Miracle-dz/UniFAR-FTUs huggingface dataset:
Serum allergen-specific IgE reactivity: is there an association with clinical severity and airway eosinophilia in asthmatic cats?

Objectives The aim of this study was to evaluate the results of serum allergen-specific IgE testing in cats with a clinical diagnosis of asthma and to determine if the number of allergens with positive IgE reactivity and magnitude of positive IgE responses would be associated with the severity of clinical signs or airway eosinophilia. Methods Medical records from 2008 to 2018 were retrospectively reviewed. Inclusion required a diagnosis of feline asthma based on consistent clinicopathologic features and bronchoalveolar lavage (BAL) cytology with >10% eosinophils; additionally, cats needed to have the results of serum allergen-specific IgE tests. Results Eighteen cases satisfied the inclusion criteria. Median age was 5 years and the most common presenting clinical sign was cough (n = 10/18). Most cats lived exclusively indoors (n = 13/18). The median percentage of BAL eosinophils was 47%. Serum allergen-specific IgE testing supported an underlying allergic etiology in 14/18 (78%) cats, with all but one having polysensitization. The severity of clinical signs and magnitude of airway eosinophilia did not correlate with the degree of positive IgE reactivity. Conclusions and relevance This study identified a strong association between the identification of allergen-specific IgE and cats with asthma, and the majority of these cats were polysensitized. However, larger numbers of allergens with positive IgE reactivity or magnitude of IgE reactivity were not significantly associated with clinical severity or airway eosinophilia. Knowledge of positive allergen-specific IgE results could guide allergen avoidance, regardless of the magnitude of IgE reactivity.
Robust partial reference-free cell composition estimation from tissue expression

MOTIVATION In the analysis of high throughput omics data from tissue samples, estimating and accounting for cell composition have been recognized as important steps. High cost, intensive labor requirements and technical limitations hinder the cell composition quantification using cell sorting or single-cell technologies. Computational methods for cell composition estimation are available, but they are either limited by the availability of a reference panel or suffer from low accuracy. RESULTS We introduce TOAST/-P and TOAST/+P, two partial reference-free algorithms for estimating cell composition of heterogeneous tissues based on their gene expression profiles. TOAST/-P and TOAST/+P incorporate additional biological information, including cell type specific markers and prior knowledge of compositions, in the estimation procedure. Extensive simulation studies and real data analyses demonstrate that the proposed methods provide more accurate and robust cell composition estimation than existing methods. AVAILABILITY The proposed methods TOAST/-P and TOAST/+P are implemented as part of the R/Bioconductor package TOAST at https://bioconductor.org/packages/TOAST. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Repurposing Antihypertensive Drugs for the Management of Alzheimer's Disease.

Alzheimer's disease (AD) is a neurodegenerative disorder that has affected millions of people worldwide. However, currently there is no treatment to cure the disease. The AD drugs available in the market only manage the disease symptomatically and the effects are usually short-term. Thus, there is a need to look at alternatives AD therapies. Mid-life hypertension has not only been recognised as a risk factor for AD, but its relation with AD has also been well established. Thus, antihypertensives are postulated to be beneficial in managing AD. This literature review aims to shed some light on the potential of repurposing antihypertensives to treat AD, considering recent updates. Four classes of antihypertensives, as well as their potential limitations and future prospects in being utilised as AD therapeutics are discussed in this review.
Noninvasive follicular thyroid neoplasm with papillary‐like nuclear features and the risk of malignancy in The Bethesda System for the Reporting of Thyroid Cytopathology

The Bethesda System for the Reporting of Thyroid Cytopathology (TBSRTC) is used to categorize and diagnose thyroid nodules by fine needle aspiration biopsy (FNAB). Each category in TBSRTC is associated with an estimated risk of malignancy (ROM). A subset of noninvasive encapsulated follicular variant of papillary thyroid carcinoma (niEFVPTC) was reclassified as a nonmalignant tumor: noninvasive follicular thyroid neoplasm with papillary‐like nuclear features (NIFTP). We studied the impact of this reclassification on the reported ROM in TBSRTC.
Precision and Reliability of Tightly Coupled PPP GNSS and Landmark Monocular Vision Positioning

