jimnoneill/paper-to-field-training huggingface dataset:
Learning large-scale gene regulatory networks from single cell transcriptomic data using multivariate information theory

Networks provide powerful and flexible models for many biological systems. Gene regulatory networks model the complex biomolecular interactions that drive genetically identical cells to adopt distinct functional identities. Gene regulation is complicated and multifactorial, involving different biological mechanisms that are often well-characterized individually, but whose combinatorial effects on a large scale are poorly understood. Recent technological advances mean that highly-informative single cell data are being generated on an unprecedented scale, but these large, unwieldy datasets contain technical noise and biological heterogeneity, and must be analyzed carefully. Here we make use of information theory to address the complexities and nonlinearities of these data, drawing on recent developments in quantifying information within multivariate systems. We first provide a comprehensive review of single cell analysis and the multiple definitions of gene regulatory networks. Then we develop a network inference algorithm using multivariate information, and use it to learn networks from several developmental systems. We next present a method for quantifying significance in a large-scale information theoretic context, and use it to control the accuracy of our networks for different applications. Finally we infer a network from over 11,000 expressed genes and, using graph theoretic and bioinformatic analyses, characterize the biological processes occurring during early neural development. Throughout this work, we take a data-driven approach, favouring statistical methods that make minimal assumptions. Alongside our analyses, we provide efficient, reusable software, culminating in a collection of free, open source software libraries.

Topic: Gene expression and cancer classification
Subfield: Molecular Biology
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Real Time Backpack Detection in Visual Surveillance based on Verticals Contour Analysis

In this paper, we aim to propose a method to detect backpacks and sling bags which pedestrians are carrying in visual surveillance. A real time video analysis and processing on passive recording provided from surveillance camera could give more valuable information for a variety of applications. We detect backpacks without protrusion supposition or any training data. We propose an algorithm to find expectable vertical lines inside or near a human body contours using some fuzzy rules. To improve detection accuracy, area of carried object is compared with next several frames. It influences our detection result greatly. As a result, we detect carried objects including backpack and sling bag successfully. We run several experiments with previously designed VIRAT ground video dataset and result shows that our method is promising.

Topic: Video Surveillance and Tracking Methods
Subfield: Computer Vision and Pattern Recognition
Field: Computer Science
Domain: Physical Sciences
Efficiency of fungicides in the fight against winter rye diseases

A sharp decrease in the area under winter rye is primarily due to the deterioration of the phytosanitary situation in the agrocenosis. Therefore, the use of seed dressings and fungicides to combat dangerous diseases of the crop is a mandatory technique aimed at limiting their harmfulness. The studies were conducted on the zoned variety Saratovskaya 6. The field experiment included seed dressings Oplot, VSK, Lamador, KS, Sistiva, KS and Tir, TPS, which were used to disinfect winter rye seeds from saprophytic and pathogenic mycoflora, stem smut, root rot of various etiologies. Fungicides Alto Super, KE, ProTeb, KME, Folicur, KE and Titul Duo, KKR were used to treat vegetative plants against powdery mildew, brown rust and septoria. The biological efficiency of the studied preparations application on winter rye crops is demonstrated. Seed treatment reduced the contamination with pathogenic and saprophytic mycoflora by 70.9–78.4 and 72.5–74.1%, respectively. The intensity of root rot development decreased by 61.7–74.5% in autumn and by 47.6–36.6% in spring. The efficiency of fungicides against stem smut varied from 100 to 92.0%. The studies showed that the implementation of a set of protective measures contributed to obtaining additional products from 9.5 to 7.6 to %.

Topic: Agriculture, Plant Science, Crop Management
Subfield: Plant Science
Field: Agricultural and Biological Sciences
Domain: Life Sciences
Paleolithic Art Panel 26 - Cueva de Los Casares

Cueva de Los Casares near the village of Riba de Saelices (Guadalajara) contains some of the most important Paleolithic engraving in Spain. This model of Panel 26, Lam. XXI (Juan Cabre, 1934) shows what is believed to be an engraving of a wolverine. Source: Objaverse 1.0 / Sketchfab

Topic: Archaeological and Geological Studies
Subfield: Archeology
Field: Arts and Humanities
Domain: Social Sciences
Qigong in Perceptual Auditory Attention: Tool to Improve Sound Integration in Autism Spectrum Disorders.

