Miracle-dz/UniFAR-FTUs huggingface dataset:
Limitations of Detecting Genetic Variants from the RNA Sequencing Data in Tissue and Fine-Needle Aspiration Samples

Background: Genetic profiling of resected tumor or biopsy samples is increasingly used for cancer diagnosis and therapy selection for thyroid and other cancer types. Although mutations occur in cell DNA and are typically detected using DNA sequencing, recent attempts focused on detecting pathogenic variants from RNA. The aim of this study was to determine the completeness of capturing mutations using RNA sequencing (RNA-Seq) in thyroid tissue and fine-needle aspiration (FNA) samples. Methods: To compare the detection rate of mutations between DNA sequencing and RNA-Seq, 35 tissue samples were analyzed in parallel by whole-exome DNA sequencing (WES) and whole-transcriptome RNA-Seq at two study sites. Then, DNA and RNA from 44 thyroid FNA samples and 47 tissue samples were studied using both targeted DNA sequencing and RNA-Seq. Results: Of 162 genetic variants identified by WES of DNA in 35 tissue samples, 77 (48%) were captured by RNA-Seq, with a detection rate of 49% at site 1 and 46% at site 2 and no difference between thyroid and nonthyroid samples. Targeted DNA sequencing of 91 thyroid tissue and FNA samples detected 118 pathogenic variants, of which 57 (48%) were identified by RNA-Seq. For DNA variants present at >10% allelic frequency (AF), the detection rate of RNA-Seq was 62%, and for those at low (5–10%) AF, the detection rate of RNA-Seq was 7% (p < 0.0001). For common oncogenes (BRAF and RAS), 94% of mutations present at >10% AF and 11% of mutations present at 5–10% AF were captured by RNA-Seq. As expected, none of TERT promoter mutations were identified by RNA-Seq. The rate of mutation detection by RNA-Seq was lower in FNA samples than in tissue samples (32% vs. 49%, p = 0.02). Conclusions: In this study, RNA-Seq analysis detected only 46–49% of pathogenic variants identifiable by sequencing of tumor DNA. Detection of mutations by RNA-Seq was more successful for mutations present at a high allelic frequency. Mutations were more often missed by RNA-Seq when present at low frequency or when tested on FNA samples. All TERT mutations were missed by RNA-Seq. These data suggest that RNA-Seq does not detect a significant proportion of clinically relevant mutations and should be used with caution in clinical practice for detecting DNA mutations.
NASH, Fibrosis and Hepatocellular Carcinoma: Lipid Synthesis and Glutamine/Acetate Signaling

Primary liver cancer is predicted to be the sixth most common cancer and the fourth leading cause of cancer mortality worldwide. Recent studies identified nonalcoholic fatty liver disease (NAFLD) as the underlying cause in 13–38.2% of patients with hepatocellular carcinoma unrelated to viral hepatitis and alcohol abuse. NAFLD progresses to nonalcoholic steatohepatitis (NASH), which increases the risk for the development of liver fibrosis, cirrhosis, and hepatocellular carcinoma. NAFLD is characterized by dysregulation of lipid metabolism. In addition, lipid metabolism is effected not only in NAFLD, but also in a broad range of chronic liver diseases and tumor development. Cancer cells manipulate a variety of metabolic pathways, including lipid metabolism, in order to build up their own cellular components. Identifying tumor dependencies on lipid metabolism would provide options for novel targeting strategies. This review article summarizes the research evidence on metabolic reprogramming and focuses on lipid metabolism in NAFLD, NASH, fibrosis, and cancer. As alternative routes of acetyl-CoA production for fatty acid synthesis, topics on glutamine and acetate metabolism are included. Further, studies on small compound inhibitors targeting lipid metabolism are discussed. Understanding reprogramming strategies in liver diseases, as well as the visualization of the metabolism reprogramming networks, could uncover novel therapeutic options.
Health and Well-Being in Protected Natural Areas—Visitors’ Satisfaction in Three Different Protected Natural Area Categories in Catalonia, Spain

