Miracle-dz/UniFAR-FTUs huggingface dataset:
The role of CT-scan in the diagnosis and prognosis of COVID-19 in a sample of Iraqi patients referred to Al-Diwaniyah Teaching Hospital, Iraq

The respiratory system is the primary target of the SARS-CoV-2 virus, leading to clinical manifestations such as dry cough, fever, and shortness of breath. Other reported manifestations include generalized weakness, dizziness, headache, vomiting, and diarrhea. A chest CT scan is one of the best imaging tools to screen and diagnose COVID-19. This prospective observational study was conducted at Al-Diwaniyah Teaching Hospital in the mid-Euphrates region of Iraq to assess the prognostic role of chest CT examinations in COVID-19 patients between February 2020 and July the 15th, 2020. The study included 100 patients suspected of COVID-19 based on clinical features and microbiological investigations, comprising 72 males and 28 females aged between 30 and 55. All patients were SARS-CoV-2 PCR positive and had no history of chronic lung disease. We categorized patients into two groups based on changes in density and lesion area: patients with changes (n=55) and patients without changes (n=45). Furthermore, we divided all patients into three groups according to treatment requirements and symptom severity: group 1 included patients with severe symptoms who required CPAP and admission to the Respiratory Care Unit, group 2 consisted of patients with moderate symptoms who needed oxygen therapy and hospital admission, and group 3 comprised patients with mild symptoms who were treated as outpatients with medication. Upon correlating the change in density and lesion area with these groups, we observed that most patients with no changes were in group 1, while patients with changes were predominantly seen in group 2. Additionally, the ratio of lesion area in the mediastinal CT window to lung CT was identified as a potential prognostic factor for COVID-19 patients.
Selective RNAi-silencing of Schwann cell Piezo1 alleviates mechanical hypersensitization following peripheral nerve injury

Abstract We previously reported functional Piezo1 expression in Schwann cells of the peripheral nervous system. This study is designed to further investigate the role of Schwann cell Piezo1 in peripheral nociception. We first developed an adeno-associated viral (AAV) vector that has primary Schwann cell tropism after delivery into the sciatic nerve. This was achieved by packing AAV-GFP transcribed by a hybrid CMV enhancer/chicken β-actin (CBA) promoter using a capsid AAVolig001 to generate AAVolig001-CBA-GFP. Five weeks after intrasciatic injection of AAVolig001-CBA-GFP in naïve rats, GFP expression was detected selectively in the Schwann cells of the sciatic nerve. A short hairpin RNA against rat Piezo1 (PZ1shRNA) was designed that showed efficient physical and functional knockdown of Piezo1 in NG108 neuronal cells. A dual promoter and bidirectional AAV encoding a U6-driven PZ1shRNA and CBA-transcribed GFP was packed with capsid olig001 (AAVolig001-PZ1shRNA), and AAV was injected into unilateral sciatic nerve immediately after induction of common peroneal nerve injury (CPNI). Results showed that the development of mechanical hypersensitivity in the CPNI rats injected with AAVolig001-PZ1shRNA was mitigated, compared to rats subjected with AAVolig001-scramble. Selective in vivo Schwann cell transduction and functional block of Piezo1 channel activity of primary cultured Schwann cells was confirmed. Together, our data demonstrate that 1) AAVolig001 has unique and selective primary tropism to Schwann cells via intrasciatic delivery and 2) Schwann cell Piezo1 contributes to mechanical hypersensitivity following nerve injury.
Efficacy of water application of a humic substance, butyric acid, vitamins C, D, and E and/or electrolytes on performance and mortality in health-challenged nursery pigs¹

