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Differential Expression of Anthocyanin Biosynthesis Genes and Transcription Factors Causes Color Variation of Lilium cernum
Shaopeng Chen , Shihao Li , Ruirui Li , Tingyu Yin , Qianqian Zhuang
Jilin Agricultural Science and Technology University, Jilin, 132101, China
Received: 31&nbspOct., 2022 Accepted: 08&nbspNov., 2022 Published: 17&nbspNov., 2022
Chen S.P., Li S.H., Li R.R., Yin T.Y., and Zhuang Q.Q., 2022, Differential expression of anthocyanin biosynthesis genes and transcription factors causes color variation of Lilium cernum, International Journal of Horticulture, 12(5): 1-12 (doi: 10.5376/ijh.2022.12.0005)
In order to explore the variation mechanism of two different colors of Lilium cernum, the floral organs of Lilium cernum with different colors and same habitat were used as materials. A high-throughput sequencing technique applied used to establish the process of flower development and the transcriptome database of the two types of flowers. The structural genes and transcription factors of anthocyanin biosynthesis pathway were screened differentially. The results revealed that a total of 57521 Unigenes were obtained by sequencing. Compared the expression differences of structural genes of anthocyanin synthesis in floral organs at different stages, 5 structural genes were screened out, including DFR, CHS, ANR, ANS and FOMT, and 11 transcription factors, such as MYB14, MYB98, MYBC1, PHL7, PHL8, cytochrome P45094A1, bHLH30, bHLH51, MYB13, bHLH52 and bHLH35. These structural genes and transcription factors are speculated to be closely related to the regulation of anthocyanin synthesis. At the same time, it is believed that pink Lilium cernum may be caused by the flowering process, during which the color conversion stage is not completely completed.
Lilium cernum; Flower color; High-throughput sequencing technology; Anthocyanin; Transcription factor
Lilium spp., one of the world's famous ornamental flowers, is mainly cultivated as cut flower, whose ornamental value lies in the floral organ. It usually comes in colors of red, orange, white and pink with the absence of blue or purple. Lilium cernum., also known as Lilium pinifolium, falls into the Sect. Sinomartagon of Lilium genus and is also one of the most important wild species in Asiatic hybrids. Among such distribution areas as Northeast China (Jilin Province and Liaoning Province), the Korean Peninsula and Russia, the Changbai Mountains are the major one of Lilium cernum., the only wild fragrant purplish-red Lilium spp. in the Northeast China. Plants on the Changbai Mountain (the Baekdu Mountain in North Korea) have been in the cycle of glaciation and interglaciation due to height change of the mountain, resulting in that a series of low and medium density populations have been subjected to extensive genetic variation (Chung et al., 2014). The case is same for the wild Lilium cernum species, which are under different color variations.
The main reason causing color variations rests on the different types and contents of anthocyanidins, wherein the carotenoids, flavonoids and alkaloids are the major pigments contributing to color formation of flowers. Purple, crimson, pink and other colors of Lilium spp. are generally caused by different contents of flavonoid (anthocyanin), for example the 'Holean', 'Monte Negro' and 'Red Carrpet' of purplish-red Lilium Asiatic., while the white Lilium spp. does not contain any anthocyanin or flavonol (Yamagishi et al., 2012; Nørbæk and Kondo, 1999). Many studies have pointed out that the biosynthesis of anthocyanins in flowers are primarily regulated at the transcriptional level of biosynthesis genes, which involves multiple transcription factors. LhR3MYB1 and LhR3MYB2 in Lilium spp are capable of inhibiting the accumulation of anthocyanin while the latter is more intensely involved in the negative regulation to inhibit the same (Sakai et al., 2019). CmMYB4 and CmMYB5 in Chrysanthemum×Morifolium negatively regulate the biosynthesis of its anthocyanin (Hong et al., 2019) and additionally, the MYB6 in Populus tomentosa (Wang et al., 2019) and VvMYBA1 and VvMYBA1-1in Vitis vinifera (Xu et al., 2019) are conducive to the biosynthesis of their anthocyanins and proanthocyanidins. In addition, the application of the exogenous ABA can increase the up-regulated expression of MdMYB110ac in Malus pumila. and further increase the content of anthocyanin in the pericarp of Malus pumila (Cho et al., 2020), which demonstrate that the MYB gene family and various subfamilies are conducive to the positive and negative regulations on anthocyanin synthesis.
However, MYB gene alone cannot regulate the anthocyanin synthesis, the bHLH and WD40 are also required to form MBW compound so as to activate the promoter of anthocyanin synthesis structure. The FhTTG1 gene, which can highly activate the gene promoter relating to biosynthesis of anthocyanin (Shan et al., 2019), in the WD40 family of Freesia hybrida is expressed in parallel with the accumulation of proanthocyanidin and anthocyanin in Freesia hybrida. 138 transcription factors bHLH are screened out from the genome of Ziziphus jujube, wherein the ZjTT8, ZjGL3a and ZjGL3b of the III subfamily are highly correlated with the anthocyanin synthesis (Shi et al., 2019).
The research group discovered in the field survey that the wild Lilium cernum experienced color variation, with colors ranging from dark purple to white. The shades and coloration area proportions vary in individuals (Figure 1) and pink ones (Figure 1B) are common while the white (Figure 1A), purple (Figure 1D) and even pinkish white ones (Figure 1C) quite rare. Some studies believe that the pink Lilium Asiatic may be generated from the Lilium cernum (Yamagishi et al., 2014). Furthermore, recent reports suggest that the Japanese scholars divide the Lilium cernum into 2 categories based on the flower color, namely the ordinary pink ones and the variable white ones (L.cernuum var.album) (Yamagishi, 2020), which are consistent with the varieties discovered by the research group in the field (Figure 1A). In addition, the research group also discovered the Purplish-red ones and the pinkish white ones apart from the two categories mentioned above. The purple one has always been a rare one of all the species of Lilium spp., which is also a variation seldomly observed in the wild Lilium spp. Moreover, the purplish-red one and the pinkish white one is completely the same in the early stage. Therefore, the change of color of Lilium cernum from white to dark purple provides an opportunity for the research on the molecular regulation mechanism of anthocyanin biosynthesis of Lilium spp. and is of vital significance to the cultivation of new species of Lilium spp.
Figure 1 Four flower colors type and flower bud development of Lilium cernum
Note: A, white type; B, normal type; C, pink-white type; D, purple-red type; E~L, bud development at different stages
1 Results and Analysis
1.1 Quality of sequencing data
The transcriptome data obtained were assembled (Table 1), from which it could be seen that the number of transcripts was 118 091 with length of 992.93 bp on average. After screening and assembly, 57 521 Unigenes were obtained and the length of N50 was 1 227 bp (870.01 bp on average), ranging from 300 to 1 000 bp mostly. The obtained genes accounted for 73.29% of the total amount of Unigenes, indicating a high assembly integrity.
Table 1 Assembly result statistics
1.2 Unigene function annotation
25 678 annotated Unigene were obtained eventually after selecting the BLAST parameter with E-value not greater than 1e-5 and HMMER parameter with E-value not greater than 1e-10 (Table 2), among which 12 531 annotated ones were with lengths ranging from 300 to1 000 bp and 13 147 annotated ones were above 1 000 bp in length.
Table 2 Unigene annotation statistics
1.3 Differently expressed genes
The number of differential genes of different samples were quite different. In Group Bud Stage versus Purplish-red, the number of differential genes was the largest (up to 3 665) and that of the up-regulated genes was also the largest (up to 2 746). In Group Purplish-red versus Pinkish-white, the number of down-regulated genes was larger than that of the up-regulated genes, while differentially expressed gene sets of other comparison groups indicated that the number of up-regulated genes was larger than that of down-regulated genes. However, in Group Color Conversion Stage versus Pinkish-white, there were only 23 differential genes, wherein the number of up-regulated genes was 3 and that of the down-regulated genes 20 (Table 3).
Table 3 Statistics of the number of differentially expressed genes
1.4 Annotation of KEGG differentially expressed genes
1.4.1 Annotation of differential genes in the metabolic pathway of anthocyanin
6 structural genes differentially expressed in the synthetic pathway of anthocyanin were screened out via the screening of differential genes in metabolic pathway of anthocyanin during different flower development processes of Lilium cernum with specific names, expressions and function annotations of the genes (Table 4). In Group Bud Stage versus Color Conversion Stage during the early flower development, the expressions of DFR, CHS, ANR and ANS were all up-regulated while the expression of FOMT was down-regulated (Table 5). As the flower development continued (in Group Color Conversion vs Purplish-red), the expression of ANS was up-regulated and that of agmatine coumaroyl transferase (ACT) down-regulated, while the expressions of other genes remained the same. In Group Purplish-red versus Pinkish-white, the expression of CHS was down-regulated and that of ACT up-regulated; in Group Bud Stage versus Purplish-red, the expressions of DFR and ANS were up-regulated and the expression of FOMT was down-regulated; in Group Bud Stage versus Pinkish-white, the expressions of 6 differential genes are as follows: the expressions of DFR, CHS, ANR and ANS were up-regulated and the expression of FOMT was down-regulated. Nevertheless, in the Group Color Conversion versus Pinkish-white, the 6 differential genes in metabolic pathway of anthocyanin remained the same.
Table 4 Changes in gene expression levels and functional annotations of differential anthocyanin metabolic pathways
Table 5 Annotation of differentially expressed genes in transfection period and pink-white
1.4.2 Annotation of differential genes (Color Conversion Stage and Pinkish-White)
In terms of two different colors of Lilium cernum., samples at color conversion stage and the pinkish-white state were quite similar in color but different in blossoming state. In the course of sequencing comparison, there were only 23 differentially expressed genes, which were annotated then. Among the 23 differentially expressed genes related to the metabolic process and energy synthesis, there were 5 genes related to cell control and movement. The results of functional annotation showed that (Table 5) 3 out of the 5 differentially expressed genes were from the MCO family and all associated with the synthesis and decomposition of lignin; While the wood cellulose synthase was related to the biosynthetic process and cell movement of cellulose. The expressions of such 5 genes were down-regulated in the process of transformation from the color conversion stage to the pinkish-white state.
1.5 Transcription factors regulation
1.5.1 MYB transcription factors
There were 2 125 transcription factors in the transcriptome database, wherein 244 were MYB and MYB family transcription factors. The MYB and its family members subjected to expression change in the blossoming process of Lilium cernum (Table 6). In the process of transformation from bud stage to color conversion stage, there were 15 genes including MYB2 with expressions up-regulated and 6 genes including MYB52 with expressions down-regulated and the rest 222 remained the same. Additionally, in the process of transformation from color conversion stage to purplish-red state, 7 genes including MYB98 were up-regulated, 3 genes including MYB73 were down-regulated and the rest 234 remained the same. Among the differential genes in Group Purplish-red versus Pinkish-white, 4 including MYB58 were up-regulated and 8 including MYB14 down-regulated, while the rest 232 remained the same. In Group Bud Stage versus Purplish-red, 3 genes including MYB98 were up-regulated and 3 genes including MYB protein L subtype×1 down-regulated, while the rest 238 remained the same. In Group Bud Stage versus Pinkish-white, 1 gene including MYB118 was up-regulated and 2 genes including MYB56 and MYB protein 3R-1 subtype×2 were down-regulated, while the rest 241 remained the same. In Group Color Conversion Stage versus Pinkish-white, expressions of 244 genes remained the same.
Table 6 MYB transcription factors
1.5.2 Transcription factors bHLH
There were 103 bHLH and bHLH family transcription factors, the bHLH and its family members subjected to expression change in the blossoming process of Lilium cernum (Table 7). In Group Bud Stage versus Color Conversion Stage, 2 genes including bHLH54 and bHLH-MYC were up-regulated and 3 genes including bHLH82 down-regulated, while the rest 98 remained the same. In Group Color Conversion State versus Purplish-red, 5 genes including bHLH30 were up-regulated and 2 genes including bHLH35 and bHLH52 down-regulated, while the rest 96 remained the same. In Group Purplish-red versus Pinkish-white, 3 genes including bHLH35 were up-regulated and 3 genes including bHLH30 down-regulated, while the rest 97 remained the same. In Group Bud Stage versus Purplish-red, 6 genes including bHLH30 were up-regulated and 4 genes including bHLH35 down-regulated, while the rest 93 remained the same. In Group Bud Stage versus Pinkish-white, 2 genes including bHLH54 and bHLH-MYC were up-regulated and 3 genes including bHLH52down-regulated, while the rest 98 remained the same. However, in Group Color Conversion Stage versus Pinkish-white, expressions of 103 genes remained the same.
Table 7 bHLH transcription factors
1.6 qRT-PCR verification of differentially expressed genes
