jimnoneill/paper-to-field-training huggingface dataset:
Combined substrate micropatterning and FFT analysis reveals myotube size control and alignment by contact guidance

Field: Agricultural and Biological Sciences (Life Sciences)

Abstract Most important evaluating criteria for in vitro skeletal muscle models include the extent of differentiation and the degree of alignment in the tissue model. Substrate micropatterning is considered as an effective tool as it recreates in vivo like cellular microenvironment and helps in understanding the fundamental concepts and mechanisms underlying myogenesis. However, the influence of micropatterning based contact guidance cues over satellite cell alignment and myotube formation needs to be explored and studied further. In the present work, we demonstrate the regulation of myotube size control and alignment through the substrate micropatterning. For this purpose, primary myoblast cells (i.e., satellite cells) isolated from rat hind limb muscle were characterized and cultured for a period of 14 days on micropatterned glass substrates processed by the microchannnel flowed plasma process. Several characteristic parameters of muscle differentiation, including the fusion index, maturation index, and average width of the myotubes were quantified. The functional behavior of cultured myotubes exhibiting spontaneous contractions was assessed through kymograph to determine the twitch frequency. In addition, we evaluated the degree of alignment of myotubes on micropatterned substrates through examining orientation order parameter and two‐dimensional fast Fourier transform analysis. Altogether, the outcomes reveal that the contact guidance cues arising due to micropatterning of the substrates could be a key regulator for controlling the size and degree of alignment of myotubes during the myogenesis process.
Trait Interactions and Yield Enhancement in Linseed (Linum usitatissimum L.): Insights from Correlation and Path Analysis

Field: Agricultural and Biological Sciences (Life Sciences)

Linseed (Linum usitatissimum L.) is a self-pollinated (2n = 30) annual Rabi season crop mainly cultivated for flax fiber and oil due to its commercial use. The present investigation was carried out to study an association analysis among the yield and yield attributes using 75 linseed genotypes including 10 checks in a randomized block design with three replications at Oilseeds Research Farm, Kalyanpur, Chandra Shekhar Azad University of Agriculture and Technology, Kanpur, Uttar Pradesh, (India) during Rabi season of 2019-20. The correlation analysis revealed that the traits number of secondary branches per plant followed the number of primary branches per plant and number of capsules per plant at both the genotypic and phenotypic levels. The results of the path coefficient analysis revealed that traits such as the number of secondary branches per plant, number of capsules per plant, number of seeds per capsule, and plant height exhibited a strong and positive direct effect on seed yield per plant at both the genotypic and phenotypic levels. The seed yield can be improved by selecting traits such as number of primary branches per plant, number of secondary branches, number of capsules per plant, and plant height. It is recommended that the breeder focus on these traits in linseed to enhance its commercial value for the farming community.
[The detection of antibodies, antigens and circulating immune complexes in acute and chronic fascioliasis. Preliminary results].

Field: Medicine (Health Sciences)

24 patients with fascioliasis were studied. 19 of them were in the chronic stage and 5 in acute stage. The presence of antigens and of circulating immune complexes (CIC) was detected in 100% of the patients suffering from acute fascioliasis with less than 30 days of evolution of the clinical symptoms; whereas coproantigens were present in 100% of the chronic patients. In this group it was observed a considerable number of cases with elevated levels of antibodies. 43.7% of the cases with CIC were detected by using the precipitation technique with PEG and that of Clq deviation. A highly significant correlation was found between the eggs counting and the CIC levels by both techniques. Another important correlation was established between the eggs counting and the levels of coproantigens.
[Sexually transmitted diseases, HIV infection and AIDS in Mudzi, Zimbabwe. A study of knowledge, attitudes and practice in a rural area in southern Africa].