Abstract Health challenges continue to be rampant in nursery pigs which has led to increased industry-wide mortality trends. Therefore, the objective of these three studies was to evaluate a water supplement (HV; HydraVantage, Kent Nutrition Group, Muscatine, IA) which is a proprietary blend of a humic substance, butyric acid, and vitamins C, D, and E, as well as an electrolyte blend on nursery pig performance and mortality. Experiment 1 consisted of 196 crossbred weanling pigs (7 pigs per pen with 14 pens per treatment) which were randomly allotted by BW to two treatments consisting of control (water for 33 d) or HV at 15 g/L of stock solution and proportioned through a medicator (1:128) for 11 d followed by water for 22 d. There were no performance differences. However, mortality was reduced (P < 0.01) from 6.12% for the control to 0.00% for HV. In experiment 2, there were 488 weanling pigs (6 to 10 pigs/pen with 14 pens per treatment) which were randomly allotted by BW to four treatments in a 34-d trial. Treatment 1 was control (water), and treatments 2 and 4 were HV at 15 g/L of stock solution for 11 and 34 d, respectively. Treatment 3 utilized HV at 15 g/L stock solution during days 0 to 11 with 7.5 g HV/L stock solution utilized during days 11 to 21 followed by water. No performance differences were observed among the four treatments. Mortality was 10.89%, 4.82%, 5.54%, and 7.26% for treatments 1 to 4, respectively, with treatment 1 having a higher mortality (P < 0.05) compared to treatments 2 to 4. In experiment 3, a 2 × 2 factorial study was conducted (7 pigs per pen with 14 pens per treatment) in which the treatments were: 1) water; 2) HV at 15 g/L stock solution for 34 d; 3) electrolytes at 241 g/L stock solution for 34 d; and 4) HV at 15 g/L of stock solution and electrolytes at 226 g/L of stock for 34 d. Overall pen gain tended to be improved (P = 0.09) with supplemental HV. Moreover, mortality was reduced (P = 0.06) by 36% (16.86% mortality for treatments 1 and 3 vs. 10.73% mortality for treatments 2 and 4). Supplemental electrolytes had no effect on mortality. These data suggest that HV has a positive effect by reducing mortality in nursery pigs undergoing health challenges.
The data quality and applicability of a Danish prehospital electronic health record: A mixed-methods study

Background Without accurate documentation, it can be difficult to assess the quality of care and the impact of quality improvement initiatives. Prehospital lack of documentation of the basic measurements is associated with a twofold risk of mortality. The aim of this study was to investigate data quality in the electronic prehospital patient record (ePPR) system in the Region of Southern Denmark. In addition, we investigated ambulance professionals’ attitudes toward the use of ePPR and identified barriers and facilitators to its use. Method We used an explanatory sequential mixed-methods design. Phase one consisted of a retrospective assessment of the data quality of ePPR information, and phase two included semi-structured interviews with ambulance professionals combined with observations. We included patients who were acutely transported to an emergency department by ambulance in the Region of Southern Denmark from 2016 to 2020. Data completeness was calculated for each vital sign using a two-way table of frequency. Vital signs were summarised to calculate data correctness. Interviews and observations were analysed using thematic analysis. Results Overall, an improvement in data completeness and correctness was observed from 2016–2020. When stratified by age group, children (<12 years) accounted for the majority of missing vital sign registrations. In the thematic analysis, we identified four themes; ambulance professionals’ attitudes, emergency setting, training and guidelines, and tablet and software. Conclusion We found high data quality, but there is room for improvement. The ambulance professionals’ attitudes toward the ePPR, working in an emergency setting, a notion of insufficient training in completing the ePPR, and challenges related to the tablet and software could be barriers to data completeness and correctness. It would be beneficial to include the end-user when developing an ePPR system and to consider that the tablet should be used in emergency situations.
Mammalian cells internalize bacteriophages and use them as a resource to enhance cellular growth and survival

