jimnoneill/paper-to-field-training huggingface dataset:
Comparative Genomics Reveals Chd1 as a Determinant of Nucleosome Spacing <i>in Vivo</i>

Abstract Packaging of genomic DNA into nucleosomes is nearly universally conserved in eukaryotes, and many features of the nucleosome landscape are quite conserved. Nonetheless, quantitative aspects of nucleosome packaging differ between species because, for example, the average length of linker DNA between nucleosomes can differ significantly even between closely related species. We recently showed that the difference in nucleosome spacing between two Hemiascomycete species—Saccharomyces cerevisiae and Kluyveromyces lactis—is established by trans-acting factors rather than being encoded in cis in the DNA sequence. Here, we generated several S. cerevisiae strains in which endogenous copies of candidate nucleosome spacing factors are deleted and replaced with the orthologous factors from K. lactis. We find no change in nucleosome spacing in such strains in which H1 or Isw1 complexes are swapped. In contrast, the K. lactis gene encoding the ATP-dependent remodeler Chd1 was found to direct longer internucleosomal spacing in S. cerevisiae, establishing that this remodeler is partially responsible for the relatively long internucleosomal spacing observed in K. lactis. By analyzing several chimeric proteins, we find that sequence differences that contribute to the spacing activity of this remodeler are dispersed throughout the coding sequence, but that the strongest spacing effect is linked to the understudied N-terminal end of Chd1. Taken together, our data find a role for sequence evolution of a chromatin remodeler in establishing quantitative aspects of the chromatin landscape in a species-specific manner.

Topic: Genomics and Chromatin Dynamics
Subfield: Molecular Biology
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
COVID-19 Patients at the First University Clinic of Tbilisi State Medical University, Georgia

The outbreak COVID-19 which had begun from China at the end of 2019 is a major public health issue. Public health and infection control measures are urgently required to limit the spread of this global viral infection. 160 COVID-19patients were admitted to the First University Clinic of Tbilisi State Medical University (TSMU) during March-June 2020. We provided the retrospectivestudy of these cases according to gender and age of patients, lethal outcome rate, hospitalization days and frequency of different comorbid diseases. Also, observations were carried out on patients taking angiotensin converting enzyme(ACE) inhibitors and angiotensin-AT1 receptor blockers due to heart failure or arterial hypertension. Among COVID-19 patients, frequency of lethal outcome was not significantly different between female and male genders (44.4% vs. 55.6%). Prevalence of this disease was the most common in patients with 30-59 years of ages (45.3%). Average hospitalization days were 21. Mortality rate was 5.6%, mostly in age above 60 (88.8%). Among lethal outcome patients, 88.8% had comorbid diseases. Heart failure, acute kidney injury, sepsis, essential arterial hypertension III, mitral valve defect, nontoxic diffuse goiter and etc; were the most common underlying conditions. Recovering of COVID- patients 19with arterial hypertension(55%) who were not treated with angiotensin-converting enzyme inhibitors and angiotensin-AT1 receptor blockers required fewer hospitalization days to recover (approximately 2-3 days or 62 hours less) in comparing to patients which were treated using the above mentioned medications.

Topic: COVID-19 Clinical Research Studies
Subfield: Infectious Diseases
Field: Medicine
Domain: Health Sciences
Microparametric Syntax: <i>Some Introductory Remarks</i>

Abstract Comparative syntax can be thought of as that facet of syntactic theory directly concerned with the question of how best to characterize the properties of human languages that are not universal. Put another way, comparative syntax directly addresses the question of how best to understand the notion of parameter taken to underlie syntactic variation.

Topic: Syntax, Semantics, Linguistic Variation
Subfield: Language and Linguistics
Field: Arts and Humanities
Domain: Social Sciences
Improving productive performance of crossbred cattle in cold arid conditions of Kargil through UMMB supplementation

The study was carried-out to assess the response of urea molasses mineral block (UMMB) supplementation on milk yield and cost effectiveness with lactating crossbred cows, maintained under smallholder mixed farming system at cold arid conditions, Kargil. Crossbred cows (20) in early to mid lactation were selected; 10 cows were given free access to UMMB in addition to normal ration and the other 10 cows served as control. Supplementation of UMMB licks significantly increased feed intake, milk yield and maintained live weight and body condition score of the cows. UMMB improved general health of the animals with enhanced cash benefit of over ` 41.1/cow/day. The UMMB supplementation technology was found a cost-effective approach to maximize the utilization of locally available feed resources which are scarce in the region as it remains covered with snow and cutoff from rest of world for 6 months.

