jimnoneill/paper-to-field-training huggingface dataset:
COBRA improves the quality of viral genomes assembled from metagenomes

Field: Computer Science (Physical Sciences)

Abstract

Microbial and viral diversity, distribution, and ecological impacts are often studied using metagenome-assembled sequences, but genome incompleteness hampers comprehensive and accurate analyses. Here we introduce COBRA (Contig Overlap Based Re-Assembly), a tool that resolves de Bruijn graph based assembly breakpoints and joins contigs. While applicable to any short-read assembled DNA sequences, we benchmarked COBRA by using a dataset of published complete viral genomes from the ocean. COBRA accurately joined contigs assembled by metaSPAdes, IDBA_UD, and MEGAHIT, outcompeting several existing binning tools and achieving significantly higher genome accuracy (96.6% vs 19.8-59.6%). We applied COBRA to viral contigs that we assembled from 231 published freshwater metagenomes and obtained 7,334 high-quality or complete species-level genomes (clusters with 95% average nucleotide identity) for viruses of bacteria (phages), ~83% of which represent new phage species. Notably, ~70% of the 7,334 species genomes were circular, compared to 34% before COBRA analyses. We expanded genomic sampling of ≥ 200 kbp phages (i.e., huge phages), the largest of which was curated to completion (717 kbp in length). The improved phage genomes from Rotsee Lake provided context for metatranscriptomic data and indicated in situ activity of huge phages, WhiB and cysC/cysH encoding phages from this site. In conclusion, COBRA improves the assembly contiguity and completeness of microbial and viral genomes and thus, the accuracy and reliability of analyses of gene content, diversity, and evolution.
General method of assignment of relative stereochemistry in C-1-substituted 2,4-dimethyl-8-oxabicyclo[3.2.1]oct-6-en-3-one by1H and13C NMR correlations

Field: Chemistry (Physical Sciences)

The 1H and 13C NMR spectra of cis-endo (a) and cis-exo (b) diastereoisomeric pairs of five differently C-1-functionalized 2,4-dimethyl-8-oxabicyclo[3.2.1]oct-6-en-3-ones were completely assigned. Several trends regarding the variation of chemical shifts and coupling constants of hydrogen and carbon atoms, on changing the configuration at C-2 and C-4 in both diastereoisomers, were observed by correlation of spectral data: methyl groups attached at C-2 and C-4 in a appear in 1H NMR at higher field than in diastereoisomer b. Simultaneously, H-2 and H-4 result in a lower field in a than in b. Both effects are due to the different interactions of hydrogens H-2, H-4, H-9 and H-10 with the bridging oxygen. In 13C NMR spectra it is possible to observe an upfield shift of C-9, C-10 and C-3 in b versus a. The difference observed in chemical shifts of the aforementioned hydrogens and carbons, between both diastereoisomers, allows one to assign the configuration at C-2 and C-4 in such structures. This phenomenon has wide scope and validity and could be applied to the stereochemical determination of any pair of diastereoisomers (a and b), independently of the function attached to C-1 of the oxabicyclic system. ©1998 John Wiley & Sons, Ltd.
Weak Positional Games on Hypergraphs of Rank Three

Field: Mathematics (Physical Sciences)

In a weak positional game, two players, Maker and Breaker, alternately claim vertices of a hypergraph until either Maker wins by getting a complete edge or all vertices are taken without this happening, a Breaker win. For the class of almost-disjoint hypergraphs of rank three (edges with up to three vertices only and edge-intersections on at most one vertex) we show how to find optimal strategies in polynomial time. Our result is based on a new type of decomposition theorem which might lead to a better understanding of weak positional games in general.
Establishment of environmentally sensitive DNA methylation states in the very early human embryo - Supplementary Materials

Field: Biochemistry, Genetics and Molecular Biology (Life Sciences)