This paper presents an approach to analyse the quality, in terms of precision and reliability, of a system which integrates—at the observation-level—landmark positions and GNSS measurements, obtained with a single camera and a digital map, and a single frequency GNSS receiver respectively. We illustrate the analysis by means of design computations, and we present the actual performance by means of a small experiment in practice. It is shown that the integration model is able to produce a position solution even when both sensors individually fail to do so. With realistic assumptions on measurement noise, the proposed integrated, low-cost system can deliver a horizontal position with a precision of better than half a meter. The external reliability of the integrated system is at the few decimetre-level, showing that the impact of undetected faults in the measurements, for instance incorrectly identified landmarks in the image, on the horizontal position is limited and acceptable, thereby confirming the fault-robustness of the system.
Personality and anxiety are related to health-related quality of life in unruptured intracranial aneurysm patients selected for non-intervention: A cross sectional study

Background Personality traits and mental health problems have been previously reported in unruptured intracranial aneurysm (UIA) patients; however, few studies have clarified the relations between these variables and health-related quality of life (HRQoL). This study was designed to characterize the personality traits, HRQoL and mental health of patients with UIA and to evaluate whether personality has an influence on HRQoL and whether this is mediated by the patients' emotional symptoms. Methods Sixty-three patients with UIAs (mean age 62.6 years, 83.9% women) answered questionnaires for depression, anxiety, HRQoL and personality traits between June 2016 and May 2019. Results Eight percent of the sample had depression, and 27.4% had anxiety. Participants showed high levels of responsibility, kindness and neuroticism and low levels of extraversion and openness. HRQoL scores were normal compared with the Colombian population. Structural equation analysis showed that patients' HRQoL was negatively affected by anxiety levels and that the latter are associated with the patient's personality, where neuroticism is directly associated with symptomatology and inversely associated with extraversion. Conclusions The results of this study showed the importance of personality and emotional symptoms in the HRQoL of UIA patients. These results are important for developing strategies for psychological counseling in patients with UIAs.
Detecting heart failure using wearables: a pilot study

Objective: Heart failure (HF) can be difficult to diagnose by physical examination alone. We examined whether wristband technologies may facilitate more accurate bedside testing. Approach: We studied on a cohort of 97 monitored in-patients and performed a cross-sectional analysis to predict HF with data from the wearable and other clinically available data. We recorded photoplethysmography (PPG) and accelerometry data using the wearable at 128 samples per second for 5 min. HF diagnosis was ascertained via chart review. We extracted four features of beat-to-beat variability and signal quality, and used them as inputs to a machine learning classification algorithm. Main results: The median [interquartile] age was 60 [51 68] years, 65% were men, and 54% had heart failure; in addition, 30% had acutely decompensated HF. The best 10-fold cross-validated testing performance for the diagnosis of HF was achieved using a support vector machine. The waveform-based features alone achieved a pooled test area under the curve (AUC) of 0.80; when a high-sensitivity cut-point (90%) was chosen, the specificity was 50%. When adding demographics, medical history, and vital signs, the AUC improved to 0.87, and specificity improved to 72% (90% sensitivity). Significance: In a cohort of monitored in-patients, we were able to build an HF classifier from data gathered on a wristband wearable. To our knowledge, this is the first study to demonstrate an algorithm using wristband technology to classify HF patients. This supports the use of such a device as an adjunct tool in bedside diagnostic evaluation and risk stratification.
Contribution of Cross-Linker and Silica Morphology on Cr(VI) Sorption Performances of Organic Anion Exchangers Embedded into Silica Pores

