Miracle-dz/UniFAR-FTUs huggingface dataset:
Viral causes of severe acute respiratory infection in hospitalized children and association with outcomes: A two-year prospective surveillance study in Suriname

Background Viruses are the most frequent cause of severe acute respiratory infection (SARI) in children. It is currently unknown whether presence of a virus, the number of viruses, or type of virus, are associated with clinical outcomes of pediatric SARI in developing countries. Methods Between 2012 and 2014 nasopharyngeal swabs and demographic and clinical variables were prospectively collected for surveillance of viral causes of SARI in Surinamese children within 48 hours after hospitalization. These swabs were tested for 18 respiratory viruses using a multiplex polymerase chain reaction (PCR) panel to identify the specific viral causes of SARI, unknown to the treating physicians. In post hoc analyses we evaluated if the PCR results, and demographic and clinical characteristics, were associated with course of disease, duration of respiratory support, and length of stay (LOS). Results Of a total of 316 analyzed children, 290 (92%) had one or more viruses. Rhinovirus/enterovirus (43%) and respiratory syncytial virus (34%) were most prevalent. Course of disease was mild in 234 (74%), moderate in 68 (22%), and severe in 14 (4%) children. Neither presence of a single virus, multiple viruses, or the type of virus, were different between groups. Prematurity and lower weight-for-age-z-score were independent predictors of a severe course of disease, longer duration of respiratory support, and longer LOS. Conclusions Viruses are common causes of pediatric SARI in Suriname, yet not necessarily associated with clinical outcomes. In developing countries, demographic and clinical variables can help to identify children at-risk for worse outcome, while PCR testing may be reserved to identify specific viruses, such as influenza, in specific patient groups or during outbreaks.
Differences in Biomarkers of Inflammation Between Novel Subgroups of Recent-Onset Diabetes

A novel clustering approach identified five subgroups of diabetes with distinct progression trajectories of complications. We hypothesized that these subgroups differ in multiple biomarkers of inflammation. Serum levels of 74 biomarkers of inflammation were measured in 414 individuals with recent adult-onset diabetes from the German Diabetes Study (GDS) allocated to five subgroups based on data-driven cluster analysis. Pairwise differences between subgroups for biomarkers were assessed with generalized linear mixed models before (model 1) and after (model 2) adjustment for the clustering variables. Participants were assigned to five subgroups: severe autoimmune diabetes (21%), severe insulin-deficient diabetes (SIDD) (3%), severe insulin-resistant diabetes (SIRD) (9%), mild obesity-related diabetes (32%), and mild age-related diabetes (35%). In model 1, 23 biomarkers showed one or more pairwise differences between subgroups (Bonferroni-corrected P < 0.0007). Biomarker levels were generally highest in SIRD and lowest in SIDD. All 23 biomarkers correlated with one or more of the clustering variables. In model 2, three biomarkers (CASP-8, EN-RAGE, IL-6) showed at least one pairwise difference between subgroups (e.g., lower CASP8, EN-RAGE, and IL-6 in SIDD vs. all other subgroups, all P < 0.0007). Thus, novel diabetes subgroups show multiple differences in biomarkers of inflammation, underlining a prominent role of inflammatory pathways in particular in SIRD.
Optic Nerve Head Parameters and Peripapillary Retinal Nerve Fiber Layer Thickness in Patients with Coronavirus Disease 2019

