Miracle-dz/UniFAR-FTUs huggingface dataset:
Core self-evaluations as resilience and risk factors of psychological distress during the COVID-19 pandemic

ABSTRACT In view of the grave consequences of distress reactions to the COVID-19 pandemic, this study investigated CSE (Core Self-evaluations) – internal/external health locus of control, generalized self-efficacy and trait optimism – and intolerance of uncertainty as potential correlates of distress reactions. We conducted an online questionnaire-based cross-sectional study with 422 Israeli respondents. Pandemic-related distress was defined by perceived stress, negative and positive affect, and worries. Predictors were: health locus of control, generalized self-efficacy, trait optimism, and intolerance of uncertainty. The findings show that CSEs and intolerance of uncertainty added between 11% (to perceived stress) and 22% (to negative affect) of explained variance beyond the background variables. Specifically, higher trait optimism and generalized self-efficacy were associated with less distress, and greater intolerance of uncertainty was correlated with higher distress. In conclusion, the CSE framework is useful for explaining psychological distress during the COVID-19 pandemic. Beyond their theoretical contribution, the findings may have practical implications for increasing resilience and ameliorating distress during a pandemic.
A simple guide to de novo transcriptome assembly and annotation

Abstract A transcriptome constructed from short-read RNA sequencing (RNA-seq) is an easily attainable proxy catalog of protein-coding genes when genome assembly is unnecessary, expensive or difficult. In the absence of a sequenced genome to guide the reconstruction process, the transcriptome must be assembled de novo using only the information available in the RNA-seq reads. Subsequently, the sequences must be annotated in order to identify sequence-intrinsic and evolutionary features in them (for example, protein-coding regions). Although straightforward at first glance, de novo transcriptome assembly and annotation can quickly prove to be challenging undertakings. In addition to familiarizing themselves with the conceptual and technical intricacies of the tasks at hand and the numerous pre- and post-processing steps involved, those interested must also grapple with an overwhelmingly large choice of tools. The lack of standardized workflows, fast pace of development of new tools and techniques and paucity of authoritative literature have served to exacerbate the difficulty of the task even further. Here, we present a comprehensive overview of de novo transcriptome assembly and annotation. We discuss the procedures involved, including pre- and post-processing steps, and present a compendium of corresponding tools.
Biomimicking interfacial fracture behavior of lizard tail autotomy with soft microinterlocking structures

Biological soft interfaces often exhibit complex microscale interlocking geometries to ensure sturdy and flexible connections. If needed, the interlocking can rapidly be released on demand leading to an abrupt decrease of interfacial adhesion. Here, inspired by lizard tail autotomy where such apparently tunable interfacial fracture behavior can be observed, we hypothesized an interlocking mechanism between the tail and body based on the muscle-actuated mushroom-shaped microinterlocks along the fracture planes. To mimic the fracture behavior of the lizard tail, we developed a soft bilayer patch that consisted of a dense array of soft hemispherical microstructures in the upper layer acting as mechanical interlocks with the counter body part. The bottom control layer contained a microchannel that allowed to deflect the upper layer when applying the negative pressure, thus mimicking muscle contraction. In the microinterlocked condition, the biomimetic tail demonstrated a 2.7-fold and a three-fold increase in adhesion strength and toughness, respectively, compared to the pneumatically released microinterlocks. Furthermore, as per the computational analysis, the subsurface microchannel in the control layer enabled augmented adhesion by rendering the interface more compliant as a dissipative matrix, decreasing contact opening and strain energy dissipation by 50%. The contrasting features between the microinterlocked and released cases demonstrated a highly tunable adhesion of our biomimetic soft patch. The potential applications of our study are expected in soft robotics and prosthetics.
Perpendicular magnetization anisotropy induced dynamical coherence reduction in stripe domain film

