Miracle-dz/UniFAR-FTUs huggingface dataset:
Report of Low Incidence of Thrombosis with Early Prophylaxis in Hospitalized Patients with COVID-19 from Two Saudi Tertiary Centers

Background Thrombotic events can increase the COVID-19 associated disease mortality. The administration of prophylactic anticoagulants had been shown to decrease the incidence of thrombosis, mortality, and ICU admission rates in COVID-19 patients. Aims The present study investigates the rate of thrombosis with early anticoagulation prophylaxis, the various risk factors for thrombotic events, and the overall survival rate in hospitalized COVID-19 cases. Methods In this prospective observational study, 425 patients aged ≥14 years were included in the study who were hospitalized with COVID-19 related symptoms from March to October 2020 at two tertiary care hospitals in the Kingdom of Saudi Arabia. Venous thromboembolism (VTE) score was evaluated, and VTE prophylaxis was administered according to the hospital guidelines. Patients’ demographics, comorbidities, disease presentation, and sequential hematological profiles were also recorded. Samples were collected at different time points to determine the hematological profiles. Results Out of 425 with positive COVID-19 subjects, eight (1.9%) patients developed thrombosis during admission, with pulmonary embolism being the most common type. VTE prophylaxis was administered to 394 (92.7%) patients. These anticoagulants included enoxaparin (86.3%), heparin (12.7%), warfarin (0.8%) and apixaban (0.3%). Comorbid conditions were recorded in 253 (59.5%) patients. ICU admission rate was 28% (n = 119), with a median time to transfer to ICU of 1 day (r: 0-33 days). A trend of high VTE score (5.0) with ICU admission and mortality (P = <.001) was observed. The observed mortality rate for our cohort was 5.9% (25 events out of 425); however, for patients admitted in ICU, it was 16% (19 events out of 119 admissions). Conclusion We are reporting a low incidence of thrombosis in COVID-19 patients. We have demonstrated that the early administration of prophylactic anticoagulants might reduce the risk of thrombotic events and the associated mortality. We observed a higher VTE score and thrombosis in patients admitted to the ICU.
Re‐infection in COVID‐19: Do we exaggerate our worries?

Protective long‐term immunity following coronavirus disease 2019 (COVID‐19) is unclear. The study evaluated the relationship between the vaccination status and risk factors in the re‐infection of patients with a diagnosis of COVID‐19 who reported to the Public Health Management System in a province in south‐eastern Turkey.
‘I need time to start antiretroviral therapy’: understanding reasons for delayed ART initiation among people diagnosed with HIV in Lusaka, Zambia’

Abstract Introduction Rapid antiretroviral therapy (ART) initiation can improve patient outcomes such as viral suppression and prevent new infections. However, not everyone who can start ART does so immediately. Methods We conducted a qualitative study to inform interventions supporting rapid initiation in the ‘Test and Start’ era. We purposively sampled 20 adult patients living with HIV and a previous gap in care from ten health facilities in Lusaka, Zambia for interviews. We inductively analysed transcripts using a thematic, narrative approach. In their narratives, seven participants discussed delaying ART initiation. Results Drawing on messages gleaned from facility-based counselling and community information, many cited greater fear of rapid sickness or death due to imperfect adherence or treatment side effects than negative health consequences due to delayed initiation. Participants described needing time to ‘prepare’ their minds for a lifetime treatment commitment. Concerns about inadvertent HIV status disclosure during drug collection discouraged immediate initiation, as did feeling healthy, and worries about the impact of ART initiation on relationship dynamics. Conclusion Findings suggest that counselling messages should accurately communicate treatment risks, without perpetuating fear-based narratives about HIV. Identifying and managing patient-specific concerns and reasons for the ‘need for time’ may be important for supporting individuals to rapidly accept lifelong treatment. Key messages Fear-based adherence messaging in health facilities about the dangers of missing a treatment dose or changing the time when ART is taken contributes to Zambian patients’ refusals of immediate ART initiation Responsive health systems that balance a stated need for time to accept one's diagnosis and prepare to embark on a lifelong treatment plan with interventions to identify and manage patient-specific treatment related fears and concerns may support more rapid ART initiation Perceived social stigma around HIV continues to be a significant challenge for treatment initiation.
Determinants of socioeconomic and rural-urban disparities in stunting: evidence from Indonesia.