The molecular mechanisms responsible for the developmental origins of later disease are currently unknown. We previously demonstrated that women’s periconceptional nutrition predicts their offspring’s DNA methylation at metastable epialleles (MEs). We present a genome-wide screen yielding 687 MEs and track their trajectories across nine developmental stages in human in vitro fertilization embryos. MEs exhibit highly unusual methylation dynamics across the implantation-gastrulation transition, producing a large excess of intermediate methylation states, suggesting the potential for differential programming in response to external signals. Using a natural experiment in rural Gambia, we show that genomic regions sensitive to season of conception are highly enriched for MEs and show similar atypical methylation patterns. MEs are enriched for proximal enhancers and transcription start sites and are influenced by genotype. Together, these observations position MEs as distinctive epigenomic features programmed in the early embryo, sensitive to genetic and periconceptional environment, and with the potential to influence phenotype.
Lateral resolution of secondary ion mass spectrometry–results of an inter‐laboratory comparison

Field: Materials Science (Physical Sciences)

Abstract Recently, BAM organised an inter‐laboratory comparison focussed on lateral resolution and accuracy of sub‐micron length measurements by secondary ion mass spectrometry (SIMS). Results were submitted by 16 laboratories from 10 countries. The task was to analyse a cross‐sectioned semiconductor multilayer stack. The resulting strip pattern in the surface of the sample shows narrow strips, step transitions and gratings of different periods. Imaging analysis of this pattern enables the determination of relevant parameters related to the lateral resolution: (i) The width (FWHM) of the primary ion beam, (ii) the distance between 16% and 84% intensity points in a profile across the image of a step transition and (iii) the modulation of intensity in the images of gratings with different periods. The parameter's data reported by the participants vary in a wide range. A strong variation in the data of primary ion beam width was observed for results measured with the same type of instrument. The distance between two narrow strips was measured with high accuracy. Twelve of sixteen of the submitted values are within the limits of uncertainty of the reference value 964 ± 35 nm. This result shows that the calibration of the length scale of the SIMS instruments is already rather precise in most of the participating laboratories. Copyright © 2006 John Wiley & Sons, Ltd.
The Effects of Situational and Individual Factors on Algorithm Acceptance in COVID-19-Related Decision-Making: A Preregistered Online Experiment

Field: Psychology (Social Sciences)

In times of the COVID-19 pandemic, difficult decisions such as the distribution of ventilators must be made. For many of these decisions, humans could team up with algorithms; however, people often prefer human decision-makers. We examined the role of situational (morality of the scenario; perspective) and individual factors (need for leadership; conventionalism) for algorithm preference in a preregistered online experiment with German adults (n = 1,127). As expected, algorithm preference was lowest in the most moral-laden scenario. The effect of perspective (i.e., decision-makers vs. decision targets) was only significant in the most moral scenario. Need for leadership predicted a stronger algorithm preference, whereas conventionalism was related to weaker algorithm preference. Exploratory analyses revealed that attitudes and knowledge also mattered, stressing the importance of individual factors.
DERMOID CYSTS OF THE OVARY PRESENTING AS A CAUSE OF ACUTE ABDOMINAL PAIN IN CHILDHOOD

Field: Medicine (Health Sciences)

Benign dermoid ovarian cysts uncommonly cause symptoms in young girls. It is estimated that they constitute 0.35% of all tumors occurring in children of both sexes less than 15 years of age. Symptoms produced by the cysts may mimic other intra-abdominal disease, and in three of the four cases reported in this series the girls were initially considered to have either acute appendicitis or infection of the urinary tract. All three had a pelvic mass palpable per rectum. The fourth girl was found to have bilateral calcified densities in the ovaries when examined roentgenographically for low back pain. In three of the four children, calcified or ossified material in the pelvis was seen in roentgenograms of the lower abdomen, and this finding was considered by the radiologist to be indicative of ovarian dermoid cyst. In two patients the cysts and associated Fallopian tubes had undergone torsion with infarction, and salpingo-oophorectomies were performed. In one girl, a simple oophorectomy was carried out, and, in the fourth child with bilateral dermoids, a bilateral ovarian cystectomy with preservation of tubes and as much ovarian tissue as possible was performed. All four girls have subsequently made satisfactory progress.
Analysis of solid waste management practices in rural settings of Tanzania

Field: Environmental Science (Physical Sciences)

