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The low-growing evergreen shrub is popular in nearly every European cuisine and is used variously to flavor various proteins, soups, puddings, cheeses and vegetables. It is stimulating to hydrochloric acid, pepsinogen, and other gut secretions. White sagebrush - Artemisia ludoviciana (Other names: Dakota sage, Man sage, Grandfather sage, Badlands Sage, Silver wormwood, Old man sage, Silver king, Western mugwort) Another Artemisia smudge, this one grows all over the badlands of South Dakota and out west and down south to Louisiana. This makes the tea beneficial to the body's digestive process for some people. California sagebrush is considered one of the most medicinally useful plants. #126835798 - Cup of herbal tea - tutsan, sagebrush, oregano, helichrysum,.. Sage tea might have multiple health benefits, but none have been proven. Artemisia, "White Sagebrush" essential oil. delicious sagebrush tea in a beautiful glass bowl on table - sagebrush stock pictures, royalty-free photos & images. A poultice of the leaves can be applied to spider bites, blisters and burst boils[257]. Sage can also be brewed as a tea or eaten. It has small yellow flowers on the ends of the twigs, and the entire shrub smells wonderful. Local adaptation means that plants from a local habitat out-perform plants from places farther away because of natural selection of optimal genetic types. Chemistry. Its leaves were used for multiple health concerns, most notably as a natural remedy for colds. Silver wormwood, white sagebrush, wild sage, prairie sage, wormwood, white mugwort, western mugwort, Louisiana sage, darkleaf mugwort, Mexican sagewort, Chihuahua sagewort, Garfield tea, lobed cudweed, man sage . RANGE & HABITAT. Diviner's sage (Salvia divinorum), for instance, is a plant with hallucinogenic properties that is used in some indigenous cultures for religious purposes. Cut stalks used for fragrant wreaths and floral arrangements. Sagebrush is locally adapted. White Sage (Salvia apiana) is a plant native to high desert ecosystems and grows prevalently in California and in the Mountain West.For hundreds of years, White Sage has been considered a sacred, cleansing, purifying, and protective plant. This website has photos and descriptions of native plants found in the province of Saskatchewan, Canada. CDN$50.56. Common names are from state and federal lists. As a tea, Sagebrush is an aromatic bitter. Wikipedia tells us this: A hot tea of the herb (just a tsp in 1 cup of water is sufficient, steeped in recently boiled water for 10–15 min with a lid) will also promote sweating and coughing early in infectious processes. (Its Latin name refers to its main pollinator, the honeybee.) Use. Shallow dof. Tea from leaves for ceremonial bathing. Take a mouthful at a time, swishing the liquid in your mouth for several minutes before swallowing. They contain a range of aromatic compounds that give them their distinctive fragrance; some are considered too strong to be taken internally. Add to Likebox #118051041 - Mugwort Herbal and curry leaves. White sage is a shrubby herb and gets six feet tall and four feet wide, so give it plenty of room. White sage the ideal plant if you're doing xeriscaping because it doesn't need much water and it looks great next to broadleaf desert plants such as aloe and yucca. Artemisia species (Sagebrush, ... (A. dracunculus), white sagebrush (A. ludoviciana), and big sagebrush (A. tridentata). As explained above, there are various uses for white sage, including brewing a tea, binding dried leaves and burning them as incense, or applying them as a topical compress on the body. The Kumeyaay, from the San Diego region, dried out sagebrush leaves then prepared a tea from the foliage. There are many species of sage. The wood was used as fuel, and the stringy bark was used in the manufacture of ropes and baskets. Tea was made from various parts of the plant, and it was used extensively in medicine. The common garden sage has been known and used for culinary and herbal purposes for centuries. Produces small yellow blooms. The wash was also applied to eczema and as an underarm deodorant[257]. flora of gran canaria - artemisia thuscula - sagebrush stock pictures, royalty-free photos & images. Tea made with white sagebrush was used in Mexican traditional medicine to alleviate intestinal pain . The two most common of these are Artemisia cana (silver sagebrush, also referred to as Badlands sage or South Dakota sage) and Artemisia tridentata (big sagebrush, desert sage, mountain sage, and many other names). subsp. Use: In natural perfumery used in sacred incense perfumes, herbaceous notes, chypre, fougere, colognes, forest bouquets. Michigan . Other common names. Threatened and Endangered Information: This plant is listed by the U.S. federal government or a state. Updated 2020.09.06 and just as an FYI, this post contains affiliate links. For centuries, the plant was used in a variety of traditional methods including for its healthful qualities as well as in ceremonial use. Native plants have been photographed from the province's Prairie, Cypress Upland, Parkland, and Boreal eco-regions. Amazon Business: For business-only pricing, quantity discounts and FREE Shipping. Similar Images . of dried sage leaves into the bathwater is another effective way to purify the body. Asarum … Odor: fresh, herbaceous-fruity bouquet with a soft, green, resinous, tea-like undertone. An essential oil extracted from white sagebrush ( A. l . Register a free business account . What Does Burning Sage Do; 9 Impressive Benefits of Sage; Tea – To make a tea from sacred sage, place two teaspoons of fresh sage leaves (or 1 teaspoon of dried sage leaves) in a mug. White sage has been an important botanical for many indigenous cultures. The leaf is used to make medicine. The taste of white sagebrush is incredibly bitter to humans but perfectly fine for other species, including cattle. Landscaping With White Sage. Sagebrush plants grow best if they come from the same habitat they are planted into. Here are some of the benefits of burning white sage: Physical Healing. In addition, the cold tea is a diuretic and the hot tea is diaphoretic. mexicana ) has been demonstrated to give symptomatic relief of diarrhea [ 144 ]. Thrush or Candidiasis Tea 2 tsp common sagebrush root 1 Tbsp pau d'arco bark 1 cup water Place the above herbs in a glass container and cover with the water; let soak overnight; strain. Mexican White Sagebrush and Mugwort . Sagebrush leaves themselves—which are strongly aromatic and a shade of light green that seems to change with the weather— provide food to a variety of birds and fauna, including mule deer, white-tailed deer, elk, pronghorn antelope, bighorn sheep, and jackrabbit. Overview Information Sage is an herb. Adding about 1 oz. Mountain Rose Herbs recognizes the long-established cultural and spiritual significance white sage holds for many tribes and the stewardship that has ensued for generations. This is useful for helping to break a fever and induce a sweat. Similar Images . This decoction was used to treat skin lesions. Have a question? A weak tea was used in the treatment of stomach ache and menstrual disorders[222]. Steep for 10 minutes and do not strain out the leaves as they may be ingested safely. Externally, a wash of the leaves was applied to itching, rashes, swellings, boils, sores, etc[222]. Sage tea shows some promise for helping with cognition, menopause and other maladies. Click on a place name to get a complete protected plant list for that location. Understanding the reason for this is easy after visiting the area: sagebrush is nearly everywhere. Add to Likebox ... #129006022 - Sagebrush on white wooden background. Prairie sage can be grown from seeds, roots, or cuttings of the plant. Special offers and product promotions. Nearly 100 bird species depend on sagebrush country for their habitat needs. FREE Shipping on orders over $25 shipped by Amazon. It has lots of branches and grey bark. Common sage (Salvia officinalis) is the type of sage available in most grocery stores and used to make most commercial sage tea bags.It should not be confused with other types of sage species. Editor's pick. White sage can be made into a tea by crinkling up a few sage leaves into the bottom of a tea cup and adding boiling water. White Sage is the bread and butter of any smudging kit. Add to Likebox #116328736 - A close-up wide-angle shot of a single pine tree located on the.. 99 $16.99 $16.99. Sagebrush is the common name of several woody and herbaceous species of plants in the genus Artemisia.The best known sagebrush is the shrub Artemisia tridentata.Sagebrushes are native to the North American west. white sagebrush Legal Status. Similar Images . White Sage (Salvia apiana—also known as Bee Sage, California Sage, Sacred Sage) For many people, "smudging" means one thing only—White Sage. Sage leaves can be infused as tea, macerated as an extract, and used as a culinary spice. Eating or drinking too much sage may result in complications including dizziness, rapid heart rate, and even seizures. Smoke for ceremonial uses. Silver wormwood, western mugwort, Louisiana wormwood, white sagebrush, and gray sagewort - Artemisia ludoviciana. The twigs are very hairy and the leaves have three teeth at the end. White sagebrush in bloom (Artemisia ludoviciana Valerie Finnis), Asteraceae. This plant grows in the … Big sagebrush is a tall green-grey shrub that grows up to two metres high. Similar Images . Artemisia ludoviciana (Mexican white sagebrush) is medicinally quite close to the famed Chinese herb Artemisia vulgaris (mugwort, ai ye). 6" 6 Pack White Sage Smudge Sticks | 6-inch Large Smudging Wand Incense Stick for Cleansing, Purifying, Healing, Meditation, Yoga, Blessing New Home (6 Pack) 4.6 out of 5 stars 944. 100 Silver Sagebrush (White Sagebrush/Silver King) Artemisia Ludoviciana Flower Seeds ... Starwest Botanicals Organic Tea, 1 Pound 4.6 out of 5 stars 705. thyme, estragon and rosemary essential oil or infusion - sagebrush stock pictures, royalty-free photos & images . Louisiana Artemisia, Louisiana Sage, White Sage, Prairie Sage, Silver Sage, White Sagebrush, Louisiana Wormwood, Silver Wormwood, Louisiana Sagewort, Gray Sagewort. Following is an alphabetical list of common names for various species of the genus Artemisia, along with their corresponding scientific name. White sage has many properties. Other Common Names: Good Tasting Cow Plant, Man Sage, Pasture Sage, White Sagebrush Characteristics: Edible, aromatic silver-green leaves.
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An unusual cause of anemia and encephalopathy
Kothari
Sanjeev Kumar Sharma, Dharma Choudhary, Anil Handoo, Gaurav Dhamija, Gaurav Kharya, Vipin Khandelwal, Mayank Dhamija and Sweta Kothari
Department of Hemato-Oncology and Bone Marrow Transplantation, BLK Superspeciality Hospital, New Delhi, India.
Corresponding author: Sanjeev Kumar Sharma, MD, DM, Consultant and Principal Coordinator, Department of Hemato-oncology and Bone Marrow Transplantation, BLK Superspeciality Hospital, New Delhi, India. Mobile: +91-9968756303. Email: sksanjeev13@yahoo.com
Published: May 1, 2015
Received: March 16, 2014
Accepted: April 6, 2014
Mediterr J Hematol Infect Dis 2015, 7(1): e2015036, DOI 10.4084/MJHID.2015.036
(http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Although severe anemia can theoretically result in anemic hypoxia and can then lead to hypoxic encephalopathy, it is not a primary cause of encephalopathy. More frequently anemia can contribute with other multiple causes of encephalopathy such as infection, metabolic abnormalities, trauma, hepatic dysfunction, hypertension, toxins, etc. We present here an interesting case of recent onset anemia that was associated with an encephalopathy of unusual cause.