INTRODUCTION Stunting continues to be a prominent health problem in Indonesia. Stunting prevalence is higher in children from poor families or living in rural areas; however, there has been a lack of information on predictors of stunting disparities and stunting risk factors by socioeconomic status (SES) and location of residence (rural or urban). This study aims to examine the factors associated with stunting by SES and rural-urban status, and to assess determinants of stunting disparities by SES and rural-urban status in Indonesia. METHODS This study analysed data from the Indonesian Family and Life Survey (IFLS) wave 5, conducted in 2014. Data for 3887 children aged 0-59 months, including individual, family and community variables, were analysed. Stratified logistic regression was conducted to assess differences in determinants of stunting by household expenditure (poor or non-poor, representing SES) and rural-urban status. The Oaxaca-Blinder decomposition method was used to assess determinants of stunting disparities by household expenditure and rural-urban status. RESULTS The analyses showed differences in factors associated with stunting among children in rural versus urban areas, or children in poor versus non-poor households. Mother's short stature and low education level increased the odds of stunting across all groups. However, in children of families with a higher household expenditure, unhealthy snacks were a significant predictor of stunting (adjusted odds ratio (aOR) 1.23, 95% confidence interval (CI) 1.04-1.47). This finding was not found in other groups. Good sanitation significantly reduced stunting in children in families with higher household expenditure and children from urban communities. Nutrition services were significantly associated with stunting in poor children and children from urban areas. The decomposition analyses showed that differences in characteristics explained 55.35% stunting disparity by household expenditure. Meanwhile, rural-urban disparity was mostly explained by differences in responses (56.20%), with low birth weight and unexplained variables as predominant contributors. CONCLUSION There were slight differences in stunting determinants by household expenditure and rural-urban status in Indonesia. Stunting disparities were attributed to differences in characteristics and responses between the less and more advantaged populations. To improve the effectiveness of stunting reduction programs, specific interventions tailored to address the differences between the more and less advantaged population are needed.
Meditation‐based lifestyle modification in mild to moderate depression—A randomized controlled trial

Depression is a global key challenge in mental health care. The implementation of effective, low‐risk and cost‐effective interventions to reduce its disease burden is a necessity. The aim of this study was to investigate the efficacy of the new Meditation‐Based Lifestyle Modification (MBLM) program, a “second‐generation” mindfulness‐based intervention, in depressive outpatients.
Prognostic accuracy and impact of cerebral collateral status on clinical and safety outcomes in acute ischemic stroke patients receiving reperfusion therapy: a systematic meta-analysis

Background Cerebral collateral status has a potential role in mediating postreperfusion clinical and safety outcomes in acute ischemic stroke (AIS). Purpose To investigate the prognostic accuracy and impact of collateral status on clinical and safety outcomes in patients with AIS receiving reperfusion therapy. Material and Methods Studies with AIS patients treated with reperfusion therapy, collateral status assessed using Tan, ASITN/SIR, or similar collateral grading methods and data stratified according to collateral status were included. Relevant data on clinical outcomes, such as functional outcome at 90 days, mortality at 90 days, angiographic reperfusion, symptomatic intracerebral hemorrhage (sICH) and hemorrhagic transformation (HT), were collated and analyzed. Results A meta-analysis of 18 studies involving 4132 patients with AIS was conducted. Good collateral status was significantly associated with angiographic reperfusion (odds ratio [OR]=1.97, 95% confidence interval [CI]=1.38–2.80; P < 0.0001), sICH (OR=0.67, 95% CI=0.46–0.99; P = 0.042), and 90-day functional outcome (OR=3.05, 95% CI=1.78–5.24; P < 0.0001). However, its association with HT (OR=0.76, 95% CI=0.38–1.51; P = 0.425) and three-month mortality (OR=0.53, 95% CI=0.17–1.69; P = 0.280) did not reach statistical significance. The prognostic accuracy of collaterals for predicting angiographic reperfusion, HT, functional outcome (at 90 days), and mortality (at 90 days) were 63%, 49%, 66%, and 48%, respectively. Conclusion Cerebral collaterals are significantly associated with clinical and safety outcomes, albeit with a prognostic accuracy range of 48%–66%; thus, evaluation of their patency is a useful prognostic tool in patients with AIS receiving reperfusion therapy.
Contribution of skeletal muscle and serum lipids to muscle contraction induced by neuromuscular electrical stimulation in older individuals