Field: Medicine (Health Sciences)

We describe a study conducted in a rural area of Zimbabwe. We examined all patients who attend for treatment of a presenting sexually transmitted disease for a period of one month in 1989 and 1992. In addition we studied the knowledge of, attitudes towards and practices as regards HIV-infection and AIDS in 1992. The annual rate of sexually transmitted diseases was not different in the two periods studied. Most of the females with symptoms of sexually transmitted diseases were married and had been infected by their husbands. Most males too were married, but had been infected by prostitutes. There was a reduction in the proportion of patients who were employed as teachers, policemen or in the army. The use of condoms seems to have increased. Males were generally better informed about HIV-infection and AIDS than females were. As much as 26% of the females and 40% of the males had a close friend/relative who had died from AIDS and 69% of the females and 81% of the males had found it necessary to change their sexual behaviour after hearing about AIDS. Most people knew the most important parts of transmission, and about condoms as a means of protection, but the rate of sexually transmitted diseases remains very high. New strategies are needed in the preventive work.
Effects of a Lactobacillus salivarius mixture on performance, intestinal health and serum lipids of broiler chickens

Field: Agricultural and Biological Sciences (Life Sciences)

The ban or severe restriction on the use of antibiotics in poultry feeds to promote growth has led to considerable interest to find alternative approaches. Probiotics have been considered as such alternatives. In the present study, the effects of a Lactobacillus mixture composed from three previously isolated Lactobacillus salivarius strains (CI1, CI2 and CI3) from chicken intestines on performance, intestinal health status and serum lipids of broiler chickens has been evaluated. Supplementation of the mixture at a concentration of 0.5 or 1 g kg-1 of diet to broilers for 42 days improved body weight, body weight gain and FCR, reduced total cholesterol, LDL-cholesterol and triglycerides, increased populations of beneficial bacteria such as lactobacilli and bifidobacteria, decreased harmful bacteria such as E. coli and total aerobes, reduced harmful cecal bacterial enzymes such as β-glucosidase and β-glucuronidase, and improved intestinal histomorphology of broilers. Because of its remarkable efficacy on broiler chickens, the L. salivarius mixture could be considered as a good potential probiotic for chickens, and its benefits should be further evaluated on a commercial scale.
An Evaluation of Thrombophilia Screening in an Urban Tertiary Care Medical Center

Field: Medicine (Health Sciences)

To evaluate the utilization of thrombophilia screening at a large urban academic tertiary care center, we retrospectively examined the indications, appropriateness, and results of 200 consecutive thrombophilia panels. Of the panels, 103 (51.5%) were ordered for venous thromboembolism; 124 (62.0%) were ordered during acute thrombotic episodes, and at least 40 (20.0%) had abnormal protein C and S results, of which 25 (63%) were attributable to anticoagulation and the remainder to pregnancy. Of the 200 panels, 46 (23.0%) had a significant abnormality; the most common abnormal result was a lupus anticoagulant, occurring in 23 cases (11.3%). Thrombophilia screening seems to be overutilized in our population, especially considering that the majority of tests are ordered during suboptimal conditions, eg, acute thrombosis, pregnancy, or anticoagulation. At present, outside the research setting, thrombophilia panels should be reserved for special circumstances, targeted to factors for which there would be a specific clinical impact, and performed in the absence of confounding clinical variables.
Richter Transformation in Chronic Lymphocytic Leukemia: Update in the Era of Novel Agents

Field: Medicine (Health Sciences)

Richter transformation (RT) is a poorly understood complication of chronic lymphocytic leukemia (CLL) with a dismal prognosis. It is associated with a switch in histopathology and biology, generally with a transformation of the original CLL clone to diffuse large B-cell lymphoma (DLBCL) or less frequently to Hodgkin’s variant of Richter transformation (HVRT). It occurs in 2–10% of CLL patients, with an incidence rate of 0.5–1% per year, and may develop in treatment-naïve patients, although it is more common following therapy. In recent years, there has been a deeper understanding of the molecular pathogenesis of RT that involves the inactivation of the TP53 tumor suppressor gene in 50–60% of cases and the activation of aberrations of NOTCH1 and MYC pathways in about 30% of cases. Compared to the preceding CLL, 80% of cases with DLBCL-RT and 30% of HVRT harbor the same IGHV-D-J rearrangements, indicating a clonal evolution of the disease, while the remaining cases represent de novo lymphomas that are clonally unrelated. Despite advances in understanding the molecular variations and the pathogenesis of the disease, there is still no significant improvement in patient outcomes. However, if no clinical trials were designed for patients with RT in the past, now there many studies for these patients that incorporate new drugs and novel combinations that are being explored. In this review, we summarize the new information accumulated on RT with special emphasis on results involving the novel therapy tested for this entity, which represents an unmet clinical need.
Expressed and cryptic flagellin genes in the H44 and H55 type strains of Escherichia coli