Clinical history: A 49-years-old non-hypertensive, non-diabetic male was admitted to the hospital with the complaints of progressive weakness lasting three months. For the last two weeks, the patient also had drowsiness. The patient was hospitalized in the neurology ward for evaluation of encephalopathy. The patient became increasingly confused during his hospital stay. There was no history of fever, bleeding from any site, jaundice, head trauma or drug abuse. He was a non-vegetarian, non-alcoholic and non-smoker. Patient had a history of deep vein thrombosis one year back and was treated with warfarin.
Clinical examination: On examination he had pallor; there was no icterus, cyanosis, pedal edema and lymphadenopathy. On per abdominal examination, there was no abdominal distension and no dilated veins over the abdomen. He did not have hepatosplenomegaly or ascites, and bowel sounds were normal. Central nervous system evaluation revealed him in altered sensorium with irritability and
restlessness. There was no neck rigidity, and bilateral planters were flexor. Bilateral pupils were normal in size and well reacting to light. Examination of his respiratory and cardiovascular systems did not reveal any abnormality.
Initial laboratory investigations: His hemogram showed pancytopenia with hemoglobin 7.6 g/dl, total leukocyte count 3.1x109/l and platelet count 108x109/l with normal differential count on peripheral smear. Mean corpuscular volume was 85 fl. His liver and kidney function tests were normal except for total serum protein 5.79 g/dl and albumin of 2.6 g/dl with reversal of albumin globulin ratio. His serum electrolytes including calcium and magnesium were in normal range. The workup for altered sensorium including cerebrospinal fluid examination and magnetic resonance imaging (MRI) of the brain was inconclusive. The screening for viral infections including HIV/Hepatitis-B virus/Hepatitis-C virus was negative. Blood culture was sterile. Peripheral smear did not show malarial parasites or schistocytes. His antinuclear antibody (ANA) and serum vitamin B12 and folate levels were also within the standard range. The thyroid stimulating hormone (TSH) was within normal range.
Differential diagnosis:
1. Infective causes of altered consciousness were evaluated and ruled out. Moreover, the patient did not have a fever and cerebrospinal fluid, and MRI findings were inconclusive. Also, the screening for infection including bacterial, malarial and viral pathogens was negative.
2. There was no vitamin deficiency/drug abuse/toxin or heavy metal exposure/head trauma.
3. Since the patient had a history of deep vein thrombosis, he was evaluated for paroxysmal nocturnal hemoglobinuria.
4. Bone marrow examination was planned considering myelodysplastic syndrome as a possibility.
Further workup: Study for paroxysmal nocturnal hemoglobinuria (PNH) did not reveal any PNH clone. His bone marrow done for evaluation of cytopenias revealed sheets and clusters of plasma cells suggestive of multiple myeloma (Figure 1). Serum protein electrophoresis showed M band of 0.4 g/dl. Serum immunofixation electrophoresis showed kappa light chain only. Serum free light assay showed kappa-lambda ratio of 165. CT pulmonary angiography, performed for breathlessness and history of deep vein thrombosis, showed no evidence of pulmonary embolism, but the ribs showed multiple lytic lesions. A diagnosis of multiple myeloma was made. Liver-function tests and abdominal CT showed no evidence of hepatic dysfunction. Because of increasing altered sensorium and restlessness the patient required sedation and prophylactic intubation. Electrolytes, blood urea nitrogen, creatinine and calcium levels were unremarkable. Though the patient had multiple myeloma, the cause of altered sensorium could not be found, as all the usual causes of encephalopathy had been ruled out.
Further evaluation of encephalopathy showed that serum ammonia levels were high, 170 µg/dl (normal range 25-95 µg/dl).
Figure 1. Bone marrow biopsy (200X) showing plasma cells in sheets and clusters (picture on the left side). CD 138 immunostain on bone marrow biopsy (100X) highlighting the plasma cells that are seen in sheets and clusters (picture on the right side).
Treatment: He was started on anti-myeloma therapy with cyclophosphamide, bortezomib, and dexamethasone. Bortezomib was given 1.3 mg/m2 on day 1, 4, 8 and 11, dexamethasone 40 mg/m2 on day 1-4 and cyclophosphamide 500 mg once weekly. On fourth day patient's sensorium improved, and he was extubated. His repeat ammonia levels done on day 4 of chemotherapy were 84 µg/dl and decreased to 50.6 µg/dl after three weeks of therapy. His karyotype showed tetraploidy. With continued treatment, the patient showed complete improvement in his sensorium and was discharged on day 22. His hemoglobin was 11.4 g/dl, total leucocyte count 4.7x109/l and platelets 224x109/l at the time of discharge. On day 60 of anti-myeloma therapy patient had no M-band in serum protein electrophoresis and kappa-lambda ratio was 2.14.
Central nervous system can be involved in various ways in multiple myeloma.[1,2] Encephalopathy occurring in multiple myeloma is frequently due to metabolic disturbances related to the underlying plasma cell disorder, such as hypercalcemia and uremia.[1] In addition, a direct invasion of CNS and leptomenings by the myeloma cells has also been reported.[2] In our case hypercalcemia, and renal insufficiency were excluded by biochemical tests and MRI/CSF examination excluded CNS involvement by myeloma. Therefore, we considered hyperammoniemia a possible cause of encephalopathy. Hyperammonemia is involved mostly in the pathogenesis of hepatic encephalopathy that may present with an identical clinical syndrome, characterized by altered sensorium and impaired counsciousness.[3] However, there were hepatic causes of hyperammonemia in our patient. Although it is not always possible to establish a right correlation between ammonemia level and neurologic symptoms, severe acute hyperammonemia causes a rapidly progressive, often fatal, encephalopathy with brain edema. Chronic milder hyperammonemia causes a neuropsychiatric illness.[3] Therefore, prompt recognition can be lifesaving.[3] Among the possible extra-hepatic causes of hyperammonemia, the literature also reports adult-onset inborn error of metabolism (a urea cycle disorder), carbamazepine or valproate use, and urinary tract infection with a urea-hydrolysing organism. Though rare, the underlying cause may be reversible, and potentially curable with the appropriate therapy of underlying disease.[3,4]
Encephalopathy associated with hyperammonemia is a rare event in myeloma.[5-11] However, it is a life threatening condition with an overall mortality of 40-48%.[5,10,11] The diagnosis needs a high level of suspicion, and treatment should start as soon as possible. The cause of hyperammonemia in myeloma is not known though excess of ammonia production has been found in human myeloma cell lines,[12] but also concomitant features could be significant. Chemotherapy directed against multiple myeloma is the most efficient treatment to achieve an improvement of neurological conditions in these patients. Thus, hyperammonemia should be considered in any patient with multiple myeloma and a low level of consciousness. Our patient presented with anemia and disturbance of consciousness. He was diagnosed to have multiple myeloma with hyperammonemia, and there was a dramatic and fast improvement in sensorium on treating him with chemotherapy. The improvement was clearly associated with the rapid decline in serum ammonia levels and progressive increase in hemoglobin level (Figure 2). The reduction in M band and free light chain ratio as well the rise of hemoglobin were late and then could not have any correlation with neurological improvement.
Figure 2. Serum ammonia level (µg/dl) showing dramatic reduction after starting chemotherapy. Black dots represent time points of measuring serum ammonia levels. Redline and dots represent the Haemoglobin level
The more frequent causes of altered sensorium in multiple myeloma include infections, hypercalcemia, uremia or dyselectrolemia, but when none of those could be found then hyperammonemia should be suspected, and treatment for myeloma should be started immediately. Therefore ammonemia should be tested in any patient with myeloma having an altered sensorium. The presentation of this case was unusual and misleading because the patient had pancytopenia and altered sensorium, without any routine biochemical data and radiological imaging suggesting any causes of encephalopathy. Only the bone marrow infiltration of plasma cells and the presence of osteolysis, while making evident the diagnosis of myeloma, suggested checking ammonemia. Anti-myeloma therapy was able to retrieve cytopenias and, by reducing ammonemia, also the altered sensorium.
We are thankful to Ms. Bharti, Ms. Sujata, Ms. Ankita and Dr. Sandeep Kumar Sharma for formatting the manuscript.
Sobol U, Stiff P. Neurologic aspects of plasma cell disorders. Handb Clin Neurol. 2014;120:1083-99. doi: 10.1016/B978-0-7020-4087-0.00073-5. http://dx.doi.org/10.1016/B978-0-7020-4087-0.00073-5 PMid:24365373 .
Schluterman KO, Fassas AB,Van Hemert RL, Harik SI. Multiple myeloma invasion of the central nervous system. Arch Neurol. 2004;61:1423-29. doi:10.1001/archneur.61.9.1423,
http://dx.doi.org/10.1001/archneur.61.9.1423 PMid:15364689 .
Hawkes ND, Thomas GA, Jurewicz A, Williams OM, Hillier CE, McQueen IN, Shortland G. Non-hepatic hyperammonaemia: an important, potentially reversible cause of encephalopathy. Postgrad Med J. 2001; 77:717–22. doi:10.1136/pmj.77.913.717 http://dx.doi.org/10.1136/pmj.77.913.717 PMid:11677282 .
Walker V. Ammonia metabolism and hyperammonemic disorders. Adv Clin Chem.2014;67:73-150. doi:10.1016/bs.acc.2014.09.002. http://dx.doi.org/10.1016/bs.acc.2014.09.002 PMid:25735860 .
Lora-Tamayo J, Palom X, Sarrá J. Multiple myeloma and hyperammonemic encephalopathy: review of 27 cases. Clin Lymphoma Myeloma. 2008;8:363-69. doi: 10.3816/CLM.2008.n.054, http://dx.doi.org/10.3816/CLM.2008.n.054 PMid:19064403 .
Kwan L, Wang C, Levitt L. Hyperammonemic Encephalopathy in Multiple Myeloma. N Engl J Med. 2002;346:1674-75. http://dx.doi.org/10.1056/NEJM200205233462119 PMid:12024007 .
Martinelli G, Peccatori F, Ullrich B, Ghielmini M, Roggero E, Goldhirsch A. Clinical manifestation of severe hyperammonaemia in patients with multiple myeloma. Ann Oncol. 1997;8:811. http://dx.doi.org/10.1023/A:1008236018377 PMid:9332693 .
Matsuzaki H, Hata H, Sonoki T, Matsuno F, Kuribayashi N, Yoshida M, Nagasaki A, Murata H, Fujiyama S, Takatsuki K. Serum amino acid disturbance in multiple myeloma with hyperammonemia. Int J Haematol. 1995; 61:131-37. http://dx.doi.org/10.1016/0925-5710(95)00359-Z PMid:7599324 .
Holahan JR. Hyperammonemia: elevated ammonia levels in multiple myeloma. Am J Med. 2004;116:210-11. doi:10.1016/j.amjmed.2003.06.010, http://dx.doi.org/10.1016/j.amjmed.2003.06.010 PMid:14749172 .
Talamo G, Cavallo F, Zangari M, Barlogie B, Lee CK, Pineda-Roman M, Kiwan E, Krishna S, Tricot G. Hyperammonemia and encephalopathy in patients with multiple myeloma. Am J Hematol. 2007; 82:414-15. http://dx.doi.org/10.1002/ajh.20808 PMid:17133420 .
Pham A, Reagan JL, Castillo JJ. Multiple myeloma-induced hyperammonemic encephalopathy: An entity associated with high in-patient mortality. Leuk Res. 2013;37:1229-32. doi: 10.1016/j.leukres.2013.07.014, http://dx.doi.org/10.1016/j.leukres.2013.07.014 PMid: 23932549 .
Otsuki T, Yamada O, Sakaguchi H, Ichiki T, Kouguchi K, Wada H, Hata H, Yawata Y, Ueki A. In vitro excess ammonia production in human myeloma cell lines. Leukemia. 1998;12:1149-58. http://dx.doi.org/10.1038/sj.leu.2401077 PMid:9665203 .