Intramyocellular lipids (IMCL) stored in droplets in muscle cells and free fatty acids (FFA) from fat cells in the blood are the main substrates of adenosine triphosphate during continuous muscle contractions of relatively lower intensity. Although it is known that the lipid oxidative capacity decreases with aging, the effect of IMCL and FFA on muscle contraction in older individuals remains unclear. The purpose of this study was to investigate the contribution of skeletal muscle lipids and blood lipids as energy sources for muscle contraction in older individuals. Eighteen older individuals (mean age: 70.4 ± 3.5 years) underwent muscle contraction intervention induced by intermittent neuromuscular electrical stimulation (NMES) to the vastus lateralis for 30 min. Fasting blood samples were obtained and proton magnetic resonance spectroscopy (1H‐MRS) was performed before and after NMES, and the parameters (including IMCL and extramyocellular lipid [EMCL]) from 1H‐MRS, along with FFA and adiponectin levels, were analyzed using the blood samples of all participants. Levels of IMCL and EMCL did not change (p > 0.05); however, FFA and adiponectin levels decreased from 1.1 ± 0.5 mEq/L to 0.8 ± 0.2 mEq/L and 12.0 ± 5.3 μg/ml to 11.4 ± 5.0 μg/ml, after NMES (p < 0.05), respectively. These findings indicate that serum lipids, but not skeletal muscle lipids, are the energy substrate utilized during involuntary muscle contraction in older individuals.
Obesity is associated with a distinct brain-gut microbiome signature that connects Prevotella and Bacteroides to the brain’s reward center

ABSTRACT The prevalence of obesity has risen to its highest values over the last two decades. While many studies have either shown brain or microbiome connections to obesity, few have attempted to analyze the brain-gut-microbiome relationship in a large cohort adjusting for cofounders. Therefore, we aim to explore the connection of the brain-gut-microbiome axis to obesity controlling for such cofounders as sex, race, and diet. Whole brain resting state functional MRI was acquired, and connectivity and brain network properties were calculated. Fecal samples were obtained from 287 obese and non-obese participants (males n = 99, females n = 198) for 16s rRNA profiling and fecal metabolites, along with a validated dietary questionnaire. Obesity was associated with alterations in the brain’s reward network (nucleus accumbens, brainstem). Microbial diversity (p = .03) and composition (p = .03) differed by obesity independent of sex, race, or diet. Obesity was associated with an increase in Prevotella/Bacteroides (P/B) ratio and a decrease in fecal tryptophan (p = .02). P/B ratio was positively correlated to nucleus accumbens centrality (p = .03) and negatively correlated to fecal tryptophan (p = .004). Being Hispanic, eating a standard American diet, having a high Prevotella/Bacteroides ratio, and a high nucleus accumbens centrality were all independent risk factors for obesity. There are obesity-related signatures in the BGM-axis independent of sex, race, and diet. Race, diet, P/B ratio and increased nucleus accumbens centrality were independent risk factors for obesity. P/B ratio was inversely related to fecal tryptophan, a metabolite related to serotonin biosynthesis, and positively related to nucleus accumbens centrality, a region central to the brain’s reward center. These findings may expand the field of therapies for obesity through novel pathways directed at the BGM axis.
Mortality and disease related comorbidities in systemic lupus erythematosus: Data from an Egyptian cohort

