Miracle-dz/UniFAR-FTUs huggingface dataset:
Let’s lower the floor: Clinical utility of the D-KEFS TMT with a forensic psychiatric inpatient population

Abstract Trail-making tests are widely used as part of neuropsychological assessments, although the prevalence of processing speed deficits in schizophrenia spectrum disorders may limit their utility when administered to this population. In response, our study sought to explore D-KEFS TMT performance among a forensic-oriented schizophrenia spectrum sample, with the goal of generating normative data to enhance the utility of the TMT with this population. Archival data was collected from a sample of patients admitted to a forensic maximum-security psychiatric facility. Analyses revealed a large percentage of individuals achieved an “impaired” result across D-KEFS TMT trials, ranging from 20% to more than 60%. The most noteworthy finding was for Number-Letter Switching, in which approximately 48% of participants performed at the floor level. Following reclassification of performance, 36% of our sample were identified as “below average,” while greater than 60% of individuals were captured as average to above average. The current analyses revealed a problematic skew in TMT performance among schizophrenia spectrum patients, in turn complicating interpretation of cognitive status as well as the ability to compare performance between patients and over time. The present adjustments account for this skew and yield more variability in standardized scoring.
Identification of an ATP/P2X7/mast cell pathway mediating ozone-induced bronchial hyperresponsiveness

Ozone is a highly reactive environmental pollutant with well-recognized adverse effects on lung health. Bronchial hyperresponsiveness (BHR) is one consequence of ozone exposure, particularly for individuals with underlying lung disease. Our data demonstrated that ozone induced substantial ATP release from human airway epithelia in vitro and into the airways of mice in vivo and that ATP served as a potent inducer of mast cell degranulation and BHR, acting through P2X7 receptors on mast cells. Both mast cell–deficient and P2X7 receptor–deficient (P2X7–/–) mice demonstrated markedly attenuated BHR to ozone. Reconstitution of mast cell–deficient mice with WT mast cells and P2X7–/– mast cells restored ozone-induced BHR. Despite equal numbers of mast cells in reconstituted mouse lungs, mice reconstituted with P2X7–/– mast cells demonstrated significantly less robust BHR than mice reconstituted with WT mast cells. These results support a model where P2X7 on mast cells and other cell types contribute to ozone-induced BHR.
Cohort profile: a national, community-based prospective cohort study of SARS-CoV-2 pandemic outcomes in the USA—the CHASING COVID Cohort study

Purpose The Communities, Households and SARS-CoV-2 Epidemiology (CHASING) COVID Cohort Study is a community-based prospective cohort study launched during the upswing of the USA COVID-19 epidemic. The objectives of the cohort study are to: (1) estimate and evaluate determinants of the incidence of SARS-CoV-2 infection, disease and deaths; (2) assess the impact of the pandemic on psychosocial and economic outcomes and (3) assess the uptake of pandemic mitigation strategies. Participants We began enrolling participants from 28 March 2020 using internet-based strategies. Adults≥18 years residing anywhere in the USA or US territories were eligible. 6740 people are enrolled in the cohort, including participants from all 50 US states, the District of Columbia, Puerto Rico and Guam. Participants are contacted regularly to complete study assessments, including interviews and dried blood spot specimen collection for serologic testing. Findings to date Participants are geographically and sociodemographically diverse and include essential workers (19%). 84.2% remain engaged in cohort follow-up activities after enrolment. Data have been used to assess SARS-CoV-2 cumulative incidence, seroincidence and related risk factors at different phases of the US pandemic; the role of household crowding and the presence of children in the household as potential risk factors for severe COVID-19 early in the US pandemic; to describe the prevalence of anxiety symptoms and its relationship to COVID-19 outcomes and other potential stressors; to identify preferences for SARS-CoV-2 diagnostic testing when community transmission is on the rise via a discrete choice experiment and to assess vaccine hesitancy over time and its relationship to vaccine uptake. Future plans The CHASING COVID Cohort Study has outlined a research agenda that involves ongoing monitoring of the incidence and determinants of SARS-CoV-2 outcomes, mental health outcomes and economic outcomes. Additional priorities include assessing the incidence, prevalence and correlates of long-haul COVID-19.
Bibliometric analysis of the keratoconus literature

