Miracle-dz/UniFAR-FTUs huggingface dataset:
The RD‐Connect Genome‐Phenome Analysis Platform: Accelerating diagnosis, research, and gene discovery for rare diseases

Rare disease patients are more likely to receive a rapid molecular diagnosis nowadays thanks to the wide adoption of next‐generation sequencing. However, many cases remain undiagnosed even after exome or genome analysis, because the methods used missed the molecular cause in a known gene, or a novel causative gene could not be identified and/or confirmed. To address these challenges, the RD‐Connect Genome‐Phenome Analysis Platform (GPAP) facilitates the collation, discovery, sharing, and analysis of standardized genome‐phenome data within a collaborative environment. Authorized clinicians and researchers submit pseudonymised phenotypic profiles encoded using the Human Phenotype Ontology, and raw genomic data which is processed through a standardized pipeline. After an optional embargo period, the data are shared with other platform users, with the objective that similar cases in the system and queries from peers may help diagnose the case. Additionally, the platform enables bidirectional discovery of similar cases in other databases from the Matchmaker Exchange network. To facilitate genome‐phenome analysis and interpretation by clinical researchers, the RD‐Connect GPAP provides a powerful user‐friendly interface and leverages tens of information sources. As a result, the resource has already helped diagnose hundreds of rare disease patients and discover new disease causing genes.
Development and Evaluation of a Web-Based Educational Toolkit on the Knowledge, Attitudes, and Practices of Psychiatric Prescribers Regarding Long-Acting Injectable Antipsychotics

Background: Long-acting injectable antipsychotics (LAIs) are unique and effective pharmacological treatment options for schizophrenia that are underutilized in clinical practice. Research surrounding prescriber barriers to the underuse of LAIs are limited to a few seminal studies which identified psychiatric prescriber barriers to the use of LAIs as knowledge deficits, uninformed attitudes, and poor prescribing practices. There is a gap in the literature regarding effective educational interventions to target the identified psychiatric prescriber barriers to the use of LAIs. Aims: The study aimed to develop a web-based educational toolkit that would positively affect the knowledge, attitudes, and practices of psychiatric prescribers regarding LAIs. Methods: A one-group, before and after design with a convenience, purposive sample of 17 psychiatric prescribers to assess the knowledge, attitudes, and practices (KAP) using a 20-item KAP questionnaire before and after a presentation of a web-based educational toolkit about LAIs was chosen. Results: The web-based educational toolkit slightly improved the total and three subscales KAP scores of psychiatric prescribers. However, only the difference in total KAP scores was found to be statistically significant. Conclusions: The developed and evaluated web-based educational toolkit could provide a foundation for positive change to psychiatric prescribers’ KAP regarding LAIs.
L-Carnitine alleviates hepatic and renal mitochondrial-dependent apoptotic progression induced by letrozole in female rats through modulation of Nrf-2, Cyt c and CASP-3 signaling

Abstract Letrozole (LTZ) is a non-steroidal aromatase inhibitor that is commonly used in breast cancer therapy. It has several side effects that might lead to the drug's cessation and data of LTZ's potential adverse effects on the hepatorenal microenvironment was conflicting. In addition, searching for therapeutic interventions that could modulate its adverse effects will be very beneficial. So, this study aims to determine the impact of LTZ on the hepatorenal microenvironment in cyclic female rats with a proposed regulatory role of L-Carnitine (LC) supplementation giving molecular insights into its possible mechanism of action. LTZ (1 mg/kg using 0.5% carboxy methyl cellulose as a vehicle for 21 consecutive days orally) to assess its impact on hepatorenal microenvironment. After treatment with LC (100 mg/kg orally) for 14 days, hepatorenal redox state (lipid peroxides (MDA), reduced glutathione (GSH) and catalase enzyme (CAT)), as well as relative gene expression of nuclear factor erythroid 2-related factor 2 (Nrf-2), cytochrome-c (Cyt c) and caspase-3 (CASP-3) were evaluated. Histopathological examination and immunohistochemical staining of CASP-3 in both liver and kidney were done. LTZ altered hepatic and renal functions. Relative gene expression of hepatorenal Nrf-2, Cyt c and CASP-3 as well as redox state revealed significant deterioration. Also, the liver and kidney tissues showed several micromorphological changes and intense reaction to CASP-3 upon immunohistochemical staining. It can be concluded that LC alleviates LTZ induced hepatorenal oxidative stress (OS) and mitochondrial-dependent apoptotic progression through modulation of Nrf-2, Cyt c, and CASP-3 signaling in female rats.
Erythroid Differentiation of Induced Pluripotent Stem Cells Co-cultured with OP9 Cells for Diagnostic Purposes