Background Systemic lupus erythematosus (SLE) is a complex autoimmune disorder with significant disease-related comorbidity and considerably high mortality. Aim of the work Explore the survival rates and the spectrum of disease related comorbidities in an Egyptian cohort afflicted by SLE. Methods This is a single center observational cohort study performed in one of the leading medical Schools governmental hospitals for teaching and training in the North African region and Middle East sectors Kasr Alainy School of Medicine—Cairo University. Inclusion criteria: the investigators of the research question went for planned review of the medical records of adult SLE patients ≥16 years classified according to American College of Rheumatology (ACR) 1997 SLE classification criteria set forth by Hochberg, 1997 who received longitudinal clinical care during the time period from 1999 to 2019. Exclusion criteria: patients seen only once, other collagen vascular diseases, endocrinal, cardiovascular, or other multisystem disease diagnosed prior to the onset of SLE. Data analysis Survival was determined from the time of SLE diagnosis to the last contact or date of death. The cumulative probability of survival was estimated using Kaplan–Meier method. Differences in survival between patient groups were determined using the long-rank test. Results The study included records of two hundred and two SLE patients, 184 (91.1%) were females and 18 (8.9%) patients were males. The mean age at the time of diagnosis was 26.71 ± 7.93 years with a mean follow-up between mean: 6.6 ± 4.58 years, 34.15% had damage in at least one of the organ systems by Systemic Lupus International Collaborating Clinics American college of rheumatology damage index SLICC/ACR-DI in the first 6 months. Considering an outcome label of dead or alive at the end of follow-up period, results showed a total of 52 mortalities, 88.5% were females and 11.5% were males, mean age at death onset was 30.9 ± 8.8 years. Results of the Kaplan–Meier survival curve showed an overall cumulative probability of survival at 5, 10, 15, and 20 years after SLE diagnosis was 82.9, 68.8, 51.4, and 20.4%, respectively. Conclusion The cumulative probability of survival at 5, 10, 15, and 20 years after SLE diagnosis was 82.9, 68.8, 51.4, and 20.4%, respectively.
On photovoice—Applications and reflections to an intensive care context

Abstract Background In this paper, we share our experiences of using ‘photovoice’ methodology as a way to generate data in intensive care units concerning the place and space of care. We have adapted and modified ‘photovoice’ in researching people's lived experiences of ICU. Researching lived experiences in an intensive care context is challenging because of the complex nature of critical care. Aim This study aims to explore and discuss photovoice methodolgy in ICU as a data collection method. Materials and Methods: Photos and interviews collected from patients, loved ones and staff collected in a previous research proejct. Results Although there are challenges in using cameras and photographing the environment in the ICU, due to ethics and the voiceless patients therein, many advantages are presented to the researchers in capturing the meaning of lived experiences of various phenomena in the lifeworld in general and in the meaning of place and space. This paper offers applications and reflection over ontological, epistemological and methodological concerns and also offers a detailed approach on how to employ photovoice for successful and rich data generation. Discussion developing and adapting scientific methods and methodologies contributes to knowledge development in caring science and is therefore an important subject of matter. Conclusions Photovoice also presents a powerful tool in disseminating the findings as it opens up the closed world of ICU to the public and increases people's understanding of the significance of place and space of caring practice.
Presence of Natural Killer B Cells in Simian Immunodeficiency Virus-Infected Colon That Have Properties and Functions Similar to Those of Natural Killer Cells and B Cells but Are a Distinct Cell Population