There is a growing appreciation that the direct interaction between bacteriophages and the mammalian host can facilitate diverse and unexplored symbioses. Yet the impact these bacteriophages may have on mammalian cellular and immunological processes is poorly understood. Here, we applied highly purified phage T4, free from bacterial by-products and endotoxins to mammalian cells and analyzed the cellular responses using luciferase reporter and antibody microarray assays. Phage preparations were applied in vitro to either A549 lung epithelial cells, MDCK-I kidney cells, or primary mouse bone marrow derived macrophages with the phage-free supernatant serving as a comparative control. Highly purified T4 phages were rapidly internalized by mammalian cells and accumulated within macropinosomes but did not activate the inflammatory DNA response TLR9 or cGAS-STING pathways. Following 8 hours of incubation with T4 phage, whole cell lysates were analyzed via antibody microarray that detected expression and phosphorylation levels of human signaling proteins. T4 phage application led to the activation of AKT-dependent pathways, resulting in an increase in cell metabolism, survival, and actin reorganization, the last being critical for macropinocytosis and potentially regulating a positive feedback loop to drive further phage internalization. T4 phages additionally down-regulated CDK1 and its downstream effectors, leading to an inhibition of cell cycle progression and an increase in cellular growth through a prolonged G1 phase. These interactions demonstrate that highly purified T4 phages do not activate DNA-mediated inflammatory pathways but do trigger protein phosphorylation cascades that promote cellular growth and survival. We conclude that mammalian cells are internalizing bacteriophages as a resource to promote cellular growth and metabolism.
Transcriptomic Analysis Pipeline (TAP) for quality control and functional assessment of transcriptomes

Abstract Background RNA-sequencing (RNA-seq) has revolutionized the exploration of biological mechanisms, shedding light on the roles of non-coding RNAs, including long non-coding RNAs (lncRNAs), across various biological processes, including stress responses. Despite these advancements, there remains a gap in our understanding of the implications of different RNA-seq library protocols on comprehensive lncRNA expression analysis, particularly in non-mammalian organisms. Results In this study, we sought to bridge this knowledge gap by investigating lncRNA expression patterns in Drosophila melanogaster under thermal stress conditions. To achieve this, we conducted a comparative analysis of two RNA-seq library protocols: polyA + RNA capture and rRNA-depletion. Our approach involved the development and application of a Transcriptome Analysis Pipeline (TAP) designed to systematically assess both the technical and functional dimensions of RNA-seq, facilitating a robust comparison of these library protocols. Our findings underscore the efficacy of the polyA + protocol in capturing the majority of expressed lncRNAs within the Drosophila melanogaster transcriptome. In contrast, rRNA-depletion exhibited limited advantages in the context of D. melanogaster studies. Notably, the polyA + protocol demonstrated superior performance in terms of usable read yield and the accurate detection of splice junctions. Conclusions Our study introduces a versatile transcriptomic analysis pipeline, TAP, designed to uniformly process RNA-seq data from any organism with a reference genome. It also highlights the significance of selecting an appropriate RNA-seq library protocol tailored to the specific research context.
Reduced graphene oxide-embedded nerve conduits loaded with bone marrow mesenchymal stem cell-derived extracellular vesicles promote peripheral nerve regeneration

[INLINE:1] Microglia-mediated inflammatory responses have been shown to play a crucial role in Parkinson’s disease. In addition, exosomes derived from mesenchymal stem cells have shown anti-inflammatory effects in the treatment of a variety of diseases. However, whether they can protect neurons in Parkinson’s disease by inhibiting microglia-mediated inflammatory responses is not yet known. In this study, exosomes were isolated from human umbilical cord mesenchymal stem cells and injected into a 6-hydroxydopamine-induced rat model of Parkinson’s disease. We found that the exosomes injected through the tail vein and lateral ventricle were absorbed by dopaminergic neurons and microglia on the affected side of the brain, where they repaired nigral-striatal dopamine system damage and inhibited microglial activation. Furthermore, in an in vitro cell model, pretreating lipopolysaccharide-stimulated BV2 cells with exosomes reduced interleukin-1β and interleukin-18 secretion, prevented the adoption of pyroptosis-associated morphology by BV2 cells, and increased the survival rate of SH-SY5Y cells. Potential targets for treatment with human umbilical cord mesenchymal stem cells and exosomes were further identified by high-throughput microRNA sequencing and protein spectrum sequencing. Our findings suggest that human umbilical cord mesenchymal stem cells and exosomes are a potential treatment for Parkinson’s disease, and that their neuroprotective effects may be mediated by inhibition of excessive microglial proliferation.
Higher Concentration of Marijuana Dispensaries in Neighborhoods with More Disadvantage Following Legalization in Washington

