Miracle-dz/UniFAR-FTUs huggingface dataset:
Investigating the relationship between breath aerosol size and exhaled breath condensate (EBC) metabolomic content

Exhaled breath aerosols contain valuable metabolomic content due to gas exchange with blood at the alveolar capillary interface in the lung. Passive and selective filtering of these aerosols and droplets may reduce the amount of saliva contaminants and serve as an aid to enhance targeted metabolomic content when sampled in exhaled breath condensate (EBC). It is currently unknown if breath aerosol size distribution affects the types or abundances of metabolites sampled through EBC. This pilot study uses a previously described hand-held human breath sampler device with varying notch filter geometries to redirect the trajectory of breath aerosols based on size. Ten notch filter lengths were simulated with the device to calculate the effect of filter length on the breath aerosol size distribution and the proportion of aerosols which make their way through to an EBC collection tube. From three notch filter lengths, we investigate metabolite content of various aerosol fractions. We analyzed the non-volatile fraction of breath condensate with high performance liquid chromatography-mass spectrometry for broad metabolite coverage. We hypothesize that: (1) increasing the length of the notch filter in this device will prevent larger aerosols from reaching the collection tube thus altering the breath aerosol size distribution sampled in EBC; and (2) there is not a systematic large-scale difference in EBC metabolomic content that correlates with breath aerosol size. From simulation results, particles typically larger than 10 µm were filtered out. This indicates that a longer notch filter in this device prevents larger particles from reaching the collection tube thus altering the aerosol particle size distribution. Most compounds were commonly present in all three filter lengths tested, and we did not see strong statistical evidence of systematic metabolite differences between breath aerosol size distributions.
Bench Press Load-Velocity Profiles and Strength After Overload and Taper Microcyles in Male Powerlifters.

Williams, TD, Esco, MR, Fedewa, MV, and Bishop, PA. Bench press load-velocity profiles and strength after overload and taper microcyles in male powerlifters. J Strength Cond Res XX(X): 000-000, 2020-The purpose of this study was to quantify the effect of an overload microcycle and taper on bench press velocity and to determine if the load-velocity relationship could accurately predict 1-repetition maximum (1RM). Twelve male powerlifters participated in resistance training structured into an introduction microcycle, overload microcycle (PostOL), and taper (PostTP). At the end of each microcycle, subjects completed a bench press for 1RM assessment consisting of warm-up sets at 40, 55, 70, and 85% of a previously established 1RM. The mean concentric velocity (MCV) was recorded during each warm-up set. A predicted 1RM (p1RM) was calculated using an individualized load-velocity profile (LVP). The average MCV decreased after PostOL (0.66 ± 0.07 m·s) compared with baseline (BL) (p = 0.003; 0.60 ± 0.11 m·s) but increased after PostTP (0.67 ± 0.09 m·s). One-repetition maximum increased from PostOL (146.7 ± 19.8 kg) to PostTP (p = 0.002; 156.1 ± 21.0 kg), with no differences observed between other test sessions (p > 0.05). Bland-Altman analysis indicated that p1RM was consistently higher than measured 1RM (3.4-7.8 kg), and the limits of agreement were extremely wide. However, very large to near perfect correlations (r = 0.89 to 0.96) were observed between p1RM and 1RM during BL, PostOL, and PostTP. The load-velocity relationship established from submaximal sets did not accurately predict 1RM, but MCV was affected by changes in weekly training loads. Velocity-based measurements seem to be more sensitive to changes in training loads than maximal strength.
Physical and Occupational Therapy Staffing Patterns in Nursing Homes and Their Association with Long-stay Resident Outcomes and Quality of Care

ABSTRACT The purpose of this study is to examine Physical Therapy (PT) and Occupational Therapy (OT) staffing patterns in nursing homes and understand their relationship with quality performance. Bivariate analyses between PT/OT staffing and facility characteristics were performed to understand staffing patterns and random effects regressions were run to explore the link between therapy staff and quality. Findings suggest PT/OT staff have a positive influence on resident outcomes and therapy staffing patterns significantly differ across provider attributes, including size, profit status, and occupancy rate, among others. The findings can be used to inform policymakers about potential unintended consequences resulting from changes to Medicare reimbursement policies.
A Multicompartment Human Kidney Proximal Tubule-on-a-Chip Replicates Cell Polarization–Dependent Cisplatin Toxicity