redpajama_set_name: RedPajamaCommonCrawl


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Urinary CD80 is elevated in minimal change disease but not in focal segmental glomerulosclerosis.
Eduardo H Garin, Wei Mu, John M Arthur, Christopher J Rivard, Carlos E Araya, Michiko Shimada, Richard J Johnson
Kidney International 2010 August
Controversy exists as to whether minimal change disease (MCD) and focal segmental glomerulosclerosis (FSGS) represent different diseases or are manifestations within the same disease spectrum. Urinary excretion of CD80 (also known as B7.1) is elevated in patients with MCD and hence we tested whether urinary CD80 excretion might distinguish between patients with MCD from those with FSGS. Urinary CD80 was measured in 17 patients with biopsy-proven MCD and 22 with proven FSGS using a commercially available enzyme-linked immunosorbent assay and its molecular size determined by western blot analysis. A significant increase in urinary CD80, normalized to urinary creatinine, was found in patients with MCD in relapse compared to those in remission or those with FSGS. No significant differences were seen when CD80 urinary excretion from MCD patients in remission were compared to those with FSGS. In seven of eight MCD patients in relapse, CD80 was found in glomeruli by immunohistochemical analysis of their biopsy specimen. No CD80 was found in glomeruli of two patients with FSGS and another MCD patient in remission. Thus, our study supports the hypothesis that MCD and FSGS represent two different diseases rather than a continuum of one disease. Urinary CD80 excretion may be a useful marker to differentiate between MCD and FSGS.


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JUST IN: Man slain in West Palm late Sunday recalled as loving boyfriend
Romy Ellenbogen
Jul 30, 2018 at 12:01 AM Jul 31, 2018 at 2:35 AM
D'Monte Davis made his own family.
Davis, 25, didn't have his mother or father in his life. Instead, he lived with his aunt, took care of nieces and nephews and found comfort and a home with his girlfriend of eight years, Alyssa Dejesus.
The two met in 2009 at Royal Palm Beach High School and instantly connected, she said Monday from Maryland. They moved in with each other at 18.
"When we met, it was just like, 'We're never gonna leave each other,' " Dejesus said. " 'We're gonna be the people who don't leave.' "
RELATED 'I felt him leave me:' Man killed in West Palm shooting had baby on the way
On Sunday night, Davis was struck by a bullet and killed near 20th Street and Division Avenue. He died at the hospital after what West Palm Beach police say was a targeted attack. They have offered no other details on the fatal shooting or information about any suspects.
Davis was the 16th confirmed homicide death in West Palm Beach this year and the 57th in Palm Beach County, according to a Palm Beach Post online database.
The Palm Beach Post homicides tracker records and remembers homicide victims from Palm Beach County
Dejesus said Davis was different than any man she knew. He was bright, loved to joke around and worked hard, she said.
When the two of them spent time together, they would go to the beach or drive around aimlessly. Other times, they'd pick up their younger nieces and nephews and play hide and seek.
"We wanted a family because that was something we never had," Dejesus said.
Alyssa Dejesus and D'Monte Davis. (Family photo)
In April 2017, someone shot into the couple's home and hit Davis four times. It took him nearly five months to recover, Dejesus said. Before then, he had been working two jobs and going to college. After the shooting, Davis became frustrated but still kept trying to apply for work, Dejesus said.
It was in that period of time that Davis and Dejesus broke up. But even after they did and Dejesus moved away, not a day went by that they didn't speak to each other, she said.
RELATED Man found not guilty by insanity in 2014 slaying of Boca diner owner
She remembers him as endlessly curious, saying it took forever to order at a restaurant because Davis would ask so many questions. His own cooking was better, though. For her 17th birthday, Davis got a cheap bottle of wine to pair with the spaghetti and meatballs he made her.
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He sent flowers to her work, or lit candles for when she would come home, she said.
"He just wanted the struggle in his life to stop so he could take care of his family," Dejesus said. "He was a good kid."
Anyone with information about Sunday's shooting is asked to contact West Palm police or Crime Stoppers of Palm Beach County at 800-458-TIPS (8477).
The first photo Alyssa Dejesus and D'Monte Davis took together. They met in 2009 while students at Royal Palm Beach High School. (Family photo)


We investigated 335 landslides (including rockslides, rock avalanches, soil slides, and slides) in the Zagros mountain belt of southwest Iran using a digital elevation model (DEM) with 30 m resolution, Google Earth™ images, and field investigation. Individual landslides have volumes ranging from 104 (the lower limit of resolution) to 3 × 1010 m3 and cover surface areas ranging from 103 to 108 m2. The relationship between landslide volume (VL) and area (AL) is well described by a power law of the form VL = ALα, where α = 1.49 over five orders of magnitude of AL and seven orders of magnitude of VL. We also show that the frequency-size (i.e., volume) distribution is heavy tailed, following a power law for the largest landslides (>107 m3) with a scaling exponent β = 1.51. Non-power-law behavior for smaller landslides is probably an artifact due to the relatively low resolution of our data, such that we are essentially missing many small landslides. Comparison of these results with the other published data sets around the globe shows that the Zagros landslides are relatively larger, and they show similar scaling behavior to those observed in other regions, especially with regard to data sets where landslides are deep-seated or relatively large and occur in relatively resistant materials (e.g., consolidated rocks, as opposed to soil). In addition, we used principal component analysis (PCA) to investigate links between the size of landslides and causative factors (e.g., geological, geomorphological, and physical factors). Our results highlight that although the size of landslides is not controlled by any single factor, their geographic distribution is strongly influenced by lithology, elevation, and slope.


Thanksgiving is almost here! I assure you that if you asked the guests at the original Thanksgiving table if they prefer their stuffing out of a box or the kind in a bag, they'd look at you like you had three heads. They knew something then that we're all striving to get back to now – farm fresh dishes are the best!
Below, you'll find some of the more amazing farm-fresh Thanksgiving side dish recipes from some of the best bloggers on the web. Give them a try and let us know what you think!
The following are appetizers rather than side dishes, but they looked so delicious I thought I'd add them!
What's your favorite Farm Fresh Thanksgiving side dish?


2012 Summer Olympics in London also give an impact on the sales of the car. Penske Automotive Group is predicting to have a boost in the sales of their luxury cars in the UK stores due to the London Olympics.
As there is a presidential appointment ahead in the Penske's U.S. business, it is very thorny to calculate any prospect. As the second –quarter wages call at the moment reported by the Roger Penske's Chairman.
There is about a 26 percent boost in the second-quarter net income of the Penske Automotive Group motivated by the strong retail vehicle sales particularly in the dealership of the Toyota and Honda.
In a statement from the company published today, the net income of the company in the second quarter of this year is $49.1 million as compared with the $39.6. Million of the previous year in the retailer group.
The second quarter income of the Penske is the preceding in the public retailer. As the largest part of the retailer reported profit earlier and revealed the rise in the sale of the latest automobile and also have a burly investment and insurance deal.
As compared with the previous quarter year, the income per vehicle of the Penske's F&I revenue is downstairs from $989 to $980.
"The entire assemblage is lowered in an average due to the dealership group in Belfast of the Northern Ireland having a huge acquisition in the preliminary of this year" said by the Roger Penske.
Penske also added in his statement "On a "same-store" foundation, not including the acquisition, F&I income per vehicle was flat to some extent further on of a year ago"
"For the third-quarter there are a lot more opportunities to grow as of the summer Olympics in London is a head" said by the Roger Penske.
"I saw lots of the BMW in the Olympics when I was there for the two days, it will be good used cars for all of us" in his statement.
There are more than 170 franchises of the Penske outside the united states and among them most of them were in the United Kingdom."As the car of the Olympic " Bmw will put around its 4,000 vehicles in the service during the Olympic , a statement from the Penske.
Penske further added "In a hope that the dealers will buy, it's all the opportunities we have".
As BMW only makes the 24 percentage of the total Penske's brand revenue.
In the united States Penske Automotive is confident regarding their third quarter as there is a strong demand of the premium luxury vehicles there will be a sale of the 14 million to 14.5 million is forecasted in the united states for the 2012 due to the easy availability of the credit and a slowly rebounding market.
The election of the president of the US ahead. If the tax rate change, then there could be a big impact on the sale of the luxury vehicles.


On Thursday 24 and Friday 25 May 2018, a two-day international conference was held in University College Dublin, Ireland, examining comparative and interdisciplinary approaches to partition and border studies. 2020 marks the centenary of the 1920 Government of Ireland Act which legislated for a two-state solution to the Irish question. Nationally, this conference prefaced this event by considering the wider history and contexts of partition. Internationally, the conference provided a forum in which scholars can come together in a focused manner to explore their differing approaches to this pivotal issue in the history of the modern world.
Jointly organised by University College Dublin and Jawaharlal Nehru University, New Delhi, this conference brought together scholars working on aspects of partition and border studies from multiple disciplines. The conference aimed to consider multiple geographical regions and time periods drawing parallels through a targeted analysis of the phenomenon of partition in history and society.
Learn more about the full programme.


The Roman Blind Company has a showroom at 25 Spencer Road, Derry / Londonderry.
All our roman blinds are hand crafted in our workroom.
We have an extensive range of fabrics to choose from, or you can bring along your own choice of fabric if you wish.
From our collection of floral fabrics in many colours you will find the perfect choice.
Roman blinds made with striped fabrics are an excellent choice for a timeless window dressing.
Contact us to check if your team has made our league table of roman blinds.


