Miracle-dz/UniFAR-FTUs huggingface dataset:
Benchmarking RNA-seq differential expression analysis methods using spike-in and simulation data

Benchmarking RNA-seq differential expression analysis methods using spike-in and simulated RNA-seq data has often yielded inconsistent results. The spike-in data, which were generated from the same bulk RNA sample, only represent technical variability, making the test results less reliable. We compared the performance of 12 differential expression analysis methods for RNA-seq data, including recent variants in widely used software packages, using both RNA spike-in and simulation data for negative binomial (NB) model. Performance of edgeR, DESeq2, and ROTS was particularly different between the two benchmark tests. Then, each method was tested under most extensive simulation conditions especially demonstrating the large impacts of proportion, dispersion, and balance of differentially expressed (DE) genes. DESeq2, a robust version of edgeR (edgeR.rb), voom with TMM normalization (voom.tmm) and sample weights (voom.sw) showed an overall good performance regardless of presence of outliers and proportion of DE genes. The performance of RNA-seq DE gene analysis methods substantially depended on the benchmark used. Based on the simulation results, suitable methods were suggested under various test conditions.
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Wheat contains abundant xylan in cell walls of all tissues, but in endosperm, there is an unusual form of xylan substituted only by arabinose (arabinoxylan; AX) that has long chains and low levels of feruloylation, a fraction of which is extractable in water (WE-AX). WE-AX acts as soluble dietary ﬁbre but also gives rise to viscous extracts from grain, a detrimental trait for some non-food uses of wheat. Here, we show that a glycosyl transferase family 43 wheat gene abundantly expressed in endosperm complements the Arabidopsis irx9 mutant and so name the three homoeologous genes TaIRX9b. We generated wheat lines with a constitutive knockout of TaIRX9b by stacking loss-of-function alleles for these homeologues from a mutagenized hexaploid wheat population resulting in decreases in grain extract viscosity of 50% – 80%. The amount and chain length of WE-AX molecules from grain of these triple-stack lines was decreased accounting for the changes in extract viscosity. Imaging of immature wheat grain sections of triple-stacks showed abolition of immunolabelling in endosperm with LM11 antibody that recognizes epitopes in AX, but also showed apparently normal cell size and shape in all cell types, including endosperm. We identiﬁed differentially expressed genes from endosperm of triple-stacks suggesting that compensatory changes occur to maintain this endosperm cell wall integrity. Consistent with this, we observed increased ferulate dimerization and increased cross-linking of WE-AX molecules in triple-stacks. These novel wheat lines lacking functional TaIRX9b therefore provide insight into control of wheat endosperm cell walls.
Readmission Outcomes of Sliding Scale Insulin Compared to Basal-Bolus Insulin Prescribed at Discharge in an Insulin-Naive Patient Population

Background: Limited data are available that examine hospital readmission outcomes of sliding scale compared to basal-bolus insulin in indigent and insulin-naive patients. Objective: To evaluate hospital readmission outcomes in patients who are insulin naive with type 2 diabetes mellitus who are initiated on either sliding scale or basal-bolus insulin upon hospital discharge. Methods: A retrospective chart review was conducted of adult patients with a history of type 2 diabetes mellitus, who were insulin naive, had a hemoglobin A1c (HbA1c) 10% or greater, and were discharged with a prescription for sliding scale or basal-bolus insulin from January 2015 to July 2018. The primary objective measured all-cause 30-day hospital readmissions. The secondary objectives measured diabetes-related 30-day hospital readmissions and HbA1c change after 3 months of initial hospital admission. Data were analyzed using descriptive statistics, χ2 test, paired sample t test, and logistic regression. Results: Forty-one patients were prescribed sliding scale insulin and 105 patients were prescribed basal-bolus insulin. The majority were male (60%), spoke English (84%), were self-pay (39%), and had a mean age of 51 ± 10.2 years, initial HbA1c of 13% ± 1.9%, and LACE+ score of 51 ± 15.6 upon discharge. All-cause 30-day hospital readmissions occurred in 14.6% of sliding scale and 6.7% of basal-bolus insulin groups (odds ratio [OR]: 2.40, 95% confidence interval [CI]: 0.75-7.63). Hyperglycemia occurred in 7.3% of sliding scale and 0.9% of basal-bolus insulin groups. Mean HbA1c difference for basal-bolus and sliding scale insulin was 3.3 ± 3.1 and 2.9 ± 2.7, respectively (P = 0.459). Conclusion: There was no significant difference in all-cause 30-day hospital readmissions comparing sliding scale to basal-bolus insulin.
Gastrointestinal microbiology in autistic spectrum disorder: a review