Drug-induced kidney injury is a major clinical problem and causes drug attrition in the pharmaceutical industry. To better predict drug-induced kidney injury, kidney in vitro cultures with enhanced physiologic relevance are developed. To mimic the proximal tubule, the main site of adverse drug reactions in the kidney, human-derived renal proximal tubule epithelial cells (HRPTECs) were injected in one of the channels of dual-channel Nortis chips and perfused for 7 days. Tubes of HRPTECs demonstrated expression of tight junction protein 1 (zona occludens-1), lotus lectin, and primary cilia with localization at the apical membrane, indicating an intact proximal tubule brush border. Gene expression of cisplatin efflux transporters multidrug and toxin extrusion transporter (MATE) 1 (SLC47A1) and MATE2-k (SLC47A2) and megalin endocytosis receptor increased 19.9 ± 5.0–, 23.2 ± 8.4–, and 106 ± 33–fold, respectively, in chip cultures compared with 2-dimensional cultures. Moreover, organic cation transporter 2 (OCT2) (SLC22A2) was localized exclusively on the basolateral membrane. When infused from the basolateral compartment, cisplatin (25 µM, 72 hours) induced toxicity, which was evident as reduced cell number and reduced barrier integrity compared with vehicle-treated chip cultures. Coexposure with the OCT2 inhibitor cimetidine (1 mM) abolished cisplatin toxicity. In contrast, infusion of cisplatin from the apical compartment did not induce toxicity, which was in line with polarized localization of cisplatin uptake transport proteins, including OCT2. In conclusion, we developed a dual channel human kidney proximal tubule-on-a-chip with a polarized epithelium, restricting cisplatin sensitivity to the basolateral membrane and suggesting improved physiologic relevance over single-compartment models. Its implementation in drug discovery holds promise to improve future in vitro drug-induced kidney injury studies. SIGNIFICANCE STATEMENT Human-derived kidney proximal tubule cells retained characteristics of epithelial polarization in vitro when cultured in the kidney-on-a-chip, and the dual-channel construction allowed for drug exposure using the physiologically relevant compartment. Therefore, cell polarization–dependent cisplatin toxicity could be replicated for the first time in a kidney proximal tubule-on-a-chip. The use of this physiologically relevant model in drug discovery has potential to aid identification of safe novel drugs and contribute to reducing attrition rates due to drug-induced kidney injury.
Aptamer-Based Detection of Ampicillin in Urine Samples

The misuse of antibiotics in health care has led to increasing levels of drug resistant infections (DRI’s) occurring in the general population. Most technologies developed for the detection of DRI’s typically focus on phenotyping or genotyping bacterial resistance rather than on the underlying cause and spread of DRI’s; namely the misuse of antibiotics. An aptameric based assay has been developed for the monitoring of ampicillin in urine samples, for use in determining optimal antibiotic dosage and monitoring patient compliance with treatment. The fluorescently labelled aptamers were shown to perform optimally at pH 7, ideal for buffered clinical urine samples, with limits of detection as low as 20.6 nM, allowing for determination of ampicillin in urine in the clinically relevant range of concentrations (100 nM to 100 µM). As the assay requires incubation for only 1 h with a small sample volume, 50 to 150 µL, the test would fit within current healthcare pathways, simplifying the adoption of the technology.
Utility of screening tools to differentiate beta thalassemia trait and iron-deficiency anemia - do they serve a purpose in blood donors?