Background Reagent red blood cells (RBCs) are prepared from donated whole blood, resulting in various combinations of blood group antigens. This inconsistency can be resolved by producing RBCs with uniform antigen expression. Induced pluripotent stem cells (iPSCs) generated directly from mature cells constitute an unlimited source for RBC production. We aimed to produce erythroid cells from iPSCs for diagnostic purposes. We hypothesized that cultured erythroid cells express surface antigens that can be recognized by blood group antibodies. Methods iPSCs were co-cultured with OP9 stromal cells to stimulate differentiation into the erythroid lineage. Cell differentiation was examined using microscopy and flow cytometry. Hemoglobin electrophoresis and oxygen-binding capacity testing were performed to verify that the cultured erythroid cells functioned normally. The agglutination reactions of the cultured erythroid cells to antibodies were investigated to confirm that the cells expressed blood group antigens. Results The generated iPSCs showed stemness characteristics and could differentiate into the erythroid lineage. As differentiation progressed, the proportion of nucleated RBCs increased. Hemoglobin electrophoresis revealed a sharp peak in the hemoglobin F region. The oxygen-binding capacity test results were similar between normal RBCs and cultured nucleated RBCs. ABO and Rh-Hr blood grouping confirmed similar antigen expression between the donor RBCs and cultured nucleated RBCs. Conclusions We generated blood group antigen-expressing nucleated RBCs from iPSCs co-cultured with OP9 cells that can be used for diagnostic purposes. iPSCs from rare blood group donors could serve as an unlimited source for reagent production.
Frontal Eye Fields in Macaque Monkeys: Prefrontal and Premotor Contributions to Visually Guided Saccades.

Neuronal spiking was sampled from the frontal eye field (FEF) and from the rostral part of area 6 that reaches to the superior limb of the arcuate sulcus, dorsal to the arcuate spur when present (F2vr) in macaque monkeys performing memory-guided saccades and visually guided saccades for visual search. Neuronal spiking modulation in F2vr resembled that in FEF in many but not all respects. A new consensus clustering algorithm of neuronal modulation patterns revealed that F2vr and FEF contain a greater variety of modulation patterns than previously reported. The areas differ in the proportions of visuomotor neuron types, the proportions of neurons discriminating a target from distractors during visual search, and the consistency of modulation patterns across tasks. However, between F2vr and FEF we found no difference in the magnitude of delay period activity, the timing of the peak discharge rate relative to saccades, or the time of search target selection. The observed similarities and differences between the 2 cortical regions contribute to other work establishing the organization of eye fields in the frontal lobe and may help explain why FEF in monkeys is identified within granular prefrontal area 8 but in humans is identified within agranular premotor area 6.
Testing an mHealth System for Individuals With Mild to Moderate Alcohol Use Disorders: Protocol for a Type 1 Hybrid Effectiveness-Implementation Trial