We investigated the magnetization dynamics of the 350 nm permalloy film with in plane domain (IPD), stripe domain (SD), and labyrinth domain (LD) patterns. Experimental and micromagnetic simulation results showed that the change in magnetic domain structure from IPD to LD was due to the increasing perpendicular magnetic anisotropy (PMA) of the film. The magnetization dynamics indicated that the resonant modes of the film strongly depended on the magnetic domain structure. IPD films presented a uniform precession mode. The film with well-regular SD exhibited clear acoustic and optical resonance modes, and the formation of LD suppressed both resonance modes. Finally, the dynamics of magnetization dependent on the domain structure in these films were discussed by using the phenomenological resonance models.
Effects of a physical activity intervention on schoolchildren fitness

The global prevalence of childhood obesity is high. Obesity main causes are linked to sedentary lifestyles. Increasing physical activity (PA) and reducing sedentary activities are recommended to prevent and treat obesity. This study aimed to evaluate the effectiveness of a 6‐month school PA intervention on obesity prevention and healthy behaviors in school‐aged children. Participating students (10–11 years of age) were randomly divided into an intervention group and a control group. Children in the intervention group (n = 80) participated in a multicomponent PA that included improvement in extracurricular physical activities (with an additional 40 min per day for 5/6 days per week). Children (n = 80) in the control group participated in usual practice. Participants had mean body mass index of 19.7 ± 2.9 kg/m2, and 33.7% of them were overweight or with obesity at T0. The change in body mass index in intervention group (−2.4 ± 0.6 kg/m2) was significantly different from that in control group (3.01 ± 1.8 kg/m2). The effects on waist circumference, waist‐to‐height ratio, and physic fitness were also significant in intervention group compared with control group (all p < 0.05). Furthermore, there is a significant decrease in overweight or children with obesity in the experimental group (to 17.5%, p < 0.05). These findings suggest that a school‐based intervention program represents an effective strategy for decreasing the number of overweight and children with obesity.
Homozygous missense variant in POPDC3 causes recessive limb‐girdle muscular dystrophy type 26

Limb‐girdle muscular dystrophy (LGMD) comprises a heterogeneous group of diseases, affecting different muscles, predominantly skeletal muscles and cardiac muscles of the body. LGMD is classified into two main subtypes A and B, which are further subclassified into eight dominant and thirty recessive subtypes. Three genes, namely POPDC1, POPDC2 and POPDC3, encode popeye domain‐containing protein (POPDC), and the variants of POPDC1 and POPDC3 genes have been associated with LGMD.
Application of the Buccal Fat Pad in Oral Reconstruction: Covered With Collagen Membrane or Not?

Objective: To evaluate the clinical effectiveness of collagen membrane as biological dressing in protecting the covered buccal fat pad (BFP) from physical damage during postoperative healing phase in the reconstruction of oral soft tissue defect. Methods: A retrospective cohort study was performed in patients undergoing oral defects reconstruction using BFP. The predictor variable was the application of collagen membrane or not. The primary outcome variable was the wound healing. Other variables considered included age, gender, pain score, time taken for epithe-lialization, defect size and site. Postoperative follow-up was done at 1 week, 3 weeks, 6 months, and 1 year. Results: Thirty patients in Zhuhai People’s Hospital were selected and randomly divided in 2 groups. Group i patients were reconstructed using BFP alone, whereas collagen membrane was used as a covering over BFP in group II patients. In group I, 4 patients developed dehiscence 1-week postoperative, and underwent infection with food lodgment along with another 1 patient at 3-week follow-up, whereas none of the group II patients developed dehiscence or infection. Pain score was lesser in group II patients as compared to group I. Time taken for epithelialization was about 3 weeks in both groups. Conclusions: Combined application of collagen membrane protects the covered BFP from masticatory physical damage and food lodgment, which reduces infection and graft loss. It is worthy of consideration as an effective method for the reconstruction of selected moderate-sized oral defects, especially in larger size or at distant location.
Short Breastfeeding Duration is Associated With Premature Onset of Female Breast Cancer