6 differentially expressed genes were screened out for qRT-PCR verification (Table 8). The results showed that the expression of CHS is the highest at color conversion stage and the second highest at the pinkish-white state, between which the difference was not significant. However, the expression of CHS was the lowest at bud stage, showing an extremely significant difference in comparison with that at color conversion stage, purplish-red state and pinkish-white state; the expression of ANS increased constantly in the process of transformation from bud stage to purplish-red state and there was a significant difference between expressions at color conversion stage and pinkish-white state; the expression of MYB98 kept increasing in the process of transformation from bud stage to purplish-red state, while the difference among expressions at pinkish-white state, bud stage and color conversion stage was not significant, but the difference between expressions at pinkish-white state and the purplish-red state was extremely significant; the expression of MYB14 was not significantly different at bud stage, color conversion stage or pinkish-white state while that at the purplish-red state was the highest, showing an extremely significant difference in comparison with other stages or state; the expression of bHLH52 was the highest at bud stage and the lowest at purplish-red state, while the difference between expressions at color conversion stage and pinkish-white state was not significant; the expression of bHLH95 at purplish-red state was the highest and showed an extremely significant difference in comparison with that at bud stage, color conversion stage and pinkish-white state.
Table 8 qRT-PCR verification of some differentially expressed genes
Note: The data in the table is the mean±standard deviation; different capital letters indicate significant differences between treatments (P<0.01); different lowercase letters indicate significant differences between treatments (P<0.05)
Based on filed observation, the research group divided the blossoming process of Lilium cernum. into two primary stages: the pre-color conversion stage, which included the bud stage and color conversion stage, where there was no obvious change in flower color and the bud kept growing; the post-color conversion stage, at which the floral organs of Lilium cernum. developed into such two states as purplish-red state and the pinkish-white state and the colors kept or stopped being darkened. Therefore, discussions were carried out on the basis of two stages and two color states.
In the research of flowering mechanism, many researches suggested that the color change was mainly caused by the differences in types and contents of anthocyanin and anthocyanidin, while genes involved in the anthocyanin synthesis could be divided into two major categories, namely the structural genes of anthocyanin synthesis, such as GSH and ANS, and the transcription factors activating or inhibiting the enzyme expression. 6 structural genes were screened out after transcriptome sequencing based on the different development states and states of the floral organs of Lilium cernum. and comparing the difference in expression of structural genes of anthocyanin synthesis of floral organs at different stages, and they were: DFR, CHS, ANR, ANS, FOMT and ACT. Wherein, the DFR is able to catalyze the colorless anthocyanin products into colorless pelargonidin, colorless cyanidin and colorless delphinidin; CHI is the first important structural enzyme in the pathway of anthocyanin synthesis, which can catalyze the 4-coumaroyl-CoA into CHI, and CHI is then transformed into colorless anthocyanin by a series of catalytic reactions; ANS then catalyze the colorless anthocyanidin into anthocyanin. This process is also obtained from such flowers as Osmanthus fragrans (Ma et al., 2017) and Brunfelsia acuminata (Min et al., 2016). However, the color change was not obvious in the pre-color conversion stage of Lilium cernum. with a little appearance of purple. In this process, the ANR and FOMT were both up-regulated, which might inhibit or restore the pigments subjected to color conversion. It was pointed out in researches of regulation on colors of Malus crabapple (Li et al., 2019) and Camellia sinensis (Zhao et al., 2017) that the function of ANR was opposite to that of ANS, while ANR was responsible for reducing the anthocyanin synthesis; FOMT was a member of the methyltransferase family of transferases, which regulated the color response of plant tissues by changing the types, chemical stability, water solubility and other characters of anthocyanin. The purple trait in petals of Paeonia spp. were regulated by the methylation of anthocyanin (Du et al., 2015). In lilium cernum colors might be regulated through a similar pathway since DFR, CHS and ANS were up-regulated to increase anthocyanidin at the pre-color conversion stage and ANR and FOMT are up-regulated to reduce the synthesized anthocyanidin, while the same differential expression of genes also occurred in the process of development of Lilium cernum from the bud stage to the white state. Meanwhile, CHS and ANS were verified by qRT-PCR and it was also indicated that the expressions of CHS and ANS increased at the pre-color conversion stage, which was consistent with the sequencing results.
Additionally, the colors of Lilium cernum at color conversion stage and pinkish-white state were basically the same, while the blossoming states were different. After comparing the differentially expressed genes at this stage and state, there were only 23 differentially expressed genes, among which 5 were related to cell movement and cellulose synthesis. Meanwhile, after comparing the expressions of DFR, CHS, ANR, ANS, FOMT and ACT in the pathways of anthocyanin synthesis at color conversion stage and pinkish-white state, it was discovered that the expressions of said 6 genes remained the same. According to comparison by qRT-PCR between the expressions of CHS and ANS at color conversion stage and pinkish-white state, the expressions of CHS at color conversion stage and pinkish-white state was not significantly different, and that of ANS was not extremely different neither, which were basically consistent with the sequencing results. It was proved that the anthocyanin synthesis processes at color conversion stage and pinkish-white state were consistent but the blossoming states were different. As a result, it was speculated that the blossoming process of pinkish-white flowers might be advanced at the color conversion stage due to internal and external environmental changes or other reasons, resulting in blossoming before the completion of color conversion. Nevertheless, since there are few researches on morphological changes during the blossoming process and some scholars point out that the curvature or wrinkle of petals is caused by uneven expansion of the cells in petals (Kawabata et al., 2011), the internal mechanism of the uneven distribution of anthocyanidins on the petals of Lilium cernum.caused by advanced blossoming needs to be supported by more experiments.
According to many researches and reports, the MYB, bHLH and WD40 transcription factors played a significant role in flower color regulation. A large number of MYB and bHLH transcription factors were found in the blossoming process of Lilium cernum. and the MYB and bHLH transcription factors differed in the type and amount of differential expression at different development stages of flowers. Based on the sequencing results, the differentially expressed MYB and bHLH transcription factors were mostly concentrated in the whole process transformation from bud stage to purplish-red state, but less concentrated in the process of transformation from bud stage to pinkish-white state. The MYB and bHLH transcription factors of Lilium cernum. were related to the change of flower colors. For instance, the MYB14, MYB98, MYBC1, PHL7, PHL8, cytochrome P45094A1, bHLH30 and bHLH51 in the process of transformation from color conversion stage to purplish-red state (from light to dark) were all up-regulated, while such same transcription factors in the process of transformation from purplish-red state to pinkish-white state (from dark to light) were down-regulated. The same phenomenon also occurred to transcription factors MYB13, bHLH52 and bHLH35. Such four transcription factors as MYB98, MYB14, bHLH52 and bHLH95 were selected for qRT-PCR verification and the results also indicated that the expressions of MYB98 and MYB14increased in the process of transformation from color conversion stage to purplish-red state the difference was extremely significant, and that compared with the pinkish-white state, the expressions of MYB98 and MYB14 at purplish-red state decreased and the difference was extremely significant. The expressions of bHLH52 and bHLH95 were also consistent with the sequencing results. These phenomena indicated that such transcription factors as MYB14, MYB98, MYBC1, PHL7, PHL8, cytochrome P45094A1, bHLH30, bHLH51, MYB13,bHLH52 and bHLH35 played important positive and negative regulatory roles in the process of anthocyanin synthesis and accumulation. In addition, many researches also pointed out that MYB, bHLH and WD40 interacted with each other to form a binary or ternary complex for the joint regulation on structural genes and anthocyanin metabolic synthesis. However, the differentially expressed transcription factor WD40 was not discovered in this research, which may be that the anthocyanin of Lilium cernum. was regulated by the binary complex of bHLH and R2R3-MYB instead of the ternary complex (Sakai et al., 2011).
Unfortunately, the whole genome sequencing of Lilium spp. has not been completed yet. The MYB and bHLH transcription factor families are considerably large and there are many differences among transcription factors of different species of Lilium spp.Furthermore, no research of the color regulation transcription factors of Lilium spp. has been conducted with respect to the types mentioned above at home and abroad, consequently, specific functions of these transcription factors need to be further verified by more experiments.
3 Materials and Methods
3.1 Sampling
The well-grown Lilium cernum planted in the horticultural farm of Jilin Agricultural Science and Technology University were selected as the experimental materials. Seeds of the Lilium cernum were from Huashan Village, Linjiang City, Jiling Province (N41.881277, E126.829992 and 567.5m above sea level) and floral organs were collected on June 23rd, 2019. With respect to the four colors of Liliun cernum (Figure 1), two more obvious variations (Figure 1D (Purplish-red) and Figure 1C (Pinkish-white)) were selected for sampling since there was only 1 white Liliun cernum with 2 flowers only, which were unable to meet the demands of subsequent experiments. Meanwhile, the development processes of Type C and Type D Liliun cernum before the H stage were identical and their colors began to change after the color conversion stage. Therefore, 2 flower development processes (Figure 1K (Bud Stage) and Figure 1H (Color Conversion Stage)) were selected for sampling. Afterwards, samples were put in pre-sterilized sterile bags. Three parallel samplings were counted as three repetitions. Stamens and pistils were removed after samples in each group were marked. The petals were immediately frozen with liquid nitrogen and brought back to the lab for storage in refrigerator at -80°C.
Total RNA from the petals of Lilium cernum. was extracted by using the polysaccharide and polyphenol total RNA isolation kit (TIANGEN, CHINA). After the total RNA was tested and qualified by agarose gel electrophoresis, the OD value was measured with the microvolume UV-Vis spectrophotometer (NanoPhotometerTM P-Class, USA). A260/280 ranged from 1.70 to 1.90, and the DNA concentration was above 100 μg·L-1. The extraction was stored in refrigerator at -80℃ after satisfying demands of subsequent experiments.
3.3 Database establishment and sequencing
Transcriptome sequencing was performed on the total RNA of the extracted petals by Beijing Biomarker Technologies Co., Ltd. with the adoption of Illumina novaseq 6000 (Illumina, The United States). In order to ensure the data quality, the raw data was filtered and Trinity (v2.4.0) was used for data assembly. After the assembly, BLAST (https://blast.ncbi.nlm.nih.gov/Blast.cgi) was applied to compare the gene annotations with such databases as NR (ftp://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/nr.gz), Swiss-Prot (ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gz), GO (http://geneontology.org), COG (https://www.ncbi.nlm.nih.gov/COG/), KOG (ftp://ftp.ncbi.nih.gov/pub/COG/KOG/kyva), eggNOG4.5 (http://eggnogdb.embl.de/) and KEGG (http://www.kegg.jp/kegg). Afterwards, DESeq2 (v1.23.10) was used to analyze the differential expressions between sample groups, and the differentially expressed genes were classified into COG and eggNOG respectively. After comparing with the KEGG database, the differential genes in the anthocyanin metabolic pathway were screened out.
3.4 Screening of differentially expressed genes
DESeq2 (v1.25.9) was applied to the analysis of differential expressions between sample groups so as to obtain differentially expressed gene sets between different samples. Among which, FC (Fold Change) ≥ 2 was marked as up-regulated genes and FC<0.05 was marked as down-regulated genes, which was of statistical significance (P<0.05).
3.5 Determination by qRT-PCR
Quantitative real-time PCR (qRT-PCR) was used to determine the transcript level of differentially expressed genes in the four developmental processes of Lilium spp. SYBR Premix Ex Tag (Tli RnaseH Plus, TaKaRa) was used for qRT-PCR while cDNA (diluted to 20×) served as the template, and the operation was carried out according to the instructions. The gene-specific primers for qRT-PCR were designed by Primer Express (v3.0), and the reference gene adopted the general actin of Lilium spp. (LhActin, NCBI accession number: JX826390). qRT-PCR specific primers and endogenous reference were listed (Table 9).
Table 9 Specific primers and internal reference primers
CSP and ZQQ designed and executed the experiments of this research; WW collected the samples and LSH performed the data analysis; LRR participated in experiment design and experiment result analysis; YTY wrote and revised the paper. All authors read and approved the final manuscript.
This study was supported by the "Thirteenth Five-Year" Science and Technology Project of the Education Department of Jilin Province (JJKH20190982KJ) and the Central Finance Forestry Science and Technology Promotion Demonstration Project (JLT2020-39).
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. Shaopeng Chen
. Shihao Li
. Ruirui Li
. Tingyu Yin
. Qianqian Zhuang
. Lilium cernum
. Flower color
. High-throughput sequencing technology
. Anthocyanin
. Transcription factor