Background The extent of human interaction needed to achieve effective and cost-effective use of mobile health (mHealth) apps for individuals with mild to moderate alcohol use disorder (AUD) remains largely unexamined. This study seeks to understand how varying levels of human interaction affect the ways in which an mHealth intervention for the prevention and treatment of AUDs works or does not work, for whom, and under what circumstances. Objective The primary aim is to detect the effectiveness of an mHealth intervention by assessing differences in self-reported risky drinking patterns and quality of life between participants in three study groups (self-monitored, peer-supported, and clinically integrated). The cost-effectiveness of each approach will also be assessed. Methods This hybrid type 1 study is an unblinded patient-level randomized clinical trial testing the effects of using an evidence-based mHealth system on participants’ drinking patterns and quality of life. There are two groups of participants for this study: individuals receiving the intervention and health care professionals practicing in the broader health care environment. The intervention is a smartphone app that encourages users to reduce their alcohol consumption within the context of integrative medicine using techniques to build healthy habits. The primary outcomes for quantitative analysis will be participant data on their risky drinking days and quality of life as well as app use from weekly and quarterly surveys. Cost measures include intervention and implementation costs. The cost per participant will be determined for each study arm, with intervention and implementation costs separated within each group. There will also be a qualitative assessment of health care professionals’ engagement with the app as well as their thoughts on participant experience with the app. Results This protocol was approved by the Health Sciences Minimal Risk Institutional Review Board on November 18, 2019, with subsequent annual reviews. Recruitment began on March 6, 2020, but was suspended on March 13, 2020, due to the COVID-19 pandemic restrictions. Limited recruitment resumed on July 6, 2020. Trial status as of November 17, 2021, is as follows: 357 participants were enrolled in the study for a planned enrollment of 546 participants. Conclusions The new knowledge gained from this study could have wide and lasting benefits related to the integration of mHealth systems for individuals with mild to moderate AUDs. The results of this study will guide policy makers and providers toward cost-effective ways to incorporate technology in health care and community settings. Trial Registration ClinicalTrials.gov NCT04011644; https://clinicaltrials.gov/ct2/show/NCT04011644 International Registered Report Identifier (IRRID) DERR1-10.2196/31109
Constitutive nuclear accumulation of endogenous alpha-synuclein in mice causes motor impairment and cortical dysfunction, independent of protein aggregation

Abstract A growing body of evidence suggests that nuclear alpha-synuclein (αSyn) plays a role in the pathogenesis of Parkinson’s disease (PD). However, this question has been difficult to address as controlling the localization of αSyn in experimental systems often requires protein overexpression, which affects its aggregation propensity. To overcome this, we engineered SncaNLS mice, which localize endogenous αSyn to the nucleus. We characterized these mice on a behavioral, histological and biochemical level to determine whether the increase of nuclear αSyn is sufficient to elicit PD-like phenotypes. SncaNLS mice exhibit age-dependent motor deficits and altered gastrointestinal function. We found that these phenotypes were not linked to αSyn aggregation or phosphorylation. Through histological analyses, we observed motor cortex atrophy in the absence of midbrain dopaminergic neurodegeneration. We sampled cortical proteomes of SncaNLS mice and controls to determine the molecular underpinnings of these pathologies. Interestingly, we found several dysregulated proteins involved in dopaminergic signaling, including Darpp32, Pde10a and Gng7, which we further confirmed was decreased in cortical samples of the SncaNLS mice compared with controls. These results suggest that chronic endogenous nuclear αSyn can elicit toxic phenotypes in mice, independent of its aggregation. This model raises key questions related to the mechanism of αSyn toxicity in PD and provides a new model to study an underappreciated aspect of PD pathogenesis.
The generalized Fisher's combination and accurate p‐value calculation under dependence

Combining dependent tests of significance has broad applications but the related p‐value calculation is challenging. For Fisher's combination test, current p‐value calculation methods (eg, Brown's approximation) tend to inflate the type I error rate when the desired significance level is substantially less than 0.05. The problem could lead to significant false discoveries in big data analyses. This paper provides two main contributions. First, it presents a general family of Fisher type statistics, referred to as the GFisher, which covers many classic statistics, such as Fisher's combination, Good's statistic, Lancaster's statistic, weighted Z‐score combination, and so forth. The GFisher allows a flexible weighting scheme, as well as an omnibus procedure that automatically adapts proper weights and the statistic‐defining parameters to a given data. Second, the paper presents several new p‐value calculation methods based on two novel ideas: moment‐ratio matching and joint‐distribution surrogating. Systematic simulations show that the new calculation methods are more accurate under multivariate Gaussian, and more robust under the generalized linear model and the multivariate t‐distribution. The applications of the GFisher and the new p‐value calculation methods are demonstrated by a gene‐based single nucleotide polymorphism (SNP)‐set association study. Relevant computation has been implemented to an R package GFisher available on the Comprehensive R Archive Network.
Cell migration orchestrates migrasome formation by shaping retraction fibers