We specialize in packing goods in Vietnam according to customer requirements and orders. With all kinds of goods, quantity and weight according to international standard packing.
With modern packaging technology and abundant staff with many years of experience in the packaging industry of HD Asean VietNam Co., Ltd, we believe that it will bring absolute satisfaction to customers.
What benefits do you receive when packing goods at our company?
Goods are guaranteed during packaging and shipping.
⪼Move in large quantities to ensure safety for customers' goods.
Receive information that requires the customer's type of goods to be closed.
Measuring and determining the size and weight of goods to be packed.
Determine delivery time, time to affect products.
Selecting necessary materials and carrying out packing according to the packaging standard.
Checking the packaging process to ensure proper packaging techniques.
Handover of packaged products and confirm work performance.


text:
Q: What are the group and artifact names for individual ImageJ2 libraries through Maven? I've spent most of yesterday trying to figure out what to use in my pom.xml file so I can get the ImageJ2 libraries that I need without inheriting from the ImageJ parent pom. I figured out the following settings, but they are far from optimal:
    ...
    <repository>
        <id>imagej.public</id>
        <url>http://maven.imagej.net/content/groups/public</url>
    </repository>
    ...
    <dependency>
        <groupId>net.imagej</groupId>
        <artifactId>imagej</artifactId>
        <version>2.0.0-rc-28</version>
    </dependency>
    ...

The problem I have is that it appears that all of ImageJ2 is downloaded this way. There is a massive dependency tree and some 60+ jar files are now in my classpath in eclipse.
How can I pick and choose the individual libraries that I need, and which one of them is the base version (like ij.jar was for ImageJ1)? And how can I find the available version number(s)?

A:
all of ImageJ2 is downloaded this way.

net.imagej:imagej is indeed the application-level project that aggregates all the ImageJ2 components.

How can I pick and choose the individual libraries that I need
  And how can I find the available version number(s)?

All components of ImageJ2 are Mavenized and can be consumed directly/independently, the same way you included net.imagej:imagej. There are several ways to browse the components and available versions - for example:

*

*Browse components on GitHub. The source code is divided into projects across several organizations. Each project will have its own pom (e.g. imagej-common) and list of releases.

*Look at the BOMs for each project. For example, pom-imagej will give you the list of ImageJ components at versions that work together.

*Search Maven central (not all projects hosted here - search by groupId, e.g. net.imagej, io.scif, org.scijava)

*Search the ImageJ nexus

without inheriting from the ImageJ parent pom.

Even if you don't declare pom-imagej as a parent pom, if you end up using multiple ImageJ components you would benefit from scope:importing it (or another appropriate BOM). Leaning on BOM dependency management will help ensure your components are at versions that work well together.

which one of them is the base version (like ij.jar was for ImageJ1)

It really depends on what you are trying to develop. The ImageJ wiki gives an overview of how functionality is divided in ImageJ2. There is also a comprehensive development section.
For more technical questions about ImageJ2 development, you may also want to try the ImageJ-devel mailing list.

redpajama_set_name: RedPajamaStackExchange


text:
Tim Hardaway, Jr., No. 3 Michigan outlast No. 10 Ohio State in overtime thriller
By Daniel MartinFeb 5, 2013, 11:33 PM EST
Michigan junior Tim Hardaway, Jr. has spent much of the 2012-13 season proving that he has become more than just a three-point shooter in his third year in with the Wolverines.
But on Tuesday night, he leaned on that three-point shot again and led No. 3 Michigan to a grueling 76-74 overtime win against No. 10 Ohio State at Crisler Center in Ann Arbor, Mich.
Over a two-minute stretch in the middle of the second half, Hardaway, Jr. hit threes on three straight possessions, pulling Michigan from five points down to two points up, 52-50, with 10:16 to play.
He hit another two threes in the half, finishing with 23 points on 7-of-14 from the floor, including 6-of-9 from distance.
The focus Tuesday, too, was the point guard matchup between Michigan's Trey Burke and Ohio State's Aaron Craft.
In no place was that better exemplified than on three straight possessions in overtime when Craft stripped Burke with 0:26 to play, only to be stripped by Burke on the fastbreak in the other direction.
Ohio State retained possession, but a jumpshot by Craft was blocked by Burke and grabbed by Michigan to preserve a 75-74 lead. Craft then fouled Glenn Robinson III, giving the Wolverines a chance to go up by three with free throws. Robinson III hit one of two free throws, allowing Ohio State one more possession.
Craft drove the length of the floor with Burke on his hip, going in for the layup before being blocked by Hardaway, Jr. Craft and the Ohio State bench were looking for a foul after what appeared to be a lot of contact around the rim, but there was no call as time expired, giving Michigan the victory.
Craft finished with 11 points, seven rebounds, and three steals, while Burke had 16 points and eight assists.
In the first half, Michigan's hot shooting got the Wolverines out to a 13-4 start, thanks to aggressiveness in attacking the basket and three-pointers from Robinson III and Nik Stauskas.
Robinson III showed he could bounce back after an Indiana game where he looked to be more out of sorts than at any other point in the season. He finished with 10 points and four rebounds.
Ohio State then tightened up on defense with the help of Craft. That defensive effort allowed the Buckeyes to get out in transition.
Eight Buckeyes scored in the first half, led by Deshaun Thomas' seven points. Though Ohio State spread the ball around, Thomas still had a similar percentage of the Buckeyes' overall scoring with his team-high 17 points on the night.
The problem was, though, Thomas did not score and was not the focus of an offense that struggled to score just one basket in overtime. Craft was 1-of-4 from the floor in the extra period with a turnover.
To OSU's credit, though, Thomas is typically counted on for the bulk of the scoring. Tuesday night, LaQuinton Ross had one of the best games of his career with 16 points on 7-of-10 shooting from the floor. Craft and Lenzelle Smith, Jr. also scored in double figures.
Mitch McGary brought the interior toughness that Michigan needed, tallying 10 of his 14 points in the first half and adding six rebounds.
The Wolverines then began to find the hot-shooting Hardaway, Jr., though they struggled to get stops on the defensive end. He hit another two three-pointers to keep it close, but Ohio State exploited Michigan's lack of size inside.
The Buckeyes worked the ball inside to Amir Williams on consecutive possessions, resulting in a layup and dunk to pull Ohio State ahead, 64-60, with 5:12 to play.
After trading baskets down the stretch, Lenzelle Smith, Jr. hit a jumper with a hand in his face to tie the game at 72-72 with 0:29 to play, ultimately forcing overtime.


Conference at the celebration of CIANO and INIA's 25th Anniversary.
Dr. Alejandro Ortega describes the process of experimental varieties of maize and the information of some of them in the experimental station of Poza Rica.
Conference regarding the fertilization requirements on maize plants.
An introduction to the processes usted to evaluate wheat quality for bread wheat, durum wheat and triticale.


text:
French court to rule on claim over 1994 ferry disaster
George Zimmerman banned from popular dating app
By: Cox Media Group National Content Desk
FLORIDA - The ex-neighborhood watch volunteer who killed an unarmed black teen in Florida in 2012 has been banned from the dating app Tinder.
An emailed statement from Tinder cited users safety as a reason for removing George Zimmerman's profile.
An article by Tampa, Florida, weekly Creative Loafing, Zimmerman had a phony profile and using a fake name "Carter."
In screen grabs captured by Creative Loafing Tampa, Zimmerman described himself as a self-employed consultant and a graduate from Liberty University.
TRENDING STORIES:
'You told me to': Video shows Charlotte police officer kill man following orders to drop gun
1 killed, several injured after driver fleeing police on I-75/85 hits 2 cars, police say
Gang members sentenced for 'most brutal murder in recent Atlanta history'
According to The Washington Post, Zimmerman was blocked and banned from Bumble in 2018.
Zimmerman was acquitted in the shooting of Trayvon Martin on the grounds of self-defense.
He has had several run-ins with the law, including a 2015 arrest after he was accused of throwing a wine bottle at his girlfriend. The case was dropped.
In November he entered a no contest plea to resolve a charge of stalking a private investigator associated with a documentary on Martin.
The Associated Press contributed to this story.
Former UGA star buys his mom a house (VIDEO)


ㅋㅋㅋㅋㅋㅋㅋㅋㅋ으앍 뭐야 나 여기 왜나와 ㅋㅋㅋㅋㅋㅋ스티븐연 의상만 체크하고 후딱 도망쳤어야했엌ㅋㅋㅋㅋㅋㅋㅋㅋㅋㅋㅋㅋㅋㅋㅋㅋㅋㅋㅋㅋㅋㅋㅋㅋㅋ웃음이 멈추질 않는다.
Last week, we spoke to South Korean megastar Zico about his volcanic rise from Block B boy band leader to fearless, no-fucks-given rapper, and how he has been existing with one foot in both worlds. But before that, he released this candy-coated visual for new track "I Am You, You Are Me", which sees the artist sing, rap and dance in a supermarket, his eyes firmly directed towards a bored-looking shop assistant. Eventually the pair realise they've been wearing the same outfits, from a multi-coloured woollen jumper to a big, biker jack and a fuzzy, canary yellow top and a shirt with a rose pin. Watch right to the end to see if you can spot a copy of Dazed leaning against one of the shop shelves.
음. 보시다시피. 네. 그렇습니다. 워낙 유명한 잡지니까 자세한 이야기는 생략. 아무튼 오밤중에 미감님 인스타를 보고 알았음. 참여했던 작업이 해외 유명잡지에 실린다는 것은 기사가 길고 짧음을 떠나서 갱장히 뿌듯한 느낌! 마무리는 영어한줄정리 > This work has been featured on Dazed & Confused. Thank you all you guys!


text:
"""
====================================================================
pipeline_chiptools - homer and deeptools implimentation
====================================================================

Overview
========

The aim of this pipeline is to create peaklists in :term:`bed` files from
aligned reads in :term:`bam` files that can then be taken on to downstream
analysis (e.g., quantification of peaks etc.). The pipeline wraps up
homer and deeptools software for ATAC and ChIP-seq analysis.

This pipeline also performs motif analysis and basic QC analysis
(i.e., basic tag information, read length distribution, clonal tag distribution
(clonal read depth), autocorrelation analysis (distribution of distances
between adjacent reads in the genome) and sequence bias analysis).

Principal targets
-----------------

standard
    perform all workflows minus the motif generation

full
    run all chiptools tasks

Functionality
+=============

- Takes paired-end or single end :term:`Bam` files you want to call peaks on
  (e.g. ChIP-Seq or ATAC-Seq samples and their appropriate 'input' controls).
- Creates Tag directories for ChIP and Input :term:'Bam' files
- Runs homer peakcaller (findPeaks)
- Produces peak lists in bed files to take forward for downstream analysis.
- Performs motif discovery analysis
- Performs peak annotation
- Finds differential and common  peaks between replicates (reproducibility)
  and between samples (differential binding)

Usage
=====

See :ref:`PipelineSettingUp` and :ref:`PipelineRunning` on general
information how to use CGAT pipelines.

Configuration
-------------

For homer to work with your desired genome please follow the instructions:

   perl {path_to_cgat_pipelines}/conda-install/envs/py36-v1/share/homer-4.9.1-5/configureHomer.pl -install hg19

This will download the genome and you can now use homer to process your samples.

The pipeline requires a configured :file:`pipeline.ini` file.
CGATReport report requires a :file:`conf.py` and optionally a
:file:`cgatreport.ini` file (see :ref:`PipelineReporting`).