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Freesia Lane
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In Defense of Biden
I must start with full disclosure. Biden is not my first choice for the Democratic candidate for the presidency. I can't really say why, actually. If I think about it without any personal prejudice, he might just be what our country needs. He is liked by many on both sides of the aisle. No one has a visceral negative response to him, unlike people have for many other candidates. So, when I think about it, he probably has the power to heal our divided nation.
But that's not what this post is about. This post is about what happened last night.
What took place last night on the debate floor is that all those ridiculous candidates sold their ethics and their party down the river because the pundits said that is what they needed to do in order to to stand out. Pundits drive all behavior now, and they spent much of yesterday laying the groundwork for what they wanted: TV soundbites of everyone attacking Biden. Most candidates took the bait and made that their mission. They betrayed themselves and their party — and our country. Instead of coming across as candidates I want to lead our nation, they acted like praying mantises. After praying mantises mate, the woman bites off the head of her partner, killing him instantly. Biden has been good to everyone on that stage. He has supported them all along.
Since Biden did not return the "favor" last night, he's now being called lackluster. I'll take being called "lackluster" over selling out my party and trading in my soul for a soundbite on CNN that will be forgotten when the news cycle ends. Last night, those candidates who went after him were like the GOP going after good people just to get Trump's approval, or I should say, to stay out of Trump's destruction-driven Twitter feed.
Discourse like this is beneath us all. Last night's debate was a disaster for those running, for the party, and for the country.
Joe Biden is a good guy — in many ways, a great guy — and he will always be uncomfortable in aggressively attacking people with whom he sits on the same side of the fence. At one point last night, he turned to someone who was angrily addressing him, and said, "Good to know, because you and I speak all the time." What he was saying, in my opinion, was, "This is not how you and I speak; I'm saddened that you think it will help you and that you are willing to check our relationship at the door." He also said, "That is malarkey!" Malarkey?! I'm surprised Google didn't report that as a top keyword search last night. The younger generations haven't heard that word before; even I haven't heard it since my dad passed away a few years ago.
When his wife and small daughter were killed in a car accident years ago and his two small sons were in the hospital, Joe Biden resigned his newly gained senatorial seat. He explained that he had to give his sons all of his attention. The senators on both sides of the aisle replied that they would cover for him, but that he wasn't going anywhere and that he should come back when he could. Joe Biden values family and work. He hails from a labor union home, where his dad taught him about country and loyalty. He is the best of Americans. Yes, Biden does invade people's personal space; I have felt it. BUT, he does so in the way an overexcited puppy does, not in a sexually predatorial way; at least, that is my opinion. He means no harm, and intention does matter.
Whoever stands up and starts talking about the difference between his/her ideas and those of the others, stressing that we all want the same thing: "a great America for all who call her home," and does so with a cool, kind, compelling, "I would like to date that person" presence will seize the day, in my opinion.
Here are some soundbites that would have brought them all to higher ground:
"I simply will not put down the other candidates here. I will tell you, as I tell them across the table when we are together, why I like my idea better. So, let me tell you my plan for health care."
"I will not speak about Donald Trump. If I am chosen to go up against him next fall, I can promise you, I have much I would like to say to him. But right now, it's about showing you who I am and what I stand for, and how I can serve you. He is not worth my time right now."
"Donald Trump? Seriously? I believe the American people have seen through him; they don't need me to tell them why. They need me to show them who I am and what I will do and how I will represent them. That's what I'm here to do tonight."
"I watch 'The Handmaid's Tale,' and the phrase 'under his eye' haunts me. Under the eye of those in power now, we are putting people in cages. People are dying because they can't pay for health care. People are not reaping the benefits of what we keep being told is the best economy in the history of the universe. 'Under his eye' has new meaning in today's world. Enough said."
"Gun control is not what it's about. It's about not needing to have an instrument that shoots off more than 50 bullets a second. It's about degree. It's always about degree, and there is always a middle ground that is palatable to all. I do not believe that anyone who supports the NRA likes the headlines in today's shooting-every-single-day world."
It's not about attacking Biden. It's not about attacking Trump. And that strategy, in my opinion, will not beat Trump. Besides, it's beneath all of you. Stop it.
August 2nd, 2019 | Leave a comment
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Science Fiction & Fantasy Meta
Science Fiction & Fantasy Stack Exchange is a question and answer site for science fiction and fantasy enthusiasts. It only takes a minute to sign up.
What is The Culture's industrial capacity?
I'm looking for information on the production power of the Culture. Especially useful would be answers to:
How long does it take a ship to produce another ship equivalent to itself (i.e. the doubling time of any fleet)?
Does productive power scale linearly with ship size?
What are the bottlenecks for exponential growth, or what parts of new ships take most of the industrial effort to create and which require minimal effort (e.g. new Minds, effectors, hyperspace drives, the body of the ship)?
Are ships constructed primarily by effectors (so effector power is a limiting factor), or by something else (nanobots?).
the-culture
eteete
As a rule of thumb nano-machines are small (very small) and as we currently understand the technology work best when doing small things under the command of larger computer/Minds. If you want to build megastructures, nanomachines are not the best way. Megastructure usually require facilities nearly as large as themselves, even in the advanced technology of the Culture. – Thaddeus Howze♦ May 18 '14 at 19:08
@Thaddeus - Or a very long time. – Valorum May 18 '14 at 19:33
@Thaddeus Makes sense. My reason for thinking nanobots may play a role (directed by minds) is that self-replicating nanobots should have a vastly lower doubling time than the apparent doubling times for larger Culture constructs, so would be able to scale up much faster with abundant materials and a Mind providing instructions+displacer transport. Perhaps they have self-rep nanobot technology, but avoid it at all costs because it's hegeswarmy? – ete May 19 '14 at 1:36
There are no objective 'in universe' answers to the question you've posed. We can make some educated guesses and on-the-back-of-a-napkin calculations if you'd like:
How long does it take a ship to produce another ship equivalent to itself?
If we assume that the constructed fleet seen at the end of the book "Excession" is roughly equivalent to a "replicating event" then the answer is that the single largest ship-type seen in the Culture fleet (a GSV) can probably be constructed in as little as 20-30 years, assuming adequate materials were to hand. This tallies nicely with the events of the Idiran war, in which we see the Culture create a brand new class of vessel, the GOU and ROU (roughly half the size of a GSV) which then takes approximately 15-20 years to go from design to production.
The largest GSVs seem to agglomerate in size as they age, starting at around 25KM and growing to as much as 200KM at the upper end of their lifecycle.
Yes, absolutely. The principle, well established in the Contact novels, as well as in Bank's own "Notes on the culture" is that a General Systems Vehicle or a completed Orbital is an holographic representation of the Culture, capable of reproducing any object or structure found elsewhere in the Culture up to and including a viable Culture population
Smaller ships (Offensive Units and the like) seem to be restricted to producing their own drones, munitions and small "lifeboat" style units controlled by AI cores. The production of mind-controlled craft is left to larger System- and Contact- Class vessels as well as Rings.
What are the bottlenecks for exponential growth?
Culturally, the Culture spurns exponential growth. They view this as crass and akin to the actions of an homogenising swarm. Per Banks' own notes;
"why? What is the point? To put it in what we might still regard as frivolous terms but which the Culture would have the wisdom to take perfectly seriously, where is the fun in that?
Interest - the delight in experience, in understanding - comes from the unknown; understanding is a process as well as a state, denoting the shift from the unknown to the known, from the random to the ordered... a universe where everything is already understood perfectly and where uniformity has replaced diversity, would, I'd contend, be anathema to any self-respecting AI."
Which part of a ship is the hardest part to build?
Arguably the most valuable part is the Mind. We see a factory tasked with the production of ships in Consider Phlebas. They prioritise the Mind above all else when the facility is attacked and there is some suggestion that the production of a Mind is considered the highest faculty of Culture technology.
Are ships constructed by nano-machines or effectors?
It is only within the most recent Culture novels that there's been a mention of increasing use of eDust and nano-machines in the Culture's culture. The majority of production in previous novels is either managed by effectoring pieces into their correct configuration or, as we see in Player of Games, allowing humans to have a small (and largely trivial) role in physically manhandling the parts into place.
ValorumValorum
Useful information, thanks! Re: Culture avoiding exponential growth/doubling times, I'm planning on running a game where an initially tiny Culture Ulterior fleet has a goal of having a large effect on a galaxy in trouble (40k). I'm struggling to square decade+ industrial doubling times with their level of tech, is there any indication that they're massively holding back on growth even during the Iridian war? Maybe self-repair feats would be at least partly relevant? And any hints about how much direct from gridfire production slows them compared to using available matter? – ete May 18 '14 at 16:07
@ete - At the start of the Idiran war, the aim was pure survival, moving ships and populations out of harm's way as well as fighting holding actions. By year 20(ish) the pendulum had swung towards war production and essentially unlimited growth – Valorum May 18 '14 at 16:14
@ete - Any ship larger than an LCU should, in principle be able to perform a complete repair on anything up to and including near-total destruction; en.wikipedia.org/wiki/… – Valorum May 18 '14 at 16:16
Re: Iridian war, so perhaps fitting with a much higher production power per ship than doubling times in the decades would indicate (maybe low years or months?), but in the early stages all resources were needed on the front lines not production? Re: Repair, anything about how long a near total destruction repair would take? I remember a drone speculating about taking ~a month to self repair from extreme damage, but self-repair is less helpful other than establishing a lower limit for repair speed because the repair tools are also likely damaged. – ete May 18 '14 at 16:41
@ete - No canon confirmation. It would depend on how damaged you are and how repaired you want to be. The shipyard in Consider Phlebas was able to cobble together a rudimentary spaceship within days out of a "depleted stock of components, even though most of the weapon, power and sensory systems were either faulty, superseded or due for overhaul". The smart move would be to make something capable of getting you to a dockyard, not effecting a total repair. – Valorum May 18 '14 at 16:55
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A total of 53% of US participants admitted to having lied in their online dating profile.Women apparently lied more than men, with the most common dishonesties being about looks.
Teens have much more free will than children, and there are a number of new options available to them.
This Sims 3 Guide was originally written for the PC and Mac versions of the game, but also will help owners of the console versions - PS3, Xbox 360 and Wii.