Topic: Livestock Management and Performance Improvement
Subfield: Agronomy and Crop Science
Field: Agricultural and Biological Sciences
Domain: Life Sciences
Patent controversy: don’t let breast cancer gene genie out of the bottle

The US Court of Appeals for the Federal Circuit has found Myriad Genetics is entitled to patents on two sets human genetic mutations used to predict if women have an increased risk of breast and ovarian cancer.

The case has been closely monitored here for two reasons:

1) The Australia Patent Amendment (Human Genes and Biological Materials) Bill 2011 is currently with the Senate and Community Affairs Legislation Committee, whose report on the Bill is due on August 25.

2) The Federal Court of Australia is slated to hear an Australian test case (discussed below) in February 2012.

Dr Luigi Palombi, who has previously written about the Patent Amendment (Human Genes and Biological Materials) Bill 2011 for The Conversation, gives his response about the implications of the decision for Australia:

The US decision is disappointing because it doesn’t provide a definitive resolution of the real question – should naturally occurring genes be patentable subject matter?

Topic: Science, Research, and Medicine
Subfield: Reproductive Medicine
Field: Medicine
Domain: Health Sciences
[Use of nutrient density in etiologic studies on stomach cancer].

Role of nutrient density played in the genesis of stomach cancer was analyzed with a pair-matched case-control design to explore further the association between dietary nutrient and incidence of stomach cancer. Investigation of 88 pairs of cases with stomach cancer and controls showed high nutrient density of dietary vitamins C and A could protect from stomach cancer with OR of 0.34 and 0.46, respectively, and high of carbohydrate could increase risk of it with an OR of 2.20. Some problems in the use of nutrient density were discussed in the paper.

Topic: Nutrition, Genetics, and Disease
Subfield: Genetics
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Traditional chinese medicine in the treatment of gastroesophageal reflux in newborns

Introduction: Gastroesophageal reflux (GER) is common in the pediatric population. Most cases represent physiologic GER and as the lower esophageal sphincter (LES) matures and a solid diet is introduced, many of these patients (>65%) experience spontaneous resolution of symptoms by two years of age. Those who continue to have symptoms and develop complications such as failure to thrive, secondary respiratory disease, and others are classified as having gastroesophageal reflux disease. 
Purpose of this stud: To demonstrate that gastroesophageal reflux can be controlled quickly with auricular acupuncture in a new born baby without the necessity of using any kind of medications. Methods: a case report of a new born baby girl, with symptoms of vomiting constantly after days of birth. The parents were very worried about this situation because the baby was losing weight and cannot breastfeed adequately. The Chinese medicine´s doctor only did one session of auricular acupuncture in the right ear of the patient using mustard seeds. 
Results: with only one session, the baby can feed adequately and don´t want to intake any other medications to control this symptom of gastroesophageal reflux. 
Conclusion: the conclusion of this study is that gastroesophageal reflux can be treated using Chinese medicine´s tools such as auricular acupuncture in a new born baby and the adequate orientations of this patient parents regarding the exposition of the external pathogenic factor and what the mother of the baby need to eat, is an important tool to control this symptom.

Topic: Infant Health and Development
Subfield: Pharmacy
Field: Health Professions
Domain: Health Sciences
Effect of combined inoculations of Rhizobium-Arbuscular Mycorrhiza in Leucaena leucocephala CV: Perú

The work was conducted at the Experimental Station of Soil and Fertilizer “Escambray” land of farmers and associated rural extension. The experimental design was randomized blocks, and treatments: Rizhobium loti V-4033 (Research Institute of Pastures and Forages), mycorrhizal fungi trainers, Rhizobium +mycorrhiza fungi trainers, nitrogen and total control. Inoculation with my corrhiza forming fungi was performed at 10 g/bag Certificate MicoFert Strain the Institute of Ecology and Systematics-3: Glomus spurcum, Topes de Collantes, 85 % colonization of rootlets, while the Rhizobium was inoculated in a dose of 50 g/kg of seed. Variant was nitrogen at 25 kg/ha of urea. The plots occupied 18m2 , with an area of 9 m2 evaluable. When the plants reached 7.5 months and an average height of 143.4 cm proceeded to make the Court of establishment and then four foliage cuts were made every 90 days. Each cut dry biomass yield, and phosphorus content was determined crude protein. The combined inoculation of Rhizobium and mycorrhiza fungi Makers increased the yield of dry biomass, and phosphorus content of crude protein. We conclude proposing the adoption of an alternative methodology using mycorrhiza formers Fungi and Rhizobium in Leucaena leucocephala as a way to increase the yield of dry biomass, decreasing mineral fertilization and contribute to environmental protection