Default configuration files can be generated by executing:

   python <srcdir>/pipeline_chiptools.py config

Input files
-----------

The pipeline requres a sample `bam` file and an optional input `bam` file to
perform background evaluation. The bam file should be indexed.

The pipeline requires a pipeline.ini file that needs to be popeluated with information
that will allow the pipeline to execute correctly. This can be generated using the
command:

       cgatflow chiptools config

A folder called design.tsv, which is a tab seperated file also needs to be supplied
for running both homer and deeptools. The file needs to be specified with the following
headers

SampleID Tissue Factor Condition Treatment Replicate bamReads ControlID bamControl

For running deeptools you also need to specify a bed file of interested regions. Please
see the pipeline.ini under the deep options for more details.

Code
====

"""
from ruffus import *
import sys
import os
import CGAT.Experiment as E
import CGATPipelines.Pipeline as P
import CGATPipelines.PipelinePeakcalling as PipelinePeakcalling
import CGAT.BamTools as Bamtools
import CGAT.IOTools as IOTools
import matplotlib.pyplot as plt
import pandas as pd

# load options from the config file
PARAMS = P.getParameters(
    ["%s/pipeline.ini" % os.path.splitext(__file__)[0],
     "../pipeline.ini",
     "pipeline.ini"])

#######################################################################
# Check for design file & Match ChIP/ATAC-Seq Bams with Inputs ########
#######################################################################

# This section checks for the design table and generates:
# 1. A dictionary, inputD, linking each input file and each of the various
#    IDR subfiles to the appropriate input, as specified in the design table
# 2. A pandas dataframe, df, containing the information from the
#    design table.
# 3. INPUTBAMS: a list of control (input) bam files to use as background for
#    peakcalling.
# 4. CHIPBAMS: a list of experimental bam files on which to call peaks on.

# if design table is missing the input and chip bams  to empty list. This gets
# round the import tests

if os.path.exists("design.tsv"):
    df, inputD = PipelinePeakcalling.readDesignTable("design.tsv", "none")

    INPUTBAMS = list(df['bamControl'].values)
    CHIPBAMS = list(df['bamReads'].values)
    TOTALBAMS = INPUTBAMS + CHIPBAMS

    # I have defined a dict of the samples to I can parse the correct
    # inputs into bamCompare
    SAMPLE_DICT = {}
    for chip, inputs in zip(CHIPBAMS, INPUTBAMS):
        key = chip
        value = inputs
        SAMPLE_DICT[key] = value

else:
    E.warn("design.tsv is not located within the folder")
    INPUTBAMS = []
    CHIPBAMS = []
    TOTALBAMS = []
    SAMPLE_DICT = {}

#########################################################################
# Connect to database
#########################################################################

def connect():
    '''
    Setup a connection to an sqlite database
    '''

    dbh = sqlite3.connect(PARAMS['database'])
    return dbh

###########################################################################
# start of pipelined tasks
# 1) Preprocessing Steps - Filter bam files & generate bam stats
###########################################################################

@transform("design.tsv", suffix(".tsv"), ".load")
def loadDesignTable(infile, outfile):
    ''' load design.tsv to database '''
    P.load(infile, outfile)

#####################################################
# makeTagDirectory Inputs
#####################################################

@active_if(PARAMS['homer'])
@follows(mkdir("homer"))
@follows(mkdir("homer/Tag.dir"))
@follows(loadDesignTable)
@transform(INPUTBAMS, regex("(.*).bam"),
           r"homer/Tag.dir/\1/\1.txt")
def makeTagDirectoryInput(infile, outfile):
    '''
    This will create a tag file for each bam file
    for a CHIP-seq experiment
    '''

    bamstrip = infile.strip(".bam")
    samfile = bamstrip + ".sam"

    statement = '''
                   samtools view %(infile)s > homer/Tag.dir/%(samfile)s;
                   cd homer/Tag.dir/ ;
                   makeTagDirectory %(bamstrip)s
                   %(samfile)s
                   -genome %(homer_maketagdir_genome)s -checkGC
                   &> %(bamstrip)s.makeTagInput.log;
                   touch %(bamstrip)s/%(bamstrip)s.txt &&
                   sleep 60'''

    P.run()

#####################################################
# makeTagDirectory ChIPs
#####################################################

@active_if(PARAMS['homer'])
@follows(mkdir("homer"))
@follows(mkdir("homer/Tag.dir"))
@follows(makeTagDirectoryInput)
@transform(CHIPBAMS, regex("(.*).bam"),
           r"homer/Tag.dir/\1/\1.txt")
def makeTagDirectoryChips(infile, outfile):
    '''
    This will create a tag file for each bam file
    for a CHIP-seq experiment
    '''

    bamstrip = infile.strip(".bam")
    samfile = bamstrip + ".sam"

    statement = '''
                   samtools view %(infile)s > homer/Tag.dir/%(samfile)s &&
                   cd homer/Tag.dir/ &&
                   makeTagDirectory %(bamstrip)s
                   %(samfile)s
                   -genome %(homer_maketagdir_genome)s -checkGC
                   &> %(bamstrip)s.makeTagChip.log &&
                   touch %(bamstrip)s/%(bamstrip)s.txt &&
                   sleep 60'''

    P.run()

@active_if(PARAMS['homer'])
@transform((makeTagDirectoryChips),
           regex("homer/Tag.dir/(.*)/(.*).txt"),
           r"homer/Tag.dir/\1/regions.txt")
def findPeaks(infile, outfile):

    '''
    This function will find peaks in your samples.

    Arguments
    ---------
    infiles : string
         this is a list of tag directories
    directory: string
         This is the directory where the tag file will be placed
    '''

    directory = infile.strip(".txt")
    _, _, directory, _ = directory.split("/")
    bamfile = directory + ".bam"

    df_slice = df[df['bamReads'] == bamfile]
    input_bam = df_slice['bamControl'].values[0]
    input_bam = input_bam.strip(".bam")

    statement = '''cd homer/Tag.dir/ &&
                   findPeaks %(directory)s -style %(homer_findpeaks_style)s -o %(homer_findpeaks_output)s
                   %(homer_findpeaks_options)s -i %(input_bam)s &> %(directory)s.findpeaks.log'''
    P.run()

@active_if(PARAMS['homer'])
@transform(findPeaks,
           regex("homer/Tag.dir/(.*)/regions.txt"),
           r"homer/Tag.dir/\1/\1.bed")
def bedConversion(infile, outfile):

    '''
    The peaks identified will be converted to a bed file for further downstream
    processing outside of this pipeline.
    '''

    statement = '''pos2bed.pl %(homer_bed_options)s %(infile)s > %(outfile)s'''

    P.run()

@active_if(PARAMS['homer'])
@transform(findPeaks,
           regex("homer/Tag.dir/(.*)/regions.txt"),
           r"homer/Tag.dir/\1/annotate.txt")
def annotatePeaks(infile, outfile):

    '''
    The peaks identified in your tag directory will be annotated according
    to the specified genome.
    '''

    statement = '''annotatePeaks.pl %(infile)s %(homer_annotatepeaks_genome)s &> Annotate.log > %(outfile)s'''

    P.run()

@active_if(PARAMS['homer'])
@follows(mkdir("homer/motif.dir"))
@transform(findPeaks,
           regex("homer/Tag.dir/(.*)/regions.txt"),
           r"homer/motif.dir/\1/motifs.txt")
def findMotifs(infile, outfile):

    '''
    This will find known motifs enrched in yopur peaks lists using the
    Jaspar database.
    '''

    _, _, directory, _ = infile.split("/")

    statement = '''findMotifsGenome.pl %(infile)s %(homer_motif_genome)s homer/motif.dir/%(directory)s -size %(homer_motif_size)i
                   &> homer/motif.dir/%(directory)s.log'''

    P.run()

@active_if(PARAMS['homer'])
@active_if(PARAMS['homer_diffannotat_raw'])
@follows(mkdir("homer/raw_annotate.dir"))
@merge(makeTagDirectoryChips, "homer/raw_annotate.dir/countTable.peaks.txt")
def annotatePeaksRaw(infiles, outfile):

    '''
    This function will annotate peaks according to the genome that is specified in the
    pipeline.ini section. It will take an unprocessed Tag directory as an input.
    '''

    directories = []

    for infile in infiles:
        directory = infile.split("/")[2]
        directories.append("homer/Tag.dir/" + directory + "/")

    directories = " ".join(directories)

    statement = '''annotatePeaks.pl %(homer_annotate_raw_region)s %(homer_annotate_raw_genome)s
                   -d %(directories)s > homer/raw_annotate.dir/countTable.peaks.txt'''

    P.run()

@active_if(PARAMS['homer'])
@active_if(PARAMS['homer_diff_expr'])
@follows(mkdir("homer/diffExprs.dir"))
@transform(annotatePeaksRaw,
           suffix(".peaks.txt"),
           r"homer/raw_annotate.dir/\1.diffexprs.txt")
def getDiffExprs(infile, outfile):

    '''
    Once the peaks have been annotated and the reads counted, differential
    expression is then performed.
    '''
    # in the future this should be read from the design file AC 11/12/2017

    statement = '''getDiffExpression.pl %(infile)s
                  %(homer_diff_expr_options)s %(homer_diff_expr_group)s
                  > homer/diffExprs.dir/diffOutput.txt'''

    P.run()

@active_if(PARAMS['homer'])
@active_if(PARAMS['homer_diff_repeats'])
@follows(mkdir("homer/Replicates.dir"))
@follows(makeTagDirectoryChips)
@originate("homer/Replicates.dir/outputPeaks.txt")
def getDiffPeaksReplicates(outfile):

    '''
    The function will determine the statistically enriched peaks accross
    replicates.