Protected natural areas (PNAs) can be a source of health and well-being, but little research has been carried out regarding outcomes in terms of satisfaction (the difference between motivations and benefits). Inspired by previous research that examines the motivations and benefits perceived by visitors to various PNAs in Canada, and based on importance–performance analysis (IPA) and service quality gap (GAP) analysis theory, the aim of this study was to identify the outcomes generated by protected areas in terms of satisfaction, especially with regard to the PNAs’ individual protection categories. The study was based on survey data from visitors (n = 360) to three PNAs in Catalonia: one national park, one natural park and one periurban park. The results indicate that anticipated environmental, psychological, physical and social benefits were of major personal value in choosing to visit a PNA. The results indicate that, generally, visitors were satisfied with regard to the benefits anticipated. Differences between parks in this respect could be explained in part by sociodemographic factors and visitors’ behavior. The results are discussed in terms of their applicability and how they relate to the role of PNAs in the promotion of visitors’ health and well-being.
Capturing cell type-specific chromatin compartment patterns by applying topic modeling to single-cell Hi-C data

Single-cell Hi-C (scHi-C) interrogates genome-wide chromatin interaction in individual cells, allowing us to gain insights into 3D genome organization. However, the extremely sparse nature of scHi-C data poses a significant barrier to analysis, limiting our ability to tease out hidden biological information. In this work, we approach this problem by applying topic modeling to scHi-C data. Topic modeling is well-suited for discovering latent topics in a collection of discrete data. For our analysis, we generate nine different single-cell combinatorial indexed Hi-C (sci-Hi-C) libraries from five human cell lines (GM12878, H1Esc, HFF, IMR90, and HAP1), consisting over 19,000 cells. We demonstrate that topic modeling is able to successfully capture cell type differences from sci-Hi-C data in the form of “chromatin topics. ” We further show enrichment of particular compartment structures associated with locus pairs in these topics.
Study on mechanism of Tianzhu Powder in treatment of vascular dementia based on systems pharmacology

Objective: To determine the gene expression difference of rats and elucidate the anti-vascular dementia mechanism mediated by Tianzhu Powder. Methods: The differential expression genes were determined by using genome-wide chip detection technology, and the expression proteins of the differential expression genes were searched in database, then the biological network between protein of the differential expression genes and vascular dementia related targets was established by the inference rule of directed TCM entity grammar system(d TGS), and the interaction between them was inferred. Results: There were 229 differentially expressed genes which including 219 up-regulated genes(2) and 10 down-regulated genes(0.5). There were 3 anti-vascular dementia pathways of Tianzhu Powder by analyzing biological network. Conclusion: By mediating the gene expression of rat and affecting the biological network of the differential expression gene downstream, Tianzhu Powder plays the role of anti-vascular dementia.
Biological Role of Arrestin-1 Oligomerization

Members of the arrestin superfamily have great propensity of self-association, but the physiological significance of this phenomenon is unclear. To determine the biological role of visual arrestin-1 oligomerization in rod photoreceptors, we expressed mutant arrestin-1 with severely impaired self-association in mouse rods and analyzed mice of both sexes. Members of the arrestin superfamily have great propensity of self-association, but the physiological significance of this phenomenon is unclear. To determine the biological role of visual arrestin-1 oligomerization in rod photoreceptors, we expressed mutant arrestin-1 with severely impaired self-association in mouse rods and analyzed mice of both sexes. We show that the oligomerization-deficient mutant is capable of quenching rhodopsin signaling normally, as judged by electroretinography and single-cell recording. Like wild type, mutant arrestin-1 is largely excluded from the outer segments in the dark, proving that the normal intracellular localization is not due the size exclusion of arrestin-1 oligomers. In contrast to wild type, supraphysiological expression of the mutant causes shortening of the outer segments and photoreceptor death. Thus, oligomerization reduces the cytotoxicity of arrestin-1 monomer, ensuring long-term photoreceptor survival. SIGNIFICANCE STATEMENT Visual arrestin-1 forms dimers and tetramers. The biological role of its oligomerization is unclear. To test the role of arrestin-1 self-association, we expressed oligomerization-deficient mutant in arrestin-1 knock-out mice. The mutant quenches light-induced rhodopsin signaling like wild type, demonstrating that in vivo monomeric arrestin-1 is necessary and sufficient for this function. In rods, arrestin-1 moves from the inner segments and cell bodies in the dark to the outer segments in the light. Nonoligomerizing mutant undergoes the same translocation, demonstrating that the size of the oligomers is not the reason for arrestin-1 exclusion from the outer segments in the dark. High expression of oligomerization-deficient arrestin-1 resulted in rod death. Thus, oligomerization reduces the cytotoxicity of high levels of arrestin-1 monomer.
Changes in biochemical properties of rice rhizosphere as influenced by tillage and herbicide application