Topic: Plant and soil sciences
Subfield: General Agricultural and Biological Sciences
Field: Agricultural and Biological Sciences
Domain: Life Sciences
Holdup, Pressure Drop, and Flooding in Packed Countercurrent Columns for the Gas Extraction

The hydrodynamic behavior, i.e., flooding, liquid holdup, and pressure drop of countercurrent columns with two random packings, Raschig rings and Berl saddles, and two gauze packings, Sulzer CY and Sulzer EX, is scrutinized at temperatures between 313 and 373 K and pressures between 8 and 30 MPa using carbon dioxide as the supercritical solvent and water and olive oil deodorizer distillate as liquid phases. Two models are employed to correlate the experimental data: a sophisticated mechanistic approach based on the liquid holdup and a well-known empirical approach for the flooding point. The experimental data for the dry pressure drop and the liquid holdup below the loading point are successfully correlated using modified models from normal pressure operation. The flooding points can be correlated with good accuracy as well.

Topic: Phase Equilibria and Thermodynamics
Subfield: Biomedical Engineering
Field: Engineering
Domain: Physical Sciences
Inaccurate, exploitative, and very popular: the problem with ‘Poverty Porn’

With politicians, media, and much of public opinion already framing welfare as a problem, what is the impact of television shows that claim to ‘expose’ the daily lives of claimants? Ruth Patrick draws on her latest book to explain the mismatch between such portrayals and claimants’ realities. She writes that while some of Britain’s poorest are being exploited for entertainment, the impact of those portrayals is anything but entertaining.

Topic: Gender, Feminism, and Media
Subfield: Gender Studies
Field: Social Sciences
Domain: Social Sciences
Characterization of Chitosanase from Indralaya Swamp Bacteria, South Sumatera, Indonesia

The extracellular chitosanase-production capacity of 14 bacterial isolates taken from Indralaya Swamp South Sumatera, was evaluated in liquid cultures. The GB2 isolate was selected due to its high chitosanase activity. The optimum pH and temperature of chitosanase
produced by GB2 were 8 and 30 oC, respectively. Ca2+ and Fe2+ increased GB2 chitosanase whereas Na+ and K+inhibited the enzyme.Study on the effect of metals ion indicated that chitosanase GB2 was metaloenzyme.Moleculer weights were determined by using SDSPAGE and zymogram technique. Moleculer weight of chitosanase isolate GB2 was 36-110 kD.

Key Words: Chitosanase, Characterization, Bacteria, Indralaya swamp.

Topic: Studies on Chitinases and Chitosanases
Subfield: Molecular Biology
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
2165-P: In Vivo Islet Imaging Reveals that GLP-1 Paradoxically Increases Insulin Content