This study explores the causes of ineffective solid waste management services in Tanzania’s rural settings which are made up of district councils. It is inspired by the fact that only 7.6% of the generated waste in the district councils which makes up 74% of the total local government authorities in the country is collected. The study variables include data availability, waste minimization initiatives, financial reliability, service reliability, technological flexibility, convenient waste collection systems, responsive market, supportive legal framework, and stakeholder inclusivity. Literature review, direct observation, interviews, and questionnaires constitute part of the data collection methods. Questionnaires were distributed to 137 (100%) district councils with over 95% responses. Zonal consultative meetings were conducted in six (6) zones representing 26 regions of Tanzania’s Mainland and attended by 26(100%) Regional Environmental Experts; and 56 (30%) District Environmental Management Officers (DEMOs). The findings show inadequacy in data availability, waste minimization initiatives, financing, stakeholders’ inclusiveness, waste management options, technological flexibility, and service reliability. The findings also show the presence of a supportive legal framework and a responsive market for the provision of waste management services. The study recommends; Improvement of waste management infrastructure; promotion of waste minimization initiatives, enhancement of waste management financing, and formalization of informal waste collection service providers.
Refuge Denied: The St. Louis Passengers and the Holocaust

Field: Arts and Humanities (Social Sciences)

In May of 1939, the Cuban government turned away the Hamburg-America Line's MS St. Louis, which carried more than 900 hopeful Jewish refugees escaping Nazi Germany. The passengers subsequently sought safe haven in the United States, but were rejected once again, and the St. Louis had to embark on an uncertain return voyage to Europe. Finally, the St. Louis passengers found refuge in four western European countries, but only the 288 passengers sent to England evaded the Nazi grip that closed upon continental Europe a year later. Over the years, the fateful voyage of the St. Louis has come to symbolize U.S. indifference to the plight of European Jewry on the eve of World War II. Although the episode of the St. Louis is well known, the actual fates of the passengers, once they disembarked, slipped into historical obscurity. Prompted by a former passenger's curiosity, Sarah Ogilvie and Scott Miller of the United States Holocaust Memorial Museum set out in 1996 to discover what happened to each of the 937 passengers. Their investigation, spanning nine years and half the globe, took them to unexpected places and produced surprising results. Refuge Denied chronicles the unraveling of the mystery, from Los Angeles to Havana and from New York to Jerusalem. Some of the most memorable stories include the fate of a young toolmaker who survived initial selection at Auschwitz because his glasses had gone flying moments before and a Jewish child whose apprenticeship with a baker in wartime France later translated into the establishment of a successful business in the United States. Unfolding like a compelling detective thriller, Refuge Denied is a must-read for anyone interested in the Holocaust and its impact on the lives of ordinary people.
Rational use and interpretation of urine drug testing in chronic opioid therapy.

Field: Medicine (Health Sciences)

Urine drug testing (UDT) has become an essential feature of pain management, as physicians seek to verify adherence to prescribed opioid regimens and to detect the use of illicit or unauthorized licit drugs. Results of urine drug tests have important consequences in regard to therapeutic decisions and the trust between physician and patient. However, reliance on UDT to confirm adherence can be problematic if the results are not interpreted correctly, and evidence suggests that many physicians lack an adequate understanding of the complexities of UDT and the factors that can affect test results. These factors include metabolic conversion between drugs, genetic variations in drug metabolism, the sensitivity and specificity of the analytical method for a particular drug or metabolite, and the effects of intentional and unintentional interferants. In this review, we focus on the technical features and limitations of analytical methods used for detecting drugs or their metabolites in urine, the statistical constructs that are pertinent to ordering UDT and interpreting test results, and the application of these concepts to the clinical monitoring of patients maintained on chronic opioid therapy.
sampling interval

Field: Chemistry (Physical Sciences)

Citation: 'sampling interval' in the IUPAC Compendium of Chemical Terminology, 3rd ed.; International Union of Pure and Applied Chemistry; 2006. Online version 3.0.1, 2019. 10.1351/goldbook.S05465 • License: The IUPAC Gold Book is licensed under Creative Commons Attribution-ShareAlike CC BY-SA 4.0 International for individual terms. Requests for commercial usage of the compendium should be directed to IUPAC.
Guanyl Nucleotide Regulation of Human Chorionic Gonadotropin Binding to Rat Luteal Tissue*