Fan et al. quantitatively dissect the decisive regulation of migration paradigm (persistence and velocity) to the formation of the migrasome, a cellular organelle with vesicle-like morphology that mediates migracytosis. Their work adds up our current understanding of the role of cell behavior in migrasome studies.
Spatial Separation of Cocatalysts on Z‐Scheme Organic/Inorganic Heterostructure Hollow Spheres for Enhanced Photocatalytic H2 Evolution and In‐Depth Analysis of the Charge‐Transfer Mechanism

A Z‐scheme heterojunction with spatially separated cocatalysts is proposed for overcoming fundamental issues in photocatalytic water splitting, such as inefficient light absorption, charge recombination, and sluggish reaction kinetics. For efficient light absorption and interfacial charge separation, Z‐scheme organic/inorganic heterojunction photocatalysts are synthesized by firmly immobilizing ultrathin g‐C3N4 on the surface of TiO2 hollow spheres via electrostatic interactions. Additionally, two cocatalysts, Pt and IrOx, are spatially separated along the Z‐scheme charge‐transfer pathway to enhance surface charge separation and reaction kinetics. The as‐prepared Pt/g‐C3N4/TiO2/IrOx (PCTI) hollow sphere photocatalyst exhibits an exceptional H2 evolution rate of 8.15 mmol h−1 g−1 and a remarkable apparent quantum yield of 24.3% at 330 nm in the presence of 0.5 wt% Pt and 1.2 wt% IrOx cocatalysts on g‐C3N4 and TiO2, respectively. Photoassisted Kelvin probe force microscopy is used to systematically analyze the Z‐scheme charge‐transfer mechanism within PCTI. Furthermore, the benefits of spatially separating cocatalysts in the PCTI system are methodically investigated in comparison to randomly depositing them. This work adequately demonstrates that the combination of a Z‐scheme heterojunction and spatially separated cocatalysts can be a promising strategy for designing high‐performance photocatalytic platforms for solar fuel production.
Liquid-Phase Microextraction Approaches for Preconcentration and Analysis of Chiral Compounds: A Review on Current Advances

Abstract Chirality is a critical issue in pharmaceutics, forensic chemistry, therapeutic drug monitoring, doping control, toxicology, or environmental investigations as enantiomers of a chiral compound can exhibit different activities, i.e., one enantiomer can have the desired effect while the other one can be inactive or even toxic. To monitor enantioselective metabolism or toxicokinetic/toxicodynamic mechanisms in extremely low content in biological or environmental matrices, sample preparation is vital. The present review describes current status of development of liquid-phase microextraction approaches such as hollow fiber liquid-phase microextraction (HF-LPME), electromembrane extraction (EME), dispersive liquid-liquid microextraction (DLLME), and supramolecular solvent-based microextraction (SSME), used for sample preparation of enantiomers/chiral compounds. The advantages and limitations of the above techniques are discussed. Attention is also focused on chiral separation approaches commonly applied to study the stereo-selective metabolism or toxicokinetic/toxicodynamic mechanisms of enantiomers in the biological and environmental samples.
Sex life and sexuality among tongqi: doing gender and heterosexuality

Abstract The term tongqi refers to cisgender, heterosexual women who unwittingly marry non-straight men. In mainland China, their adverse social position and health have been the subject of concern. This study aims to broaden and diversify perceptions of the lived experiences of tongqi by focusing on sex and sexualities in mixed-orientation marriages. Four themes (lack of sexuality-related exploration before marriage, the unsatisfactory nature of marital sex life, the exercise of sexual agency, and increased self-awakening) were developed from observations of a tongqi online support group and 12 semi-structured interviews with members. Using inductive thematic analysis, findings reveal how heteronormativity oppresses and punishes both tongqi and their non-straight husbands. In most cases, husbands not ‘doing heterosexuality’ as expected were still found to be ‘doing gender’ in patriarchal ways, with wives’ subordinate status thereby being reinforced, making them more vulnerable. However, despite women’s sexual autonomy and agency being constrained by normative forces, some were able to navigate their conjugal relationships by practising sexual autonomy and agency within and outside their marriage.
Clinicians’ perspectives on equity of access to dialysis and kidney transplantation for rural people in Australia: a semistructured interview study