    The output of the function is a homer peak file that contains several
    columns of annotation, normalised read counts and differential enriched statistics
    from DESEq2.
    '''
    replicates = set(df["Replicate"])

    for x in replicates:
        subdf = df[df["Replicate"] == x]

        bams = subdf["bamReads"].values

        bam_strip = []
        for bam in bams:
            bam = bam.strip(".bam") + "/"
            bam_strip.append(bam)

    bam_strip = " ".join(bam_strip)

    inputs = subdf["bamControl"].values

    input_strip = []
    for inp in inputs:
        inp = inp.strip(".bam") + "/"
        input_strip.append(inp)

    input_strip = " ".join(input_strip)

    statement = '''getDifferentialPeaksReplicates.pl -t %(bam_strip)s
                       -i %(input_strip)s -genome %(homer_diff_repeats_genome)s %(homer_diff_repeats_options)s>
                       homer/Replicates.dir/Repeat-%(x)s.outputPeaks.txt'''

    P.run()

##################################################################################################
# This is the section where the deeptool (http://deeptools.readthedocs.io/en/latest/index.html#)
# deepTools is a suite of python tools particularly developed for the efficient analysis
# of high-throughput sequencing data, such as ChIP-seq, RNA-seq or MNase-seq
# Functions are specified
##################################################################################################

@active_if(PARAMS['deeptools'])
@follows(mkdir("deepTools/Plot.dir/Coverage.dir"))
@follows(loadDesignTable)
@merge([CHIPBAMS, INPUTBAMS], "deepTools/Plot.dir/Coverage.dir/coverage_plot.eps")
def coverage_plot(infiles, outfile):

    '''
    This tool is useful to assess the sequencing depth of a given sample.
    It samples 1 million bp, counts the number of overlapping reads and
    can report a histogram that tells you how many bases are covered how
    many times. Multiple BAM files are accepted, but they all should
    correspond to the same genome assembly.
    '''

    infile = [item for sublist in infiles for item in sublist]
    infile = " ".join(infile)

    if PARAMS['deep_ignore_dups']:
        duplicates = "--ignoreDuplicates"
    elif not PARAMS['deep_ignore_dups']:
        duplicates = ""
    else:
        raise ValueError('''Please set a ignore_dups value in the
                   pipeline.ini''')

    statement = '''plotCoverage -b %(infile)s
                   --plotFile %(outfile)s
                   --plotTitle "coverage_plot"
                   --outRawCounts deepTools/Plot.dir/Coverage.dir/coverage_plot.tab
                   %(duplicates)s
                   --minMappingQuality %(deep_mapping_qual)s'''

    P.run()

@follows(coverage_plot)
@active_if(PARAMS['deeptools'])
@follows(mkdir("deepTools/Plot.dir/Fingerprint.dir"))
@follows(loadDesignTable)
@merge([CHIPBAMS, INPUTBAMS],
       "deepTools/Plot.dir/Fingerprint.dir/fingerprints.eps")
def fingerprint_plot(infiles, outfile):

    '''
    This quality control will most likely be of interest for you
    if you are dealing with ChIP-seq samples as a pressing question
    in ChIP-seq experiments is Did my ChIP work?, i.e. did the
    antibody-treatment enrich sufficiently so that the ChIP signal
    can be separated from the background signal? (After all, around
    90% of all DNA fragments in a ChIP experiment will represent
    the genomic background).

    This tool samples indexed BAM files and plots a profile of
    cumulative read coverages for each. All reads overlapping a
    window (bin) of the specified length are counted; these counts
    are sorted and the cumulative sum is finally plotted.
    '''

    infile = [item for sublist in infiles for item in sublist]
    infile = " ".join(infile)

    if PARAMS['deep_ignore_dups']:
        duplicates = "--ignoreDuplicates"
    elif not PARAMS['deep_ignore_dups']:
        duplicates = ""
    else:
        raise ValueError('''Please set a ignore_dups value in the
                   pipeline.ini''')

    statement = '''plotFingerprint -b %(infile)s
                   --plotFile %(outfile)s
                   --plotTitle "Fingerprints of samples"
                   --outRawCounts deepTools/Plot.dir/Fingerprint.dir/fingerprints_plot.tab
                   %(duplicates)s
                   --minMappingQuality %(deep_mapping_qual)s'''

    P.run()

@follows(fingerprint_plot)
@active_if(PARAMS['deeptools'])
@active_if(PARAMS['deep_paired_end'])
@follows(mkdir("deepTools/Plot.dir/FragmentSize.dir"))
@follows(loadDesignTable)
@merge([CHIPBAMS, INPUTBAMS],
       "deepTools/Plot.dir/FragmentSize.dir/FragmentSize.png")
def fragment_size(infiles, outfile):

    '''
    This tool calculates the fragment sizes for read pairs
    given a BAM file from paired-end sequencing.Several regions
    are sampled depending on the size of the genome and number
    of processors to estimate thesummary statistics on the fragment
    lengths. Properly paired reads are preferred for computation,
    i.e., it will only use discordant pairs if no concordant
    alignments overlap with a given region. The default setting
    simply prints the summary statistics to the screen.
    '''

    infile = [item for sublist in infiles for item in sublist]
    infile = " ".join(infile)

    if PARAMS['deep_logscale']:
        logscale = ("--logScale %s") % (PARAMS['deep_logscale'])
    else:
        logscale = ""

    statement = '''bamPEFragmentSize -b %(infile)s
                   --histogram %(outfile)s
                   %(logscale)s &&
                   sleep 60'''

    P.run()

@follows(fragment_size)
@active_if(PARAMS['deeptools'])
@active_if(PARAMS['deep_bam_coverage'])
@follows(mkdir("deepTools/Bwfiles.dir/bamCoverage.dir"))
@transform(TOTALBAMS, regex("(.*).bam"),
           r"deepTools/Bwfiles.dir/bamCoverage.dir/\1.bw")
def bamCoverage(infiles, outfile):

    '''
    This tool takes an alignment of reads or fragments as
    input (BAM file) and generates a coverage track (bigWig
    or bedGraph) as output. The coverage is calculated as
    the number of reads per bin, where bins are short
    consecutive counting windows of a defined size. It is
    possible to extended the length of the reads to better
    reflect the actual fragment length. bamCoverage offers
    normalization by scaling factor, Reads Per Kilobase per
    Million mapped reads (RPKM), and 1x depth (reads per
    genome coverage, RPGC).
    '''

    if PARAMS['deep_ignore_norm'] is not "":
        normalise = '--ignoreForNormalization '
        norm_value = PARAMS['deep_ignore_norm']

    else:
        normalise = ''
        norm_value = ''

    if PARAMS['deep_extendreads']:
        extend = '--extendReads'
    elif not PARAMS['deep_extendreads']:
        extend = ''
    else:
        raise ValueError('''Please set the extendreads to a value 0 or 1''')

    statement = '''bamCoverage --bam %(infiles)s
                   -o %(outfile)s
                   -of bigwig
                   --binSize %(deep_binsize)s
                   %(normalise)s %(norm_value)s
                   %(extend)s
                   %(deep_bamcoverage_options)s &&
                   sleep 60'''

    P.run()

@follows(fragment_size)
@active_if(PARAMS['deeptools'])
@active_if(PARAMS['deep_bam_compare'])
@follows(loadDesignTable)
@follows(mkdir("deepTools/Bwfiles.dir/bamCompare.dir"))
@transform(CHIPBAMS,
           suffix('.bam'),
           add_inputs(SAMPLE_DICT),
           r"deepTools/Bwfiles.dir/bamCompare.dir/\1.bw")
def bamCompare(infiles, outfile):

    '''
    This tool compares two BAM files based on the number of
    mapped reads. To compare the BAM files, the genome is
    partitioned into bins of equal size, then the number of reads
    found in each bin is counted per file, and finally a summary
    value is reported. This value can be the ratio of the number
    of reads per bin, the log2 of the ratio, or the difference.
    This tool can normalize the number of reads in each BAM file
    using the SES method proposed by Diaz et al. (2012) Normalization,
    bias correction, and peak calling for ChIP-seq. Statistical
    Applications in Genetics and Molecular Biology, 11(3).
    Normalization based on read counts is also available. The
    output is either a bedgraph or bigWig file containing the
    bin location and the resulting comparison value. By default,
    if reads are paired, the fragment length reported in the
    BAM file is used. Each mate, however, is treated independently
    to avoid a bias when a mixture of concordant and discordant
    pairs is present. This means that each end will be extended
    to match the fragment length.
    '''

    chipbam = infiles[0]
    inputbams = infiles[1]
    inputbam = inputbams[chipbam]

    statement = '''
                   bamCompare -b1 %(chipbam)s
                       -b2 %(inputbam)s
                       -o %(outfile)s
                       -of bigwig
                       %(deep_bamcompare_options)s &&
                   sleep 60'''

    P.run()

@follows(bamCompare)
@active_if(PARAMS['deeptools'])
@follows(loadDesignTable)
@follows(mkdir("deepTools/Summary.dir"))
@merge([CHIPBAMS, INPUTBAMS], "deepTools/Summary.dir/Bam_Summary.npz")
def multiBamSummary(infiles, outfile):

    '''
    multiBamSummary computes the read coverages for genomic regions
    for typically two or more BAM files. The analysis can be
    performed for the entire genome by running the program in
    bins mode. If you want to count the read coverage for
    specific regions only, use the BED-file mode instead.
    The standard output of multiBamSummary is a compressed
    numpy array (.npz). It can be directly used to calculate
    and visualize pairwise correlation values between the read
    coverages using the tool plotCorrelation. Similarly,
    plotPCA can be used for principal component analysis of
    the read coverages using the .npz file. Note that using
    a single bigWig file is only recommended if you want to
    produce a bedGraph file (i.e., with the --outRawCounts
    option; the default output file cannot be used by ANY
    deepTools program if only a single file was supplied!).
    '''

    infile = [item for sublist in infiles for item in sublist]
    infile = " ".join(infile)

    if PARAMS['deep_mode_setting'] == 'None':
        mode_set = 'bins'
        mode_region = ''
    else:
        mode_set = 'BED-file --BED '
        mode_region = PARAMS['deep_mode_setting']

    if PARAMS['deep_ignore_dups']:
        duplicates = "--ignoreDuplicates"
    elif not PARAMS['deep_ignore_dups']:
        duplicates = ""
    else:
        raise ValueError('''Please set a ignore_dups value in the
                   pipeline.ini''')

    statement = '''
                   multiBamSummary %(mode_set)s %(mode_region)s
                   -b %(infile)s
                   -o %(outfile)s
                   --outRawCounts deepTools/Summary.dir/Bam_Summary.tab
                   --minMappingQuality %(deep_mapping_qual)s
                   %(deep_summary_options)s &&
                   sleep 60'''

    P.run()

@active_if(PARAMS['deeptools'])
@merge([bamCoverage, bamCompare], "deepTools/Summary.dir/bw_summary.npz")
def multiBwSummary(infiles, outfile):

    '''
    This performs and summary accross all of the big wig files
    and is similar to that impliemnted for the multi bam Summary.
    '''

    infiles = " ".join(infiles)

    if PARAMS['deep_mode_setting'] == 'None':
        mode_set = 'bins'
        mode_region = ''
    else:
        mode_set = 'BED-file --BED '
        mode_region = PARAMS['deep_mode_setting']

    statement = '''multiBigwigSummary %(mode_set)s %(mode_region)s
                   -b %(infiles)s
                   -out %(outfile)s
                   --outRawCounts deepTools/Summary.dir/Bw_Summary.tab
                   %(deep_summary_options)s &&
                   sleep 60'''

    P.run()

@active_if(PARAMS['deeptools'])
@follows(mkdir("deepTools/Plot.dir/Summary.dir/"))
@transform((multiBamSummary, multiBwSummary),
           regex("\S+/(\S+).npz"),
           r"deepTools/Plot.dir/Summary.dir/\1corr")
def plotCorrelation(infiles, outfile):