Removal of Cr(VI) from the environment represents a stringent issue because of its tremendous effects on living organisms. In this context, design of sorbents with high sorption capacity for Cr(VI) is getting a strong need. For this purpose, poly(vinylbenzyl chloride), impregnated into porous silica (PSi), was cross-linked with either N,N,N’,N’-tetramethyl-1,2-ethylenediamine (TEMED) or N,N,N’,N’-tetramethyl-1,3-propanediamine, followed by the reaction of the free -CH2Cl groups with N,N-diethyl-2-hydroxyethylamine to generate strong base anion exchangers (ANEX) inside the pores. The PSi/ANEX composite sorbents were deeply characterized by FTIR spectroscopy, SEM-energy dispersive X-ray spectroscopy (EDX), thermogravimetric analysis (TGA), and water uptake. The sorption performances of composites against Cr(VI) were investigated as a function of pH, contact time, initial concentration of Cr(VI), and temperature. It was found that the cross-linker structure and the silica morphology are the key factors controlling the sorption capacity. The adsorption process was spontaneous and endothermic and well described by pseudo-second-order kinetic and Sips isotherm models. The maximum sorption capacity of 311.2 mg Cr(VI)/g sorbent was found for the composite prepared with mesoporous silica using TEMED as cross-linker. The PSi/ANEX composite sorbents represent an excellent alternative for the removal of Cr(VI) oxyanions, being endowed with fast kinetics, equilibrium in about 60 min, and a high level of reusability in successive sorption/desorption cycles.
Insights to correlations and discrepancies between impaired lung function and heart failure in Eisenmenger patients

Impaired lung function and spirometric signs of airway obstruction without common risk factors for chronic obstructive pulmonary disease could be found in patients with Eisenmenger syndrome. This study aimed to analyse the association between lung function parameters and disease severity (including heart failure markers, associated congenital heart defect) as well as the possible reasons for airflow obstruction in Eisenmenger syndrome. The data of 25 patients with Eisenmenger syndrome were retrospectively evaluated. The patients were divided into groups according to airflow obstruction and a type of congenital heart defect. Airflow obstruction was found in nearly third (32%) of our cases and was associated with older age and worse survival. No relation was found between airway obstruction, B-type natriuretic peptide level, complexity of congenital heart defect and bronchial compression. Most of the patients (88%) had gas diffusion abnormalities. A weak negative correlation was noticed between gas diffusion (diffusing capacity of the lung for carbon monoxide) and B-type natriuretic peptide level (r = −0.437, p = 0.033). Increased residual volume was associated with higher mortality (p = 0.047 and p = 0.021, respectively). A link between B-type natriuretic peptide and lung diffusion, but not airway obstruction, was found. Further research and larger multicentre studies are needed to evaluate the importance of pulmonary function parameters and mechanisms of airflow obstruction in Eisenmenger syndrome.
The role of nutrition in asthma prevention and treatment

Abstract Asthma is a chronic respiratory condition characterized by airway inflammation and hyperreactivity. Prevalence has continued to rise in recent decades as Western dietary patterns have become more pervasive. Evidence suggests that diets emphasizing the consumption of plant-based foods might protect against asthma development and improve asthma symptoms through their effects on systemic inflammation, oxidation, and microbial composition. Additionally, increased fruit and vegetable intake, reduced animal product consumption, and weight management might mediate cytokine release, free radical damage, and immune responses involved in the development and course of asthma. The specific aim of this review paper is to examine the current literature on the associations between dietary factors and asthma risk and control in children and adults. Clinical trials examining the mechanism(s) by which dietary factors influence asthma outcomes are necessary to identify the potential use of nutritional therapy in the prevention and management of asthma.
Maternal depression in Latinas and child socioemotional development: A systematic review