Background The aim of this study was to estimate the prevalence of the beta thalassemia trait (BTT) and differentiate it from iron-deficiency anemia (IDA) among blood donors. Methods A total of 1,000 samples from blood donors were subjected to complete hemogram with red blood cell indices. Further, Mentzer index (MI) was calculated for samples with mean corpuscular volume (MCV) below 80 fL and mean corpuscular hemoglobin (MCH) below 27 pg. Samples with Mentzer index <12 were subjected to naked-eye single-tube red cell osmotic fragility test (NESTROFT) followed by hemoglobin electrophoresis in positive cases. Serum ferritin was assessed in NESTROFT-negative cases. Results The prevalence of BTT among blood donors was 3.7% and that of microcytosis among donors was 8.6%. The prevalence of BTT among microcytic donors was 41.8% while that among those with IDA was 11.6%. A value of MI <13 was highly sensitive in the diagnosis of BTT. MI >13 was found to have both high specificity and high sensitivity for diagnosing IDA. Conclusion A moderately high prevalence of BTT was observed among blood donors. Presently, no screening program is mandatory for screening of BTT among blood donors. Indices like MCV, MCH, and Mentzer Index were thus found to be effective to screen for BTT and IDA among blood donors, and NESTROFT was a cost-effective mass screening method to differentiate BTT and IDA.
Electrochemical Immuno- and Aptamer-Based Assays for Bacteria: Pros and Cons over Traditional Detection Schemes

Microbiological safety of the human environment and health needs advanced monitoring tools both for the specific detection of bacteria in complex biological matrices, often in the presence of excessive amounts of other bacterial species, and for bacteria quantification at a single cell level. Here, we discuss the existing electrochemical approaches for bacterial analysis that are based on the biospecific recognition of whole bacterial cells. Perspectives of such assays applications as emergency-use biosensors for quick analysis of trace levels of bacteria by minimally trained personnel are argued.
Cells expressing PAX8 are the main source of homeostatic regeneration of adult mouse endometrial epithelium and give rise to serous endometrial carcinoma

ABSTRACT Humans and mice have cyclical regeneration of the endometrial epithelium. It is expected that such regeneration is ensured by tissue stem cells, but their location and hierarchy remain debatable. A number of recent studies have suggested the presence of stem cells in the mouse endometrial epithelium. At the same time, it has been reported that this tissue can be regenerated by stem cells of stromal/mesenchymal or bone marrow cell origin. Here, we describe a single-cell transcriptomic atlas of the main cell types of the mouse uterus and epithelial subset transcriptome and evaluate the contribution of epithelial cells expressing the transcription factor PAX8 to the homeostatic regeneration and malignant transformation of adult endometrial epithelium. According to lineage tracing, PAX8+ epithelial cells are responsible for long-term maintenance of both luminal and glandular epithelium. Furthermore, multicolor tracing shows that individual glands and contiguous areas of luminal epithelium are formed by clonal cell expansion. Inactivation of the tumor suppressor genes Trp53 and Rb1 in PAX8+ cells, but not in FOXJ1+ cells, leads to the formation of neoplasms with features of serous endometrial carcinoma, one of the most aggressive types of human endometrial malignancies. Taken together, our results show that the progeny of single PAX8+ cells represents the main source of regeneration of the adult endometrial epithelium. They also provide direct experimental genetic evidence for the key roles of the P53 and RB pathways in the pathogenesis of serous endometrial carcinoma and suggest that PAX8+ cells represent the cell of origin of this neoplasm. Summary: The study describes a single-cell transcriptomic atlas of the mouse uterus and shows that PAX8+ cells are responsible for long-term maintenance of endometrial epithelium and might represent the cell of origin of serous endometrial carcinoma.
IntAPT: integrated assembly of phenotype-specific transcripts from multiple RNA-seq profiles