ABSTRACT Clinical Relevance Clinicians, researchers funding agencies and indeed the general public can benefit from knowledge of the most highly cited papers and most impactful authors, institutions, countries and journals in the field of keratoconus. Background Bibliometrics relating to the keratoconus literature were derived to enable identification of the most impactful papers published, as well as the leading authors, institutions, countries and journals. Methods A search was undertaken of the titles of papers on the Scopus database to identify keratoconus-related articles. The 20 most highly cited papers were determined from the total list of 4,419 papers found. Rank-order lists by count were assembled for the ‘top 20ʹ in each of four categories: authors, institutions, countries and journals. A subject-specific keratoconus-related h-index (hKC-index) was derived for each constituent of each category to serve as a measure of impact in the field. The top 10 constituents of each category were ranked by hKC-index and tabulated for consideration. Results The hKC-index of the keratoconus field is 125. The 4,419 papers have been cited a total of 98,010 times, and 18.5% of these papers have never been cited. The most highly cited paper is a general review of keratoconus by Yaron Rabinowitz, who is also the most impactful author in the field (hKC = 31). The Cedars Sinai Medical Center in the United States produces the most impactful keratoconus-related papers (hKC = 36), and the United States is the most impactful country (hKC = 91). The Journal of Cataract and Refractive Surgery is the most impactful journal (hKC = 55). Conclusion Keratoconus is a topic of high interest in the clinical and scientific literature. Highly cited papers and impactful authors, institutions, countries and journals are identified.
Pain conditions and suicide attempts in military veterans: A case-control design.

OBJECTIVE Specific pain conditions such as back pain and migraines are associated with increased risk of suicide mortality after accounting for key covariates. The purpose of the current study was to assess the associations of specific pain conditions with suicide attempts. DESIGN Case-control. SETTING Veterans Health Administration (VHA). SUBJECTS Individuals who utilized VHA services with a record of a suicide attempt (n = 30,051) in Fiscal Years 2013 and 2014 were identified and propensity score matched with controls with no such record (n = 30,051). METHODS Data on pain condition diagnoses (back pain, arthritis, migraine, headaches, psychogenic pain, neuropathy, fibromyalgia) psychiatric diagnoses, medical comorbidity, and demographics were extracted from VHA medical record and suicide surveillance datasets. RESULTS Unadjusted logistic regression analyses found that each of the pain conditions were associated with suicide attempts (e.g., back pain: Odds ratio [OR]=3.25, 95% Confidence Interval [CI]=3.12-3.39). After adjusting for mental health conditions, medical comorbidity, and each of the pain conditions, the effects were attenuated across pain conditions; however, remained significant for each of the pain conditions except for fibromyalgia. Specifically, back pain (OR = 1.25, 95% CI = 1.19-1.32), migraines (OR = 1.29, 95% CI = 1.14-1.46), headaches (OR = 1.33, 95% CI = 1.19-1.48), and neuropathic pain (OR = 1.52, 95% CI = 1.33-1.74) were each associated with increased odds of a suicide attempt. Fibromyalgia was the only pain condition associated with re-attempt status (OR = 1.25, 95% CI = 1.08-1.45). CONCLUSIONS Specific pain conditions are associated with increased odds of suicide attempts even after including key covariates. LIMITATIONS Limitations of the study include the retrospective study design and lack of examination into additional variables including prescription opioid use, pain intensity, and pain duration. The case-control design also limits the ability to draw causal or temporal conclusions.
Outcomes of early repeat sweat testing in infants with cystic fibrosis transmembrane conductance regulator‐related metabolic syndrome/CF screen‐positive, inconclusive diagnosis

Reaching early and definitive diagnosis in infants with cystic fibrosis (CF) transmembrane conductance regulator‐related metabolic syndrome (CRMS)/CF screen‐positive, inconclusive diagnosis (CFSPID) is a priority of all CF newborn screening programs. Currently, sweat testing (ST) is the gold standard for CF diagnosis or exclusion. We assessed outcomes in a cohort of Italian CRMS/CFSPID infants who underwent repeat ST in the 1st year of life.
Tracheostomy in Mechanically Ventilated Patients With SARS-CoV-2-ARDS: Focus on Tracheomalacia