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

Bacterial H antigens are specified by flagellin molecules, which constitute the flagellar filament. Escherichia coli 781-55 and E2987-73 are the type strains for H44 and H55 antigens, respectively. Unlike E. coli K-12, they possess two flagellin genes, fliC and fllA, on their chromosomes. However, they are monophasic, expressing exclusively the fllA genes, which specify the type antigens. In this study, the flagellin genes were cloned from these strains and their structure and expression were analyzed. It was found that the fliC genes encode apparently intact flagellin subunits but possess inefficient sigma28-dependent promoters, which may result in these genes being silent. The chromosomal locations of the fllA genes are approximately, but not exactly, identical with that of the phase-2 flagellin gene, fljB, of diphasic Salmonella strains. However, unlike the Salmonella fljB gene, the invertible H segment and the fljA gene responsible for the control of flagellar phase variation are both absent from the fllA loci. The fllA genes are highly homologous to the E. coli fliC gene but distantly related to the Salmonella fljB gene. These results suggest a hypothesis that the fllA genes may have emerged by an intra-species lateral transfer of the fliC gene. This hypothesis is further supported by the observation that the fllA genes are flanked by several IS elements and located within cryptic prophage elements.
Synthesis and larvicidal and adult topical activity of some hydrazidehydrazone derivatives against Aedes aegypti

Field: Pharmacology, Toxicology and Pharmaceutics (Life Sciences)

A series of novel hydrazide-hydrazone derivatives weresynthesized and evaluated for their larvicidal and adulttopical activity against Aedes aegypti. The proposedstructures of all the synthesized compounds were confirmedusing elemental analysis, UV, IR, 1H-NMR, 13C-NMR andmass spectroscopy. Compounds 4a-h were screened in larvalbioassays at concentrations of 100, 50 and 25 ppm in a dosedependent manner and data for their mortality was recorded.Among the tested compounds, 1-(4-nitrophenyl)-3-(4-{2-oxo-2-[2-(2-oxo-1,2-dihydro-3H-ylidene)hydrazinyl] ethyl}phenyl)urea (4b) showed noteworthy larvacidal activityagainst Aedes aegypti. Dose-response data of compound 4bshowed LC50 and LC90 values of 30.5 (15.4 – 22.7) and 95.9(73.8 – 139.4) ppm, respectively. Screening of compounds4a-h at four doses by topical bioassay indicated a range ofactivity between 10000 and 1000 ppm.Keywords: Hydrazide-hydrazone, mosquito control, Aedesaegypti, larvicidal activity, adult topical activity
CHAI: consensus clustering through similarity matrix integration for cell-type identification

Field: Computer Science (Physical Sciences)

Abstract Several methods have been developed to computationally predict cell-types for single cell RNA sequencing (scRNAseq) data. As methods are developed, a common problem for investigators has been identifying the best method they should apply to their specific use-case. To address this challenge, we present CHAI (consensus Clustering tHrough similArIty matrix integratIon for single cell-type identification), a wisdom of crowds approach for scRNAseq clustering. CHAI presents two competing methods which aggregate the clustering results from seven state-of-the-art clustering methods: CHAI-AvgSim and CHAI-SNF. CHAI-AvgSim and CHAI-SNF demonstrate superior performance across several benchmarking datasets. Furthermore, both CHAI methods outperform the most recent consensus clustering method, SAME-clustering. We demonstrate CHAI’s practical use case by identifying a leader tumor cell cluster enriched with CDH3. CHAI provides a platform for multiomic integration, and we demonstrate CHAI-SNF to have improved performance when including spatial transcriptomics data. CHAI overcomes previous limitations by incorporating the most recent and top performing scRNAseq clustering algorithms into the aggregation framework. It is also an intuitive and easily customizable R package where users may add their own clustering methods to the pipeline, or down-select just the ones they want to use for the clustering aggregation. This ensures that as more advanced clustering algorithms are developed, CHAI will remain useful to the community as a generalized framework. CHAI is available as an open source R package on GitHub: https://github.com/lodimk2/chai.
Peer Review #1 of "Geographic population genetic structure and diversity of Sophora moorcroftiana based on genotyping-by-sequencing (GBS) (v0.1)"

