights into zigzag-shaped shoot formation in tea plants and serve as a valuable foundation for further investigations of architecture formation in woody plants. MethodsPlant materials The tender stems (between the first and third leaves from the apical bud) of tea plants with erect (C. sinensis var. Meizhan, MZ) and zigzag-shaped (C. sinensis var. Qiqu, QQ; C. sinensis var. Lianyuanqiqu, LYQQ) shoots were collected from the germplasm resource garden of in October 2018. A portion of each sample was immediately frozen in liquid nitrogen and then stored at -80°C until use for transcriptome sequencing and metabolite analysis. The remaining samples were fixed in cold fixative solution (4°C) for section observation. All samples were examined in triplicate and used as biological replicates. Tissue section observation Longitudinal stem sections were sliced and stained as previously described by Ile, et al. [61] with minor modifications. At least seven stems from each tea plant cultivar were cut into fragments (<0. 5 cm) and fixed in fixative solution over 72 h at 4°C.

Output: pass


Input: Claim: Epigenetics explores how certain environmental factors can influence gene expression across generations. [SEP] Text: Citation1 Transposable elements, also referred to as “jumping genes,” have accumulated throughout millions of years as evolutionary ancient DNA in the form of transposons and retrotransposons, which are reverse transcribed long-terminal repeat (LTR) retroviruses. Citation2 Today, active non-LTR retrotransposons (i. e. , Alu and LINEs) perpetuate transgenerational genetic diversities through genomic DNA variation among humans. While the evolution of DNA occurs at a slow pace, expedient heritable changes to the epigenome allow dynamic and flexible modification to suit rapid environmental adaptation. Citation3 While the epigenome has more influence on the temporal phenotype, the collective effects of change to the genome and the epigenome contribute to observable physical or biochemical characteristics of an organism. Throughout the life cycle, dynamic epigenetic control over the phenotype is influenced by a time component responsible for maturation and senescence from conception to adulthood. Environmental epigenetic factors affecting long-term phenotypic change are largely initiated during in utero/perinatal periods, when introduction to the external world is being established. Citation4 It is believed that since epigenetic patterns are inherited through mitosis, the earlier the stage of development, the more critical the environmental impact on the resulting phenotype. During fetal development, environmental cues can induce the modification of a pliable epigenome, which can result in long-term changes in gene expression that occur in a self-sustaining manner in the absence of the original stimulus. Citation5 Adverse gestational conditions that arise from inadequate healthcare, poor nutrition, socioeconomic disadvantage and racial disparities are often associated with long-lasting phenotypic consequences in adults, yielding greater risk of diabetes and heart disease,Citation6,Citation7 as well as low birth weight and congenital defects in progeny. Citation8–Citation10 It is now becoming evident that these effects are inextricably linked to altered epigenetic patterns. Offspring exposed to gestational malnutrition due to extended famine in certain populations also show higher prevalence of adult onset obesity and schizophrenia, tantamount to altered DNA methylation patterns for specific genes such as insulin like growth factor 1/2 and the obesity factor gene leptin.