Glucagon-like peptide-1 (GLP-1) is an incretin, secreted in response to a meal that promotes glucose-stimulated insulin secretion in animal models and diabetic and nondiabetic humans. GLP-1 analogues have been successfully used as an effective treatment for both obesity and type 2 diabetes. While the general mechanisms of actions of GLP-1 on β-cell growth and function have been extensively studied, a number of questions regarding the dynamic and heterogeneity of the response of individual islets to GLP-1 in vivo remain. Using a fluorescent reporter mouse model originally created by the Arvan Lab, we have optimized a platform allowing us to monitor the content of individual islets in live animals. In this model, a super-folded GFP is bound to the C-Peptide, allowing the fluorescent visualization and quantification of insulin content within the islets without altering their normal physiology. After an overnight fast, the pancreas is exposed by laparotomy in anesthetized mice and the reporter in individual islets can be imaged repeatedly to quantify their insulin content. Upon glucose challenge, the GFP intensity within the islets progressively decreases in control mice, correlating with the insulin secretion within the bloodstream. In order to study the effects of GLP-1 on individual islet secretion, mice were either treated either with Liraglutide, a stable GLP-1 analog, or subjected to Vertical Sleeve Gastrectomy (VSG), a surgical procedure known to increase GLP-1 levels in obese mice. Surprisingly, with both approaches, in addition to increasing insulin secretion upon a glucose challenge, we could also observe insulin content actually increasing within the islets over the course of the excursion. This finding was later confirmed by measuring total insulin content in liraglutide-treated mice. This data indicates that despite causing enhanced insulin secretion, GLP-1 can also very rapidly increase insulin content within islets. Disclosure C.M.H. Cras-Méneur: None. H. Frikke-Schmidt: None. P. Arvan: None. R.J. Seeley: Consultant; Self; Ironwood Pharmaceuticals, Inc., Novo Nordisk A/S, Scohia Pharma Inc. Research Support; Self; MedImmune, Novo Nordisk A/S, Zafgen, Inc. Stock/Shareholder; Self; Zafgen, Inc.

Topic: Pancreatic function and diabetes
Subfield: Surgery
Field: Medicine
Domain: Health Sciences
C-MYC Induces KIR Expression Via a Novel Control Region Upstream of the Conventional Adult KIR Promoter.

Abstract KIR determine whether NK cells will be alloreactive against targets. Although epigenetic control is thought to play a role in KIR expression, the mechanism of KIR repertoire formation is unknown. Recently, a probabilistic transcriptional mechanism has been shown to control the acquisition of mouse Ly49 receptors using a switch region upstream of each Ly49 promoter (S. Anderson). Based on this information, the DNA upstream of known KIR genes was scanned for similar motifs to test the hypothesis that similar control mechanisms are operant in human NK cells. A putative c-myc/AML binding site was found approximately 1Kb upstream of the traditional KIR promoters. Initiation of transcription in this region was observed by RNAse protection, and spliced KIR mRNAs originating in the upstream region were cloned. To look at the effects of c-myc on KIR expression, we transduced NK92 cells using retroviral murine stem cell virus vectors containing either c-myc/eGFP or eGFP alone. Cells expressing high levels of c-myc were 18% KIR positive as compared to 0.9% of control cells. To further look at the effect of c-myc on KIR from primary cells, we transduced CD34+ progenitors isolated from umbilical cord blood with c-myc/eGFP and eGFP vectors. eGFP+ cells were plated on the murine fetal liver line AFT024 and cultured with IL-15, IL-7, IL-3, Flt3 ligand, and c-kit ligand, all known to induce NK cell differentiation. Although c-myc is an oncogene, it did not promote autonomous growth of NK cells in the absence of exogenous cytokines. Proliferation was significantly increased in single cell progenitors over-expressing c-myc with 739.3x103 NK cell progeny compared to 0.56x103 from each control cell after 21 days (p&amp;lt;0.0001). At this early time point, 21.68 ± 3.25% of c-myc cells were KIR positive while 0.0% of control cells were KIR positive (p&amp;lt;0.0001) suggesting that c-myc targets KIR expression. Furthermore, bulk-transduced cells over expressing c-myc had 3.9 times the level of early non-coding transcripts originating from the upstream promoter as compared to eGFP transduced cells. A direct effect of c-myc on the upstream promoter was supported by ChIP assays demonstrating increased binding to the c-myc/AML site. The presence of these upstream transcripts directly correlates with increased conventional KIR transcripts as shown by Q-RT-PCR and an increase of KIR expression as shown by flow cytometry. These data show that c-myc play an important role in the differentiation of NK cells and in KIR acquisition. Experiments are currently in progress to look at the effects of the competing AML site on KIR expression and to investigate how non-coding RNA affects adult KIR expression. Understanding the mechanisms of KIR expression may lead to development of novel strategies to manipulate NK cells for therapeutic benefit.