Field: Agricultural and Biological Sciences (Life Sciences)

Sophora moorcroftiana is a perennial leguminous low shrub endemic to the Yarlung Zangbo River basin in Tibet with irreplaceable economic and ecological value.To determine the drivers of evolution in this species, 225 individuals belonging to 15 populations from different geographic locations were sampled and population genetics was studied using high-throughput genotyping-by-sequencing (GBS).Based on genetic diversity analysis, phylogenetic analysis, principal component analysis, and structure analysis, 15 natural populations could be clustered into five subgroups: subgroup I (Shigatse subgroup) was located in the upper reaches of the Yarlung Zangbo River with a relatively high level of population genetic variation (means for PIC, Shanon and PI were 0.173, 0.326 and 0.0000305, respectively), and gene flow within the subgroup was also high (mean value for Nm was 4.67).Subgroup II (including Pop 7 and Pop 8, means for PIC, Shanon and PI were 0.182, 0.345 and 0.0000321, respectively), located in the middle reaches of the Yarlung Zangbo River had relatively high levels of gene flow with the populations distributed in the upper and lower reaches, The Nm between subgroup II with subgroup I and III were 3.271 and 2.894, respectively Taking all genetic diversity indices into account, Pop 8 had relatively high genetic diversity.Subgroup III (the remaining mixed subgroup of Lhasa and Shannan) was located in the middle reaches of Yarlung Zangbo River and the means for PIC, Shanon and PI were 0.172, 0.324 and 0.0000303, respectively.Subgroup IV (Nyingchi subgroup), located in the lower reaches of the Yarlung Zangbo River basin, had further genetic distance with the other subgroups and the means for PIC, Shanon and PI were 0.147, 0.277 and 0.0000263, respectively.Subgroup V (Nyingchi Gongbu Jiangda subgroup), located in the upper reaches of the Niyang River,
Sales Force – Customer Relationship and Ethical Behaviours in the Nigerian Banking Industry: A Synthesis

Field: Business, Management and Accounting (Social Sciences)

This study examined 'Sales force -Customer Relationship and Ethical Behaviours in NigerianBanking Industry.The objectives include: to assess the differences in the ethical behaviours of bank sales force; to determine the effects of sales quotas, social ties and personal moral judgment on salespeople's ethical behaviours; to identify the congruence between bank salespeople's and customers' perceptions of ethical behaviours.Survey research design and six banks were used for the study.203 bank salespeople and 150 customers were sampled.Convenience sampling technique was used for selecting respondents.Questionnaire was used for data collection.The reliability of the research instrument yielded 0.83 co-efficient using Cronbach Alpha test.ANOVA, Regression Analysis and Pearson's Product Moment Correlation were used to test hypotheses.Findings show a significant difference in the salespeople's ethical behaviours; sales target, social ties and low personal moral judgment are responsible for salespeople's unethical behaviours; there is a significant congruence between the salespeople's and customers' perceptions of ethical behaviours and there is a strong negative influence of bank's corporate code of ethics on salespeople's ethical behaviours.This study is a case of ethical dilemma.The study recommends that the bank management should adopt discretional measures in approaching ethical issues
Navigating the Boundaries of Political Tolerance: Environmental Litigation in China

Field: Social Sciences (Social Sciences)

This is a dissertation about lawyers, judges, international NGOs and legal action in an authoritarian state. The state is contemporary China. The type of legal action is civil environmental lawsuits, as when herdsmen from Inner Mongolia sue a local paper factory over poisoned groundwater and dead livestock or a Shandong villager demands compensation from a nearby factory for the noise that allegedly killed 26 foxes on his farm. Empirically, this is a close-to-the-ground account of everyday justice and the factors that shape it. Drawing on fifteen months of field research in China, along with in-depth exploration of four cases, legal documents, government reports, newspaper articles and blog archives, this dissertation unpacks how law as litigation works: how judges make decisions, why lawyers take cases and how international influence matters. Conceptually, civil environmental lawsuits illustrate one pathway between litigation and social change in China and, by implication, possibly other illiberal states. With the exception of the first chapter, each chapter introduces a new actor's perspective on the interaction between state signals and legal professionals' response. The key theme, which cuts across chapters on the state, judges, lawyers and international NGOs, is what I call political ambivalence: conflicting official (or quasi-official) signals regarding the desirability of certain types of citizen action. Simultaneous impulses to promote law but control courts, to protect the environment and yet pursue economic growth, generate a medley of statements, cases and regulations that do not necessarily concord. For legal professionals on the ground, these mixed messages translate into a degree of opportunity. Without official sanction or intent, conflicting signals crack open enough political space to allow limited judicial innovation (chapter 3), legal activism (chapter 4), sustained international encouragement (chapter 5) and policy promotion (chapter 6). Even on tough terrain, political ambivalence over law can provide a limited opportunity to probe new roles and, in so doing, gently push the limitations of political tolerance.
An Efficient Deep Learning Model to Detect COVID-19 Using Chest X-ray Images

