jimnoneill/paper-to-field-training huggingface dataset:
Chimira: analysis of small RNA sequencing data and microRNA modifications

Abstract Summary: Chimira is a web-based system for microRNA (miRNA) analysis from small RNA-Seq data. Sequences are automatically cleaned, trimmed, size selected and mapped directly to miRNA hairpin sequences. This generates count-based miRNA expression data for subsequent statistical analysis. Moreover, it is capable of identifying epi-transcriptomic modifications in the input sequences. Supported modification types include multiple types of 3′-modifications (e.g. uridylation, adenylation), 5′-modifications and also internal modifications or variation (ADAR editing or single nucleotide polymorphisms). Besides cleaning and mapping of input sequences to miRNAs, Chimira provides a simple and intuitive set of tools for the analysis and interpretation of the results (see also Supplementary Material). These allow the visual study of the differential expression between two specific samples or sets of samples, the identification of the most highly expressed miRNAs within sample pairs (or sets of samples) and also the projection of the modification profile for specific miRNAs across all samples. Other tools have already been published in the past for various types of small RNA-Seq analysis, such as UEA workbench, seqBuster, MAGI, OASIS and CAP-miRSeq, CPSS for modifications identification. A comprehensive comparison of Chimira with each of these tools is provided in the Supplementary Material. Chimira outperforms all of these tools in total execution speed and aims to facilitate simple, fast and reliable analysis of small RNA-Seq data allowing also, for the first time, identification of global microRNA modification profiles in a simple intuitive interface. Availability and implementation: Chimira has been developed as a web application and it is accessible here: http://www.ebi.ac.uk/research/enright/software/chimira. Contact: aje@ebi.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.

Topic: MicroRNA in disease regulation
Subfield: Cancer Research
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Combined Transcriptome and Proteome Analysis Provides Insights into Petaloidy in Pomegranate

Petaloidy leads to a plump floral pattern and increases the landscape value of ornamental pomegranates; however, research on the mechanism of petaloidy in ornamental pomegranates is limited. In this study, we aimed to screen candidate genes related to petaloidy. We performed transcriptomic and proteomic sequencing of the stamens and petals of single-petal and double-petal flowers of ornamental pomegranates. Briefly, 24,567 genes and 5865 proteins were identified, of which 5721 genes were quantified at both transcriptional and translational levels. In the petal and stamen comparison groups, the association between differentially abundant proteins (DAPs) and differentially expressed genes (DEGs) was higher than that between all genes and all proteins, indicating that petaloidy impacts the correlation between genes and proteins. The enrichment results of transcriptome, proteome, and correlation analyses showed that cell wall metabolism, jasmonic acid signal transduction, redox balance, and transmembrane transport affected petaloidy. Nine hormone-related DEGs/DAPs were selected, among which ARF, ILR1, LAX2, and JAR1 may promote petal doubling. Sixteen transcription factor DEGs/DAPs were selected, among which EREBP, LOB, MEF2, MYB, C3H, and trihelix may promote petal doubling. Our results provide transcriptomic and proteomic data on the formation mechanism of petaloidy and a theoretical basis for breeding new ornamental pomegranate varieties.

Topic: Plant Molecular Biology Research
Subfield: Plant Science
Field: Agricultural and Biological Sciences
Domain: Life Sciences
Host-dependent variation of asparagine-linked oligosaccharides at individual glycosylation sites of Sindbis virus glycoproteins.