Output: corroborate


Input: Claim: Desert agriculture yields the same crop productivity as traditional farming everywhere. [SEP] Text: Diammonium phosphate (DAP) fertiliser application led to a substantial increase in the average grain yield (0. 66 t ha−1), but a large variability in responses implied that its use would be economically worthwhile for roughly half of the farmers. For the sake of targeting agricultural innovations to those households that are most likely to adopt, the Ubudehe household typology – a Rwandan government system of wealth categorisation – could be a useful and easily available tool to structure rural households within regions of Rwanda that are relatively uniform in agro-ecology. 10. 1017/S0014479716000028 [Opens in a new window] This is an 4. 0/), which permits unrestricted re-use, distribution, and reproduction in any medium, provided the original work is properly cited. © Press 2016 sub-(SSA), there is a strong need to intensify crop production sustainably due to poor crop yields, rapid expansion of human population and increasing pressure on remaining non-cultivated areas with a high-biodiversity value (Pretty et al. , Reference Pretty, Toulmin and Williams2011; Vanlauwe et al. , and Van Asten2014). Legumes provide opportunities for sustainable intensification. Legumes can fix atmospheric nitrogen and yield well without nitrogen fertiliser, improve the N status of soils and prevent the build-up of weeds, pests and diseases associated with continuous monoculture of cereal or root and tuber crops. Moreover, they provide nutritious food and feed, which often have a good market demand (Giller, Reference Giller2001). Common bean (Phaseolus vulgaris L. ) is the key staple grain legume in the highlands of East and Central Africa. While bush varieties have been widely grown since common bean was introduced in the 16th Century, climbing bean varieties were only found in a few locations in the highlands until a targeted breeding programme was started in the mid 1980s including the introduction of new varieties from (Sperling and Muyaneza, and Muyaneza1995). Climbing bean is now an important crop at elevations above 1600 m above sea level (masl) in the highlands of East and Central Africa. Its adoption cuts across socio-economic class and gender boundaries (Sperling and Muyaneza, and Muyaneza1995).

Output: contrast


Input: Claim: Fossilized plants provide insights into ancient climates and ecosystems. [SEP] Text: The stems were dehydrated by transferring them sequentially through a series of increasing concentrations of ethanol (75 to 100% absolute ethanol), followed by 100% ethanol, ethanol:xylene (2:1), ethanol:xylene (1:1), ethanol:xylene (1:2), pure xylene, pure xylene (each for 1 h), xylene:Paraplast (1:1) for 24 h, and molten Paraplast (melting point 65°C) for 48 h and finally embedded in freshly molten Paraplast. Central longitudinal sections of 5 μm thickness per stem were cut using a disposable-blade rotary microtome (RM2016, Leica, Shanghai, China), allowed to stand overnight and dried at 40°C for 4 h. Sections were dewaxed in xylene, hydrated gradually in decreasing concentrations of ethanol (from 100 to 70%) and stained with safranine (1. 0% for 2. 5 h) followed by (1. 0% for 8 s) in ethanol. After staining, the stem sections were observed under a Leica DMi8 inverted microscope (Leica, Shanghai, China). UPLC-ESI-MS/MS analysis and differential metabolite identification A total of 100 mg of powder from crushed freeze-dried samples was weighed and extracted overnight at 4°C with 1. 0 ml of 70% aqueous methanol containing 0. 1 mg/L lidocaine as an internal standard. Following centrifugation at 10,000 ×g for 10 min, the supernatant was absorbed and filtered (SCAA-104, 0. 22-μm pore size; ) before liquid chromatography-tandem mass chromatography (LC-MS/MS) analysis. Quality control samples were mixed with all the samples to ensure the reproducibility of the entire experiment. The extracted compounds were analysed using an ultra performance liquid chromatography-electrospray ionization-tandem mass spectrometry (UPLC-ESI-MS/MS) system (UPLC, Shim-pack 30A; MS/MS, 6500 QTRAP) [62]. Two microliters of each sample was injected onto a 3 C18 column (2. 1 mm*100 mm, 1. 8 μm) operating at 40°C and a flow rate of 0. 4 mL/min.