The WB Qigong had a positive effect on the AA mechanism, with a significant reduction in RT. The results support the importance of practice to achieve positive effects. People with neurodevelopmental disorders, such as autism and ADHD, struggle every day for sensory integration of AA mechanisms. Qigong can be taught and easily learned from the age of 2 years until senior ages, and it's a safe and very low-cost intervention that deserves to be researched further in clinical trials. These potential benefits of Qigong should be confirmed by future studies.

Topic: Biofield Effects and Biophysics
Subfield: Physiology
Field: Medicine
Domain: Health Sciences
AOTV bow shock location

Hypersonic bow-shock location and geometry are of central importance to the aerodynamics and aerothermodynamics of aeroassisted orbital transfer vehicles (AOTVs), but they are difficult to predict for a given vehicle configuration. This paper reports experimental measurements of shock standoff distance for the 70 deg cone AOTV configuration in shock-tunnel-test flows at Mach numbers of 3.8 to 7.9 and for angles of attack from 0 deg to 20 deg. The controlling parameter for hypersonic bow-shock standoff distance (for a given forebody shape) is the mean normal-shock density ratio. Values for this parameter in the tests reported are in the same range as those of the drag-brake AOTV perigee regime. Results for standoff distance are compared with those previously reported in the literature for this AOTV configuration. It is concluded that the AOTV shock standoff distance for the conical configuration, based on frustrum (base) radius, is equivalent to that of a sphere with a radius about 35 percent greater than that of the cone; the distance is, therefore, much less than reported in previous studies. Some reasons for the discrepancies between the present and previous are advanced. The smaller standoff distance determined here implies there will be less radiative heat transfer than was previously expected.

Topic: Gas Dynamics and Kinetic Theory
Subfield: Applied Mathematics
Field: Mathematics
Domain: Physical Sciences
The mechanism of the influence of peer relational skills on social anxiety: The mediational effect of self-presentational expectancy moderated by self-insight

본 연구에서는 경미한 비행을 보이는 중학교 청소년들을 대상으로 그들의 비행을 감소시키는 것을 목표로 하는 문제해결기술훈련 프로그램을 시행하여, 그 효과를 검증하였고, 1개월 후 사후조사에서 비행의 감소여부를 검증하였다. 통제집단으로는 심성훈련 프로그램을 실시한 집단이 비교되었다. 서울시 소재 중학교 선생님들로부터 경미한 비행 범주에 포함되는 부적응 행동으로 의뢰된 남녀 학생 총 58명(문제해결기술 훈련 집단 31명, 심성 훈련 집단 27명)에게 한 회기에 120분 씩 5일 연속으로 총 5회기의 프로그램을 시행한 결과, 문제해결기술 훈련 집단은 가설적 상황에서 가능한 한 많은 대안수를 생각해 내는 능력과 적절한 대안을 생각해 내는 능력에서 유의미한 향상을 보인 반면, 심성훈련 집단은 두 가지 항목 모두에서 유의미한 향상을 보이지 않았다. 1개월 후에 측정한 자기보고식 청소년 비행 척도에서는 문제해결기술훈련 집단의 비행 감소량이 유의미하게 더 많았고, 성별에서는 남학생 집단의 자기보고 비행 감소량(변화량)이 더 많았다. 교사의 문제행동 적발빈도에서는 집단 간이나 성별 차이는 통계적으로 유의하지 않았으나 집단 및 성별 간 상호작용 효과가 유의미하였다. 즉, 문제해결기술훈련 집단에서 교사가 평가한 문제행동 적발빈도의 감소량은 여학생 집단이 남학생 집단보다 더 많았고, 심성훈련 집단에서는 남학생 집단이 여학생 집단보다 더 많았다. 교사의 문제행동 평가점수에서는 성별 차이가 통계적으로 유의해서 여학생 집단의 문제행동평가 점수의 감소량이 더 많았다. 프로그램 자체의 효과, 문제해결능력 향상과 비행 감소의 관계, 연구의 제한점 및 후속 연구에 대해 제언하였다.