We examined the Asn-linked oligosaccharides at individual glycosylation sites of the two envelope glycoproteins of Sindbis virus, E1 and E2. The analysis was done by separating tryptic glycopeptides by reverse phase high performance liquid chromatography and analyzing the oligosaccharides from isolated glycopeptides by gel filtration chromatography. Both E1 and E2 have two glycosylation sites each in virus grown in chick embryo fibroblasts, baby hamster kidney cells, and Chinese hamster ovary cells. Our results indicate that previously observed host-dependent variation in the oligosaccharides of Sindbis virus glycoproteins are probably attributable to differences in oligosaccharide composition at individual sites of E1 and E2 and not to differences in the frequency of glycosylation of these sites. One of the two glycosylation sites in E1 has exclusively complex type oligosaccharides regardless of the host cell type. However, the second glycosylation site in E1 has high mannose oligosaccharides in virus grown in chick embryo fibroblasts, complex oligosaccharides in virus from baby hamster kidney cells, and both complex and high mannose oligosaccharides in virus from Chinese hamster ovary cells. E2 has one glycosylation site which has primarily high mannose oligosaccharides and one site which has primarily complex type oligosaccharides. Certain sites which have predominantly complex type glycans also have a small number of two specific classes of oligosaccharides which are cleaved by endo-beta-N-acetylglucosaminidase H and may be high mannose type. Our findings are discussed with regard to regulation of oligosaccharide processing in animal cells.

Topic: Glycosylation and Glycoproteins Research
Subfield: Molecular Biology
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Analyzing over-dispersed count data in two-way cross-classification problems using generalized linear models

Abstract Several methods of testing factor effects in a two-way cross-classification analysis are compared in a Monte Carlo simulation study, using over-dispersed count data generated from the family of negative binomial distributions. Tests compared are based on general linear models, using raw and transformed data, and on generalized linear models specifying either the Poisson or negative binomial distribution. The general linear model is recommended, especially in the case of small means and small numbers of replications. Keywords: Count datageneralized linear modelnegative binomial distributionoverdispersioncross-classification

Topic: Statistical Methods and Bayesian Inference
Subfield: Statistics and Probability
Field: Mathematics
Domain: Physical Sciences
Local Injection of Botulinum Toxin Type A to Prevent Postoperative Scar: Comment

Journal of Craniofacial Surgery: September 2020 - Volume 31 - Issue 6 - p 1852-1853 doi: 10.1097/SCS.0000000000006664

Topic: Botulinum Toxin and Related Neurological Disorders
Subfield: Neurology
Field: Medicine
Domain: Health Sciences
Analysis and Research on Safety Evaluation of Tour Traffic Based on BP Neural Network

The paper expounds the basic theory,algorithm,disfigurement and improving methods of BP neural network.It studies the safety about tour traffic through an example,chooses the suitable study sample and parameters to train,receives better evaluation results,and provides theoretical basis for the tour safety of tourists and the managers of relevant sectors.

Topic: Advanced Sensor and Control Systems
Subfield: Control and Systems Engineering
Field: Engineering
Domain: Physical Sciences
Electrocardiographic Reference Values for a Population of Older Adults in Sub‐Saharan Africa

Background/Objectives Older adults in sub‐Saharan Africa (SSA) are at greatest risk of an impending noncommunicable diseases epidemic, of which cardiac disease is the most prevalent contributor. Thus, it is essential to establish electrocardiographic reference values for a population that is likely to differ genetically and environmentally from others where reference values are established. Methods Two thousand two hundred thirty‐two apparently healthy community‐based participants without known cardiac disease aged 70+ in rural Tanzania underwent 12‐lead electrocardiography. Electrocardiograms were digitally analyzed and gender‐specific reference values for P duration (P D ), P amplitude (P AMP ), P area (P AREA ), P terminal negative force (V 1 ) (P TNF ), PR interval, QRS duration (QRS D ), QT/QTc, R amplitude (II, V 5 ) (R AMP ) LVH index (LVHI), R axis and R/S ratio (V 1 ) reported, following univariate analysis of covariance using a multiple linear regression model, adjusting for age, systolic blood pressure (SBP), body mass index (BMI), and RR interval. Results Data from 1824 subjects were suitable for analysis. Adjusted mean values for men/women were: P D 115/110 ms, P AMP (avg) 123/114 μV, P AMP (II) 203/190 μV, P AREA (avg) 5.3/4.6 mV*s, P AREA (II) 9.3/8.1mV*s, P TNF 1.7/1.4 mV*s, PR 158/152 ms, QRS D 89/84 ms, QT 370/375 ms, QTc 421/427 ms, R AMP (II) 805/854 μV, (V 5 ) 2022/1742 μV, LVHI 3.0/2.8 mV (Sokolow‐Lyon), 1.293/1.146 mV (Cornell), R axis 51/49°, R/S 0.2/0.2. Excluding P TNF , R axis and R/S ratio, all gender differences were significant (P &lt; 0.001 apart from LVHI [Sokolow‐Lyon; P &lt; 0.005)] and R AMP (II) [P &lt; 0.05]) following adjustment for age, SBP, BMI, and RR interval. Conclusions Our description of comprehensive electrocardiographic parameters establishes reference values in this genetically and environmentally diverse SSA population thereby allowing identification of “outliers” with potential cardiac disease.