Output: pass


Input: Claim: Epigenetics explores how certain environmental factors can influence gene expression across generations. [SEP] Text: Citation11 Altered epigenetic patterns acquired during early development involve changes in DNA methylation patterns, genomic imprinting,Citation12 histone modifications and the establishment of specific expression profiles of non-coding miRNAs. Citation13,Citation14Given the enormous impact of early epigenetic programming and the serious nature of related developmental conditions, such as Praeder-Willi, Angelman and Beckwith-Wiedemann syndromes, neural tube defects, adult onset psychiatric disorders, obesity, cancer and schizophrenia,Citation15–Citation19 considerable attention is given to the “nurture of the epigenome” prior to birth. A number of community outreach projects such as the CDC's on promote awareness about reducing the risk of epigenetic related defects such as spina bifida by suggesting an adequate intake of epigenetic-related nutrients (e. g. , choline, vitamin B12, B6 and folate) during pregnancy. Citation20–Citation25 The epigenome appears to remain pliable after birth and during the first years of life. This is evidenced by correlations described in infants exposed to stress or lack of emotional nurturing who show overactive hypothalamic-pituitary-adrenal stress response, glucocorticoid feedback or decreased hypothalamic corticotropin-releasing factor. Citation26 Once established in the offspring, epigenetic marks can become transgenerational, continuing transmittance to future descendants—including the very trait of maternal nurturing in females. Citation27 The longevity of transgenerational epigenomic inheritance pattern is further influenced by the severity and repetition of a similar environmental stimulus among individuals of the same lineage. If the stimuli are discontinued, phenotypic traits could dissipate after the first or second generation. Citation27,Citation28 In other instances, longer lasting epigenetic changes adversely affect the phenotype of the third or fourth generation,Citation29 often initiated by environmental factors adverse to human health that perpetuate aberrant patterns of transgenerational transmission of phenotype. Citation30The purpose of this review is to simplify the enormous complexity of epigenetic biochemistry that links nuclear DNA to the environment. On one hand, the concept of epigenetics is relatively simple in that it describes a means by which genes are either turned on or off by a heritable epigenome.

Output: corroborate


Input: Claim: Desert agriculture yields the same crop productivity as traditional farming everywhere. [SEP] Text: In the of Rwanda, up to 95% of the households grow climbing beans (Franke and de Wolf, and de Wolf2011; NIS, 2010). Province has good rainfall (1000–1500 mm per annum) with two distinct growing seasons and relatively cool temperatures due to its mid to high elevation (Franke et al. , Reference Franke, Rufino and Farrow2011). The province harbours relatively fertile volcanic soils, which have a long history of arable farming. Population densities in the are very high, with on average 528 persons km−2 (NIS, 2012). Farming/fishing is the prime economic activity of 90% of rural males and 97% of rural females in Rwanda (SNR, 2005). Dense populations and limited opportunities for income generation off-farm have resulted in tiny landholdings, on average 0. 65 ha per household in the (NIS, 2010), and intensive land use. Climbing bean fits well within this farming system as a high yielding, though labour demanding crop. Other major crops include maize, sorghum, sweet potato, highland banana and potato. The indeterminate growth of climbing beans allows them to take advantage of the long growing seasons at high elevations, providing edible yield over a prolonged period (and Francis, Clark and Francis1985; Wortmann, Reference Wortmann2001). Climbing beans tend to nodulate more prolifically than bush beans (Bliss, Reference Bliss1993) and their climbing habit allows them to capture a greater proportion of the available radiation, giving a greater yield and N2-fixing potential than bush beans (Wortmann, Reference Wortmann2001). Climbing beans are less suited for intercropping than bush varieties due to their prolific growth pattern, though farmers do intercrop climbing beans with maize, cassava and banana (Ruganzu et al. , and Blomme2014). Climbing bean productivity and N2-fixation is constrained by poor soil P and K availability (Burleig et al. , Reference Burleig, Yamoah, Regas and Mukaruzika1992; Graham and Ranalli, and Ranalli1997).