There is low-level but significant mucosal inflammation in the gastrointestinal tract secondary to human immunodeficiency virus (HIV) infection that has long-term consequences for the infected host. This inflammation most likely originates from the immune response that appears as a consequence of HIV. Here, we show in an animal model of HIV that the chronically SIV-infected gut contains cytotoxic natural killer B cells that produce inflammatory cytokines and proliferate during infection. ABSTRACT Here, we report the appearance of natural killer B (NKB) cells within the colon during simian immunodeficiency virus (SIV) infection of susceptible monkeys. Using RNA sequencing (RNAseq) and flow cytometry, we show that NKB cells are unique cells with features and functions of both NK and B cells. NKB cells express receptors and ligands found on B cells that are important for (i) antigen presentation; (ii) activities associated with class switching, affinity maturation, and B-cell memory formation in secondary lymphoid follicles; and (iii) antigen recognition. The predominant immunoglobulins (Igs) expressed on NKB cells are IgA, although NKB cells can express surface IgM and IgG. There is dominant lambda expression over the kappa light chain characteristic of mucosal B cells. In addition to B-cell aspects, NKB cells express NK cell activation receptors and Fas ligand. We show in this study that NKB cells express perforin and granzymes and lyse cells in a lytic assay. In addition to NK cell cytolytic function, NKB cells also produce the inflammatory cytokines interferon gamma, tumor necrosis factor alpha, and interleukin-18 (IL-18). Finally, we noted the increased capacity of NKB cells to proliferate compared to NK cells and CD8+ T cells from the SIV-infected colon. The increased proliferation and inflammatory cytokine production may be related to the relatively high expression levels of IL-15 receptor beta, IL-7 receptor, IL-18 receptor, and 41BB relative to the same receptors on CD8 and NK cells. The properties of NKB cells may point to their role in the enhanced inflammation observed in the SIV-infected gut. IMPORTANCE There is low-level but significant mucosal inflammation in the gastrointestinal tract secondary to human immunodeficiency virus (HIV) infection that has long-term consequences for the infected host. This inflammation most likely originates from the immune response that appears as a consequence of HIV. Here, we show in an animal model of HIV that the chronically SIV-infected gut contains cytotoxic natural killer B cells that produce inflammatory cytokines and proliferate during infection.
Arthrogenic muscle inhibition manifests in thigh musculature motor unit characteristics after anterior cruciate ligament injury

ABSTRACT Joint trauma induces a presynaptic reflex inhibition termed arthrogenic muscle inhibition (AMI) that prevents complete activation of muscles. Reduced motor unit (MU) output is a hypothesised mechanism for persistent strength deficits. The objective of this study was to determine MU characteristics of thigh musculature and determine how they change with anterior cruciate ligament (ACL) injury compared to healthy controls. A randomised protocol of knee flexion/extension isometric contractions (10–50% maximal voluntary isometric contraction) was performed for each leg with surface EMG 5-pin array electrodes placed on the vastus medialis, vastus lateralis, semitendinosus and biceps femoris. Longitudinal assessments for average rate coding, recruitment thresholds and MU action potentials were acquired at 6-month intervals. With exception of the vastus medialis, all thigh musculature of ACL-injured demonstrated smaller MU action potential peak-to-peak amplitude. For average rate coding, ACL-injured demonstrated lower coding rates than Controls for the quadriceps (p < .05) and higher rates than Controls for the hamstrings (p < .05). These MU characteristics were different from Controls after ACL reconstruction up to 12 months post-surgery, yet maximal strength increased during this time frame. As thigh MU characteristics are known across phases of ACL rehabilitation, future studies can assess these patterns of motor control and their potential to determine risk of re-injury. Further, future rehabilitation can target specific intervention programmes to restore motor control. Highlights Motor unit strategies of arthrogenic muscle inhibition are characterised for the first time via decomposed EMG. Motor unit deficits of thigh musculature persist throughout all phases of ACL rehabilitation, even after return-to-sport. After ACL injury, motor unit sizes at similar recruitment thresholds were smaller than those of healthy controls.
NetworkSIR and EnvironmentalSIR: Effective, Open-Source Epidemic Modeling in the Absence of Data

The rapidly changing situation characterized by the COVID-19 pandemic highlighted a need for new epidemic modeling strategies. Due to an absence of computationally efficient models robust to paucity of reliable data, we developed NetworkSIR, a model capable of making predictions when only the approximate population density is known. We then extend NetworkSIR to capture the effect of indirect disease spread on the progression of an epidemic (EnvironmentalSIR).