ABSTRACT Purpose To quantify the optic nerve head (ONH) and peripapillary retinal nerve fiber layer (pRNFL) thickness in patients with Coronavirus Disease-2019 (COVID-19) and compare the measurements with a healthy control group. Methods In a comparative cross-sectional observational study, ONH and pRNFL thickness were evaluated in patients with a history of COVID-19, at least 2 weeks after recovery from the systemic disease, and compared with an age-matched, normal control group. Results Thirty COVID-19 patients along with 60 age- and gender-matched healthy controls were studied. Mean average pRNFL thickness was 105.0 ± 16.3 µm in the COVID-19 patients, compared to 99.0 ± 9.0 µm in the controls (p = .31). The pRNFL thicknesses in all sectors was higher in patients with a history of COVID-19; however, this did not reach statistical significance. Similarly, ONH parameters were not significantly different between the groups. Conclusion Patients recovered from COVID-19 had unremarkable alterations in the peripapillary RNFL thickness. Abbreviations ONH: Optic Nerve HeadRNFL: Retinal Nerve Fiber LayerSD-OCT: Spectral-Domain Optical Coherence TomographyCOVID-19: Coronavirus Disease 2019SARS-CoV-2: Severe Acute Respiratory Syndrome Coronavirus 2CNS: Central Nervous SystemACE: Angiotensin-Converting EnzymeRT-PCR: Reverse Transcription-Polymerase Chain Reaction
Assessment of plasma BMP-2, BMP-7, BMP-10, vitamin D, and TGF β1 in simple fractures among Sudanese patients

Background Bone morphogenetic proteins (BMP) are multifunctional proteins. They work as cytokines regulating osteogenesis during fracture healing process. The objectives of this study were to assess changes in BMPs during fracture and their correlations to Fracture’s healing. Methods Case-Control hospital–based study conducted from January 2018 to January 2019. Demographic data, anthropometric measurements, and blood samples were collected from patients and controls (18–65 years old). Plasma concentrations of selected BMPs and vitamin D were measured using quantitative enzyme linked immunosorbent assay (ELISA). SPSS version 25 was used to calculate frequencies, Pearson correlation tests, chi-square and unpaired t-test. Results Sixty-five patients with fractures and Sixty-five controls were studied. Means of plasma concentrations were (TGFβ1 = 21.07 ng/ml ±8.49 and 19.8 ng/ml ±7.2) (BMP-2 = 76.3 pg/ml ± 156.6 and 55.5 ng/ml ± 127.9) (BMP-7 = 13.02 pg/ml ±43.5 and 64.6pg/ml ±250) (BMP-10 = 8.14 pg/ml ±12.7 and 5.48 pg/ml ±11.3) (Vitamin D mean was 24.94 ng/ml ±13.2 and 26.2 ng/ml ±11.6) in patients and controls, respectively. Forty-five subjects were enrolled into follow up study: 30 males, 15 females. Healing time mean was 4.13± 2.6 months. No significant correlation between BMP-2/BMP-7 with healing time. Conclusions BMP-7 was significantly lowers in the plasma of patients that controls (P = 0.042). Low Vitamin D was observed among Sudanese participants.
Population structure, inbreeding and admixture in local cattle populations managed by community‐based breeding programs in Burkina Faso

Abstract High‐throughput genomic markers provide an opportunity to assess important indicators of genetic diversity for populations managed in livestock breeding programs. While well‐structured breeding programs are common in developed countries, in developing country situations, especially in West Africa, on‐farm performance and pedigree recordings are rare, and thus, genomic markers provide insights to the levels of genetic diversity, inbreeding and introgression by other breeds. In this study, we analysed key population parameters such as population structure, admixture and levels of inbreeding in three neighbouring populations of African taurine and taurine × Zebu crosses managed by community‐based breeding programs in the South‐West of Burkina Faso. The three populations were pure Baoulé (called Lobi locally) in sedentary production systems, Baoulé x Zebu crossbreds in sedentary systems and Zebu × Baoulé crossbreds in transhumant production systems, respectively. The total sample analysed included 631 animals and 38,207 single nucleotide polymorphisms after quality control. Results of principal component and admixture analyses confirmed the genetic background of two distinct ancestral populations (taurine and zebuine) and levels of admixture in all three breeding populations, including the presumably pure Baoulé group of animals. Inbreeding levels were moderate, compared to European dairy and beef cattle populations and higher than those of Brazilian Nellore cattle. Very few animals with inbreeding levels indicating parent–offspring or full sib mating were observed, and inbreeding levels indicating half sib mating were also rare. For the management of breeding populations, farmers were advised to exchange best young bulls. The crossbreeding levels of presumably pure Baoulé animals are of concern to the breeding program due to the high level of endangerment of pure African taurine cattle populations across West Africa. Future rounds of bull selection in the community‐based breeding program will make use of genomic information about admixture levels.
Salmonella enterica BcfH is a trimeric thioredoxin-like bifunctional enzyme with both thiol oxidase and disulfide isomerase activities.