Output: contrast


Input: Claim: Fossilized plants provide insights into ancient climates and ecosystems. [SEP] Text: The mobile phases used were acidified water (0. 04% acetic acid) (phase A) and acidified acetonitrile (0. 04% acetic acid) (phase B). The compounds were separated using the following gradient: 95:5 phase A/phase B at 0 min; 5:95 phase A/phase B at 11. 0 min; 5:95 phase A/phase B at 12. 0 min; 95:5 phase A/phase B at 12. 1 min; 95:5 phase A/phase B at 15. 0 min. The effluent was connected to an ESI-triple quadrupole-linear ion trap (QTRAP)-MS. For metabolite identification, data filtering, peak detection, alignment, and calculations were performed using Analyst 1. 6. 1 software. In particular, the T-test was also used as a univariate analysis for screening differential metabolites. Metabolites with T-test P values <0. 05 and VIP ≥ 1 were considered differential metabolites between the two groups. Metabolites were mapped to KEGG metabolic pathways for pathway enrichment analysis [63]. The pathway enrichment analysis identified significantly enriched metabolic pathways or signal transduction pathways associated with differential metabolites compared with the background. The calculated p value was subjected to false discovery rate (FDR) correction, taking FDR ≤ 0. 05 as a threshold. Pathways meeting this condition were defined as significantly enriched pathways associated with differential metabolites. RNA isolation, library construction, Illumina sequencing, and data processing The total RNA from each sample, which consisted of at least 30 shoots collected from over 10 tea individuals, was extracted using the (). The total RNA quantity and integrity were evaluated and estimated using an 2100 system () and a NanoDropTM ultraviolet spectrophotometer (), respectively. cDNA libraries were constructed using the kit (Gene, Beijing, China) and sequenced using an Illumina HiSeq TM 2500 instrument (Co. , Guangzhou, China). High-quality clean reads were acquired by removing adaptor sequences, reads containing more than 10% unknown nucleotides (N), and low-quality reads containing more than 50% low-quality (Q value≤20) bases; then, the Q20 and Q30 values, GC content, and sequence duplication levels of the clean reads were calculated. The clean reads of each sample were then mapped to the tea plant genome by TopHat2 [64] (version 2.

Output: pass


Input: Claim: Epigenetics explores how certain environmental factors can influence gene expression across generations. [SEP] Text: On the other hand, the environmental and biological controls that mediate these events are extraordinary in number, compounded by instances of similar methylation events that have opposite effects when occurring at different histone amino acids (e. g. , H3K36me3 and H3K9me3) and by variation in the interpretation of studies performed in diverse organisms such as flies, plants, worms, yeast, ciliated protozoans, tumor cells and mammals. Citation31DNA MethylationMore than 30 million base pairs of the human genome are CG dinucleotides (CpGs). CpG sites are target platforms for methylation, which consist of the covalent attachment of a methyl group to the 5′ position of the cytosine (C). CpG methylation patterns correlate with transcriptional silencing patterns observed in 60–90% of the human genes. Citation32 Methylated CpGs reinforce silencing by a number of processes including direct ability to block transcription initiation complexes from binding to DNA promoter regions, inhibition of RNA polymerase (RNAP) and recruitment of transcriptional repressor complexes that bind through Krüppel-like C2H2 zinc fingers, such as Kaiso, and human zinc finger and BTB domain-containing proteins 4 and 38 (ZBTB4 and ZBTB38). Citation33–Citation35 Methylation of CpG sites is performed by DNA methyltransferases DNMT3A and DNMT3B, which carry out de novo methylation, and DNMT1, which ensures heritable epigenome replication through cell division. Citation36 A closer look at DNMT1 shows that this enzyme not only methylates DNA, but also docks directly to methyl-CpG binding proteins (MBPs), such as MeCP2, MBD2 and MBD3. MBPs can equally dock to constrictive histone enzymes, such as histone deacetylases HDAC1 and HDAC2, human H3K9 methyltransferase (Suv39 h1) and heterochromatin protein 1 (HP1), all synergistic components of gene silencing. DNMT1 ensures that silencing remains heritable during cell division by binding to the replication fork, through its UHRF1 domain, and to methylated CpGs, through its SRA domain.