Currently, there is controversy concerning potential factors that contribute to the development of breast cancer. Our study analyzed the possible association between weight status, cigarette consumption, lactation period, serum estrogen levels, family history of breast cancer, and age at breast cancer diagnosis. We conducted a retrospective study at a University Hospital in Granada (Spain) by consulting the medical records of 524 women aged 19 to 91 years, all of them diagnosed and treated for breast cancer from 2011 to 2019. Our findings indicated that in non-morbidly obese females who were also non-smokers, a maternal lactation period of more than 3 months (p = .013) and the absence of family antecedents of cancer (p = .025) were statistically significant factors that led to a more advanced age at breast cancer diagnosis. Thus, maternal lactation seems to have a potential protective effect on breast cancer.
Plasma metabolomics study reveals the critical metabolic signatures for benzene-induced hematotoxicity

Metabolomics has been used to explore the molecular mechanism and screen biomarkers. However, the critical metabolic signatures associated with benzene-induced hematotoxicity remain elusive. Here, we performed a plasma metabolomics study in 86 benzene-exposed workers and 76 healthy controls, followed by a validation analysis in mice, to investigate the dynamical change of the metabolic profile. We found that 8 fatty acids were significantly altered in both benzene-exposed worker and benzene-exposed animal models. These metabolites were significantly associated with S-phenylmercapturic acid and WBC, and they mediated the benzene-induced WBC decline. Furthermore, in vivo results confirm that fatty acid levels were dynamically altered, characterized by a decrease at 15 days and then sharp increases at 30 and 45 days. Following these identified fatty acids, the potential metabolic pathways were investigated. Fatty acids, as precursors for fatty acid oxidation, may disturb the balance of fatty acid biosynthesis and degradation. Our results reveal that fatty acid metabolism was strongly reprogrammed after benzene exposure. This abnormal change of fatty acids might be the key metabolic signature associated with benzene-induced hematotoxicity.
Orbital Volume and Axial Length Development in Individuals Ages 12 to 60 Years With Congenital Microphthalmia: A Retrospective Cohort Study

Objective: To analyze the stimulating effect of axial length development on orbital volume development in patients (ages 12–60 years) with congenital microphthalmia. Methods: This retrospective cohort study included 43 patients (86 eyes) with congenital microphthalmia. Three-dimensional images of the orbit were generated from past computed tomography scans, and digital orbital volume and axial length measurements were taken. The patients were divided into four age groups for analyses. Paired t tests and one-way analysis of variance tests were used to compare orbital volume and axial length between the affected and unaffected eyes. Pearson correlation analyses and scatter plots were used to investigate the correlations between age, orbital volume, and axial length in the affected and unaffected eyes. Linear regression analysis was used to determine the association between orbital volume and axial length. Results: The mean orbital volume in the affected and unaffected eyes was 17.08 ± 2.88 and 20.80 ± 2.55 cm3, respectively. The mean axis length in the affected and the unaffected groups was 12.73 ± 3.54 and 23.84 ± 1.43 mm, respectively. Significant differences were observed among orbital (t = 13.538, P < 0.001) volume and axial length (t = 21.339, P < 0.001) in the affected and the unaffected groups. There were no significant differences in affected orbital volume (F = 0.527, P > 0.05), unaffected orbital volume (F = 1.628, P > 0.05), affected axial length (F = 0.946, P > 0.05), and unaffected axial length (F = 2.217, P > 0.05) among the four age groups. According to the Pearson correlations, there were no significant correlations between age and affected volume, unaffected volume, affected axis, and unaffected axis (r = 0.095, 0.097, 0.084, and 0.022, respectively; all P > 0.05). Orbital volume was moderately correlated with axial length in the affected and unaffected groups (r = 0.470 and 0.410, respectively; both P < 0.01). Linear regression analysis revealed that a 1 mm change in axis length was associated with a 0.38 cm3 and 0.73 cm3 change in orbital volume in the affected and unaffected groups, respectively. Conclusions: In individuals ages 12 to 60 years old with congenital microphthalmia, the effect of axis length on the orbital volume growth of the affected eye is only half that of the unaffected eye. The eyeball, orbital tissue, and craniofacial development all play an important role in the growth of orbital volume.
Correlation between fall risk increasing drugs (FRIDs) and fall events at a rehabilitation hospital