    '''
    Tool for the analysis and visualization of sample
    correlations based on the output of multiBamSummary
    or multiBigwigSummary. Pearson or Spearman methods
    are available to compute correlation coefficients.
    Results can be saved as multiple scatter plots depicting
    the pairwise correlations or as a clustered heatmap,
    where the colors represent the correlation coefficients
    and the clusters are joined using the Nearest Point
    Algorithm (also known as single). Optionally,
    the values can be saved as tables, too.
    '''

    if PARAMS['deep_plot'] == 'heatmap':
        colormap = ("--colorMap %s") % (PARAMS['deep_colormap'])
    else:
        colormap = ""

    statement = '''plotCorrelation -in %(infiles)s -o %(outfile)s
                   --corMethod %(deep_cormethod)s -p %(deep_plot)s
                   %(colormap)s
                   --plotFileFormat %(deep_filetype)s
                   --skipZeros %(deep_plot_options)s &&
                   sleep 60'''
    P.run()

@active_if(PARAMS['deeptools'])
@transform((multiBamSummary, multiBwSummary),
           regex("\S+/(\S+).npz"),
           r"deepTools/Plot.dir/Summary.dir/\1PCA")
def plotPCA(infiles, outfile):

    '''
    This will plot a PCA of the samples.
    '''
    statement = '''plotPCA -in %(infiles)s -o %(outfile)s
                   --plotFileFormat %(deep_filetype)s
                   %(deep_plot_options)s'''
    P.run()

@active_if(PARAMS['deeptools'])
@follows(mkdir("deepTools/Plot.dir/matrix.dir/"))
@merge([bamCoverage, bamCompare],
       "deepTools/Plot.dir/matrix.dir/matrix.gz")
def computeMatrix(infile, outfile):

    '''
    This computes a count matrix for downstream processing of the data.
    '''
    infile = " ".join(infile)

    if 'reference-point' in PARAMS['deep_startfactor']:
        reference_point = '--referencePoint'
        regions = PARAMS['deep_regions']
        region_length = " "
    elif "scale-regions" in PARAMS['deep_startfactor']:
        reference_point == '--regionBodyLength'
        regions = " "
        region_length = PARAMS['deep_region_length']
    else:
        raise(ValueError("Please supply a valid startfactor"))

    if ".gz" in PARAMS['deep_bedfile']:
        infile = PARAMS['deep_bedfile']
        bedfile = IOTools.openFile(infile, "r")
    else:
        bedfile = PARAMS['deep_bedfile']

    if PARAMS['deep_brslength'] is not "":
        upstream = ("--upstream %s") % (PARAMS['deep_brslength'])

    if PARAMS['deep_arslength'] is not "":
        downstream = ("--downstream %s") % (PARAMS['deep_arslength'])

    if PARAMS['deep_matrix_bin_size'] is not "":
        binsize = ("--binSize %s") % (PARAMS['deep_matrix_bin_size'])
    else:
        binsize = ""

    if PARAMS['deep_out_namematrix'] is not "":
        outmatrix = ("--outFileNameMatrix %s") % (PARAMS['deep_out_namematrix'])
    else:
        outmatrix = ""

    if PARAMS['deep_out_sorted'] is not "":
        sortedfile = ("--outFileSortedRegions %s") % (PARAMS['deep_out_sorted'])
    else:
        sortedfile = ""

    statement = '''computeMatrix %(deep_startfactor)s -S %(infile)s
                   -R %(bedfile)s
                   %(reference_point)s %(regions)s %(region_length)s
                   %(upstream)s
                   %(downstream)s
                   %(binsize)s
                   --skipZeros
                   -o %(outfile)s
                   %(outmatrix)s
                   %(sortedfile)s'''
    P.run()

@active_if(PARAMS['deeptools'])
@transform(computeMatrix,
           regex("\S+/\S+/\S+/(\S+).gz"),
           r"deepTools/Plot.dir/matrix.dir/\1_heatmap.eps")
def plotHeatmap(infile, outfile):

    '''
    This tool creates a heatmap for scores associated with genomic regions.
    The program requires a matrix file generated by the tool computeMatrix.
    '''

    infile = "".join(infile)

    statement = '''plotHeatmap -m %(infile)s
                   -o %(outfile)s
                   --outFileNameMatrix %(deep_out_namematrix)s
                   --outFileSortedRegions %(deep_out_sorted)s
                   --dpi %(deep_dpi)s
                   --colorMap %(deep_colormap)s
                   --kmeans %(deep_kmeans)s
                   --legendLocation %(deep_legendlocation)s
                   --refPointLabel %(deep_refpointlabel)s'''

    P.run()

@active_if(PARAMS['deeptools'])
@transform(computeMatrix,
           regex("\S+/\S+/\S+/(\S+).gz"),
           r"deepTools/Plot.dir/matrix.dir/\1_profile.eps")
def plotProfile(infile, outfile):

    '''
    This tool creates a profile plot for scores over sets of genomic
    regions. Typically, these regions are genes, but any other regions
    defined in BED will work. A matrix generated by computeMatrix
    is required.
    '''

    infile = "".join(infile)

    if PARAMS['deep_pergroup'] is not "":
        pergroup = ("--perGroup %s") % (PARAMS['deep_pergroup'])
    else:
        pergroup = ""

    statement = '''plotProfile -m %(infile)s
                   -o %(outfile)s
                   --kmeans %(deep_kmeans)s
                   --plotType %(deep_plottype)s
                   --dpi %(deep_dpi)s
                   %(pergroup)s
                   --legendLocation %(deep_legendlocation)s
                   --refPointLabel %(deep_refpointlabel)s'''

    P.run()

# ---------------------------------------------------
# Generic pipeline tasks

@follows(loadDesignTable,
         bedConversion,
         annotatePeaks,
         annotatePeaksRaw,
         getDiffExprs,
         getDiffPeaksReplicates,
         coverage_plot,
         fingerprint_plot,
         bamCompare,
         bamCoverage,
         multiBamSummary,
         multiBwSummary,
         plotCorrelation,
         plotPCA,
         computeMatrix,
         plotHeatmap,
         plotProfile)
def standard():
    '''a target without the motif generation'''
    pass

@follows(makeTagDirectoryInput,
         loadDesignTable,
         bedConversion,
         annotatePeaks,
         annotatePeaksRaw,
         getDiffExprs,
         getDiffPeaksReplicates,
         coverage_plot,
         fingerprint_plot,
         bamCompare,
         bamCoverage,
         multiBamSummary,
         multiBwSummary,
         plotCorrelation,
         plotPCA,
         computeMatrix,
         plotHeatmap,
         plotProfile)
def full():
    pass

@follows(mkdir("Jupyter_report.dir"))
def renderJupyterReport():
    '''build Jupyter notebook report'''

    report_path = os.path.abspath(os.path.join(os.path.dirname(__file__),
                                               'pipeline_docs',
                                               'pipeline_chiptools',
                                               'Jupyter_report'))

    statement = ''' cp %(report_path)s/* Jupyter_report.dir/ ; cd Jupyter_report.dir/;
                    jupyter nbconvert --ExecutePreprocessor.timeout=None
                    --to html --execute *.ipynb;
                 '''

    P.run()

# We will implement this when the new version of multiqc is available
@follows(mkdir("MultiQC_report.dir"))
@originate("MultiQC_report.dir/multiqc_report.html")
def renderMultiqc(infile):
    '''build mulitqc report'''

    statement = '''LANG=en_GB.UTF-8 multiqc . -f;
                   mv multiqc_report.html MultiQC_report.dir/'''

    P.run()

@follows(renderJupyterReport)
def build_report():
    pass

def main(argv=None):
    if argv is None:
        argv = sys.argv
    P.main(argv)

if __name__ == "__main__":
    sys.exit(P.main(sys.argv))

redpajama_set_name: RedPajamaGithub


text:
Stephen Sutton (16 de dezembro de 1994 - 14 de maio de 2014) foi um blogueiro e ativista de caridade britânico conhecido pelo seu blog Stephen's Story e seus esforços de captação de fundos para a caridade Teenage Cancer Trust para ajudar jovens com câncer. Tal como em 23 de maio de 2014, Sutton ja tinha levantado £3.952.699.83, mais de 390% da meta original.

Início da vida
Sutton nasceu em 16 de dezembro de 1994, e frequentou a escola primária e secundária em sua cidade natal de Burntwood, Staffordshire. Durante sua juventude, Sutton era uma criança muito ativa, participando de esportes e atletismo, especialmente corridas de longa distância e futebol.

Sutton recebeu notas A no Chase Terrace Technology College em agosto de 2012, e teve entrevistas na Universidade de Cambridge para estudar medicina, bem como nas universidades de Leicester e Leeds. Mais tarde, ele desistiu dos seus pedidos antes de chegar um veredito, depois que seu câncer estava determinado a ser incurável.

Doença e ativismo

Sutton foi diagnosticado com estágio 3B de câncer colorretal com 15 anos de idade, posteriormente, passou por tratamentos agressivos de radiação e quimioterapia. Em dezembro de 2012, dois anos após o diagnóstico inicial, o câncer foi considerado incurável depois de se espalhar para os pulmões e fígado. Após um colapso do pulmão em 22 de abril de 2014, Sutton foi colocado no suporte de vida, mas em condição estável.

Após o diagnóstico, Sutton começou a participar de eventos de caridade com o Teenage Cancer Trust, e mais tarde começou seu próprio site e blog em janeiro de 2013. Ao mesmo tempo, ele começou a captação de fundos com o Teenage Cancer Trust, com uma meta inicial de £10.000. Depois das doações inesperadas, o objetivo foi levantado para £100.000 e £500.000 no mesmo ano, mas tarde foi levantado para £1.000.000 em março de 2014. Durante sua campanha de captação de fundos, Sutton foi apoiado por várias celebridades, principalmente Jimmy Carr, Jonathan Ross e Jason Manford. Manford doou £10.000 e deu todo o faturamento de seus próprios clubes de comédia de todo o mês de maio, para a caridade. Após a hospitalização de Sutton, em abril de 2014, Manford tornou-se o porta-voz não oficial da instituição de caridade, aparecendo em entrevistas que promovem a causa. Ele também lançou a campanha "#thumbsupforStephen", pedindo que as pessoas compartilhem selfies de si mesmos que promovem a campanha.

O objetivo de Sutton para £1.000.000 foi alcançado em 23 de abril de 2014 e em 2 de maio de 2014, Sutton teve alta do hospital após uma melhoria na sua condição. Mais tarde, naquele mesmo dia, ele também se reuniu com o primeiro-ministro David Cameron, que expressou seu apoio para a campanha. Em 4 de maio de 2014, Sutton ajudou a quebrar o recorde mundial do Guinness para o "maior número de pessoas fazendo gestos com as mãos em forma de coração", com 554 pessoas no Chase Terrace Technology College.

Morte e reação
Sutton morreu enquanto dormia no Queen Elizabeth Hospital Birmingham, na madrugada de 14 de maio de 2014, de câncer colorretal, aos 19 anos de idade. No momento da sua morte, ele havia levantado mais de £3.000.000 para o Teenage Cancer Trust. Cameron elogiou Sutton por seu "espírito e bravura", enquanto Ed Miliband disse que Sutton foi uma "inspiração". Os comediantes Ricky Gervais e John Bishop, ex-futebolista Stan Collymore, a apresentadora Clare Balding e a cantora Carol Decker também ofereceram suas condolências. Jason Manford disse:

Matthew Tuck, o vocalista do Bullet for My Valentine, uma das bandas favoritas de Sutton, também twittou sobre a morte de Sutton, chamando-o de "além da inspiração".