A field study was conducted during 2009 at Raipur in an inceptisol with rainy season rice to evaluate the effect of herbicides application on biochemical characteristics of rhizosphere soil under different tillage systems. Four different types of tillage system were evaluated viz. (i) conventional-conventional (ii) conventional-zero (iii) zero-conventional and (iv) zero-zero. Among weed control measures, comparative effects of hand weeding and recommended herbicides application (butachlor as pre-emergence and fenoxaprop-p-ethyl + ethoxysulfuron as post-emergence herbicide 1.5 kg, 56.25 g and 15 g/ha, respectively) were tested compared with a weedy check (control). The conventional-conventional tillage system was found most effective to improve the biochemical characteristics of soil. Under this system, maximum organic C content was accumulated in rhizosphere soil and also found maximum enzyme activity (dehydrogenase activity, acidic phosphatase activity and alkaline phosphatase activity). Application of preand post- emergence herbicide reduced the biochemical activities in soil after its application (3 and 22 days after sowing, respectively) to 35 days of sowing of the crop thereafter it became normalize due to degradation of applied herbicides.
Fear and Trembling of Cruise Ship Employees: Psychological Effects of the COVID-19 Pandemic

The current COVID-19 pandemic has evolved to unprecedented proportions. This research aimed to gain a deeper understanding of the psychological effects of the COVID-19 pandemic on cruise ship employees stuck at sea. Using an inductive qualitative approach, a synchronous online focus group was conducted with nine cruise ship employees who were stuck at sea during COVID-19 pandemic. The findings revealed that COVID-19 pandemic has managed to erase the feeling of joy from cruise ship employees who were stuck at sea while exposing weakness of cruise line companies such as poor human resource management leadership. Moreover, COVID-19 pandemic demonstrated that it is of paramount importance that cruise line companies create a comprehensive strategy in assisting their employees who are experiencing an anxiety disorder and depression. The managerial implications are outlined.
A Poplar Rust Effector Protein Associates with Protein Disulfide Isomerase and Enhances Plant Susceptibility

Melampsora larici-populina (Mlp), the causal agent of Populus leaf rust, secretes an array of effectors into the host through the haustorium to gain nutrients and suppress immunity. The precise mechanisms by which these effectors promote virulence remain unclear. To address this question, we developed a transgenic Arabidopsis line expressing a candidate effector, Mlp124357. Constitutive expression of the effector increased plant susceptibility to pathogens. A GxxxG motif present in Mlp124357 is required for its subcellular localization at the vacuolar membrane of the plant cell, as replacement of the glycine residues with alanines led to the delocalization of Mlp124357 to the nucleus and cytoplasm. We used immunoprecipitation and mass spectrometry (MS) to identify Mlp124357 interaction partners. Only one of the putative interaction partners knock-out line caused delocalization of the effector, indicating that Arabidopsis protein disulfide isomerase-11 (AtPDI-11) is required for the effector localization. This interaction was further confirmed by a complementation test, a yeast-two hybrid assay and a molecular modeling experiment. Moreover, localization results and infection assays suggest that AtPDI-11 act as a helper for Mlp124357. In summary, our findings established that one of Mlp effectors resides at the vacuole surface and modulates plant susceptibility.
Functional gene categories differentiate maize leaf drought-related microbial epiphytic communities