Output: corroborate


Input: Claim: Desert agriculture yields the same crop productivity as traditional farming everywhere. [SEP] Text: While the vast majority of climbing bean fields in Rwanda receive organic manure, only a small fraction (12–21%) of the farmers apply mineral fertilizers to beans (urea, DAP or NPK blend), as these are preferably applied to staple and high value crops such as potato and tomato (Franke and de Wolf, and de Wolf2011; Ruganzu et al. , and Blomme2014). Moreover, beans are sensitive to a range of pests and diseases including rodents, bean shoot fly, leafhoppers, chrysomelids and bruchids and root rots (Graham and Ranalli, and Ranalli1997; Ruganzu et al. , and Blomme2014; Sperling and Muyaneza, and Muyaneza1995). The use of appropriate staking is the key to good yields of climbing bean, yet the availability and costs of staking material represent a major limitation (Musoni et al. , and Blomme2014; Ruganzu et al. , and Blomme2014). a wide diversity of farms and farming strategies is found, even within villages (Giller et al. , Reference Giller, Tittonell, Rufino, van Wijk, Zingore, Mapfumo, Adjei-van der Burg, Sanogo, Misiko, de Ridder, Karanja, Kaizzi, K'Ungu, Mwale, Nwaga, Pacini and Vanlauwe2011). Besides biophysical factors, socio-economic characteristics of farm households such as farm size, livestock ownership, education level and off-farm income, affect the adoption or rejection of technologies (Marenya and Barrett, and Barrett2007). Categorisations of farms are frequently used to understand factors influencing technology adoption or define recommendation domains (Bidogeza et al. , Reference Bidogeza, Berentsen, 2009; Tittonell et al. , and Vanlauwe2010). of Rwanda categorised all households according to a typology called ‘Ubudehe’ (translated as ‘local collective action’). programme of the Ministry of and the was launched in 2001 (Ansoms, Reference Ansoms2008). Ubudehe stratifies households into six categories according to their resource status, enabling poverty alleviation programs to target poor households.

Output: contrast


Input: Claim: Fossilized plants provide insights into ancient climates and ecosystems. [SEP] Text: 0. 3. 12). Gene abundances were quantified with RSEM software, and the unigene expression levels were quantified using fragments per kilobase of transcript per million mapped reads (FPKM) values [65]. To identify DEGs across samples or groups, the edgeR package ( was used, and genes with |log2FC| ≥1 and FDR <0. 05 were identified as DEGs. DEGs were then subjected to enrichment analysis of GO functions and KEGG pathways using the Gpackage [66] and KOBAS software [67], respectively. Quantitative real-time PCR validation To validate the reliability of the gene expression analysis in this study, 16 genes were selected for real-time qPCR analysis. Total RNA samples were used for cDNA synthesis according to the method recommended by the SuperScript® III kit manufacturer. Information about the primers used for qRT-PCR analysis is listed in Additional file 4: Table S4. qRT-PCR was performed using ™ II (TaKaRa, Dalian, China) in a CFX96 Touch real-time PCR system (BIO-) according to the manufacturer’s protocol, and amplification was performed as previously reported [68]. The results were calculated using the 2−ΔΔCT method [69] with the CsPTB1 gene as a control [70]. Each sample was examined in triplicate. AbbreviationsDEGs: differentially expressed genes; FDR: false discovery rate; FPKM: fragments per kilobase of transcript per million mapped reads; LC-MS/MS: liquid chromatography-tandem mass chromatography; LYQQ: Lianyuanqiqu; MZ: Meizhan; PIN: PIN-; QQ: Qiqu; qRT-PCR: quantitative real-time PCR; SGR: shoot gravitropism; UPLC-ESI-MS/MS: ultra performance liquid chromatography-electrospray ionization-tandem mass spectrometry; ZIG: zigzag; ZIP: zig suppressor1DeclarationsEthics approval and consent to participate The tea cultivars ‘Meizhan’, ‘Qiqu’ and ‘Lianyuanqiqu’ used in this study were planted and grown at. No specific permits were required for plant collection.