Field: Computer Science (Physical Sciences)

The tragic pandemic of COVID-19, due to the Severe Acute Respiratory Syndrome coronavirus-2 or SARS-CoV-2, has shaken the entire world, and has significantly disrupted healthcare systems in many countries. Because of the existing challenges and controversies to testing for COVID-19, improved and cost-effective methods are needed to detect the disease. For this purpose, machine learning (ML) has emerged as a strong forecasting method for detecting COVID-19 from chest X-ray images. In this paper, we used a Deep Learning Method (DLM) to detect COVID-19 using chest X-ray (CXR) images. Radiographic images are readily available and can be used effectively for COVID-19 detection compared to other expensive and time-consuming pathological tests. We used a dataset of 10,040 samples, of which 2143 had COVID-19, 3674 had pneumonia (but not COVID-19), and 4223 were normal (not COVID-19 or pneumonia). Our model had a detection accuracy of 96.43% and a sensitivity of 93.68%. The area under the ROC curve was 99% for COVID-19, 97% for pneumonia (but not COVID-19 positive), and 98% for normal cases. In conclusion, ML approaches may be used for rapid analysis of CXR images and thus enable radiologists to filter potential candidates in a time-effective manner to detect COVID-19.
HMGB-1 Levels May be Markers of Haematological Dysfunction after Severe Trauma

Field: Medicine (Health Sciences)

Introduction: HMGB-1 is a nuclear protein that acts as an alarmin to tissue repair in sepsis and is one of multiple mediators in the systemic inflammatory response (SIRS). Its role in clinical models of severe trauma is less well studied.
Objectives: The aim of this study was to study the release pattern of HMGB-1 in the first 72 hours after severe trauma and the association of HMGB-1 levels with tissue damage, shock, coagulation disorders and thrombocytopenia.
Materials and methods: A prospective cohort study enrolling all adult trauma patients with injury severity score (ISS)>15 admitted to a Trauma Room. Analytical variables assessed were: creatine kinase (CK), myoglobin (MIO) lactate, coagulation times and platelets at admission; HMGB-1 levels were measured at admission 24, 48 and 72h.
Results: Ninety-nine patients were enrolled with median ISS of 29, age 31 (18-60) years and 83% were male. Shock was found in 17%, hyperlactacidemia in 46%, coagulopathy in 26%, and thrombocytopenia in 19%. Outcomes were ICU admission-66%, MODS-34%, and Death-28%. The HMGB-1 highest level was found at admission. The study showed correlations between HMGB-1 and shock at admission (p<0,047), coagulopathy at 24h (p<0,01), and thrombocytopenia at 48h (p<0,026). Coagulopathy was associated with death and thrombocytopenia with ICU admission and death. HMGB-1 did not show correlation with ISS, CK or MIO or with any of the outcomes.
Conclusions: In this group of patients HMGB-1 levels at admission, at 24 h and at 48 h after severe trauma were respectively associated with the existence of shock, coagulopathy and thrombocytopenia.
Effect of drugs influencing central serotonergic mechanisms on pentazocine-induced catalepsy in mice.

Field: Pharmacology, Toxicology and Pharmaceutics (Life Sciences)

Cataleptic effect of pentazocine in mice was affected by pretreatment with dexfenfluramine, fluoxetine, buspirone, p-chlorophenylalanine, cyproheptadine, mianserin, cisapride, ondansetron, pindolol and propranolol. The results suggest that drugs which influence the activity of central serotonergic systems do modulate pentazocine-induced catalepsy in mice.