Field: Biochemistry, Genetics and Molecular Biology (Life Sciences)

Guanyl nucleotides are known to have a dual effect on most hormone-sensitive adenylate cyclase systems, regulating activation of the adenylate cyclase enzyme and binding of hormone to receptor. In the ovary, guanyl nucleotides have been shown to be required for hCG stimulation of luteal adenylate cyclase, but no effect on binding has been observed. Evidence has been obtained which suggests that guanyl nucleotide regulation of hCG binding is masked in most luteal membrane preparations by the presence of a large excess of unregulated receptor. A highly purified urea-washed membrane fraction has been prepared. Binding of hCG to this preparation was decreased (approximately 45%) in the presence of 5'-guanylylimidodiphosphate (GMPPnP). The maximal effect of GMPPnP occurred at 10 microM, with the half-maximal effect at 0.2 microM. These levels compare favorably with the GTP concentrations required for hCG stimulation of luteal adenylate cyclase. Analysis of equilibrium binding experiments showed that GMPPnP acted by reducing the number of binding sites by 45%. However, kinetic experiments suggested that this effect was due to a significant decrease in the affinity of a fraction of the hCG-binding sites. Association of hCG and its receptor was unaffected by the presence of GMPPnP (100 microM), whereas the dissociation of 40-50% of bound hormone was significantly accelerated (30-fold) by its presence. The guanyl nucleotide effect required the presence of MG+2; other divalent cations (Ca+2, Mn+2, and Co+2 could not be substituted. The ratio of beta-adrenergic to hCG-binding sites in the urea-washed heavy membrane preparation was elevated, suggesting that a sizable fraction of uncoupled hCG receptor had been removed. The results show that hCG binding to its luteal receptor is modulated by guanyl nucleotide and suggest that the modulation only occurs in those receptors that are directly coupled to the adenylate cyclase enzyme.
Materials Data on BaNaZr2F11 by Materials Project

Field: Materials Science (Physical Sciences)

BaNaZr2F11 crystallizes in the tetragonal I4_1/a space group. The structure is three-dimensional. Na1+ is bonded in a distorted pentagonal pyramidal geometry to six F1- atoms. There are a spread of Na–F bond distances ranging from 2.28–2.42 Å. Ba2+ is bonded in a distorted q6 geometry to ten F1- atoms. There are a spread of Ba–F bond distances ranging from 2.72–2.85 Å. Zr4+ is bonded in a 8-coordinate geometry to eight F1- atoms. There are a spread of Zr–F bond distances ranging from 2.05–2.26 Å. There are six inequivalent F1- sites. In the first F1- site, F1- is bonded in a trigonal non-coplanar geometry to one Na1+ and two equivalent Zr4+ atoms. In the second F1- site, F1- is bonded in a 3-coordinate geometry to two equivalent Ba2+ and one Zr4+ atom. In the third F1- site, F1- is bonded in a 2-coordinate geometry to one Na1+, one Ba2+, and one Zr4+ atom. In the fourth F1- site, F1- is bonded in a trigonal non-coplanar geometry to one Na1+ and two equivalent Zr4+ atoms. In the fifth F1- site, F1- is bonded in a distorted single-bond geometry to two equivalent Ba2+ and one Zr4+ atom. In the sixth F1- site, F1- is bonded in a linear geometry to two equivalent Zr4+ atoms.
The relevance of oral history as a methodology of research in church history : the case of the Zion Christian Church

Field: Arts and Humanities (Social Sciences)

This article is intended to show how the use of oral history as a methodology can be helpful, yet may sometimes lead to distortions. Some of the information addressed in this article has already been documented, but much of it has not been given in full. The reason for this is simply that many of the African Independent Churches do not openly disclose everything about themselves. In some cases the names of the people interviewed for this article are not disclosed, for their own protection. Sometimes church leaders were present during the interview sessions to determine what should be disclosed and how. In other cases, church leaders chose who was to be interviewed and on what subject, as some information is deemed sensitive and may not be disclosed at all. It is in this context that conclusions have been drawn.
Systematisk inledning till Nordisk lexikografisk ordbok (NLO)