Cases of autism have frequently been reported in association with gastrointestinal problems. These observations have stimulated investigations into possible abnormalities of intestinal microbiota in autistic patients. The objectives of this paper were to review the possible involvement and mechanisms of gastrointestinal microbiota in autistic spectrum disorder and explain the possible role of gastrointestinal microbiota in the condition. This review addresses the possible involvement of bacteria, viruses and fungi, and their products in autism. Direct viral damage of neurons or disruption of normal neurodevelopment by immune elements such as cytokines, nitric oxide and bacterial products, including lipopolysaccharides, toxins and metabolites, have been suggested to contribute to autistic pathology. Numerous intestinal microbial abnormalities have been reported in individuals with autism. Research to date exploring possible gastrointestinal problems and infection in autism has been limited by small and heterogeneous samples, study design flaws and conflicting results. Furthermore, interventions designed to modify the intestinal microbial population of autistic patients are few and limited in their generalisation. In order to bring clarity to this field, high-quality and targeted investigations are needed to explore the role of gastrointestinal microbiology in autism. To this end, several promising avenues for future research are suggested.
Phytoplankton Production in Char Lake, a Natural Polar Lake, and in Meretta Lake, a Polluted Polar Lake, Cornwallis Island, Northwest Territories

Phytoplankton production of ultraoligotrophic Char Lake and polluted Meretta Lake Oat. 74°42′N; long. 94°50′W) were studied between 1969 and 1972. Phytoplankton production in Char Lake is approximately 4.1 g C m−2 yr−1, making it the most oligotrophic lake on record. Photosynthesis takes place virtually the whole 9 mo the sun comes above the horizon. Changes in depth of maximum photosynthesis, in efficiency of low light utilization, and in optimal light flux resulted in a much more constant production rate than suggested by the light input, which is importantly affected by amount of snow cover. Phytoplankton in nearby sewage-polluted Meretta Lake averages 11.3 g C m−2 yr−1, and chlorophyll concentrations are 20 times higher than in Char Lake. Nutrient deficiencies, especially of phosphorus, are almost certainly responsible for the low efficiency of light utilization and resulting low production in Char Lake. Benthic production is of major significance in both lakes.
Physiological and enzymatic activity of pepper seeds (Capsicum annuum) during priming

Pepper (Capsicum annuum L. cv. Keystone Resistance Giant 3) seeds were monitored during priming to determine if seed treatments which accelerate the rate of germination could be correlated with specific physiological changes within the seeds. Pepper seeds primed with −0.90 and −1.35 MPa NaCl solutions at 23°C for 18 days did not completely equilibrate with the osmotic potential of the priming solution. Seed respiratory rates indicated that priming extends the lag phase of germination following imbibition. Soluble protein levels increased 115% in primed seeds, and the uptake and incorporation of [14C(U)] labelled amino acids into the acid insoluble fraction increased throughout the priming treatments. Alcohol dehydrogenase (EC 1.1.1.1, anaerobic metabolism), glucose-6-phosphate dehydrogenase (EC 1.1.1.49) and 6-phosphogluconate dehydrogenase (EC 1.1.1.44, pentose phosphate pathway) activities remained stable throughout the priming treatment, but were higher after 6 days. than the water-imbibed controls. Aldolase (EC 4.2.1.1. glycolysis) and isocitrate lyase (EC 4.1.3.1, glyoxylate cycle) activities increased with imbibition and were 61 and 56% (respectively) higher in primed seeds as compared to the water-imbibed controls after 12 days. Treatment with the −0.90 MPa NaCl solution was more effective than the −1.35 MPa solution in improving the rate of germination, yet there were no significant differences between the protein concentrations or enzyme activities of the two priming treatments. However, the incorporation of labelled amino acids into pepper seeds was significantly higher in the −0.90 MPa priming treatment.
Stolon characteristics related to winter survival in white clover