The phyllosphere epiphytic microbiome is composed of microorganisms that colonize the external aerial portions of plants. Relationships of plant responses to specific microorganisms–both pathogenic and beneficial–have been examined, but the phyllosphere microbiome functional and metabolic profile responses are not well described. Changing crop growth conditions, such as increased drought, can have profound impacts on crop productivity. Also, epiphytic microbial communities provide a new target for crop yield optimization. We compared Zea mays leaf microbiomes collected under drought and well-watered conditions by examining functional gene annotation patterns across three physically disparate locations each with and without drought treatment, through the application of short read metagenomic sequencing. Drought samples exhibited different functional sequence compositions at each of the three field sites. Maize phyllosphere functional profiles revealed a wide variety of metabolic and regulatory processes that differed in drought and normal water conditions and provide key baseline information for future selective breeding.
Could we Spare Carbapenems for Empiric Therapy in ESBL-Enterobacteriaceae Colonized Elderly with Community-Onset Sepsis?

The preference for empiric antibiotic therapy with carbapenems over non-carbapenems in all extended-spectrum β-lactamase-producing Enterobacteriaceae (ESBL-E) colonized patients with sepsis warrants further investigation from an ecologic perspective; even more so in the elderly (≥ 65 years) because the proportion of ESBL-E in adults increases with patients’ age. In this retrospective observational study, enrolling 547 ESBL-E colonized elderly patients with community-onset sepsis, hospitalized at a single medical centre from 2011 to 2015, the positive predictive value of ESBL-E faecal colonization for ESBL-E aetiology of sepsis was significantly higher (66.1%) when sepsis originated from a urinary tract infection than from a respiratory tract infection (26.1%), other known origins (31.6%), or an unidentified origin (13.0%). Carbapenems were prescribed empirically in 145 patients (26.5%), and 402 received non-carbapenem antibiotics. Univariate analysis suggested a higher 30-day mortality in the non-carbapenem vs. carbapenem group. However, the estimated association was smaller and not significant (OR = 1.1, 95% CI, 0.6-1.9, P = 0.62) in the multiple regression analysis adjusted for age, sex, Charlson comorbidity index score, and severity, origin or aetiology of sepsis. Therefore, carbapenem-sparing empiric therapy seems appropriate for non-critically ill elderly ESBL-E carriers with community-onset sepsis, even more so when sepsis originates outside urinary tract.
Interindividual differences in incentive sensitivity moderate motivational effects of competition and cooperation on motor performance

Established research has documented the pervasive influence of incentives (i.e., food, sex, money) on animal and human behavior. Additionally, motivational theories postulating intra–individually stable preferences for specific types of incentives (i.e., motives) highlight that effects of a given incentive are highly dependent on the motive disposition of the individual. Indeed, also research on motor performance has documented the interactive effects of motives and motive–specific incentives on motor outcomes. However, the majority of this research has relied on correlational designs focusing on the effects of the achievement motive, with few studies addressing the role of the affiliation and power motive. In order to extend findings in this domain, we tested whether a fit between individuals’ power (affiliation) motive and incentives of competition (cooperation) would improve motor performance. Following baseline measures, participants performed a dart–throwing task as part of a dyadic performance (i.e., cooperative) or a one–on–one competition scenario. In the dyadic performance scenario, a stronger affiliation motive did not translate to better performance. However, in the one–on–one competition scenario a stronger power motive was associated with better performance. Results highlight the role of the power motive in predicting motor performance, particularly in competitive situations.
Identification of functional SNPs in genes and their effects on plant phenotypes