VANCOUVER — After realizing she'd won a $39.5-million Lotto Max jackpot, Michelle De Roma did something most winners don't — she put the ticket in an envelope in a safe place and waited a week to claim her prize.
The mother of three from Surrey, B.C., says she wanted to focus on enjoying the holidays and celebrating her husband's birthday before their world shifted.
"This will change our life," she said Friday at a news conference.
De Roma plays the lottery about every week and the winning Lotto Max numbers were randomly generated through a quick pick. She bought the ticket at Tsawwassen Mills shopping centre in Delta while doing some Boxing Day shopping.
When she realized she had the single winning ticket matching all seven numbers in the Dec. 28 draw, she told her husband first.
"I just hugged my husband because he's the one who supported me all the way with this. He just said, 'Wow!' And then hugged me and kissed me," De Roma said.
De Roma said she hasn't told her children yet but she wants to use the money to build a good life for them, and also travel to Rome to see St. Peter's Basilica and the Coliseum.
All lottery winners have 52 weeks from the draw date printed on their ticket to come forward to claim their prize.
The odds of winning a Lotto Max jackpot are one in 28,633,528 per play, the B.C. Lottery Corp. says.
De Roma said she considers the win an "amazing blessing," and had hoped for a miracle whenever she bought lottery tickets.
She plans to continue playing the lottery.