SUMMARY Changes in the stolon carbohydrate contents (water-soluble and total non-structural) of four white clover populations were measured at the beginning and end of winter. Three of the populations were of Swiss origin - two of these were from high-altitude pastures, and the other from a valley location. Grasslands Huia was measured as a control variety. Levels of both types of carbohydrate declined during the winter in all populations. The Swiss populations from high altitudes contained the highest levels of both carbohydrate types. An artificial freezing test was carried out on stolon segments collected from a range of clover populations (including the two high-altitude Swiss clovers) growing in field plots in January, and values of ‘lethal dose 50’ (LD50) were calculated. The two Swiss populations had the lowest LD50 values, indicating a greater intrinsic tolerance to freezing in those plants than in the other populations (of lowland temperate origin). One of the Swiss populations, Ac3785, was grown under two temperature regimes and short daylength to determine whether its tolerance to freezing increased with time. Significant increases in tolerance occurred after 8 days at 2 °C, but plants grown at 8 °C showed no change in tolerance even after 30 days. The results suggest that (i) stolon carbohydrate content is an important factor in the overwintering of white clover, (ii) there is a considerable amount of genetic variation in cold tolerance within white clover, (iii) artificial freezing tests can provide a method of predicting the survival of clover stolons during winter and (iv) the cold hardiness of white clover increases with time spent at temperatures near 0 °C under short daylengths.
A combination of depression and liver Qi stagnation and spleen deficiency syndrome using a rat model

A syndrome (Zheng in Chinese) plays a critical role in disease identification, diagnosis, and treatment in traditional Chinese medicine (TCM). Clinically, the liver Qi stagnation and spleen deficiency syndrome (LQSSDS) is one of the most common syndrome patterns. Over the past few decades, several animal models have been developed to understand the potential mechanisms of LQSSDS, but until now, simulation of the syndrome is still unclear. Recently, several studies have confirmed that an animal model combining a disease and a syndrome is appropriate for simulating TCM syndromes. Overlapping previous studies have reported that depression is highly associated with LQSSDS; hence, we attempted to develop a rat model combining depression and LQSSDS. We exposed the rats to different durations of chronic unpredictable mild stress (CUMS). Subsequently, the evaluation indicators at macrolevel consisted of behavioral tests including open field test, sucrose preference test, and forced swim test, food intake, body weight, white adipose tissue, fecal water content, visceral hypersensitivity, and small bowel transit, and the evaluation indicators at microlevel included changes of hypothalamic–pituitary–adrenal axis. Serum D‐xylose absorption was used to comprehensively confirm and assess whether the model was successful during the CUMS‐induced process. The results showed that rats exposed to 6‐week CUMS procedure exhibited significantly similar traits to the phenotypes of LQSSDS and depression. This study provided a new rat model for the LQSSDS and could potentially lead to a better understanding of the pathophysiology of LQSSDS and the development of new drugs for this syndrome.
Renin–Angiotensin–Aldosterone System Blockers and the Risk of Covid-19