AIMS Thioredoxin fold proteins are ubiquitous in nature. This redox scaffold has evolved to enable a variety of functions, including redox regulation, protein folding and oxidative stress defense. In bacteria, the thioredoxin-like disulfide bond (Dsb) family mediates the oxidative folding of multiple proteins required for fitness and pathogenic potential. Conventionally, Dsb proteins have specific redox functions with monomeric and dimeric Dsbs exclusively catalyzing thiol oxidation and disulfide isomerization, respectively. This contrasts with the eukaryotic disulfide forming machinery where the modular thioredoxin protein PDI mediates thiol oxidation and disulfide reshuffling. In this study we identified and structurally and biochemically characterized a novel Dsb-like protein from Salmonella enterica termed BcfH and defined its role in virulence. RESULTS In the conserved bcf (bovine colonization factor) fimbrial operon, the Dsb-like enzyme BcfH forms a trimeric structure, exceptionally uncommon among the large and evolutionary conserved thioredoxin superfamily. This protein also displays very unusual catalytic redox centers, including an unwound α-helix holding the redox active site and a trans-proline instead of the conserved cis-proline active site loop. Remarkably, BcfH displays both thiol oxidase and disulfide isomerase activities contributing to Salmonella fimbrial biogenesis. INNOVATION AND CONCLUSION Typically, oligomerization of bacterial Dsb proteins modulates their redox function, with monomeric and dimeric Dsbs mediating thiol oxidation and disulfide isomerization, respectively. The present study demonstrates a further structural and functional malleability in the thioredoxin-fold protein family. BcfH trimeric architecture and unconventional catalytic sites permit multiple redox functions emulating in bacteria the eukaryotic protein disulfide isomerase dual oxido-reductase activity.
The Influence of Changes in Work Stressors and Coping Resources on Sleep Disturbances: Evidence from the OHSPIW Cohort Study.

STUDY OBJECTIVES We investigated whether changes in psychosocial work conditions affect the risk of sleep disturbances. METHODS Data pertaining to 2738 males and 1431 females were obtained from the Occupational Health Study of Petroleum Industry Workers (OHSPIW), a prospective cohort study of Chinese petroleum industry workers. The subjects were assessed with regard to work-related stressors, coping resources and sleep disturbances at baseline (2012) and follow-up (2018). The variations in work stressors and coping resources, which were assessed using the Occupation Stress Inventory-Reviewed (OSI-R), were calculated. Sleep disturbances were evaluated with the self-reported Pittsburgh Sleep Quality Index (PSQI). RESULTS Increased work stressors (OR=1.57, 95% CI=1.24-1.99) and decreased coping resources (OR=2.03, 95% CI=1.48-2.78) were correlated with the likelihood of sleep disturbances in male and female workers. The primary risk factors included high role overload, increased responsibility, enhanced physical environment stressors, reduced self-care, and reduced rational coping. A reduction in work stressors was a protective factor against sleep disturbances in females only (OR=0.63, 95% CI=0.45-0.88). Coping resources had a modifying effect on the relationship between increased work stressors and sleep disturbances, with increased coping resources being associated with a lower odds of increased works stressors on sleep disturbances (OR=1.29, 95%CI=1.01-1.66) than decreased coping resources (OR=3.60, 95%CI=1.10-11.81). CONCLUSIONS Changes in work stressors and coping resources have a significant influence on the risk of sleep disturbances. Our findings highlight important precautionary strategies to abate adverse psychosocial working environments and to strengthen coping resources to prevent work-related sleep disturbances.
Reduced photosynthetic thermal acclimation capacity under elevated ozone in poplar (Populus tremula) saplings