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Very knowledable, good content to course.
Really enjoyed the course. Become more confident presenting.
Training sessions were delivered in such an interesting way. I enjoyed manual handling sessions for the first time.
A quick and through course that supports and guides you to a career as a first aid trainer.
Gerally good. Included all relevant info for the teaching + delivery + knowledge base.
Steve is engaging and knowledable in all areas. Makes learners feel at ease and would recommend. Cheers!
Would like to express my satisfaction on the trainer's course I attended last month. It was indeed a wonderful experience. Steve is absolutely an expert trainer!
Just the job for the training I ned to teach.
Very enjoyable course that I could recommend to other trainers.


text:
Jeskyně Dagmar je propasťovitá jeskyně ponorového charakteru, která leží na katastrálním území obce Lipovec v Moravském krasu asi 100 metrů od Ostrovského žlebu.

Jeskyně leží v Jedelském žlíbku a je svým vznikem vázána na Jedelský potok, který se propadá pod zem v propadání "V Jedlích". V jeskyni se nacházejí propasti, z nichž největší má hloubku 28 metrů. Je zde pestrá krápníková výzdoba, z dómů vybíhají až 15 metrů vysoké komíny. Celkově má jeskyně asi 200 metrů chodeb a síní.

Novodobě byla jeskyně Dagmar objevena v roce 1959, avšak z archeologických nálezů vyplývá její užití ve 13. a 14. století, což dosvědčují nálezy střepů z tohoto období. V 17. století sloužila jeskyně jako padělatelská dílna mincí.

Práce v jeskyni probíhaly od šedesátých let 20. století a k největším objevům došlo v letech sedmdesátých. Výzkum zde provádí Česká speleologická společnost ZO 6-08 DAGMAR, který se zabývá i zkoumáním propadání "V Jedlích" a jeskyně "U Jedelské cesty".

Fotografie

Externí odkazy

 ZO 6-08 DAGMAR

Jeskyně v Moravském krasu
Lipovec (okres Blansko)

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text:
Behind BBVA's ramp of its Banking as a Service offering in the US
BBVA built its banking as a service platform to service its own in-house banking brands.
Now, the global bank wants to white label its banking services to the broader US technology market.
This month, we're focused on banking as a service — defining it, understanding it, trying it on to see where it leads. The term BaaS is batted around a lot in the industry as it alludes to the near term evolution of a bank's role in the financial system. But, like a lot of emerging technologies, there isn't consensus on what it means. It definitely involves cloud-hosted banking services delivered to third parties applications via connections called APIs. Global bank BBVA has made a big bet on the opening up of banking tech infrastructure and in the US, is focused on ramping adoption of its banking as a service platform.
Today, on the podcast we talk with Brent Baker, the head of growth and operations at BBVA's Open Platform, which means he's in charge of bringing new customers and maintaining risk and control. We focus primarily on his work with the firm's banking as a service offering and how it fits into BBVA's global strategy of being the bank of billions of people.
BBVA's Open Platform
Open Platform is a subset of our larger Open Banking initiative that the bank is leading. For the global bank, Open Banking is a key part of its strategy, understanding that this strategy must align with the markets it participates in.
Open Banking is active in Spain (where BBVA's headquarters are), Mexico with Bancomer, and in the US with Compass. What's unique about the US is that we're really focused on our banking as a service solution. We look at it as a white label solution to let third parties take advantage of our core banking capabilities, as opposed to some other open banking settings where BaaS only gives access to existing customer data.
When we describe banking as a service at BBVA in the US, the key is that it's a white label experience. We're providing not only read functionality but write functionality. We allow a client of ours to launch their application or service, incorporate core banking capabilities that they don't typically have access to via a set of APIs. That's what makes it an open platform.
We don't view this as yet another channel for bank-branded products. You see a lot of banks rolling out developer platforms. It's become table stakes for major institutions. They often provide access to existing branded services. So, you can get access to the Wells Fargo ACH solution via API, or you can originate a Capital 360 savings account — all great services for a specific market.
We're going after clients who want to control the experience end to end but take advantage of the same services.
BBVA's move into open banking and banking as a service
When BBVA acquired Simple in 2014, as part of that acquisition, it needed to transfer Simple off its core provider and onto the Compass core. To do that, BBVA needed to build a platform that gave Simple access to the bank's functionality, from treasury management to card issuance. But, Simple needed to control the end experience, as it had up until that point.
The bank was also launching two neobanks of its own, Azlo and Denizen, and took what it had done for Simple and launched them on the same platform. Now, at the end of 2017, you have three operational banks on this platform. The bank then decided to see if there was a market for this technology outside BBVA.
We put a product in market Q1 2018 and went through a pretty extensive beta period. Our cohort group gave us feedback on the product and on the onboarding experience, and also gave us feedback on our pricing structure. This lead to the launch of our banking as a service launch at the end of Q3 2018. We've been in market for about 6 months.
We've learned that our offering is unique — there aren't that many products in the US like it. We've brought on clients who are eager to scale with us. They like the fact that they get support from our client integration team. We don't see ourselves as a vendor in this scenario. We see it as a true partnership.
Digit traditionally had a closed-loop savings program. They've done a great job of building an active and vibrant customer base and helping customers reach savings goals. Digit is taking advantage of Open Platform's payment capabilities — ACH and bill payment — to help customers set a debt reduction target and pay down their debt.
Growing the BBVA BaaS brand
Awareness and storytelling are a big emphasis for us right now. We're in market, talking to a lot of people, understanding how to position ourselves. We're covering a lot of channels and doing more with media and press. We're also leveraging our existing partnerships to help tell our story.
In 2018, we demonstrated that there was market fit, that we knew the pricing targets that would play in the market and that we could get this to market. Now that we're in market, we're focused on scalability. We're focused on how to continue to scale the onboarding of clients while still offering support to our clients in a controlled manner.
How BBVA differentiates itself
I think it's 2 things. The first is our robust suite of services. We offer a wide range of banking solutions — it's a one stop shop.
Where I feel we are really setting ourselves apart is the emphasis around the developer experience. We've spent a lot of time thinking about developer onboarding, our API documentation and the design of our APIs. We set out a mission from the beginning not to design the Open Platform the way a bank would. I don't want to offend anyone with that, but we didn't want to create an ACH API. We wanted to create a unified payments solution that minimizes the number of parameters and makes it easy for our clients to scale.
Stripe and Twilio have really well-designed APIs. Why shouldn't a bank?
Radius Bank is the first bank to offer a savings account within NerdWallet's mobile app
NerdWallet now offers a Radius savings account to its users.
Radius Bank partnered with the personal finance manager on this product launch.
The investment case for Embedded Finance
Embedded finance offers a new paradigm for the future of financial services.
Anthemis partner David Galbraith provided his firm's view on how to best invest in the changes.
Michael Deleon | November 26, 2019
What's holding Embedded Finance back?
Embedded Finance is still in its very early days with growth ahead for the industry.
We asked attendees at the Embedded Conference what one hurdle needs to be cleared in order to maximize growth.
'Skate to where the puck is heading': The state of embedded finance
Industry leaders offered their perspectives on where embedded finance is headed at the inaugural Embedded Conference
The future of embedded financial services will require better customer experiences and aligning incentives around client performance.
Zack Miller | November 20, 2019
Considered as a challenger bank, Green Dot would be one of the biggest
Green Dot's consumer bank and BaaS are a 1-2 punch.
On an end-user basis, it could be considered the largest challenger bank in the world.