Abstract Washington is one of 21 states that have legalized recreational marijuana resulting in neighborhoods that have experienced a change in physical environment with the emergence of dispensaries. This study examines the selection of dispensaries into disadvantage area, incorporating local policies and neighborhood characteristics. Marijuana and alcohol sales data were from the Washington State Liquor and Cannabis Board; and neighborhood characteristics were drawn from the American Community Survey 2010–2016 5-year estimates. Using factor analysis we created a neighborhood disadvantage index where census tracts were stratified into disadvantaged tertiles; and counties were stratified by urban/rural status. We examined the association between dispensaries, neighborhood characteristics, and local marijuana policies using Negative Binomial Regression with a natural log of land area as an offset, separately for 2014–2016. Dispensaries opened in high-disadvantaged CTs in 2014 and then dispersed across the state while retaining higher concentrations in disadvantaged urban CTs. Marijuana-specific policies (allotted dispensaries and retail cap) were found to be predictors of marijuana dispensary density. This study provides evidence that marijuana dispensaries were disproportionately located in areas with greater disadvantage. State and local marijuana policies emerged as important predictors, underscoring the importance of designing thoughtful and equitable license allocation procedures and policies.
Voluntary sports programs for individuals with mental health disorders: The trainer’s view

There is strong evidence that physical activities (PAs) are an important factor in increasing and maintaining mental health as well as in preventing relapse after mental health disorders. Physical activity is an important part of the treatment program in psychiatric hospitals. However, when individuals with mental health disorders (IMHD) leave the hospitals in Switzerland (CH), there are few possibilities to do physical activity in a given setting. One of them are voluntary sports groups for individuals with mental health disorders (SGPSY), which have been growing continuously in CH since 2016. Yet, little is known about these groups and their training settings. Therefore, the present study explores challenges, barriers, and enablers for participation in SGPSY from the point of view of the trainers of these groups. Additionally, as the sustainable implementation of SGPSY relies on the trainer, the study aims to identify reasons/motivations as well as the personality characteristics of the SGPSY trainers. Semi-structured interviews were conducted with 15 trainers of SGPSY in CH during spring 2022. Interviews were audiotaped, transcribed, and analyzed using thematic analysis in nVivo. Participants identified several intrapersonal (lack of motivation and fitness, mood problems, etc.), interpersonal (conflicts between participants), and structural barriers (time/location) that hinder IMHD from participating in SGPSY. The participating trainer reported that trainer might be helpful in overcoming the barriers by supporting IMHD as enablers. They rate social skills to be essential for the successful management and organization of SGPSY, as well as the ability to set boundaries to protect one’s private life and sports skills expertise. The reasons for their engagement as trainers of SGPSY were the satisfaction of doing sports with IMHD and to improve the physical activities habits of IMHD. The findings of the study highlight the need to upskill the trainers of SGPSY in order to improve recruitment of the future trainers of SGPSY by focusing on the assessment of appropriate personality characteristics of trainers and their motives. Additionally, these findings should be integrated in the educational materials of Swiss disabled sports systems. Further research should validate the results from SGPSY participants’ point of view.
Centella asiatica promotes antioxidant gene expression and mitochondrial oxidative respiration in experimental autoimmune encephalomyelitis

Abstract Centella asiatica (Centella) is a traditional botanical medicine that shows promise in treating dementia based on behavioral alterations seen in animal models of aging and cognitive dysfunction. In order to determine if Centella could similarly improve cognitive function and reduce disease burden in multiple sclerosis (MS), we tested its effects in the neuroinflammatory experimental autoimmune encephalomyelitis (EAE) model of MS. In two independent experiments, C57BL/6J mice were treated following induction of EAE with either a standardized water extract of Centella (CAW) or placebo for 2 weeks. At the dosing schedule and concentrations tested, CAW did not improve behavioral performance, EAE motor disability, or degrees of demyelination. However, CAW-treated mice demonstrated increases in nuclear factor (erythroid-derived 2)-like 2 and other antioxidant response element genes, and increases in mitochondrial respiratory activity. Caw also decreased spinal cord inflammation. Our findings indicate that CAW can increase antioxidant gene expression and mitochondrial respiratory activity in mice with EAE, supporting investigation of the clinical effects of CAW in people with MS.
Modelling SPM on the NW European shelf seas