BACKGROUND: The SARS-CoV-2 pandemic increased the number of patients needing invasive mechanical ventilation, either through an endotracheal tube or through a tracheostomy. Tracheomalacia is a rare but potentially severe complication of mechanical ventilation, which can significantly complicate the weaning process. The aim of this study was to describe the strategies of airway management in mechanically ventilated patients with respiratory failure due to SARS-CoV-2, the incidence of severe tracheomalacia, and investigate the factors associated with its occurrence. METHODS: This retrospective, single-center study was performed in an Italian teaching hospital. All adult subjects admitted to the ICU between February 24, 2020, and June 30, 2020, treated with invasive mechanical ventilation for respiratory failure caused by SARS-CoV-2 were included. Clinical data were collected on the day of ICU admission, whereas information regarding airway management was collected daily. RESULTS: A total of 151 subjects were included in the study. On admission, ARDS severity was mild in 21%, moderate in 62%, and severe in 17% of the cases, with an overall mortality of 40%. A tracheostomy was performed in 73 (48%), open surgical technique in 54 (74%), and percutaneous Ciaglia technique in 19 (26%). Subjects who had a tracheostomy performed had, compared to the other subjects, a longer duration of mechanical ventilation and longer ICU and hospital stay. Tracheomalacia was diagnosed in 8 (5%). The factors associated with tracheomalacia were female sex, obesity, and tracheostomy. CONCLUSIONS: In our population, approximately 50% of subjects with ARDS due to SARS-CoV-2 were tracheostomized. Tracheostomized subjects had a longer ICU and hospital stay. In our population, 5% were diagnosed with tracheomalacia. This percentage is 10 times higher than what is reported in available literature, and the underlying mechanisms are not fully understood.
The relationship between personality, season, and wounding receipt in zoo‐housed Japanese macaques (Macaca fuscata): A multi‐institutional study

It is important to those managing Japanese macaques (Macaca fuscata) in captive settings to understand predictors of wounding. While studies have demonstrated that season (breeding or nonbreeding) and sex predict rates of wounding received by zoo‐housed Japanese macaques, we investigated whether individual differences in personality ratings also might explain some of the observed interindividual variance in wounding. Such patterns were previously observed in rhesus macaques (M. mulatta), such that individuals rated higher on Anxiety and Confidence received greater wounding. Here, we collected wounding data over 24 months on 48 Japanese macaques from eight AZA‐accredited zoos. Each macaque was also rated by keepers using a 26‐item personality questionnaire. Principle components analysis of these ratings revealed four personality components: Openness, Friendliness, Dominance, and Anxiety/Reactivity. The model with the best fit revealed an interaction effect between season (breeding vs. nonbreeding) and the personality component Friendliness, such that individuals rated higher on Friendliness incurred fewer wounds in the nonbreeding season. The second‐best model revealed both a main effect of the season as well as an interaction effect between season and Openness, such that macaques rated higher in Openness received more wounds in the nonbreeding season than those rated lower in Openness. Thus, as with rhesus macaques, personality mediated wounding receipt rate in Japanese macaques, although different personality components explained interindividual variance in wounding for these two species. These differences likely reflect species differences in behavior and personality structure, as well as the influence of differing management practices, highlighting the importance of species‐specific approaches for captive primate care and welfare. This study provides further support for understanding primate personality to create individualized strategies for their care.
Effectiveness of an internet‐based intervention to improve sleep difficulties in a culturally diverse sample of international students: A randomised controlled pilot study