Abstract Background A potential association between the use of angiotensin-receptor blockers (ARBs) and angiotensin-converting–enzyme (ACE) inhibitors and the risk of coronavirus disease 2019 (Covid-19) has not been well studied. Methods We carried out a population-based case–control study in the Lombardy region of Italy. A total of 6272 case patients in whom infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was confirmed between February 21 and March 11, 2020, were matched to 30,759 beneficiaries of the Regional Health Service (controls) according to sex, age, and municipality of residence. Information about the use of selected drugs and patients’ clinical profiles was obtained from regional databases of health care use. Odds ratios and 95% confidence intervals for associations between drugs and infection, with adjustment for confounders, were estimated by means of logistic regression. Results Among both case patients and controls, the mean (±SD) age was 68±13 years, and 37% were women. The use of ACE inhibitors and ARBs was more common among case patients than among controls, as was the use of other antihypertensive and non-antihypertensive drugs, and case patients had a worse clinical profile. Use of ARBs or ACE inhibitors did not show any association with Covid-19 among case patients overall (adjusted odds ratio, 0.95 [95% confidence interval {CI}, 0.86 to 1.05] for ARBs and 0.96 [95% CI, 0.87 to 1.07] for ACE inhibitors) or among patients who had a severe or fatal course of the disease (adjusted odds ratio, 0.83 [95% CI, 0.63 to 1.10] for ARBs and 0.91 [95% CI, 0.69 to 1.21] for ACE inhibitors), and no association between these variables was found according to sex. Conclusions In this large, population-based study, the use of ACE inhibitors and ARBs was more frequent among patients with Covid-19 than among controls because of their higher prevalence of cardiovascular disease. However, there was no evidence that ACE inhibitors or ARBs affected the risk of COVID-19.
Fertility preservation for young adults, adolescents, and children with cancer

Abstract Options for fertility preservation (FP) through cryopreservation methods are currently available for young adults, adolescents, and children. Guidelines for FP have been provided by international clinical societies, and emergency procedures aimed at FP have been implemented into clinical practice worldwide. In this article, we review the current data on clinical standards of emergency FP in patients who are facing gonadotoxic effects of cancer treatment, and we also describe the methods that are still under development, usually denoted as experimental. In Sweden, programmes for FP have been established at large university hospitals, thus covering the whole country. The Swedish publicly financed health care covers both assisted reproduction for treatment of infertility and the cryopreservation of gametes or gonadal tissue when there is a medical indication, such as the risk to become infertile due to oncologic treatment; hence the access to FP is ensured for the whole population. At our centre at Karolinska University Hospital in Stockholm, methods for FP have been offered since 1988. In this article, we also review the oncologic indications for FP in our patient cohort of >3000 individuals during the period 1988–2018.
Identification of developmental disorders including autism spectrum disorder using salivary miRNAs in children from Bosnia and Herzegovina

Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by major social, communication and behavioural challenges. The cause of ASD is still unclear and it is assumed that environmental, genetic and epigenetic factors influence the risk of ASD occurrence. MicroRNAs (miRNAs) are short 21–25 nucleotide long RNA molecules which post-transcriptionally regulate gene expression. MiRNAs play an important role in central nervous system development; therefore, dysregulation of miRNAs is connected to changes in behaviour and cognition observed in many disorders including ASD. Based on previously published work, on diagnosing ASD using miRNAs, we hypothesized that miRNAs can be used as biomarkers in children with suspected developmental disorders (DD) including ASD within Bosnian-Herzegovinian (B&H) population. 14 selected miRNAs were tested on saliva of children with suspected developmental disorders including ASD. The method of choice was qRT-PCR as a relatively cheap method available in most diagnostic laboratories in low to mid-income countries (LMIC). Out of 14 analysed miRNAs, 6 were differentially expressed between typically developing children and children with some type of developmental disorder including autism spectrum disorder. Using the most optimal logistic regression, we were able to distinguish between ASD and typically developing (TD) children. We have found 5 miRNAs as potential biomarkers. From those, 3 were differentially expressed within the ASD cohort. All 5 miRNAs had shown good chi-square statistics within the logistic regression performed on all 14 analysed miRNAs. The accuracy of 5-miRNAs model training set was 90.2%, while the validation set had a 90% accuracy. This study has shown that miRNAs may be considered as biomarkers for ASD detection and may be used to identify children with ASD along with standard developmental screening tests. By combining these methods we may be able to reach a reliable and accessible diagnostic model for children with ASD in LMIC such as B&H.
Parentage analysis in Chamaelirium luteum (L.) Gray (Liliaceae): why do some males have higher reproductive contributions?