Background and aim: Falls and fall-related injuries are a major public health issue which needs global attention due to its clinical and socioeconomic impact. Important risk factors for falls are polypharmacy and the assumption of so-called Fall Risk Increasing Drugs (FRIDs). Aims of our study were to investigate the associations between falls and the use of medications among inpatients by conducting a retrospective case-control study in a rehabilitation hospital in Northern Italy in 2018. Methods: A Conditional Logistic Regression was performed to analyze the impact that 13 types of FRIDs individually and the number of administrated FRIDs had on the risk of falling. A second regression model was obtained adjusting the case-control matching for CIRS, Morse and Barthel scores. Results: We identified 148 cases and 444 controls. 3 types of FRIDs were significantly correlated (p < 0,05) with an increased risk of falling: Antipsychotics, Antidepressants, Diuretics. Antidepressants were the only type of FRID significantly correlated (p=0,008) even in the model adjusted for CIRS, Morse and Barthel scores. The unadjusted model showed that the addition of one type of FRID to therapy was significantly associated with the fall event (p<0.05). Conclusion: Assumption of drugs, in particular antidepressant and polypharmacy, can play a role in hospital falling. The fall risk assessment tools available, suffer from low specificity and sensitivity and do not assess these risk factors. A holistic approach with a multidimensional evaluation of the patient through screening tools, functional assessment tools and a full medical evaluation should be pursued to improve prediction. (www.actabiomedica.it)
Brain-Wide Synaptic Inputs to Aromatase-Expressing Neurons in the Medial Amygdala Suggest Complex Circuitry for Modulating Social Behavior

Abstract Here, we reveal an unbiased view of the brain regions that provide specific inputs to aromatase-expressing cells in the medial amygdala, neurons that play an outsized role in the production of sex-specific social behaviors, using rabies tracing and light sheet microscopy. While the downstream projections from these cells are known, the specific inputs to the aromatase-expressing cells in the medial amygdala remained unknown. We observed established connections to the medial amygdala (e.g., bed nucleus of the stria terminalis and accessory olfactory bulb) indicating that aromatase neurons are a major target cell type for efferent input including from regions associated with parenting and aggression. We also identified novel and unexpected inputs from areas involved in metabolism, fear and anxiety, and memory and cognition. These results confirm the central role of the medial amygdala in sex-specific social recognition and social behavior, and point to an expanded role for its aromatase-expressing neurons in the integration of multiple sensory and homeostatic factors, which are likely used to modulate many other social behaviors.
Perfusion system for studying dynamic metabolomics in rat brain slices exposed to oxygen–glucose deprivation using proton and phosphorus nuclear magnetic resonance

The aim of the current study was to establish a controlled and reproducible model to study metabolic changes during oxygen–glucose deprivation (OGD) in rat brain using a nuclear magnetic resonance (NMR)‐compatible perfusion system. Rat brains were cut into 400‐μm thick slices and perfused with artificial cerebrospinal fluid (aCSF) in a 10‐mm NMR tube inside a 600‐MHz NMR spectrometer. Four experimental conditions were tested: (1) continuous perfusion with aCSF with glucose and normoxia, and (2) 30‐, (3) 60‐, or (4) 120‐min periods of OGD followed by reperfusion of aCSF containing glucose and normoxia. The energetic state of perfused brain slices was measured using phosphorus (31P) NMR and metabolite changes were measured using proton (1H) NMR. aCSF samples were collected every 30 min and analyzed using 1H NMR. The sample temperature was maintained at 36.7 ± 0.1°C and was checked periodically throughout the experiments. Brain slice histology was compared before and after OGD in the perfusion system using hematoxylin–eosin–saffron staining. NMR data clearly distinguished three severity groups (mild, moderate, and severe) after 30, 60, and 120 min of OGD, respectively, compared with the control group. 31P NMR spectra obtained from controls showed that phosphocreatine levels were stable for 5 h inside the perfusion system. Control 1H NMR spectra showed that lactate, N‐acetylaspartic acid, glutamate, γ‐aminobutyric acid, and creatine metabolite levels were stable over time, with lactate levels having a tendency to gradually increase due to the recirculation of the aCSF in the perfusion system. A controlled and reproducible perfusion system was established to study the energetic and metabolic changes in rat brain slices during and after OGD of varying severity.
A multiplex real-time PCR assay for differential identification of avian Chlamydia