Sleep difficulties are widespread among international students. Internet‐based interventions are suggested as a low‐threshold treatment option but may require cultural adaptation among culturally diverse populations. The present pilot study investigated the effectiveness and acceptance of an internet‐based intervention to improve sleep difficulties in international students. A total of 81 international students of 36 nationalities were randomly assigned to the intervention (n = 41) or waitlist control group (n = 40). The intervention group received immediate access to a culturally non‐adapted unguided internet‐based sleep intervention consisting of three modules based on sleep hygiene and cognitive techniques to reduce rumination. At baseline, 4 and 12 weeks after randomisation, insomnia severity, measured by the Insomnia Severity Index, and secondary outcomes (sleep quality, depression, anxiety, perceived stress, well‐being, presenteeism, mental health literacy) were assessed. Data were analysed using linear multi‐level analyses. Additionally, satisfaction and perceived cultural appropriateness of the intervention were evaluated by international students after 4 weeks, and compared with ratings of German students, who represent the original target group. Insomnia severity improved over time in the intervention group compared to the control group, revealing a significant estimated mean difference of −5.60 (Hedges’ g = 0.84, p < 0.001) after 12 weeks. Satisfaction and perceived cultural appropriateness was high and comparable to that of German students. The present study shows that a culturally non‐adapted internet‐based sleep intervention can be a low‐threshold treatment option to help meet the high demand for mental healthcare among international students. It thus indicates that cultural adaptation might not represent a precondition for providing effective internet‐based sleep interventions to this target group.
Supplementary information for article: Revealing viscoelastic bending relaxation dynamics of isolated semiflexible colloidal polymers

Simon G. Stuij, Hannah J. Jonas, Zhe Gong, Stefano Sacanna, Thomas E. Kodger, Peter G. Bolhuis, and Peter Schall Institute of Physics, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, the Netherlands van ’t Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, the Netherlands Molecular Design Institute, Department of Chemistry, New York University, 29 Washington Place, New York 10003, USA Physical Chemistry and Soft Matter, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
A single mutation weakens symbiont-induced reproductive manipulation through reductions in deubiquitylation efficiency

Significance Wolbachia are maternally transmitted bacteria that infect most insects, making them the most common endosymbionts. Wolbachia achieved this status by manipulating host reproduction. For example, many Wolbachia cause cytoplasmic incompatibility (CI) that kills uninfected embryos. In females, Wolbachia can rescue CI, promoting their spread to high frequencies in host populations. CI strength varies in nature from weak to strong. Importantly, strong CI enables Wolbachia biocontrol strategies in mosquito systems, which protect millions of individuals from arboviruses. However, theory predicts that natural selection does not act to preserve genes that cause CI, suggesting mutations may disrupt it. We show that a single naturally observed mutation weakens CI by reducing deubiquitylation. These discoveries help elucidate the molecular basis of symbiont-induced reproductive manipulations. Animals interact with microbes that affect their performance and fitness, including endosymbionts that reside inside their cells. Maternally transmitted Wolbachia bacteria are the most common known endosymbionts, in large part because of their manipulation of host reproduction. For example, many Wolbachia cause cytoplasmic incompatibility (CI) that reduces host embryonic viability when Wolbachia-modified sperm fertilize uninfected eggs. Operons termed cifs control CI, and a single factor (cifA) rescues it, providing Wolbachia-infected females a fitness advantage. Despite CI’s prevalence in nature, theory indicates that natural selection does not act to maintain CI, which varies widely in strength. Here, we investigate the genetic and functional basis of CI-strength variation observed among sister Wolbachia that infect Drosophila melanogaster subgroup hosts. We cloned, Sanger sequenced, and expressed cif repertoires from weak CI–causing wYak in Drosophila yakuba, revealing mutations suspected to weaken CI relative to model wMel in D. melanogaster. A single valine-to-leucine mutation within the deubiquitylating (DUB) domain of the wYak cifB homolog (cidB) ablates a CI-like phenotype in yeast. The same mutation reduces both DUB efficiency in vitro and transgenic CI strength in the fly, each by about twofold. Our results map hypomorphic transgenic CI to reduced DUB activity and indicate that deubiquitylation is central to CI induction in cid systems. We also characterize effects of other genetic variation distinguishing wMel-like cifs. Importantly, CI strength determines Wolbachia prevalence in natural systems and directly influences the efficacy of Wolbachia biocontrol strategies in transinfected mosquito systems. These approaches rely on strong CI to reduce human disease.
Activating HRAS mutation in a case of inverted ductal papilloma of the salivary gland