Much of the contemporary study of adaptation in natural populations involves the regression of some component of fitness, usually survivorship or viability, on one or more characters of interest. It is difficult to apply this approach to measures of paternal reproduction, however, because paternity is typically estimated indirectly from genetic markers, rather than being measured directly from progeny counts. Here, we present maximum likelihood methods for modelling relative male reproductive success as a log‐linear function of one or more potentially predictive features, as well as providing a framework for the assessment of pairwise (male:female) effects, as they affect male reproductive performance. We also provide nonparametric statistical tests for alternative models.
Correlation of tumor necrosis factor-α -308G>A polymorphism with susceptibility, clinical manifestations and severity in Behçet syndrome: evidences from an Italian genetic case-control study CURRENT STATUS: POSTED

Background The tumor necrosis factor (TNF)α is a multifunctional proinflammatory cytokine, implicated in a variety of diseases, including Behçet syndrome (BS), a rare vasculitis with a wide spectrum of clinical manifestations. The aim of the present study was to investigate the association between a functional drug-response TNFα gene polymorphism (at the positions of -308; rs1800629) and both disease susceptibility and clinical manifestations in a cohort of Italian BS patients compared with healthy controls (HC). Methods We recruited 130 Italian patients with BS consecutively seen at Rheumatology Institute of Lucania (Italy) and 100 ethnically, age and gender matched HC. Demographic and clinical features were retrieved by medical records. Specific primer pairs were designed for TNFα coverage. Genomic DNA isolation, primer-specific PCR amplification and direct sequencing were performed for genotyping our group of patients and controls. In silico analysis was downstream performed using Mutation Surveyor software (SoftGenetics, USA) and NCBI-BlastN on line tool for the query-subject similarity analysis. Results The genotype distribution of BS patients and HC underlined a higher percentage of wild-type GG genotype in BS patients group vs HC (106/130 patients, 81.5% vs 91/100 HC, 91%; p<0.05), while the heterozygous genotype (GA) was identified in 24/130 patients (18.5%) vs 9/100 HC (9%) (p<0.05). GA genotype was significantly associated with the disease (OR=2.29, 95% CI 1.01-5.18). No significant association was recognized between the SNP and the BS clinical manifestations, as well as with disease severity (Krause's index). Conclusions We found statistically significant higher frequency of TNFα rs1800629 GA genotype in patients than in controls. No significant association was recognized between the polymorphism and the clinical parameters, as well as between the SNP and the disease severity. Our data need to be confirmed in larger cohort of patients and matched controls.
Prevalence and factors associated with overweight and central obesity among adults in the Eastern Sudan

Background A global epidemic of obesity has been documented, particularly among African countries. While central obesity and overweight have been reported for many countries, very limited information exists about the prevalence of these health problems in Sudan, and these data are nonexistent for Eastern Sudan. The present study aimed to determine the prevalence of obesity and central obesity, as well as the factors associated with both, among adults in Gadarif, Eastern Sudan. Methods A cross-sectional study was conducted in Gadarif, Eastern Sudan, during the period of January through May 2018. Sociodemographic and health characteristics data were collected through a questionnaire. Body mass index (BMI) and waist circumference (WC) were measured using the standard methods. Both descriptive and inferential statics were applied to analyze the data. Results A total of 594 adults participated in the study; 70.4% of them were female. The mean (standard deviation) age was 44.98 (16.64) years. Of the 594 enrolled participants, 33.7%, 7.4%, 26.8%, and 32.2% were normal weight, underweight, overweight, and obese, respectively. The prevalence of central obesity was (67.8%). Approximately, one-third of the participants (29.29%) were obese and had central obesity. In the multinomial regression, being married was the main risk factor associated with overweight, and older age, female sex, being married and hypertension were significantly associated with obesity. In the binary regression, the main risk factors associated with central obesity were female sex and being married. Conclusion The prevalence rates of both obesity and central obesity among the study participants were high. Older age and hypertension were only associated with obesity. Obesity and central obesity were significantly associated with female sex and being married. This study provided valuable baseline information to develop appropriate strategies for the prevention and control of obesity in Eastern Sudan.