Topic: Cardiac electrophysiology and arrhythmias
Subfield: Cardiology and Cardiovascular Medicine
Field: Medicine
Domain: Health Sciences
Correlation and High-Dimensional Consistency in Pattern Recognition

Abstract Classical discriminant analysis breaks down when the feature vectors are of extremely high dimension; for example, when the basic observation is a random function observed over a fine grid. Alternative methods have been developed assuming a simplified form for the covariance structure. We analyze the high-dimensional asymptotics of some of these methods, emphasizing the effects of correlations such as occur when the baseline is random. For instance, the Euclidean distance classifier, which has been proposed for generic use in high-dimensional classification problems, is dimensionally inconsistent under a simple repeated measurement model. We provide exponential bounds for the error rates of several classifiers. We develop new dimensionally consistent methods to deal with the effects of correlation in high-dimensional problems.

Topic: Statistical Methods and Inference
Subfield: Statistics and Probability
Field: Mathematics
Domain: Physical Sciences
Finite difference method in prolate spheroidal coordinates for freely suspended spheroidal particles in linear flows of viscous and viscoelastic fluids

A finite difference scheme is used to develop a numerical method to solve the flow of an unbounded viscoelastic fluid with zero to moderate inertia around a prolate spheroidal particle. The equations are written in prolate spheroidal coordinates, and the shape of the particle is exactly resolved as one of the coordinate surfaces representing the inner boundary of the computational domain. As the prolate spheroidal grid is naturally clustered near the particle surface, good resolution is obtained in the regions where the gradients of relevant flow variables are most significant. This coordinate system also allows large domain sizes with a reasonable number of mesh points to simulate unbounded fluid around a particle. Changing the aspect ratio of the inner computational boundary enables simulations of different particle shapes ranging from a sphere to a slender fiber. Numerical studies of the latter particle shape allow testing of slender body theories. The mass and momentum equations are solved with a Schur complement approach allowing us to solve the zero inertia case necessary to isolate the viscoelastic effects. The singularities associated with the coordinate system are overcome using L'Hopital's rule. A straightforward imposition of conditions representing a time-varying combination of linear flows on the outer boundary allows us to study various flows with the same computational domain geometry. {For the special but important case of zero fluid and particle inertia we obtain a novel formulation that satisfies the force- and torque-free constraint in an iteration-free manner.} The numerical method is demonstrated for various flows of Newtonian and viscoelastic fluids around spheres and spheroids (including those with large aspect ratio). Good agreement is demonstrated with existing theoretical and numerical results.

Topic: Fluid Dynamics and Vibration Analysis
Subfield: Computational Mechanics
Field: Engineering
Domain: Physical Sciences
La forte population de Java : deux siècles d'explications (Java : explanation of the great population density)

Abstract. - Explanation of demographic imbalance between Java and the socalled "Outer-Islands" has been numerous for almost two centuries. Authors generally considered that the great density of population was a direct consequence of the high fertility of Javanese soils. Some of them, however, connected it with an early economical "take-off". But none of these analyses can explain why marginally suitable regions from an agricultural point of view were overcrowed especially when their economical development was low. We propose another explanation scheme on an historical basis.

Topic: Asian Studies and History
Subfield: Sociology and Political Science
Field: Social Sciences
Domain: Social Sciences
Toward Robust Revenue Management: Competitive Analysis of Online Booking

In this paper, we consider the revenue management problem from the perspective of online algorithms. This approach eliminates the need for both demand forecasts and a risk-neutrality assumption. The competitive ratio of a policy relative to a given input sequence is the ratio of the policy's performance to the offline optimal. Under the online algorithm approach, revenue management policies are evaluated based on the highest competitive ratio they can guarantee. We are able to define lower bounds on the best-possible performance and describe policies that achieve these lower bounds. We address the two-fare problem in greatest detail, but also treat the general multifare problem and the bid-price control problem.