Inverted ductal papilloma (IDP) is one of the least common benign papillary/cystic neoplasms of the salivary duct system, being characterized histologically by florid hyperplasia of duct‐type epithelial cells into a cystic lumen near the orifice with occasional endophytic growth of the surface squamous epithelium along the terminus of the affected excretory duct. Given its rarity, the exact etiology of IDP remains to be defined. We herein present the first evidence of oncogenic HRAS mutation in a case of oral IDP. This finding, together with the frequent and specific BRAF mutations in sialadenoma papilliferum reported in the recent literature, supports an active role of the MAP‐kinase cascade in the pathogenesis of benign papillary neoplasms of terminal duct origin.
PeacoQC: Peak‐based selection of high quality cytometry data

In cytometry analysis, a large number of markers is measured for thousands or millions of cells, resulting in high‐dimensional datasets. During the measurement of these samples, erroneous events can occur such as clogs, speed changes, slow uptake of the sample etc., which can influence the downstream analysis and can even lead to false discoveries. As these issues can be difficult to detect manually, an automated approach is recommended. In order to filter these erroneous events out, we created a novel quality control algorithm, Peak Extraction And Cleaning Oriented Quality Control (PeacoQC), that allows for automated cleaning of cytometry data. The algorithm will determine density peaks per channel on which it will remove low quality events based on their position in the isolation tree and on their mean absolute deviation distance to these density peaks. To evaluate PeacoQC's cleaning capability, it was compared to three other existing quality control algorithms (flowAI, flowClean and flowCut) on a wide variety of datasets. In comparison to the other algorithms, PeacoQC was able to filter out all different types of anomalies in flow, mass and spectral cytometry data, while the other methods struggled with at least one type. In the quantitative comparison, PeacoQC obtained the highest median balanced accuracy and a similar running time compared to the other algorithms while having a better scalability for large files. To ensure that the parameters chosen in the PeacoQC algorithm are robust, the cleaning tool was run on 16 public datasets. After inspection, only one sample was found where the parameters should be further optimized. The other 15 datasets were analyzed correctly indicating a robust parameter choice. Overall, we present a fast and accurate quality control algorithm that outperforms existing tools and ensures high‐quality data that can be used for further downstream analysis. An R implementation is available.
Severity of SARS-CoV-2 infection and albumin levels recorded at the first emergency department evaluation: a multicentre retrospective observational study

Background The aim of this study was to investigate the association between serum albumin levels in the ED and the severity of SARS-CoV-2 infection. Methods This is a retrospective observational study conducted from 15 March 2020 to 5 April 2020 at the EDs of three different hospitals in Italy. Data from 296 patients suffering from COVID-19 consecutively evaluated at EDs at which serum albumin levels were routinely measured on patients’ arrival in the ED were analysed. Albumin levels were measured, and whether these levels were associated with the presence of severe SARS-CoV-2 infection or 30-day survival was determined. Generalised estimating equation models were used to assess the relationship between albumin and study outcomes, and restricted cubic spline (RCS) regression was used to plot the adjusted dose-effect relationship for possible clinical confounding factors. Results The mean albumin level recorded on entry was lower in patients with severe SARS-CoV-2 infection than in those whose infections were not severe (3.5 g/dL (SD 0.3) vs 4 g/dL (SD 0.5)) and in patients who had died at 30 days post-ED arrival compared with those who were alive at this time point (3.3 g/dL (SD 0.3) vs 3.8 g/dL (SD 0.4)). Albumin <3.5 g/dL was an independent risk factor for both severe infection and death at 30 days, with adjusted odd ratios of 2.924 (1.509–5.664) and 2.615 (1.131–6.051), respectively. RCS analysis indicated that there was an adjusted dose–response association between the albumin values recorded on ED and the risk of severe infection and death. Conclusion Albumin levels measured on presentation to the ED may identify patients with SARS-CoV-2 infection in whom inflammatory processes are occurring and serve as a potentially useful marker of disease severity and prognosis.