Objectives People with chronic kidney disease requiring dialysis or kidney transplantation in rural areas have worse outcomes, including an increased risk of hospitalisation and mortality and encounter many barriers to accessing kidney replacement therapy. We aim to describe clinicians’ perspectives of equity of access to dialysis and kidney transplantation in rural areas. Design Qualitative study with semistructured interviews. Setting and participants Twenty eight nephrologists, nurses and social workers from 19 centres across seven states in Australia. Results We identified five themes: the tyranny of distance (with subthemes of overwhelming burden of travel, minimising relocation distress, limited transportation options and concerns for patient safety on the roads); supporting navigation of health systems (reliance on local champions, variability of health literacy, providing flexible models of care and frustrated by gatekeepers); disrupted care (without continuity of care, scarcity of specialist services and fluctuating capacity for dialysis); pervasive financial distress (crippling out of pocket expenditure and widespread socioeconomic disadvantage) and understanding local variability (lacking availability of safe and sustainable resources for dialysis, sensitivity to local needs and dependence on social support). Conclusions Clinicians identified geographical barriers, dislocation from homes and financial hardship to be major challenges for patients in accessing kidney replacement therapy. Strategies such as telehealth, outreach services, increased service provision and patient navigators were suggested to improve access.
Isolating and cryopreserving pig skin cells for single-cell RNA sequencing study

The pig skin architecture and physiology are similar to those of humans. Thus, the pig model is very valuable for studying skin biology and testing therapeutics. The single-cell RNA sequencing (scRNA-seq) technology allows quantitatively analyzing cell types, compositions, states, signaling, and receptor-ligand interactome at single-cell resolution and at high throughput. scRNA-seq has been used to study mouse and human skins. However, studying pig skin with scRNA-seq is still rare. A critical step for successful scRNA-seq is to obtain high-quality single cells from the pig skin tissue. Here we report a robust method for isolating and cryopreserving pig skin single cells for scRNA-seq. We showed that pig skin could be efficiently dissociated into single cells with high cell viability using the Miltenyi Human Whole Skin Dissociation kit and the Miltenyi gentleMACS Dissociator. Furthermore, the obtained single cells could be cryopreserved using 90% FBS + 10% DMSO without causing additional cell death, cell aggregation, or changes in gene expression profiles. Using the developed protocol, we were able to identify all the major skin cell types. The protocol and results from this study are valuable for the skin research scientific community.
Long-term outcomes after repair for anomalous right coronary artery from the pulmonary artery

Abstract Anomalous right coronary artery from pulmonary artery (ARCAPA) is a rare congenital heart disease that can lead to abnormal coronary perfusion and a need for surgical repair. Here, we report the outcomes of patients who underwent ARCAPA surgery within the Pediatric Cardiac Care Consortium (PCCC), a North American registry of interventions for paediatric heart diseases. We queried the PCCC for patients undergoing surgical repair for ARCAPA at <18 years of age between 1982 and 2003. Outcomes were obtained from the PCCC and after linkage with the National Death Index (NDI) and the Organ Procurement and Transplantation Network (OPTN) through 2019. Twenty-four patients (males: 15) were identified having surgery for ARCAPA at a median age of 5.8 (IQR 2.7–10.3) years. Of them, 23 cases were considered “simple” (without major intracardiac disease) and one “complex” (co-existing with tetralogy of Fallot). Five patients presented with symptoms [chest pain (1), dyspnoea on exertion (2) or history of syncope (2)]; while the remaining 19 patients were referred for evaluation of either murmur or co-existing CHD. There was no in-hospital mortality after the surgical repair. Fourteen patients had sufficient identifiers for NDI/OPTN linkage; among them, only one death occurred from unrelated non-cardiac causes within a median period of 19.4 years of follow-up (IQR: 18–24.6). Outcomes were excellent after reimplantation up to 25 years later and further longitudinal monitoring is important to understand the interaction of pre-existing coronary pathology with the effects of ageing.