The sensitivity of photosynthesis to temperature has been identified as a key uncertainty for projecting the magnitude of the terrestrial carbon cycle response to future climate change. Although thermal acclimation of photosynthesis under rising temperature has been reported in many tree species, whether tropospheric ozone (O3) affects the acclimation capacity remains unknown. In this study, temperature responses of photosynthesis (light‐saturated rate of photosynthesis (Asat), maximum rates of RuBP carboxylation (Vcmax), and electron transport (Jmax) and dark respiration (Rdark) of Populus tremula exposed to ambient O3 (AO3, maximum of 30 ppb) or elevated O3 (EO3, maximum of 110 ppb) and ambient or elevated temperature (ambient +5°C) were investigated in solardomes. We found that the optimum temperature of Asat (ToptA) significantly increased in response to warming. However, the thermal acclimation capacity was reduced by O3 exposure, as indicated by decreased ToptA, and temperature optima of Vcmax (ToptV) and Jmax (ToptJ) under EO3. Changes in both stomatal conductance (gs) and photosynthetic capacity (Vcmax and Jmax) contributed to the shift of ToptA by warming and EO3. Neither Rdark measured at 25°C ( Rdark25 ) nor the temperature response of Rdark was affected by warming, EO3, or their combination. The responses of Asat, Vcmax, and Jmax to warming and EO3 were closely correlated with changes in leaf nitrogen (N) content and N use efficiency. Overall, warming stimulated growth (leaf biomass and tree height), whereas EO3 reduced growth (leaf and woody biomass). The findings indicate that thermal acclimation of Asat may be overestimated if the impact of O3 pollution is not taken into account.
Outcomes and prognostic indicators in 59 paraplegic medium to large breed dogs with extensive epidural hemorrhage secondary to thoracolumbar disc extrusion.

OBJECTIVE To evaluate outcomes and prognostic factors after decompressive hemilaminectomy in paraplegic medium to large breed dogs with extensive epidural hemorrhage (DEEH) and thoracolumbar intervertebral disc extrusion (TL-IVDE). STUDY DESIGN Retrospective, cohort, descriptive study. ANIMALS Fifty-nine client-owned dogs. METHODS Medical records and advanced imaging were reviewed for paraplegic dogs with DEEH. Ambulatory status 6 months after surgery and postoperative complications were recorded. Multiple logistic regression models were constructed to explore prognostic factors. RESULTS Records of 22 dogs with and 37 dogs without pelvic limb pain perception at presentation were included. Median age of dogs was 5 years (interquartile range, 4-7), and mean weight was 26.9 kg (SD, ±9.71). Labradors and Labrador mixes were most common (17/59 [28.8%]). Recovery of ambulation occurred in 17 of 22 (77.3%) dogs with and in 14 of 37 (37.8%) dogs without pain perception prior to surgery. Progressive myelomalacia was recorded in three of 59 (5.1%) dogs, one with pain perception and two without pain perception at presentation. Postoperative complications (14/59 [23.7%]) were common. Factors independently associated with outcome included clinical severity (odds ratio [OR] 0.179, P = .005), number of vertebrae with signal interruption in half Fourier single-shot turbo spin-echo sequences (HASTEi; OR, 0.738; P = .035), and ratio of vertebral sites decompressed to HASTEi (OR, 53.79; P = .03). CONCLUSION Paraplegic medium to large breed dogs with DEEH have a less favorable outcome after surgical decompression than paraplegic dogs with TL-IVDE. CLINICAL SIGNIFICANCE Dogs with DEEH can have severe postoperative complications. Loss of pain perception and increased HASTEi are associated with a poor outcome, while more extensive decompression improves outcome.
Development of a patient-reported outcome measure for neck pain in military aircrew: qualitative interviews to inform design and content