Topic: Optimization and Search Problems
Subfield: Computer Networks and Communications
Field: Computer Science
Domain: Physical Sciences
Growth and Development of Agricultural Education, Research, and Libraries in India

Agriculture in India, since ancient times, is the most crucial sector for ensuring food and nutritional security, sustainable development and for the alleviation of poverty. It is the key sector in India for generating employment opportunities for the vast majority of the population particularly in rural areas. The paper aims to explore the many facets related to agricultural education, research, training, and libraries in India in order to provide a historical account on these aspects. The paper discusses in detail the various committees and commissions and their salient recommendations leading to the expansive growth and development of agricultural education, research, and libraries in India. Further, the paper also highlights the critical role of the Indian Council of Agricultural Research in the growth and development of agricultural education, research, extension, and libraries.

Topic: Gender, Education, and Development Issues
Subfield: Education
Field: Social Sciences
Domain: Social Sciences
Modeling of Active Noise and Vibration Control with Finite Elements and Boundary Elements

Abstract A recently developed coupled finite element‐boundary element modeling scheme for the design of active noise and vibration control of multi‐coupled structural‐acoustic systems is presented. The approach allows the computation of structural vibrations and resulting sound fields. By means of an example, the paper describes the theoretical background of the coupled approach. In order to show the performance of the developed approach, test simulations are carried out in the frequency domain. (© 2009 Wiley‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)

Topic: Aeroelasticity and Vibration Control
Subfield: Aerospace Engineering
Field: Engineering
Domain: Physical Sciences
Regulatory emotional self-efficacy as a mediator between high-performance work system perceived by nurses on their job burnout: a cross-sectional study

The purpose of this study was to explore the correlation between the perception of high performance work system (P-HPWS) and job burnout of nurses, further to detect the mediating effect of regulatory emotional self-efficacy (RES). From November 2019 to January 2020, a cross-sectional survey on working nurses was conducted in 5 hospitals in Lanzhou, China. A total of 1266 nurses were investigated. Demographics and perception of high performance work systems, job burnout, and RES were collected. The data were statistically processed using correlation analysis, multiple linear regression analysis, and a test of mediated moderation. The P-HPWS was significantly negatively correlated with job burnout (<i>P</i> < 0.01). The RES played a mediating effect between the perception of HPWS and job burnout. The results support the important role of P-HPWS in the remission of job burnout, and the hospital can improve its management by implementing and perfecting the HPWS.<b>Abbreviations</b>: P-HPWS: Perceived high-performance work system; RES: Regulatory emotional self-efficacy; POS: Perceived self-efficacy in expressing positive emotions; ANG: Perceived self-efficacy in managing anger/irritation; DES: Perceived self-efficacy in managing despondency/distress.

Topic: Workplace Health and Well-being
Subfield: General Health Professions
Field: Health Professions
Domain: Health Sciences
To Boldly Go, Part I: Developing a Specific Legal Framework for Assessing the Regulation of International Data Trade under the CISG

The United Nations Convention on Contracts for the International Sale of Goods (‘CISG’) is an international sales law treaty concluded in 1980. Given its vintage, the CISG was drafted with traditional (physical) goods trade in mind. A significant body of scholarship has addressed the CISG’s capacity to govern electronic software transactions. However, only limited commentary has explored its digital application beyond software per se. This article develops a specific legal framework for assessing the CISG’s capacity to regulate international trade in non-software data: a framework so far missing from existing scholarship. ‘To Boldly Go, Part II’, this article’s counterpart, will go on to apply this framework to non-software data trade. Collectively, these articles establish that the CISG is capable of governing not only software trade (as previously established) but also trade in non-software data: a category of trade becoming increasingly economically important.