Topic: Perfectionism, Procrastination, Anxiety Studies
Subfield: Clinical Psychology
Field: Psychology
Domain: Social Sciences
Type 2 innate lymphoid cells–new members of the “type 2 franchise” that mediate allergic airway inflammation

Type 2 innate lymphoid cells ( ILC 2s) are members of an ILC family, which contains NK cells and Rorγt + ILC s, the latter including lymphoid tissue inducer ( LT i) cells and ILC s producing IL ‐17 and IL ‐22. ILC 2s are dedicated to the production of IL ‐5 and IL ‐13 and, as such, ILC 2s provide an early and important source of type 2 cytokines critical for helminth expulsion in the gut. Several studies have also demonstrated a role for ILC 2s in airway inflammation. In this issue of the European Journal of Immunology , Klein Wolterink et al. [Eur. J. Immunol. 2012. 42: 1106‐1116] show that ILC 2s are instrumental in several models of experimental asthma where they significantly contribute to production of IL ‐5 and IL ‐13, key cytokines in airway inflammation. This study sheds light over the relative contribution of ILC 2s versus T helper type 2 cells (Th2) in type 2 mediated allergen‐specific inflammation in the airways as discussed in this commentary.

Topic: IL-33, ST2, and ILC Pathways
Subfield: Immunology
Field: Immunology and Microbiology
Domain: Life Sciences
<i>JAMA</i>Welcomes the US Preventive Services Task Force

Albert L. Siu, MD, MSPH; and the US Preventive Services Task Force (USPSTF); Kirsten Bibbins-Domingo, PhD, MD, MAS; David C. Grossman, MD, MPH; Linda Ciofu Baumann, PhD, RN, APRN; Karina W. Davidson, PhD, MASc; Mark Ebell, MD, MS; Francisco A. R. García, MD, MPH; Matthew Gillman, MD, SM; Jessica Herzstein, MD, MPH; Alex R. Kemper, MD, MPH, MS; Alex H. Krist, MD, MPH; Ann E. Kurth, PhD, RN, MSN, MPH; Douglas K. Owens, MD, MS; William R. Phillips, MD, MPH; Maureen G. Phipps, MD, MPH; Michael P. Pignone, MD, MPH

Topic: Health Promotion and Cardiovascular Prevention
Subfield: Public Health, Environmental and Occupational Health
Field: Medicine
Domain: Health Sciences
Updating ‘stockpiling as resilience’ in the context of the cost-of-living crisis: tracking changes in resilience strategies in the U.K

Using the seven resilience strategies identified in the previous paper entitled "Stockpiling as Resilience," this study offers an update on the previous study 1 year later with interviews with the same households. The first paper was the result of interviews with 19 households held between April and May 2020 across the UK, and explored how these households managed lack of access to food during the COVID-19 lockdowns. This paper presents the same participants' experiences following the UK lockdowns in the context of the sharp rise in the cost-of-living in the UK Taken together, both phases of interviews bring into clear relief the influences affecting the UK food system, one characterized by increasing inaccessibility of food. This follow-up paper establishes that four of seven resilience strategies are still actively used, whereas three have become unnecessary. Two further themes are made salient in the interview data: weight management and convenience. Overall, this paper acts as a preliminary investigation into strategies that households are likely to utilize in the coming months and years in the context of the cost-of-living crisis.

Topic: Food Waste Reduction and Sustainability
Subfield: Food Science
Field: Agricultural and Biological Sciences
Domain: Life Sciences
Identification and Characterization of Novel Inhibitors of mPTPB, an Essential Virulent Phosphatase from <i>Mycobacterium tuberculosis</i>

Mycobacterium protein tyrosine phosphatase B (mPTPB) is an essential virulence factor required for Mycobacterium tuberculosis (Mtb) survival in host macrophages. Consequently, mPTPB represents an exciting new target with a completely novel mechanism of action. We screened a library of 7,500 compounds against mPTPB and identified several 2-oxo-1,2-dihydrobenzo[cd]indole-6-sulfonamide and piperazinyl-thiophenyl-ethyl-oxalamide derivatives as two distinct classes of mPTPB inhibitors. We showed that both classes of inhibitors are capable of blocking the mPTPB-mediated ERK1/2 inactivation. We further demonstrated that both classes of mPTPB inhibitors are effective in inhibiting the growth of Mtb in macrophages. Thus, improvement of the lead compounds may produce a novel class of anti-TB agents.

Topic: Protein Tyrosine Phosphatases
Subfield: Molecular Biology
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
A DIABATIC WEATHER PREDICTION MODEL WITH A CONSISTENT ENERGY INTEGRAL

Abstract : A vertically integrated, diabatic model is modified so that it possesses an invariant mass integral of the sum of enthalpy and the kinetic energy of the non-divergent wind in the adiabatic case. The model's linear characteristics are discussed, and a series of numerical experiments utilizing idealized initial conditions is proposed.