MOTIVATION High-throughput RNA sequencing has revolutionized the scope and depth of transcriptome analysis. Accurate reconstruction of a phenotype-specific transcriptome is challenging due to the noise and variability of RNA-seq data. This requires computational identification of transcripts from multiple samples of the same phenotype, given the underlying consensus transcript structure. RESULTS We present a Bayesian method, Integrated Assembly of Phenotype-specific Transcripts (IntAPT), that identifies phenotype-specific isoforms from multiple RNA-seq profiles. IntAPT features a novel two-layer Bayesian model to capture the presence of isoforms at the group layer and to quantify the abundance of isoforms at the sample layer. A spike-and-slab prior is used to model the isoform expression and to enforce the sparsity of expressed isoforms. Dependencies between the existence of isoforms and their expression are modeled explicitly to facilitate parameter estimation. Model parameters are estimated iteratively using Gibbs sampling to infer the joint posterior distribution, from which the presence and abundance of isoforms can reliably be determined. Studies using both simulations and real data sets show that IntAPT consistently outperforms existing methods for the integrated assembly of phenotype-specific transcripts. Experimental results demonstrate that, despite sequencing errors, IntAPT exhibits a robust performance among multiple samples, resulting in notably improved identification of expressed isoforms of low abundance. AVAILABILITY The IntAPT package is available at http://github.com/henryxushi/IntAPT. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Development and validation of the Adverse Inpatient Medication Event model (AIME)

Medication harm has negative clinical and economic consequences, contributing to hospitalisation, morbidity and mortality. The incidence ranges from 4 to 14%, of which up to 50% of events may be preventable. A predictive model for identifying high‐risk inpatients can guide a timely and systematic approach to prioritisation. The aim of this study is to develop and internally validate a risk prediction model for prioritisation of hospitalised patients at risk of medication harm.
Comparing Clinical Characteristics of Influenza and Common Coronavirus Infections Using Electronic Health Records

Abstract Background We compared outcomes in inpatients and outpatients, pre-COVID-19, who were infected with either coronavirus or influenza. Methods Using deidentified electronic health records data from the Geisinger-Regeneron partnership, we compared patients with RT-PCR–positive tests for the 4 common coronaviruses (229E, HKU1, NL63, OC43) or influenza (A and B) from June 2016 to February 2019. Results Overall, 52 833 patients were tested for coronaviruses and influenza. For patients ≥21 years old, 1555 and 3991 patient encounters had confirmed positive coronavirus and influenza tests, respectively. Both groups had similar intensive care unit (ICU) admission rates (7.2% vs 6.1%, P = .12), although patients with coronavirus had significantly more pneumonia (15% vs 7.4%, P < .001) and higher death rate within 30 days (4.9% vs 3.0%, P < .001). After controlling for other covariates, coronavirus infection still had a higher risk of death and pneumonia than influenza (odds ratio, 1.64 and 2.05, P < .001), with no significant difference in ICU admission rates. Conclusions Common coronaviruses cause significant morbidity, with potentially worse outcomes than influenza. Identifying a subset of patients who are more susceptible to poor outcomes from common coronavirus infections may help plan clinical interventions in patients with suspected infections.
Detection and biological assessment of genome structural variation in Plasmodium falciparum

by Becky Akiko Miller There are an estimated 216 million cases of malaria worldwide resulting in 655,000 deaths. Plasmodium falciparum is the intracellular parasite responsible for the 91% of the world’s malaria morbidity and mortality burden in humans. Efforts to control and eradicate malaria have been hampered by the accelerated evolution of drug resistance in the parasite. To date, the parasite has developed resistance to all major antimalarial drugs, raising concerns about the spread of drug-resistant parasites and the ability to effectively treat malaria. Understanding the genetics and genomics of P. falciparum allows for greater biological insights into drug resistance and virulence of the parasite, allowing for more informed control decisions. The development of molecular tools to assay genomic variation in P. falciparum is crucial. A novel microarray (the CNV-SNP Array) with an optimized probe design for copy number variation and SNP genotyping in the P. falciparum genome is presented
Excessive Smartphone Use and Self-Esteem Among Adults With Internet Gaming Disorder: Quantitative Survey Study