Background Although substantial research exists on the debilitating effects of maternal depression on child development, little is known about Latina mothers with depression and their young children within the broader context of sociocultural and economic stressors. Objectives What is the relationship between maternal depression in Latina mothers and their children’s socioemotional outcomes through early developmental windows (0–5 years)? Methods We searched electronic databases PubMed, CINAHL, and PsycINFO in this systematic review, pre-registered via PROSPERO (CRD42019128686). Based on pre-determined criteria, we identified 56 studies and included 15 in the final sample. After extracting data, we assessed study quality with the National Heart, Lung, and Blood Institute Quality Assessment Tool for Observational Cohort and Cross-Sectional Studies. Results We found inverse correlations between maternal depression and child socioemotional outcomes; furthermore, we found evidence of a moderating and mediating role of maternal depression between contextual stressors and child outcomes. Children of U.S.-born Latina mothers had poorer developmental outcomes than children of foreign-born Latina mothers across socioemotional domains and throughout early developmental windows. Conclusions Future research must examine underlying mechanisms for the potential Latino paradox in young Latino children’s socioemotional outcomes. Policies should support mental health of Latina mothers as early as the prenatal period.
Interventions to increase the consumption of water among children: A systematic review and meta‐analysis

The aim of this study was to conduct a systematic review and meta‐analysis on the effectiveness of interventions to increase children's water consumption. A systematic literature search was conducted in seven electronic databases. Studies published in English before 18 February 2019 that evaluated any type of intervention that measured change in water consumption among children aged 2 to 12 years by applying any type of design were included. Of the 47 interventions included in the systematic review, 24 reported a statistically significant increase in water consumption. Twenty‐four interventions (17 randomized controlled trials and seven studies with other controlled designs) were included in the meta‐analysis. On average, children in intervention groups consumed 29 mL/d (confidence interval [CI] = 13–46 mL/d) more water than did children in control groups. This effect was larger in eight interventions focused specifically on diet (MD = 73 mL/d, CI = 20–126 mL/d) than in 16 interventions focused also on other lifestyle factors (MD = 15 mL/d, CI = 1–29 mL/d). Significant subgroup differences were also found by study setting and socioecological level targeted but not by children's age group, intervention strategy, or study design. In conclusion, there is evidence that, on average, lifestyle interventions can lead to small increases in children's daily water consumption. More research is needed to further understand the specific intervention elements that have the greatest effect.
An Alternative Method for Anatomy Training: Immersive Virtual Reality

The aim of this study was to investigate the effect of immersive three‐dimensional (3D) interactive virtual reality (VR) on anatomy training in undergraduate physical therapy students. A total of 72 students were included in the study. The students were randomized into control (n = 36) and VR (n = 36) group according to the Kolb Learning Style Inventory, sex, and Purdue Spatial Visualization Test Rotations (PSVT‐R). Each student completed a pre‐intervention and post‐intervention test, consisting of 15 multiple‐choice questions. There was no significant difference between the two groups in terms of age, sex, Kolb Learning Style Inventory distribution, and the PSVT‐R (P > 0.05). The post‐test scores were significantly higher compared to pre‐test scores in both the VR group (P < 0.001) and the control group (P < 0.001). The difference between the pre‐test and post‐test results was found to be significantly higher in favor of the VR group (P < 0.001). In this study, anatomy training with a 3D immersive VR system was found to be beneficial. These results suggest that VR systems can be used as an alternative method to the conventional anatomy training approach for health students.
miRNA–mRNA Integrated Analysis Reveals Roles for miRNAs in a Typical Halophyte, Reaumuria soongorica, during Seed Germination under Salt Stress

MicroRNAs (miRNAs) are endogenous small RNAs that play a crucial role in plant growth, development, and environmental stress responses. Reaumuria soongorica is a typical halophyte that is widely distributed in saline–alkali desert regions. Under salt stress, R. soongorica can complete germination, a critical biological process in the life cycle of seed plants. To identify miRNAs and predict target mRNAs involved in seed germination during salt stress, nine small-RNA libraries were constructed and analyzed from R. soongorica seeds treated with various concentrations of NaCl. We also obtained transcriptome data under the same treatment conditions. Further analysis identified 88 conserved miRNAs representing 25 defined families and discovered 13 novel miRNAs from nine libraries. A co-expression analysis was performed on the same samples to identify putative miRNA–mRNA interactions that were responsive to salt stress. A comparative analysis of expression during germination under 273 (threshold) and 43 mM (optimal) NaCl treatments identified 13 differentially expressed miRNAs and 23 corresponding target mRNAs, while a comparison between 43 mM NaCl and non-salt-stress conditions uncovered one differentially expressed miRNA and one corresponding target mRNA. These results provide basic data for further study of molecular mechanisms involved in the germination of salt-stressed R. soongorica seeds, and also provide a reference for the improvement of salt tolerance during plant germination.
Draft Genome Sequence of Marinobacter hydrocarbonoclasticus NCT7M, Obtained from the Microbiome of a Marine Copepod