Topic: Wind and Air Flow Studies
Subfield: Environmental Engineering
Field: Environmental Science
Domain: Physical Sciences
Participating institutions per country.

&lt;div&gt;&lt;p&gt;Background&lt;/p&gt;&lt;p&gt;Recently, artificial intelligence (AI)-based applications for chest imaging have emerged as potential tools to assist clinicians in the diagnosis and management of patients with coronavirus disease 2019 (COVID-19).&lt;/p&gt;&lt;p&gt;Objectives&lt;/p&gt;&lt;p&gt;To develop a deep learning-based clinical decision support system for automatic diagnosis of COVID-19 on chest CT scans. Secondarily, to develop a complementary segmentation tool to assess the extent of lung involvement and measure disease severity.&lt;/p&gt;&lt;p&gt;Methods&lt;/p&gt;&lt;p&gt;The Imaging COVID-19 AI initiative was formed to conduct a retrospective multicentre cohort study including 20 institutions from seven different European countries. Patients with suspected or known COVID-19 who underwent a chest CT were included. The dataset was split on the institution-level to allow external evaluation. Data annotation was performed by 34 radiologists/radiology residents and included quality control measures. A multi-class classification model was created using a custom 3D convolutional neural network. For the segmentation task, a UNET-like architecture with a backbone Residual Network (ResNet-34) was selected.&lt;/p&gt;&lt;p&gt;Results&lt;/p&gt;&lt;p&gt;A total of 2,802 CT scans were included (2,667 unique patients, mean [standard deviation] age = 64.6 [16.2] years, male/female ratio 1.3:1). The distribution of classes (COVID-19/Other type of pulmonary infection/No imaging signs of infection) was 1,490 (53.2%), 402 (14.3%), and 910 (32.5%), respectively. On the external test dataset, the diagnostic multiclassification model yielded high micro-average and macro-average AUC values (0.93 and 0.91, respectively). The model provided the likelihood of COVID-19 vs other cases with a sensitivity of 87% and a specificity of 94%. The segmentation performance was moderate with Dice similarity coefficient (DSC) of 0.59. An imaging analysis pipeline was developed that returned a quantitative report to the user.&lt;/p&gt;&lt;p&gt;Conclusion&lt;/p&gt;&lt;p&gt;We developed a deep learning-based clinical decision support system that could become an efficient concurrent reading tool to assist clinicians, utilising a newly created European dataset including more than 2,800 CT scans.&lt;/p&gt;&lt;/div&gt;

Topic: COVID-19 diagnosis using AI
Subfield: Radiology, Nuclear Medicine and Imaging
Field: Medicine
Domain: Health Sciences
A SUCCESSFUL METHOD FOR ARTIFICIALLY HIBERNATING <i>MEGABOMBUS F</i>. <i>FERVIDUS</i>, AND NOTES ON A RELATED SPECIES (HYMENOPTERA: APIDAE; BOMBINAE)

Abstract Megabombus f . fervidus (F.) queens were successfully hibernated in 1961–62 under artificial conditions that are described in detail. One-half succumbed within 3 days after being removed to conditions allowing resumption of active behavior, and 68.7% perished by the end of 3 weeks. Hibernation and (or) post-hibernation survival are believed to be dependent on the amount of fat bodies metabolized prior to this dispause period. Infertile queens (and possibly large workers) are capable of hibernating. It has been discovered that during hibernation the spermatozoa encyst in the spermatheea of fervidus , and it is probable that this phenomenon is not unusual to most species hibernating under cold conditions.

Topic: Plant and animal studies
Subfield: Ecology, Evolution, Behavior and Systematics
Field: Agricultural and Biological Sciences
Domain: Life Sciences
Referral source and process of assessment: A comparative analysis of assessments for compulsory admission under The Mental Health Act, 1983

Abstract Approved social workers (ASWs) receive referrals from a wide variety of sources, and the sources may place quite different demands on them. There has, however, been no research on the relationship between referral source, process of assessment and outcome. This study compares referrals for compulsory admission under the Mental Health Act, 1983, divided into three different sources: informal network, agency and medical. There were major differences between these different groups, which were widest between agency and medical referrals. Agency referrals were characterised by vaguer requests, imprecise indications of mental health state in the referral, and were considerably more socially deprived and less socially integrated than other groups. Medical referrals were least socially deprived and had a higher proportion of women and those with children. Surprisingly, the doctors were least accurate in selecting those requiring compulsory admission. The study concludes that the characteristics of medical referrals were consistent with what Sheppard (1990) has identified as a ‘mental health orientation’, with traditional role stereotypes applied to women. The concept of ‘social insecurity’ by contrast, was most significant in understanding agency referrals. ASWs showed flexibility in their assessments, and the study demonstrates the significance of social factors in the process of assessment, and the need for wide skills in psychosocial assessment.