Em 21 de maio ele foi anunciado em uma vigília pública que será realizada na Catedral de Lichfield em 29 de maio, antes do funeral privado da família no dia seguinte.

Ligações externas
 Stephen's Story no Facebook
 Stephen's fundraising page no Justgiving
 Obituário no The Independent de Marcus Williamson

Mortes por câncer colorretal
Ativistas do Reino Unido
Blogueiros do Reino Unido

redpajama_set_name: RedPajamaWikipedia


Sieve flour, baking powder, baking soda, sugar, all together 2 to 3 times. Keep aside.
Pour condensed milk in a bowl. Add the butter, and beat well till smooth. Add the flour spoon by spoon, mixing into the condensed milk mixture. In between, add milk as required if the butter begins to get too stiff.
[Stir the mixture in one direction only all the while. This will incorporate more air and make the cake lighter].
Once all the flour is used up, beat the batter as above till light (5-7 minutes). Add the soda and mix gently till smooth.
Same as above except substitute coke or Thums up instead of soda. Replace 280 gms flour with 240 gms flour and 40 gm cocoa. Continue as above.


You can publish view and download services if the theme linked to your data set has a valid service configuration. Publishing services is done either by triggering the automated publishing process at the end of the data set creation, or through a manual command later on. When you publish services, the system always creates all configured services types at once; in other words, if your theme configuration includes a view- and a download service, it is not possible to publish just a download service. The reason for this is that the metadata of each has references to the other.
This process runs in the background and can take a while. A progress bar displaying the status of service creation, service testing and service publishing appears.
To unpublish a service, deactivate the toggle switch and click «Delete services».
Display properties configured for the theme are not used for the GetFeatureInfo in the WMS.
The ATOM Feed is not completely INSPIRE compliant, since elements for GeoRSS and Open Search are missing.


Sounds very similar to what they had in Dark Age of Camelot. The higher the stealther got his stealth ability, the closer he could get to a person without being seen. And differences in level and 'see stealth' skills effected the stealthers ability to stay undetected. The difference I see is that in DaoC the stealther had to sacrifice other abilities to be able to get close to people reliably in stealth, whereas this way every stealther would just need to get Adept III's or MI's for their ability.
Did you even read what the guy said? See stealth totems negate stealth, they are available to anyone post lvl 20 or 30 I forget which. The problem lies in track and not stealth. I do like the kind of danger sense idea though.


With 18 holes (par 72) and more than 6,000 m in length, the Royal Spanish Golf Federation (Real Federación Española de Golf) considers it to be a prestigious golf course and one of the best in Spain, both for its layout, as well as it unique beauty.
Its design makes it a spectacular course. The course has a wide variety of different species of trees: Pine, Palm, Casuarinas, Olive, Cypress, etc. which make it the ideal place to play golf, both on foot and in golf carts.


text:
How to Weigh Drugs in a Trafficking Case
Weighing stuff is pretty simple, right? Just put stuff on a scale, watch for a number to pop up on the screen, and bam–you've got a weight. When it comes to weighing drugs in a drug trafficking case, it's not so simple. Everyone has watched the crime show de jour, and been dazzled by the high tech gadgets highly paid actors use to find evidence. Unfortunately, real life is not as high tech. Unfortunately, real life government crime fighters are not always as thorough as their show biz counterparts.
Our real life crime drama comes from the case of Jackson v. State, 76 So.3d 1130 (Fla. 4th DCA 2012). Jackson was convicted of trafficking in cocaine greater than 200 grams, but less than 400 grams, and possession of cannabis. For those of you keeping score at home, this charge carries a minimum mandatory prison term of 7 years, and a minimum fine of $100,000. Even though the charge carried a minimum of 7 years, the judge gave Jackson 15 years on the trafficking (and time served on the possession of cannabis…gee, how merciful…).
Jackson's troubles began after a search warrant was served on his house, and eight baggies of cocaine were recovered. The lab analyst testified at trial that she only tested one of the eight baggies, but she did testify that each of the eight baggies appeared to contain the same drug. Add to this evidence the fact that Jackson admitted to police that he usually has in his home "approximately a quarter kilogram of cocaine", and that he "normally purchases a quarter kilogram of powder cocaine every two weeks". Id. The court of appeals overturned his trafficking in cocaine greater than 200 grams, relying upon a previous court ruling that does not allow lab analysts to visually test drugs, finding that "a visual examination of untested packets of this weight is insufficient to convict because the white powder contained therein may be milk sugar or any one of a vast variety of other white powdery chemical compounds not containing cocaine. Moreover, the fact that one or two packets containing cocaine are found among other packets containing similar-looking white powder is no assurance that the latter untested packets also contain cocaine in view of (1) the vast number of other chemical compounds which have a similar white powdery appearance, and (2) the fact that the material in the untested packets was not commingled with the material in the tested packets." Id at 1132, quoting Ross v. State, 528 So.2d 1237 (Fla. 3d DCA 1988).
Sure, Jackson was still found guilty of the weight of the baggie which was tested, and that amount turned out to be a trafficking over 28 grams, but less than 200 grams. Such a charge carries a 3 year minimum mandatory rather than 7 years. Not a complete reversal in this case, but 3 years sure beats 15 years. The deeper question is whether such decisions can ever spill over into trafficking in oxycodone cases, where citizens are caught with numerous "Watson 540" pills (for example), yet only one of the pills is actually tested. So far, our courts have been unwilling to force the government to examine each and every pill involved in a trafficking charge. Oh well, we can always hope….
How to Weigh Drugs in a Trafficking Case | Orlando Criminal Defense Lawyer


Of course, self-employment is only a crude proxy for entrepreneurship in the functional sense, but it is a widely used proxy in the empirical literature. I suppose entrepreneurship researchers, like other social scientists, resemble the drunk looking for his car keys under the lamppost. Who am I to complain?


Warner Bros. Home Entertainment has sent over a press release officially announcing and detailing their home entertainment releases of the smash hit 'IT' based on the novel by Stephen King. The film will be available to own early on Digital beginning December 19, 2017 and followed by the 4K Ultra HD, Blu-ray and DVD releases on January 9, 2018. Continue after the jump to read the full announcement for the release including bonus content listings, disc specs and more, plus front and rear artwork for the 4K Ultra HD and Blu-ray releases.
You can Pre-Order 'IT' by clicking on the Amazon Cart icon immediately below!


text:
April 19, 2016 | 4:37 pm
From Ideas to Action: Cheaply, quickly, fairly
Last week, in the Congress for the New Urbanism's "Public Square" blog, sociologist David Brain outlined strategies for a Lean charrette, which is a work-in-progress concept designed to match up with Lean Urbanism strategies. Opportunist that I am, I welcome that as an excuse to try Part 2 of the charrette discussion I offered here.
Also, there's this: PlaceMakers is a volunteer coordinator for a National Charrette Institute training in Asheville, May 16-20. David Brain will be there, along with NCI executive director Bill Lennertz. There will be lots of discussion about these ideas during that week, and we'd love to see as many folks as possible get in on the conversation. Plus, Asheville is a pretty swell place to hang out in May.
If you're not familiar with the Lean Urbanism talk, you can get the full download here. But behind the concepts is a recognition of reality: As much as we'd like to reverse all at once everything stupid we did over the last half-century in the ways we've done land and infrastructure planning, there appears to be a reluctance in most places to dedicate the megabucks and endure the time and energy-sapping political battles required for big fixes. So why not focus on making big differences in smaller, faster, more incremental ways?
Brain's blog post did a good job of explaining how to use a leaner charrette process to do that without tossing out what makes a charrette so effective at getting from visioning to idea-sorting to implementation. Here's my paraphrasing of three of Brain's keepers:
Commit to comprehensiveness. That means an inclusive, multidisciplinary approach that allows for a wide range of inputs and critiques, both from technical experts and from those who just know the turf from living and working there.
Leverage the advantages of a compressed time frame. Make it clear the goal is to have the framework of an actionable plan, and organize sessions and tasks to systematically sort through ideas, establish priorities and shape consensus-driven strategies by the end of the charrette.
Invite trust through transparency. Everybody gets to review and critique both the rules for idea-sorting and the evolution of emerging strategies. It's always easier to get buy-in for products that were co-created by customers.
Getting all that into a smaller budget, smaller team process that still delivers something actionable in the short term requires a division of labor that's almost never part of the deal planning consultants currently make with their clients. Brain is too polite to put it exactly that way, but he acknowledges the challenge:
To move efficiently, however, requires a certain amount of pre-established agreement with respect to values, goals, and some important limits to be respected. For example, a previous set of discussions and workshops might have established and branded a Lean project, linking it to a diverse set of interest and allies. Whatever the specific project might be at hand, it can be conceived as a manifestation of that initiative and thereby benefit from what is hopefully a diverse collection of allies.
So here comes the hard part:
If budgets and teams are slimmed down and we still want to get where tried-and-true charrette techniques help us go, then somebody has to take up the slack in assuring there's "a certain amount of pre-established agreement with respect to values, goals, and some important limits to be respected." So far, many municipal and regional governments have nailed the smaller-budget component of Lean. Most of the RFPs I've seen, however, invite assumptions that nothing like that kind of agreement is in place; so getting to that point is often part of the required scope and in consultants' responses, often wedged into a reduced-price charrette.
What's most helpful about the new Lean Charrette idea is the idea of re-assigning the costly and time-consuming visioning component of a charrette to an entirely separate stage of pre-charrette public engagement. The most logical responsible party for that task: The client. After all, shouldn't the establishment and maintenance of a trusting environment for talking about the future be fundamental to a government's function?
Okay, that's way too out there. Let's look at it another way. Lots of places, especially in this time of political polarization, find themselves severely disadvantaged when it comes to making the most basic plans for land use, transportation, zoning and infrastructure. So what they need is to embrace the Lean idea — small steps towards bigger ideas, starting with the crucial step of reestablishing trust that governments can get stuff done that most people agree are improvements to their quality of life.
Consultants are equipped to help with that trust building if governments can't manage it in-house. But it shouldn't be a one-off effort attached to one project or plan. The goal should be to establish that agreement about values and rules for planning in ways that make it renewable, a foundation for vision continuity enabling future planning efforts to be more focused and fast moving — and less expensive.
–Ben Brown
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Category Planning and Design, Public Engagement, Public Policy1 CommentTags Ben Brown, David Brain, Lean Urbanism, National Charrette Institute
CNU24 Detroit: Summary and celebration | PlaceMakers says:
[...] blogged on Lean Urbanism a number of times: Lean Code Tool, The Lean Charrette: From Ideas to Action: Cheaply, quickly, fairly, and Lean Urbanism: A century [...]
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Definition of Covered
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