Topic: Intellectual Property Law
Subfield: Law
Field: Social Sciences
Domain: Social Sciences
Machiavellianism, social norms, and taxpayer compliance

This study is the first to examine the relationships among Machiavellianism, social norms and taxpayer intentions to fraudulently overstate their deductions. We theorize and empirically document that (a) high Machiavellian taxpayers report significantly less ethical social norms, suggesting that reported social norms are influenced by cognitive biases such as social projection and Machiavellian cynicism; (b) reported social norms are, in general, significantly associated with tax evasion intentions; (c) social norms partially mediate the relationship between Machiavellianism and evasion intentions. Our findings imply that experimental research that controls for key personality traits such as Machiavellianism will be necessary to test the effectiveness of potential interventions designed to enhance social norms and tax compliance. Our findings also raise questions regarding the validity of certain social norm measures used in recent studies, particularly in the case of high Machiavellians. In contrast to much prior research, gender was not associated with the likelihood of committing tax fraud in our multivariate models, suggesting that the higher levels of tax compliance often associated with females may be eroding.

Topic: Taxation and Compliance Studies
Subfield: Economics and Econometrics
Field: Economics, Econometrics and Finance
Domain: Social Sciences
Lipid stability of egg and laying performance of Japanese quail feed with extract of guava (Psidium guajava L.)

Two experiments were conducted in order to evaluate the effect of dietary inclusion of guava extract on laying performance and lipid stability of egg of Japanese quails. For the first experiment, 384 Japanese quails with 42 days old were distributed in a completely randomized design with four treatments (0.0; 3.0; 6.0; 9.0 g.kg-1 guava extract), 6 replicates, and 16 birds/replicate. The experimental period lasted 84 days, divided into 4 cycles of 21 days. The parameters evaluated were: feed consumption, egg production, egg mass, feed conversion ratio, egg weight, and egg internal and external qualities. On the second experiment, 400 eggs from Japanese quails fed with diets containing four levels of guava extract were distributed in a completely randomized design with a 4x4 factorial arrangement (guava extract levels and storage time: 0, 9, 18, 27 days) with 5 replicates. Analysis of thiobarbituric acid reactive substances was performed on egg yolks. Data were submitted to regression analysis, using α=0.05. On the first experiment, the laying performance parameters were not influenced by the inclusion of guava extract in the feed, and eggshell thickness decreased linearly. On the second experiment an interaction was observed between the studied factors, affecting lipid oxidation in egg yolks. At nine days of storage, there was a quadratic effect of levels of dietary guava extract on lipid oxidation of yolk, being observed that using 4.8 g.kg-1 of guava extract on feed results in less lipid oxidation.

Topic: Psidium guajava Extracts and Applications
Subfield: Pharmacology
Field: Pharmacology, Toxicology and Pharmaceutics
Domain: Life Sciences
Biodegradable poly(urethane-urea-amide): Synthesis, characterization and mechanical studies

Biodegradable polyurethane with excellent mechanical property finds a lot of applications in the biomedical field. In this study, multi block copolymer poly(urethane-urea-amide) (PUUA) is prepared using polyethylene oxide, 1,6-hexamethylene diisocyanate and diamide (N 1 , N 4 -bis(6-aminohexyl)benzene-1,4-dicarboxamide (6T6) or N 1 , N 6 -bis(6-aminohexyl)hexanediamide (6A6)) by a method of solution/melt polymerization techniques. The polymer formation is confirmed by the 1 H NMR spectroscopic method. Other techniques such as viscosity measurements, FT-IR, DSC, TGA, and biodegradability are used to characterize the synthesized copolymers. The hard segment crystallinity is an analyzed by FT-IR spectroscopy, it revealed that the 6T6 based polymer showed 70% of crystallinity. The synthesized copolymer shows three transitions in the DSC curve. The melting enthalpy of the hard segment depends on the amide unit employed in the polymerization process. These materials are fast crystallizing due to low under cooling value. This material has a very high thermal stability and stable up to 400°C. Tensile test confirms the strain induced crystallization of hard segment occurred in the PUUA. The biodegradability of the polymer depends on the pH and chain extenders. This type of materials can be a good candidate for tissue engineering application.

Topic: Polymer composites and self-healing
Subfield: Polymers and Plastics
Field: Materials Science
Domain: Physical Sciences