Topic: Homelessness and Social Issues
Subfield: General Health Professions
Field: Health Professions
Domain: Health Sciences
Gestational Age - the Most Important Factor of Neonatal Ponderal Index

Ponderal index (fetal weight in grams X 100 / (fetal length in centimeters)3) (PI) is one of the anthropometric methods used to diagnose impaired fetal growth. Irrespective of the infant's position on the growth-weight-for-gestational age charts, PI is low in malnourished infants and high in obese ones. As fetal growth is affected by ethnicity, geographic location and socioeconomic status, we developed standards for neonatal PI, and assessed the effects of gestational age, sex and maternal parity. Data on 5798 newborns from singleton pregnancies born in the Department of Gynecology and Obstetrics, Split University Hospital, were retrospectively analyzed. Over a 15-month period in 2000/2001, 5596 newborns from 24 to 42 weeks of gestation were born. The other 202 newborns, born from 24 to 34 weeks of gestation in the ten year period, 1990-1999, were added because of the small number of preterm infants; ensuring a minimum of 30 to fill up at least infants in each gestational week. All mothers were of Caucasian origin. Stillbirths and fetuses with congenital malformations were excluded. The 10th, 50th and 90th percentiles, mean values with standard deviation of PI and the 10th, 50th, and 90th percentiles of birth weight and birth length are presented separately at weekly intervals. PI showed linear correlation with gestational age from 24 to 39 weeks, after witch the data plateaued. Sex and parity had no impact on PI in infants born between 24 and 37 weeks. Analysis of variance revealed PI to be significantly higher in female than in male newborns, and in multiparous than in nulliparous infants after 37 weeks of gestation. In conclusion, gestational age is the most important factor of neonatal PI. The effects of sex and parity on PI should only be considered in term neonates.

Topic: Birth, Development, and Health
Subfield: Pediatrics, Perinatology and Child Health
Field: Medicine
Domain: Health Sciences
Chemical inventions and chemical patents

ADVERTISEMENT RETURN TO ISSUEPREVBook and Media Revie...Book and Media ReviewChemical inventions and chemical patentsEdward Thomas Cite this: J. Chem. Educ. 1950, 27, 12, 696Publication Date (Print):December 1, 1950Publication History Received3 August 2009Published online1 December 1950Published inissue 1 December 1950https://doi.org/10.1021/ed027p696.5RIGHTS & PERMISSIONSArticle Views169Altmetric-Citations2LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (960 KB) Get e-Alerts Get e-Alerts

Topic: Various Chemistry Research Topics
Subfield: Physical and Theoretical Chemistry
Field: Chemistry
Domain: Physical Sciences
Classical Yang-Mills Mechanics: Instant vs. Light-cone Form

Two different forms of relativistic dynamics, the instant and the light‐cone form, for the pure SU(2) Yang‐Mills field theory in 4‐dimensional Minkowski space are examined under the supposition that the gauge fields depend on the time evolution parameter only. The obtained under that restriction of gauge potential space homogeneity mechanical matrix model, sometimes called Yang‐Mills classical mechanics, is systematically studied in its instant and light‐cone form of dynamics using the Dirac's generalized Hamiltonian approach. In the both cases the constraint content of the obtained mechanical systems is found. In contrast to its well‐known instant‐time counterpart the light‐cone version of SU(2) Yang‐Mills classical mechanics has in addition to the constraints generating the SU(2) gauge transformations the new first and second class constraints also. On account of all of these constraints a complete reduction in number of the degrees of freedom is performed. In the instant form of dynamics it is shown that after elimination of the gauge degrees of freedom from the classical SU(2) Yang‐Mills mechanics the resulting unconstrained system represents the ID3 Euler‐Calogero‐Moser model with a certain external fourth‐order potential, whereas in the light‐cone form it is argued that the classical evolution of the unconstrained degrees of freedom is equivalent to a free one‐dimensional particle dynamics.

Topic: Quantum Mechanics and Non-Hermitian Physics
Subfield: Atomic and Molecular Physics, and Optics
Field: Physics and Astronomy
Domain: Physical Sciences