Output: pass


Input: Claim: Epigenetics explores how certain environmental factors can influence gene expression across generations. [SEP] Text: Citation37 UHRF1 and SRA domains function synergistically in the recruitment of histones that bear constrictive epigenetic marks (e. g. , H3K9me3) and constrictive enzymes, such as G9a and HDAC1. Citation38,Citation39 DNMT1 is further stabilized by a UHRF1/HDAC1 complex containing USP7 deubiquitinase, also called “herpes virus-associated ubiquitin-specific protease,” which prevents DNMT1 proteosomal degradation. Citation39 In addition, UHRF1 both reinforces silencing at methylated CpG sites and ensures transcription at unmethylated CpG islands. CpG islands are open regions of DNA that are highly accessible to transcription initiation complexes. At transcription start sites, UHRF1 degrades DNMT1 by ubiquitin E3 ligase proteosomal targetingCitation39,Citation40 and ensures gene expression by interacting with histone expansive enzymes such as acetyltransferase Tip60, which promotes nucleosomal expansion. Citation38–Citation40 The bob and weave nature of UHRF1 contributes to the replication of DNA methylation patterns. Coordinated histone scaffold inheritance patterns occur by enabling both DNMT1 deubiquitination (stability) and DNMT1 ubiquitination (proteosomal degradation). Citation41 De novo DNA methylation enzymes, such as DNMT3a and b, work in a similar way in that they recruit constrictive silencing elements, such as transcriptional repressor domains (TRDs), a repression protein of 58 kDa also known as Zfp238 that is critical for embryonic development, HDAC1, Suv39 h1 and HP1. Citation30 All of these enzymes are tightly interwoven within compact nucleosomes surrounding methylated CpG DNA. Citation42 While de novo DNMT3s establish silencing patterns in response to environmental triggers, silencing inheritance patterns maintained throughout cell replication are carried forward by DNMT1.

Output: corroborate


Input: Claim: Desert agriculture yields the same crop productivity as traditional farming everywhere. [SEP] Text: Sites without yield data were removed from further analyses. Yield data from four other sites were removed as well: three sites reported unrealistically high yields of more than 6 t ha−1, and one site a 10-fold yield increase (from 0. 27 to 2. 70 t ha−1) with DAP fertiliser and a recording error was suspected. Soil analysis and data handling Soil samples were air-dried and sieved to 2 mm and analysed for pH (H2O 2:1), total N, available P (Bray), organic C, cation exchange capacity (CEC), and exchangeable cations (K, Ca, Mg, Na) by in Nairobi, Kenya using standard methods (Okalebo et al. , Reference Okalebo, Githua and Woomer2002). P0. 7, goats and sheep as 0. 1, pigs as 0. 2, and chicken as 0. 01 TLU (Jahnke, Reference Jahnke1982). Climbing bean grain yield from the farm characterisations was adjusted to 12% moisture and stover yield to 0%. In the demo trials, grain yield is presented as fresh yield at harvest, with an estimated moisture concentration of 12–14%. The effects of geographic region, soil parameters and agronomic and socio-economic characteristics on yield in both the farm characterisations and the demo trial were explored using Likelihood (REML), linear mixed model analyses. This approach is suitable to analyse unbalanced data (for instance the numbers of female and male farmers, the number of sites per region and the number of farmers per household class were unequal) and produce unbiased estimates of variance and covariance parameters. Several bean fields were monitoredon some farms in the detailed farm characterisations and therefore ‘farm’ was added as a factor to the random model. Since only three observations were obtained from both the ‘Very poor’ and the ‘Poor’ class we pooled data from the two poorer and the two wealthier classes. In the demo trial, ‘Sector’ was found to be confounded with gender, household class and soil characteristics and was included in the random model of the REML analysis of other variables, unless indicated otherwise in the results. First, the strength of factors such as region, household class and gender of the farmer in explaining yield variability were explored individually.

Output: contrast