text:
Q: Reading a new dataset in the same format as mnist dataset is read in TensorFlow I have a deep learning model where I have to input images of size say 100X100.  The data i have is
train images - x_train (530,100,100),
train labels - y_train (530,4),
test images - x_test(89,100,100),
test labels - y_test(89,4).
The dataset mnist is read using -
mnist = input_data.read_data_sets('MNIST_data', one_hot=True)

and it generates something like this-
Datasets(train=tensorflow.contrib.learn.python.learn.datasets.mnist.DataSet object at 0x7fd64cae76a0,
validation=tensorflow.contrib.learn.python.learn.datasets.mnist.DataSet object at 0x7fd64cae7be0,
test=tensorflow.contrib.learn.python.learn.datasets.mnist.DataSet object at 0x7fd64cae7400)

I have to transform my data in this same format so as this works with the code i Have. please help
    epochs = 20
    batch_size = 100
    image_vector = 28*28

for i in range(epochs):
    training_accuracy = []
    epoch_loss = []

    for ii in tqdm(range(mnist.train.num_examples // batch_size)):

        batch = mnist.train.next_batch(batch_size)

        images = batch[0].reshape((-1, 28, 28))
        targets = batch[1]

        c, _, a = session.run([model.cost, model.opt, model.accuracy], feed_dict={model.inputs: images, model.targets:targets})

        epoch_loss.append(c)
        training_accuracy.append(a)

    print("Epoch: {}/{}".format(i, epochs), " | Current loss: {}".format(np.mean(epoch_loss)),
          " | Training accuracy: {:.4f}%".format(np.mean(training_accuracy)))

EDIT 1 :
 As suggested , I did the following-
num_examples=271
batch_size=10
buffer_size=271
num_cpu_cores=4
dataset = tf.data.Dataset.from_tensor_slices((x_train, y_train))
dataset = dataset.shuffle(buffer_size, reshuffle_each_iteration=True).repeat()
#dataset = dataset.apply(tf.data.batch( batch_size=batch_size, num_parallel_batches=num_cpu_cores))

#batch1=dataset.batch(10)

iterator = dataset.make_one_shot_iterator()
sess = tf.Session()
sess.run(tf.global_variables_initializer())
for ii in tqdm(range(num_examples // batch_size)):
    batch = iterator.get_next()
    images = batch[0]
    targets = batch[1]

    c, _, a = sess.run([model.cost, model.opt, model.accuracy])

    epoch_loss.append(c)
    training_accuracy.append(a)

    print("Epoch: {}/{}".format(i, epochs), " | Current loss: {}".format(np.mean(epoch_loss)),
          " | Training accuracy: {:.4f}%".format(np.mean(training_accuracy)))

The images and targets are not batches but a single image and label.

(,
  )

Please suggest how to batch the data and feed into sess.run
EDIT 2 :
This is the entire code for the algorithm-
def LSTM_layer(lstm_cell_units, number_of_layers, batch_size, dropout_rate=0.8):
    '''
    This method is used to create LSTM layer/s for PixelRNN

    Input(s): lstm_cell_unitis - used to define the number of units in a LSTM layer
              number_of_layers - used to define how many of LSTM layers do we want in the network
              batch_size - in this method this information is used to build starting state for the network
              dropout_rate - used to define how many cells in a layer do we want to 'turn off'

    Output(s): cell - lstm layer
               init_state - zero vectors used as a starting state for the network
    '''

    #layer = tf.contrib.rnn.BasicLSTMCell(lstm_cell_units)
    layer = tf.nn.rnn_cell.LSTMCell(lstm_cell_units,name='basic_lstm_cell')

    if dropout_rate != 0:
        layer = tf.contrib.rnn.DropoutWrapper(layer, dropout_rate)

    cell = tf.contrib.rnn.MultiRNNCell([layer]*number_of_layers)

    init_size = cell.zero_state(batch_size, tf.float32)

    return cell, init_size

def rnn_output(lstm_outputs, input_size, output_size):
    '''
    Output layer for the lstm netowrk

    Input(s): lstm_outputs - outputs from the RNN part of the network
              input_size - in this case it is RNN size (number of neuros in RNN layer)
              output_size - number of neuros for the output layer == number of classes

    Output(s) - logits,
    '''

    outputs = lstm_outputs[:, -1, :]

    weights = tf.Variable(tf.random_uniform([input_size, output_size]), name='rnn_out_weights')
    bias = tf.Variable(tf.zeros([output_size]), name='rnn_out_bias')

    output_layer = tf.matmul(outputs, weights) + bias
    return output_layer

def loss_optimizer(rnn_out, targets, learning_rate):
    '''
    Function used to calculate loss and minimize it

    Input(s): rnn_out - logits from the fully_connected layer
              targets - targets used to train network
              learning_rate/step_size

    Output(s): optimizer - optimizer of choice
               loss - calculated loss function
    '''
    loss = tf.nn.softmax_cross_entropy_with_logits(logits=rnn_out, labels=targets)
    optimizer = tf.train.AdamOptimizer(learning_rate).minimize(loss)
    return optimizer, loss
class PixelRNN(object):

    def __init__(self, learning_rate=0.001, batch_size=10, classes=4, img_size = (129, 251), lstm_size=64,
                number_of_layers=1, dropout_rate=0.6,clip_rate=None):

        '''
        PixelRNN - call this class to create whole model

        Input(s): learning_rate - how fast are we going to move towards global minima
                  batch_size - how many samples do we feed at ones
                  classes - number of classes that we are trying to recognize
                  img_size - width and height of a single image
                  lstm_size - number of neurons in a LSTM layer
                  number_of_layers - number of RNN layers in the PixelRNN
                  dropout_rate - % of cells in a layer that we are stopping gradients to flow through
        '''

        #This placeholders are just for images
        self.inputs = tf.placeholder(tf.float32, [None, img_size[0], img_size[1]], name='inputs')
        self.targets = tf.placeholder(tf.int32, [None, classes], name='targets')

        cell, init_state = LSTM_layer(lstm_size, number_of_layers, batch_size, dropout_rate)

        outputs, states = tf.nn.dynamic_rnn(cell, self.inputs, initial_state=init_state)

        rnn_out = rnn_output(outputs, lstm_size, classes)

        self.opt, self.cost = loss_optimizer(rnn_out, self.targets, learning_rate)

        predictions = tf.nn.softmax(rnn_out)

        currect_pred = tf.equal(tf.cast(tf.round(tf.argmax(predictions, 1)), tf.int32), tf.cast(tf.argmax(self.targets, 1), tf.int32))
        self.accuracy = tf.reduce_mean(tf.cast(currect_pred, tf.float32))

        self.predictions = tf.argmax(tf.nn.softmax(rnn_out), 1)

tf.reset_default_graph()
model = PixelRNN()
num_examples=271
batch_size=10
buffer_size=271
num_cpu_cores=4
dataset = tf.data.Dataset.from_tensor_slices((x_train, y_train))
dataset = dataset.shuffle(buffer_size, reshuffle_each_iteration=True).repeat()
#dataset = dataset.apply(tf.data.batch( batch_size=batch_size, num_parallel_batches=num_cpu_cores))

dataset = dataset.batch(10) # apply batch to dataset

iterator = dataset.make_one_shot_iterator() # create iterator
sess = tf.Session()
sess.run(tf.global_variables_initializer())
for ii in tqdm(range(num_examples // batch_size)):
    batch = iterator.get_next() #run iterator
    images = batch[0]
    targets = batch[1]

    c, _, a = sess.run([model.cost, model.opt, model.accuracy],feed_dict={model.inputs: images, model.targets:targets})

    epoch_loss.append(c)
    training_accuracy.append(a)

    print("Epoch: {}/{}".format(i, epochs), " | Current loss: {}".format(np.mean(epoch_loss)),
          " | Training accuracy: {:.4f}%".format(np.mean(training_accuracy)))

When I do as suggested, I get the following error-

TypeError: The value of a feed cannot be a tf.Tensor object.
  Acceptable feed values include Python scalars, strings, lists, numpy
  ndarrays, or TensorHandles.For reference, the tensor object was
  Tensor("IteratorGetNext:0", shape=(?, 129, 251), dtype=float32) which
  was passed to the feed with key Tensor("inputs:0", shape=(?, 129,
  251), dtype=float32).