Background Smartphone overuse can harm individual health and well-being. Although several studies have explored the relationship between problematic or excessive smartphone use and mental health, much less is known about effects on self-esteem, which is essential in having a healthy life, among adults with mental health disorders, including internet gaming disorder. Furthermore, given that smartphone usage differs by gender, little is known about gender differences in the relationship between smartphone overuse and self-esteem. Objective The objective of this study was to assess self-esteem among individuals with mental health disorders and explore the relationship with excessive smartphone use. Methods Participants were selected based on their responses to the internet gaming disorder assessment, which includes 9 items developed based on Diagnostic and Statistical Manual of Mental Disorders (Fifth Edition) criteria, from among a Korean cohort of smartphone users aged 20-40 years, resulting in a sample of 189 participants (men:120, women: 69). The Rosenberg self-esteem scale and the Korean smartphone addiction proneness scale were utilized to assess the outcome self-esteem with excessive smartphone use as the primary independent variable. Guided by the Bowlby attachment theory and prior studies, we selected several covariates. Generalized linear regression analyses, as well as subgroup analyses by gender, were performed. Results Among adults with internet gaming disorder, the average Korean smartphone addiction proneness scale score was significantly higher in women than that in men (41.30 vs. 37.94; P=.001), and excessive smartphone use was significantly more prevalent in women than it was in men (30.43% vs. 20.83%; P=.02). Our findings from the generalized linear regression analyses indicated that an increase in Korean smartphone addiction proneness scale score had a negative relationship with self-esteem among those with internet gaming disorder (β=–0.18, P=.001). Furthermore, our interaction models showed that, among those with internet gaming disorder, more men than women had lower self-esteem associated with an increase in Korean smartphone addiction proneness scale score and a high degree of smartphone overuse (β=–0.19, P=.004; β=–3.73, P<.001). Conclusions Excessive smartphone use was found to be adversely associated with self-esteem among young and middle-aged adults with internet gaming disorder; notably, more men than women were negatively influenced (regarding self-esteem) by smartphone overuse. Based on our findings, more efforts should be made to reduce excessive or problematic smartphone use by considering developing public health interventions or policy, particularly among those with mental health disorders such as internet gaming disorder.
Effect of Acoustic Radiation Force on the Distribution of Nanoparticles in Solid Tumors

Acoustic radiation force (ARF) might improve the distribution of nanoparticles (NPs) in tumors. To study this, tumors growing subcutaneously in mice were exposed to focused ultrasound (FUS) either 15 min or 4 h after the injection of NPs, to investigate the effect of ARF on the transport of NPs across the vessel wall and through the extracellular matrix. Quantitative analysis of confocal microscopy images from frozen tumor sections was performed to estimate the displacement of NPs from blood vessels. Using the same experimental exposure parameters, ARF was simulated and compared with the experimental data. Enhanced interstitial transport of NPs in tumor tissues was observed when FUS (10 MHz, acoustic power 234 W/cm2, 3.3% duty cycle) was given either 15 min or 4 h after NP administration. According to acoustic simulations, the FUS generated an ARF per unit volume of $2.0\times 10^{{6}}$ N/m3. The displacement of NPs was larger when FUS was applied 4 h after NP injection compared with after 15 min. This study shows that ARF might contribute to a modest improved distribution of NPs into the tumor interstitium.
Diversity and genotypic analysis of tick‐borne pathogens carried by ticks infesting horses in Korea

Ticks account for an extensive range of health and welfare issues in horses. In addition, tick‐borne pathogens (TBPs) limit global animal trading and equine sporting events. Here, we assess the prevalence, co‐infectivity and risk factors of TBPs in horse ticks in Korea. A total of 245 hard ticks, including 103 male and 142 female adults, were obtained from horses on Jeju Island during the spring to autumn seasons of 2013–2019. All collected ticks were identified as adult Haemaphysalis longicornis. We screened and analyzed each tick for the presence of several TBPs by polymerase chain reaction (PCR) analysis. Among the 245 ticks, we detected genes for three TBPs, Candidatus Rickettsia longicornii (22.9%), Ehrlichia canis (0.4%) and Theileria luwenshuni (0.4%), while Anaplasma spp. was not detected. TBPs were most prevalent in ticks harvested during the autumn season, and more abundant in the female than male adults. This is the first report of the genera Ehrlichia, Rickettsia and Theileria in horse ticks in Korea. TBPs in horse ticks are likely a reservoir for zoonotic transmission to other animals, including humans. Our findings demonstrate the need for further understanding of the prevalence and epidemiology of TBPs in wild and domestic animals.