Single nucleotide polymorphism (SNP) is an abundant form of genetic variation within individuals of species. DNA polymorphism can arise throughout the whole genome at different frequencies in different species. SNP may cause phenotypic diversity among individuals, such as individuals with different color of plants or fruits, fruit size, ripening, flowering time adaptation, quality of crops, grain yields, or tolerance to various abiotic and biotic factors. SNP may result in changes in amino acids in the exon of a gene (asynonymous). SNP can also be silent (present in coding region but synonymous). It may simply occur in the noncoding regions without having any effect. SNP may influence the promoter activity for gene expression and finally produce functional protein through transcription. Therefore, the identification of functional SNP in genes and analysis of their effects on phenotype may lead to better understanding of their impact on gene function for varietal improvement. In this mini-review, we focused on evidences revealing the role of functional SNPs in genes and their phenotypic effects for the purpose of crop improvements.
The Effectiveness of Educational Training or Multicomponent Programs to Prevent the Use of Physical Restraints in Nursing Home Settings: A Systematic Review and Meta-Analysis of Experimental Studies

This review assesses the effectiveness of interventions to reduce physical restraint (PR) use in older people living in nursing homes or residential care facilities. A systematic search of studies published in four electronic databases (MEDLINE, CINHAL, PsycINFO, Cochrane Central Register of Controlled Trials). The review included individual and cluster randomized controlled trials that compared educational training and multicomponent programs to avoid PR use. Risk bias of randomized controlled trials (RCTs) was assessed according to the Cochrane Handbook for Systematic Reviews of Interventions. This review includes 16 studies in a qualitative synthesis that met the inclusion criteria, nine of them offered a multicomponent program and seven offered only educational training. The results of the 12 studies included in the meta-analysis showed a significant trend in favor of intervention over time and intensity of PR use tends to decrease. The review indicates that educational programs and other supplementary interventions should be effective, but the heterogeneous operative definition of physical restraints can make difficult data generalization.
Myocardial Infarction With Nonobstructive Coronary Arteries

Myocardial infarction with nonobstructive coronary arteries (MINOCA) is the current term used to describe patients who have a myocardial infarction but have normal, non-obstructed coronary arteries on a coronary angiogram. There is still much debate over the definition, diagnosis, management and treatment of MINOCA. However, MINOCA is not a benign condition; prompt recognition and diagnosis can lead to better management and treatment and thus improve patient outcomes. This review article will update the most recent definition of MINOCA, discuss epidemiology and etiology, and review the diagnostic workup and management options for patients presenting with signs and symptoms of MINOCA.
Can an increase in noradrenaline induced by brief exercise counteract sleep inertia?

ABSTRACT Emergency responders often credit ‘adrenaline’ (i.e. sympathetic activity) as the reason they respond quickly upon waking, unimpaired by sleep inertia. Movement upon waking may promote sympathetic activity in this population. This pilot study (n = 4 healthy males) tested the effects of a 30 s exercise bout (maximal sprint) upon waking during the night (02:00 h) on sympathetic activity and sleep inertia. When compared to sedentary conditions, exercise reduced subjective sleepiness levels and elicited a temporary increase in sympathetic activity, measured by plasma noradrenaline levels. These findings provide preliminary support for exercise as a potential sleep inertia countermeasure.
A Report on New Causative Agent(Gasterophilus spp.) of the Myiasis of Przewalski's Horse Occurred in China

A new causative agent attracts us in present control of the myiasis of Przewalski′s horse.The species,which is attributed to Gasterophilus,Gasterophilidae,Diptera according to the collected larva specimen,has been unrecorded in national literatures by now.Features of the 3rd instar larvae were as follows: fully-grown larvae(maggots) are 14-17 mm long(double of the width) and have green,tough skin;the body is spindly and blunt at the back end;the front part of each body segment(from the 3rd thoracic segment to the 6th abdominal segment) is ringed with single line of strong,yellow,longitudinal-narrow spines.The line of spines at the backside become incomplete since the 4th abdominal segment,and there is no spine at the backside of the 7th abdominal segment.