The gammaproteobacterium Marinobacter hydrocarbonoclasticus NCT7M was cultivated from the copepod Acartia tonsa, collected from the coastal western North Atlantic Ocean. The genome was assembled into 45 contigs for a total of 4,128,590 bp, a GC content of 57.3%, and 3,890 protein-coding genes. The genome contains the full gene cluster for denitrification. ABSTRACT The gammaproteobacterium Marinobacter hydrocarbonoclasticus NCT7M was cultivated from the copepod Acartia tonsa, collected from the coastal western North Atlantic Ocean. The genome was assembled into 45 contigs for a total of 4,128,590 bp, a GC content of 57.3%, and 3,890 protein-coding genes. The genome contains the full gene cluster for denitrification.
The DLO Hi-C Tool for Digestion-Ligation-Only Hi-C Chromosome Conformation Capture Data Analysis

It is becoming increasingly important to understand the mechanism of regulatory elements on target genes in long-range genomic distance. 3C (chromosome conformation capture) and its derived methods are now widely applied to investigate three-dimensional (3D) genome organizations and gene regulation. Digestion-ligation-only Hi-C (DLO Hi-C) is a new technology with high efficiency and cost-effectiveness for whole-genome chromosome conformation capture. Here, we introduce the DLO Hi-C tool, a flexible and versatile pipeline for processing DLO Hi-C data from raw sequencing reads to normalized contact maps and for providing quality controls for different steps. It includes more efficient iterative mapping and linker filtering. We applied the DLO Hi-C tool to different DLO Hi-C datasets and demonstrated its ability in processing large data with multithreading. The DLO Hi-C tool is suitable for processing DLO Hi-C and in situ DLO Hi-C datasets. It is convenient and efficient for DLO Hi-C data processing.
Compensatory changes in villus morphology of lactating Mus musculus in response to insufficient dietary protein

ABSTRACT Energetic challenges match intestinal size to dietary intake but less is known about how the intestine responds to specific macronutrient challenges. We examined how intestinal size responds to insufficient dietary protein at the microscopic level. Villi, enterocytes and surface area were measured across the length of the small intestine in non-reproductive and lactating Mus musculus fed isocaloric control or protein-deficient diets. Lactating mice on the protein-deficient diet exhibited a 24% increase in villus height and a 30% increase in enterocyte width in the proximal small intestine and an overall similar increase in surface area; on the control diet, changes in villus height were localized in the mid region. Flexibility localized to the proximal small intestine suggests that enterokinase, a localized enzyme, may be a candidate enzyme that promotes compensation for a protein-deficient diet. Such flexibility could allow species to persist in the face of anthropogenically induced changing dietary profiles. Summary: Insufficient dietary protein is linked to changes in enterocyte morphology resulting in increased villus height and absorptive surface in lactating mice; this flexibility may support compensatory protein assimilation through increased production of duodenally localized enzymes.
Is quality of healthcare improving in the US

Politicians and healthcare administrators have touted that under their leadership enormous strides have been made in the quality of healthcare. However, the question of how to measure quality remains ambiguous. To demonstrate improved quality that is meaningful to patients, outcomes such as life expectancy, mortality, and patient satisfaction must be validly and reliably measured. Dramatic improvements made in many of these patient outcomes through the twentieth century have not been sustained through the twenty-first. Most studies have shown no, or only modest improvements in the past several years, and at a considerable increase in cost. These data suggest that the rate of healthcare improvement is slowing and that many of the quality improvements touted have not been associated with improved outcomes.