Abstract The Proudman Oceanographic Laboratory Coastal Ocean Modelling System (POLCOMS) has been developed to tackle multidisciplinary studies in coastal/shelf environments. The central core is a sophisticated three-dimensional hydrodynamic model that provides realistic flow fields to interact with, and transport environmental parameters. The model uses realistic forcing with ocean currents and hydrography at the boundary, atmospheric forcing and tides. Suspended particulate matter (SPM) is transported within the water, like any other scalar in the model; it is advected using a high-order scheme and mixed vertically using diffusion coefficients from a second moment turbulence closure. In addition, the SPM transport is influenced by a number of processes unique to this problem, such as: the transfer between the lowest level of the model and the bed layer in which the resuspension and deposition takes place is dependent on the erosion rate, the particle settling velocity and the critical stresses for erosion and deposition. The particular application described in this paper is an annual simulation for the NW European shelf for a single sediment class. The simulation shows the expected seasonal variation in spatial patterns and a clear tidal signal in the SPM resuspension. Also evident is a fortnightly/monthly variability due to the spring-neaps and the M2-N2 cycles. There are also quarter-diurnal and semi-diurnal cycles in SPM, due to tidal resuspension and advection respectively. The above tidal suspension behaviour, as well as, the net transport direction are in agreement with historical observations of SPM.
Allelic effects on uromodulin aggregates drive autosomal dominant tubulointerstitial kidney disease

Missense mutations in the uromodulin (UMOD) gene cause autosomal dominant tubulointerstitial kidney disease (ADTKD), one of the most common monogenic kidney diseases. The unknown impact of the allelic and gene dosage effects and fate of mutant uromodulin leaves open the gap between postulated gain‐of‐function mutations, end‐organ damage and disease progression in ADTKD. Based on two prevalent missense UMOD mutations with divergent disease progression, we generated UmodC171Y and UmodR186S knock‐in mice that showed strong allelic and gene dosage effects on uromodulin aggregates and activation of ER stress and unfolded protein and immune responses, leading to variable kidney damage. Deletion of the wild‐type Umod allele in heterozygous UmodR186S mice increased the formation of uromodulin aggregates and ER stress. Studies in kidney tubular cells confirmed differences in uromodulin aggregates, with activation of mutation‐specific quality control and clearance mechanisms. Enhancement of autophagy by starvation and mTORC1 inhibition decreased uromodulin aggregates. These studies substantiate the role of toxic aggregates as driving progression of ADTKD‐UMOD, relevant for therapeutic strategies to improve clearance of mutant uromodulin.
Conformity to Masculinity Norms and Mental Health Outcomes Among Gay, Bisexual, Trans, Two-Spirit, and Queer Men and Non-Binary Individuals

Homophobia and biphobia negatively impact the mental health of gay, bisexual, trans, Two-Spirit, and queer men and non-binary individuals (GBT2Q) and sexual and gender minority men, but little is known about the impact of gender-related oppression. The current study examines the impact of pressure to conform to masculine norms in Canada-based GBT2Q individuals. Specifically, the associations between (a) gender expression and pressure to be masculine and (b) pressure to be masculine and depression, anxiety, and self-rated mental health were investigated. Drawing from an online national cross-sectional survey of 8,977 GBT2Q individuals and sexual and gender minority men living in Canada aged 15 years or older, 56.4% (n = 5,067) of respondents reported experiencing pressure to conform to masculine norms. Respondents were more likely to report masculine pressure if they were younger than 30 years, described their gender expression as fluid, identified their sexuality as queer, were an ethnoracial minority, and were trans. Pressure to be masculine was associated with increased odds of depression, anxiety, and reporting poor or fair mental health. The current study provides evidence of the detrimental impact of pressure to conform to masculine norms on the mental health of gay, bisexual, trans, Two-Spirit, and queer men and non-binary peoples.