Topic: Immune Cell Function and Interaction
Subfield: Immunology
Field: Immunology and Microbiology
Domain: Life Sciences
Games for Central Bankers: Markets v/s Politics in Public Policy Decisions

25.,1* 3$3(5 6(5,(6 *$0(6 )25 &(175$/ %$1.(56 0$5.(76 96 32/,7,&6 ,1 38%/,& 32/,&< '(&,6,

Topic: Global Financial Crisis and Policies
Subfield: Finance
Field: Economics, Econometrics and Finance
Domain: Social Sciences
CCDC 785671: Experimental Crystal Structure Determination

An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

Topic: Crystallization and Solubility Studies
Subfield: Materials Chemistry
Field: Materials Science
Domain: Physical Sciences
Inferring Generative Model Structure with Static Analysis

Obtaining enough labeled data to robustly train complex discriminative models is a major bottleneck in the machine learning pipeline. A popular solution is combining multiple sources of weak supervision using generative models. The structure of these models affects training label quality, but is difficult to learn without any ground truth labels. We instead rely on these weak supervision sources having some structure by virtue of being encoded programmatically. We present Coral, a paradigm that infers generative model structure by statically analyzing the code for these heuristics, thus reducing the data required to learn structure significantly. We prove that Coral's sample complexity scales quasilinearly with the number of heuristics and number of relations found, improving over the standard sample complexity, which is exponential in $n$ for identifying $n^{\textrm{th}}$ degree relations. Experimentally, Coral matches or outperforms traditional structure learning approaches by up to 3.81 F1 points. Using Coral to model dependencies instead of assuming independence results in better performance than a fully supervised model by 3.07 accuracy points when heuristics are used to label radiology data without ground truth labels.

Topic: Multimodal Machine Learning Applications
Subfield: Computer Vision and Pattern Recognition
Field: Computer Science
Domain: Physical Sciences
An Examination of Research to Practice Gaps in Education: Whole Language, Learning Modalities, and Brain Gym

The purpose of this thesis is to examine the documented research to practice gap in education by discussing three recent trends in education that gained momentum with little to no empirical support: (a) whole language reading instruction; (b) modality-based instruction; and (c) Brain Gym. This thesis examines the trend in education toward embracing unsubstantiated strategies by spotlighting these three educational trends and offers recommendations for addressing the research to practice gap in the field of education.

Topic: Reading and Literacy Development
Subfield: Developmental and Educational Psychology
Field: Psychology
Domain: Social Sciences
[Spondylodiscitis].

The authors present a clinical case of a female child, aged 23 months, previously healthy that 24 hours after falling down started to refuse walking and complained about back pain. She never had fever. She felt better with nonsteroidal antiinflammatory drugs, restarting the symptoms, two days after therapy suppression. At admission on hospital she presented inability to flex the lower back and loss of lumbar lordosis, being normal the remaining physical examination. There was a raise of erythrocyte sedimentation rate (ESR) and a radiological narrowing of the L1/L2 inter-vertebral disc space, a compatible image of spondylodiscitis in the MRI. Several diagnosis hipothesis have been considered, being infectious spondylodiscitis the most probable. We instituted tuberculosis therapeutic during one year and intravenous ceftriaxone for tree weeks followed by oral acetil cefuroxime (tree weeks). The spine has been immobilized with spine support. At four months disease and two months therapy, a Oerskovia xanthineolytica was isolated by intervertebral needle biopsy. A good clinical and radiological evolution has been observed. The authors stress the importance of MRI and intervertebral needle biopsy in the diagnosis of spondylodiscitis. It is also enhanced the use of MRI and ESR in the monitoring of response to the treatment.

Topic: Infectious Diseases and Tuberculosis
Subfield: Surgery
Field: Medicine
Domain: Health Sciences
Simultaneous Determination of &amp;alpha;-Tocopherol and &amp;alpha;-Tocopheryl Acetate in Plasma by Mass Fragmentography

A method for simultaneous analysis of α-tocopherol and α-tocopheryl acetate in plasma was investigated using massfragmentography for the purpose of biopharmaceutical studies of α-tocopheryl acetate administered parenterally to animals. α-Tocopherol and α-tocopheryl acetate in plasma were extracted with n-hexane, derivatized by silylation, and determined simultaneously by monitoring at m/e 502 for silylated α-tocopherol and at m/e 430 for α-tocopheryl acetate. This method was rapid and specific, and was satisfactorily employed in the biopharmaceutical studies of α-tocopheryl acetate.

Topic: Antioxidant Activity and Oxidative Stress
Subfield: Biochemistry
Field: Medicine
Domain: Health Sciences