Field: Arts and Humanities (Social Sciences)

One of the major problems of LSP lexicography is connected with the fäet that analphabetic macrostructure is not able to present a systematic overview of the subjectfield covered by the dictionary. Therefore, some modem dictionaries are providedwith an encyclopedic section which constitutes a separate dictionary componentgiving an introduction to, or a systematic and detailed exposition of, the subject.This contribution presents an encyclopedic section meant to be included in theplanned Nordic Lexicographical Dictionary.
Combining Criminology and Forensic Science to Detect Match-Fixing

Field: Social Sciences (Social Sciences)

This contribution discusses the relevance of criminology and forensic sciences approaches with regard to match-fixing detection. Existing studies on match-fixing have described offenders as rational actors, oriented to maximize their benefits in a field with low-risk detection by law enforcement systems. Often, this explanation is too simplistic, as it neglects the complexity of an offense which integrates multiple actors, with different aims in different places and various criminal activity processes. In our contribution, we further elaborate the rational choice perspective on match-fixing, by integrating the concept of crime script. Through crime scripts, it is possible to disentangle the multiple scenes that integrate the offense. This study is based on the analysis of four fixed matches, resulting in four specific crime scripts and a general script together with a set of traces that may be exploited for the investigation. These scripts detailed the modus operandi used by the fixers. Integrating the criminological perspective (rational choice theory) with the forensic science perspective (the concept of trace) may be useful to support prevention policies, monitoring activities, and investigative methodologies against match manipulation.
Variational Learning for the Inverted Beta-Liouville Mixture Model and Its Application to Text Categorization.

Field: Computer Science (Physical Sciences)

The finite invert Beta-Liouville mixture model (IBLMM) has recently gained some attention due to its positive data modeling capability. Under the conventional variational inference (VI) framework, the analytically tractable solution to the optimization of the variational posterior distribution cannot be obtained, since the variational object function involves evaluation of intractable moments. With the recently proposed extended variational inference (EVI) framework, a new function is proposed to replace the original variational object function in order to avoid intractable moment computation, so that the analytically tractable solution of the IBLMM can be derived in an effective way. The good performance of the proposed approach is demonstrated by experiments with both synthesized data and a real-world application namely text categorization.
Improved identification of heterozygotes for phenylketonuria using blood neopterin and biopterin

Field: Medicine (Health Sciences)

Summary A novel approach that combines information provided by the metabolism of pteridines and that of phenylalanine has been applied to the detection of heterozygotes for phenylketonuria. Phenylalanine, tyrosine, biopterin and neopterin have been measured in serum from normal controls and heterozygotes for classical phenylketonuria, before and after a phenylalanine oral load. Significant differences in neopterin and biopterin mean values in fasting serum and in the mean increase of biopterin induced by the phenylalanine load were found between groups. Inclusion of pteridine data in the discriminant analysis significantly improved the resolution of the classical phenylalanine loading test for the detection of heterozygotes for phenylketonuria.
ANALISIS ZAKAT PRODUKTIF DAN DAMPAKNYA TERHADAP PERTUMBUHAN USAHA MIKRO DAN PENYERAPAN TENAGA KERJA SERTA KESEJAHTERAAN MUSTAHIK DI KOTA PEKANBARU PROVINSI RIAU

Field: Social Sciences (Social Sciences)

This research was conducted on mustahik who received productive zakat from the National Amil Zakat Agency (BAZNAS) in Pekanbaru City. The purpose of this study was to see the effect of productive zakat channeled on increasing mustahik business and increasing welfare. 52 mustahik chosen in this study were conducted using purposive sampling, namely the mustahik of recipients of productive zakat. The analysis was carried out by the bineary logistic regression method because of the welfare variables and business improvement variables in the form of dummy, where the determination of mustahik welfare using the CIBEST method. The results of this study indicate that productive zakat that is distributed does not significantly influence the increase in business and also the welfare of mustahik. this is because the amount of productive zakat distributed does not meet the feasibility of business development, besides that it is still not maximized monetizing and assistance carried out by BAZNAS in the development of mustahik businesses.