Unable to figure out whats going wrong here

A: If you have your dataset as numpy array or list of image files, use from_tensor_slices.
Define parse function, use read_file and decode_image if you use list of filenames, else just apply any preprocessing
def parse_image(filename, label):
    file = tf.read_file(filename)
    image = tf.image.decode_image(file)
    #do any image/label preprocessing here
    return image, label

Then define dataset object. In general, use length of your dataset as shuffle buffer, but it may depend on size. Repeat function will control epochs(no value pass = indefinite iteration). If you don't need any preprocessing, substitute line dataset.apply, with dataset = dataset.batch(batch_size)
dataset = tf.data.Dataset.from_tensor_slices((x_train, y_train))
dataset = dataset_train.shuffle(buffer_size, reshuffle_each_iteration=True).repeat()
dataset = dataset.apply(tf.data.batch( batch_size=batch_size, num_parallel_batches=num_cpu_cores))

Create iterator. In general, there's no need to use feed dict, if only your input array will not cause 2GB graphdef limit.
iterator = dataset.make_one_shot_iterator()
batch = iterator.get_next()

Edit: You need to create iterator out of dataset, Here's the overall structure:
dataset = dataset.batch(10) # apply batch to dataset
iterator = dataset.make_one_shot_iterator() # create iterator
batch = iterator.get_next() #run iterator
images = batch[0]
targets = batch[1]

logits = Model_function(images)
loss = loss_function(logits, targets)
train_op = optimizer.minimize()

sess = tf.Session()
sess.run(tf.global_variables_initializer())

for i in range(steps):
    sess.run(train_op)

redpajama_set_name: RedPajamaStackExchange


Which is obviously exactly what I'm doing now. Not only the sharing part of it, but also the other thing: dear readers, oh "What a difference your love makes". It would be rather pointless to write a blog if I had no readers, wouldn't it. If a tree falls in a forest and no one hears it, does it make a sound? Similarly, if a blogger writes blog entries and no one reads them, does it make any difference? Well, with your love, it makes. So thanks again for reading the blog, and remember: if you like what you see, feel free to share with others as well.


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The soundtrack to Wes Anderson's second fully animated film.
Doesn't disappoint, as usual! I bought the soundtrack before even seeing the film. I enjoy the soundtrack even more after seeing the movie, which is spectacular.
I was stuck listening to my sister's piano, until THIS gem came along.
The movie is amazing, and the soundtrack mirrors that.
Another win by Alexandre Desplat just as good as Fantastic Mr.Fox soundtrack!


Summary : A drama about a woman who changes her career and eventually becomes a president of a car sales company in a male-oriented society of the 1970's. Makino Hisako quits her job at a leading textile company before turning 25, which is considered the retirement age for women at that time, and starts working as a car salesman. The drama depicts her success story along with her high school classmates, the baby-boom generation.


text:
Leading psychology professor and DMU PVC Research joins Wandsworth Council in advisory role
A leading psychology expert and the Pro Vice-Chancellor for Research at De Montfort University Leicester (DMU) has been appointed by Wandsworth Council to help tackle social isolation and loneliness.
Professor Rusi Jaspal, who lives in the London Borough, has been named the new Adult Social Care and Public Health Advisor for the council thanks to his extensive experience in the field of health and wellbeing.
As PVC Research and a Professor of Psychology and Sexual Health at DMU, Prof Jaspal's work focuses on researching and developing effective interventions for enhancing health and wellbeing in marginalised groups in society.
He will use his experience to help strengthen services across his home borough, with a focus on increasing skills and knowledge around behaviour change.
"I am particularly interested in Wandsworth because I am a resident there, so it's really great to have the opportunity to work with the council to look at ways of enhancing health and wellbeing among our residents," said Prof Jaspal.
"Combating loneliness and developing a sense of community among our residents is so important because we know that a sense of community means that people enjoy better mental health and better physical health outcomes.
"We also need to give people a sense of autonomy, resilience and independence to make the decisions that are really going to enhance their own wellbeing and the wellbeing of others in their communities."
Having conducted a wealth of research into health and wellbeing on both a local and national scale, Prof Jaspal was headhunted for the role by Councillor Paul Ellis, Wandsworth Council's former cabinet member for Adult Care and Health.
"There are a number of academics around the country who are experts in this field and we are fortunate to have one living in Wandsworth," said Councillor Ellis. "We are delighted to be working with Prof Jaspal. He will be a critical friend to the council and as an Adult Social Care and Public Health Advisor help us deliver better services for our residents."
DMU Professor wins national prize for sexual health work
Find out about Psychology at DMU - book a visit to our next open day
DMU Professor is awarded the British Psychological Society's highest honour
Social isolation and loneliness is known to have a negative impact on individual health and wellbeing at different stages of life. In Wandsworth only 41% of adult social care users surveyed say that they have as much social contact as they would like.
Carers are also at increasing risk of isolation with only 25% of carers in Wandsworth having as much social contact as they would like, compared to 37% across London.
One of the highest risk factors for experiencing loneliness is age. Around 8% (10,385) of households in the borough are occupied by a single person aged 65 or over, and around 40% (10,835) of people aged 65 are over are living alone.
Prof Jaspal added: "The other thing I would like to help the council with is to develop evidence-based strategies for changing behaviours. It's about ensuring that residents are able to change their behaviours, adopt more healthy behaviours and for those behaviours to be sustained over a period of time."
Prof Jaspal was elected a Fellow of the British Psychological Society in 2015. He is also a Chartered Scientist, Chartered Psychologist, a Fellow of the Royal Society of Arts and a Fellow of the Higher Education Academy.
Posted on: Wednesday 26 June 2019


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The convergence of the continued rise in healthcare costs and an election year is laying the groundwork for some interesting battles among pharmaceutical manufacturers, pharmacy benefits managers and insurers.
While it's too early to determine who will win the hearts and minds of our elected officials, consumers have been caught in the middle, and medical device and biotech companies need to follow these developments closely.
By way of background, according to an analysis by the Kaiser Family Foundation, total health expenditures as a percent of GDP have been rising fairly consistently since the 1970s and reached at 17.9% of GDP in 2016 (the green line in the chart). In contrast, health expenditures have been rising more slowly, particularly since the 1980s, in comparable OECD countries. Regardless, this trend is will not be sustainable.
CMS projects that national U.S. health expenditures will increase at an average rate of 5.5% per year from 2017 – 2016, higher than the average rate of increase of 4.2% per year during the period 2008 – 2016. The projection is modeled on changes in projected income growth, increases in medical goods and services prices, and insurance enrollment migrating from private health insurance to Medicare due to demographics.
Government scrutiny will likely increase because the proportion of national health spend borne by federal, state and local governments will go up (from 45% in 2016, to 47% of total spend by 2026), while that sponsored by private businesses, consumers and other private sources is expected to decline (from 55%, to 53%).
Insurers have been shifting costs to consumers through higher premiums, deductibles and co-pays. Likewise, employers are passing along increased insurance costs to their employees. The elimination of the individual mandate to purchase health insurance, part of the Act "To provide for reconciliation pursuant to titles II and V of the concurrent resolution on the budget for fiscal year 2018", passed by Congress on December 19, 2017, will push premium costs even higher as healthier individuals may opt for "skinnier", less expensive plans or forego health insurance entirely.
As we make our way through the first half of 2018, health insurers, pharmacy benefits manufacturers and pharmaceutical manufacturers are each trying to shape the conversation.
For example, Express Scripts, a pharmacy benefits manager (PBM), is trying to get Amgen to rethink its pricing model before it launches its new migraine treatment Aimovig®, currently expected to be priced at up to $10,000 per year. At issue is the industry practice of setting a higher list price and subsequently reducing it through rebates and coupons. Express Scripts says that many patients are forced to pay the list price each year until their annual deductible is met.
In response to the rise of manufacturer rebates/coupons, insurers and PBMs have increased the use of co-pay accumulators in new health insurance plans. Plans with this type of stipulation do not allow drug purchases made with coupons to apply to the beneficiary's annual deductible (or out-of-pocket maximums). When the manufacturer's coupon limit has been reached, the patient may have to pay list price (note that Medicare does not allow couponing).
Pharmaceutical manufacturers say that PBMs need to share more of the negotiated discount downstream. To this end, PhRMA has launched a public relations campaign, "Let's Talk About Cost" [sic]. One statistic from the website, based on an industry-funded study: "More than half of commercially insured patients' out-of-pocket spending for brand medicines is based on the full list price".
With CVS's proposed acquisition of Aetna and Cigna's proposed acquisition of Express Scripts, vertical integration will increase the negotiating power of the combined entities. Of course, it remains to be seen if these deals will pass muster with the U.S. Justice Department.