ABSTRACT Avian chlamydiosis is an acute or chronic disease of birds after infection by Chlamydia. Although Chlamydia psittaci is the primary agent of the disease, two additional species, Chlamydia avium and Chlamydia gallinacea, have also been recognized as potential disease agents. Therefore, the diagnosis of avian chlamydiosis requires differential identification of these avian Chlamydia species. The objective of the present study was to develop a multiplex real-time polymerase chain reaction (PCR) assay to rapidly differentiate between these three species of avian Chlamydia (C. psittaci, C. avium, and C. gallinacea) as well as to detect the genus Chlamydia. Specific genetic regions of the three species were identified by comparative analysis of their genome sequences. Also, the genus-specific region was selected based on 23S rRNA sequences. PCR primers and probes specific to the genus and each species were designed and integrated in the multiplex real-time PCR assay. The assay was highly efficient (94.8–100.7%). It could detect fewer than 10 copies of each target sequence of the genus and each species. Twenty-five Chlamydia control and field DNA samples were differentially identified while 20 other bacterial strains comprising 10 bacterial genera were negative in the assay. This assay allows rapid, sensitive, and specific detection of the genus and the three species of avian Chlamydia in a single protocol that is suitable for routine diagnostic purposes in avian diagnostic laboratories.
Rapid urine-based screening tests increase the yield of same-day tuberculosis diagnoses among patients living with advanced HIV disease

Objective: Investigation of the diagnostic yield of urine-based tuberculosis (TB) screening in patients with advanced HIV disease. Design: A cross-sectional screening study Setting: HIV outpatient clinics and wards at two hospitals in Johannesburg, South Africa, between June 2015 and October 2017. Participants: Two hundred and one patients living with advanced HIV disease (CD4+ T-lymphocytes <100 cells/μl) attending healthcare facilities following cryptococcal antigen (CrAg) screening. Intervention: Screening for TB using sputum for microscopy, culture, and Xpert MTB/Rif and urine for lipoarabinomannan (LAM) and Xpert Ultra. Main outcome measures: Proportion of positive results using each testing modality, sensitivity, and specificity of urine-based testing compared with culture, and survival outcomes during 6 months follow up. Results: Urine was obtained from 177 of 181 (98%) participants and sputum from 91 (50%). Urine-based screening increased same-day diagnostic yield from 7 (4%) to 31 (17%). A positive urine test with either LAM or Xpert Ultra had 100% sensitivity (95% confidence interval, 59–100%) for detecting culture-positive TB at any site. Patients with newly diagnosed TB on urine-based screening were initiated on treatment and did not have excess mortality compared with the remainder of the cohort. Conclusion: Urine is an easily obtainable sample with utility for detecting TB in patients with advanced HIV disease. Combining urine and sputum-based screening in this population facilitates additional same-day TB diagnoses and early treatment initiation, potentially reducing the risk of TB-related mortality. Urine-based as well as sputum-based screening for TB should be integrated with CrAg screening in patients living with advanced HIV disease.
Types, management and complications in paediatric distal radial fractures sustained during COVID-19 lockdown

In response to the coronavirus pandemic the British Orthopaedic Association Standards for Trauma and Orthopaedics (BOAST) guidelines advised treating distal radial fractures non-operatively where possible. A cohort was studied retrospectively to assess whether the COVID pandemic lockdown within the UK altered types, the management and complications of paediatric distal radial fractures. The cohort studied comprised of 194 paediatric distal radial fractures in the pre-COVID cohort and 101 fractures in the COVID cohort. There was no significant differences in the type of fractures in the two cohorts. Significantly more high energy injuries were sustained among the COVID cohort than the pre-COVID (p < 0.001). The COVID cohort had significantly more patients managed in cast (p < 0.001) and significantly more managed with K-wire fixation (p = 0.049). The COVID cohort had significantly more complications (p = 0.016) at minimum 10-month follow-up. The results suggest that treatment of paediatric distal radial fractures during lockdown was too conservative and subsequent complications may put additional strain on orthopaedic services. Level of evidence: IV