The People's Vote campaign has been accused of "overestimating" by Brexiteers after claiming one million people took part in a march through London in support of a second referendum.
Hundreds of thousands of demonstrators walked from Park Lane to Parliament Square on the 'Put It To The People March' holding placards which read 'Brexit is Rubbish', 'Revoke Article 50' and 'We Love EU'.
The demonstration followed the launch of an online petition calling on the Government to revoke Article 50 which last night had been signed by four million people.
People's Vote, the campaign group which organised the rally, said more than one million people took part and it was one of the biggest protests in British history.
The group has previously been accused of trying to mislead politicians and voters about its level of support.
A debriefing document prepared by the Greater London Authority put the number of attendees at October's People's Vote rally at 250,000 - significantly below the campaign group's claim that they were joined by more than 700,000 people.
MPs have now criticised the group's latest turnout claims and suggested the group are spreading "dubious" figures.
Peter Bone, Conservative MP for Wellingborough and part of the Brexit select committee, told The Telegraph: "I'm not really sure it can be called a People's March - it's hardly a march and more of a social gathering.
Marcus Fysh, Conservative MP for Yeovil, told The Telegraph: "They've obviously developed this march as a propaganda exercise so I wouldn't be surprised if they had overestimated their turnout figure.
"Let's be honest - they are marching against democracy and the implementation of a democratic referendum result.
"They are trying to set up a second vote where Remain is on the ballot. A 'final say' is not what they want - they want to reverse the result.
"This is a putsch that is going on this week."
The protest comes after the European Union agreed to delay the UK's departure. Meanwhile more than four million people have signed a petition calling on the Government to cancel Brexit.
People's Vote claimed there were so many people at the march that some protesters were at a standstill for 'at least an hour'.
A spokesperson said: "Our estimate is based on professional expert advice and whatever the exact number, there can be no doubt that this ranks as one of the greatest protests - possibly the biggest ever – that this country has ever seen.
March attendees included Scotland's First Minister Nicola Sturgeon, Labour MP David Lammy and Sherlock Holmes star Eddie Marsan.
Mayor of London Sadiq Khan called for Article 50 to be revoked, telling crowds: "With days to go we're in danger of falling of the cliff, which will have catastrophic consequences."
Ms Sturgeon told protesters that the Prime Minister had pitched "parliament against the people".
Labour's deputy leader Tom Watson told the crowd: "At every turn we have been ignored. At every stage Theresa May has doubled down rather than reaching out.
"She has made it impossible for anyone who cares about jobs, about solidarity at home and abroad, about friendship across borders and between communities to support this Brexit."
The London march coincided with pro-Brexit campaigners continuing their March To Leave hike from Sunderland to the capital.
They hope to arrive on March 29 - the original Brexit day.
Former Ukip leader Nigel Farage told around 200 Brexit supporters that Theresa May had reduced the nation "to a state of humiliation".


text:
5 Questions with DTES Small Arts Grant Recipient Kagan Goh
dtessag admin
Discipline: Theatre
Next place we can see your work: Richmond Cultural Centre 25th to 27th October, and Orpheum Annex Theatre 31st October to 2 November, 2018.
1. What is art to you?
Art is a medium by which we can connect on a soul to soul, heart to heart level; learn to empathize and live in someone else's shoes; to see and experience the world viscerally through different points of view. I am interested in making Art that has the power to heal.
2. What did you make in the past (and why)?
I am a multidisciplinary artist who has made films, published books, performed spoken word poetry and storytelling. My personal mission as an artist and mental health advocate and activist is to educate the public about mental health issues and help fight the stigma, discrimination, and prejudice against people with mental illness.
3. What are you making now (and why)?
I am producing a 1-hour theatrical production entitled Surviving Samsara that traces my personal struggles with manic depression, and my journey towards recovery, acceptance and unconditional self-love. Co-produced by myself and Cinevolution Media Arts Society, the work brings together acting, spoken word, music, video, film, audiovisuals, and dance.
Surviving Samsara exposes the damaging effects of the stigma of mental illness, and explores manic depression not only as a disorder, but as a spiritual emergence -- a vehicle for personal growth, healing and transcendence.
The goal of this project is to raise awareness and educate the public about mental health issues and combat the stigma and discrimination against the mentally ill. Through this work, audiences will learn firsthand the societal stigma and discrimination faced by persons with mental health challenges, and see how the power of art and creativity can be used to overcome these barriers and obstacles. I hope my personal journey of recovery will be a truly transformative experience that will inspire audiences to find courage and hope in their own journeys towards recovery.
Statistics show that 1 in 5 people will be diagnosed with a mental illness in their lifetime (making up 20% of the population). Research also demonstrates that artists are more likely to have a mental health diagnosis than their counterparts, yet this is rarely discussed within the arts community. The subject of this production is highly relevant to many people's lives, not just those with a mental illness but also their friends, relatives and family. Mental illness is so widespread that no one's life is untouched by it. However, awareness of mental health issues remains limited both within the arts community and the general public. Surviving Samsara tackles issues of stigma, discrimination and prejudice against the mentally ill, and makes tangible an experience that is typically internal and invisible. The production will create a space for dialogue through talkbacks and Q & A sessions, and invite audience members to share their own experiences with mental illness in a safe environment.
Closing the Gap Between Professional Arts and "Disability Arts." There is a perception that artists who openly identify as having a disability are more activists than artists, and that their work, while meaningful and socially significant, lacks artistic merit. At the same time, artists within the disability community are often create works catering to their own community, and lack the networks to be able to collaborate more broadly and reach out to a broader, unconverted audience disconnected from experiences of disability. Surviving Samsara strives to close the gap between professional arts and "disability arts" through its commitment to artistic excellence and the exploration of universal themes. I seek to celebrate the artistic possibilities generated by my struggles with mental illness, and to bring that narrative into a wider discussion about the human experience. We have a comprehensive marketing and outreach plan to engage and foster dialogue amongst diverse audiences.
4. What are your hopes/plans/dreams for the future?
With the support of Cinevolution, the Vancouver Foundation's DTES Small Arts Grant and the Kettle Friendship Society, I seek to build upon the earlier success of Surviving Samsara, and further develop the work under the tutelage of Artistic Director SCOTT SWAN, and through continued collaboration with award-winning choreographer & Butoh dancer SALOME NIETO. Funding for this interim stage of the production will allow us to secure strong collaborators such as Video Designer CANDELARIO ANDRADE, award-winning composer STEFAN SMULOVITZ, and allow the work to evolve from the realm of community arts to a professional arts level and garner recognition so the work can be presented nationally and internationally at professional theatres. Funding for this stage of the development will move the production forward to a new level of excellence.
Phase III: What we are building up to next.
Building upon the anticipated successful delivery of the project, I want to design the production to be portable for future use in theatrical and spoken word venues, festivals, mental health, and educational institutions. Ultimately, the goal is to create a minimalist performance that is ideally tailor-made for educational institutions such as high schools, colleges and universities.
The production of Surviving Samsara will then be followed by a 4-day theatrical run at Gallery Gachet on 9th to 12th January, 2019; and a 2-week theatrical run Vancouver Fringe Festival in 2019. The production will then tour with the Artstarts Artist on Tour Program (https://artstarts.com) in high schools, colleges and universities in 2019.
I am also applying for an Artist-in-Residence Program at the Shadbolt Centre for the Arts to further workshop and develop the project and take the production to its final phase. Our ultimate goal is to partner with an established theatre company and showcase the production of Surviving Samsara at venues like the Firehall Arts Theatre or the Cultch and tour nationally and internationally.
5. What would surprise people about your creative practice?
My creative process involves a great deal of trial and error. Artists are sometimes too precious with their work and are afraid of making mistakes. But mistakes are an essential part of the creative process for we discover what works and does not work through trial and error. You can't make an omelet without breaking eggs. As mythologist Joseph Campbell says; "Destruction before creation." Creativity is a messy process. Furthermore, mistakes may lead to surprising and unexpected discoveries -- which then can be incorporated into the evolving work. I do not strive for perfection in Art. Art, like Life, to me is a process of discovery. If I am not learning and making discoveries then the so-called "perfect" work is inert, dead, devoid of life. Art and the creative process is an evolving and breathing organic process.