Introduction The prevalence of flight-related neck pain is 70% in UK fast jet pilots; much higher than the general population. The Aircrew Conditioning Programme and direct access physiotherapy exist to minimise the impact on military capability, but a population specific patient-reported outcome measure (PROM) is required to investigate the effectiveness of these. We aimed to explore the experiences of flight-related neck pain to inform the content validity and development of a population specific PROM. Methods Qualitative semistructured interviews combining phenomenological and grounded theory methods, reported using Consolidated criteria for Reporting Qualitative research guidelines. A purposive sample of 10 fast jet pilots with neck pain was recruited. Concept elicitation interviews were audio recorded, transcribed verbatim along with field notes. Data analysis involved subject and methodological expertise used a concept elicitation approach. Results Participants included 10 male fast jet pilots, age 34.7 years. Identified themes included: (1) physical symptoms associated with flying activities; (2) occupational effects revealed modifications of flying, or ‘suboptimal’ performance owing to neck pain; (3) psychological effects revealed feelings or worry and (4) social and activity effects showed impact on out of work time. Conclusion Population-specific occupational, psychological and social factors should be considered alongside physical symptoms when managing neck pain in military aircrew. Findings support the development of a PROM specifically designed for military aircrew with neck pain.
Investigating Expressed Emotion (EE) in individuals at-risk of developing psychosis and their families over 12-months.

High levels of Expressed Emotion (EE) are present in families of individuals with an At-Risk Mental State (ARMS) of psychosis and can negatively impact on service users' functioning and symptoms, as well as relatives' psychological wellbeing. OBJECTIVES This is the first longitudinal study to assess EE from the family/carers' perspective, as well as the service users' perceptions of the family/carers' EE. We explored the effects of EE on transition risk and outcomes of depression, worry and anxiety. METHODS Questionnaires were completed by 70 ARMS individuals and 70 family/carers at three time points: baseline, 6-months and 12-months. All participants completed measures of anxiety, depression and worry, plus a version of the Family Questionnaire to assess EE. RESULTS EE scores reduced over time for both service users and family/carers. High-EE perceived by service users at 6-months was associated with higher transition to psychosis at 12-months. High-EE levels at baseline was associated with higher levels of service user depression and family/carer anxiety at 12-months. Higher family/carer total EE scores were associated with less contact with the service user and higher levels of worry. CONCLUSIONS Novel implications suggest that interventions to reduce high-EE in families of people with ARMS would benefit service users by protecting them from higher levels of depression and transition to psychosis. Reducing high-EE attitudes would also benefit the family/carers by reducing levels of anxiety and worry. Family interventions focussing on multiple perceptions of the home environment could help to direct services and prevent negative psychological outcomes for all family members.
Ecological rules for the assembly of microbiome communities

Humans and many other hosts establish a diverse community of beneficial microbes anew each generation. The order and identity of incoming symbionts is critical for health, but what determines the success of the assembly process remains poorly understood. Here we develop ecological theory to identify factors important for microbial community assembly. Our method maps out all feasible pathways for the assembly of a given microbiome—with analogies to the mutational maps underlying fitness landscapes in evolutionary biology. Building these “assembly maps” reveals a tradeoff at the heart of the assembly process. Ecological dependencies between members of the microbiota make assembly predictable—and can provide metabolic benefits to the host—but these dependencies may also create barriers to assembly. This effect occurs because interdependent species can fail to establish when each relies on the other to colonize first. We support our predictions with published data from the assembly of the preterm infant microbiota, where we find that ecological dependence is associated with a predictable order of arrival. Our models also suggest that hosts can overcome barriers to assembly via mechanisms that either promote the uptake of multiple symbiont species in one step or feed early colonizers. This predicted importance of host feeding is supported by published data on the impacts of breast milk in the assembly of the human microbiome. We conclude that both microbe to microbe and host to microbe interactions are important for the trajectory of microbiome assembly.
Nerve Graft Length and Recovery of Elbow Flexion Muscle Strength in Patients With Traumatic Brachial Plexus Injuries: Case Series

Abstract BACKGROUND Traumatic brachial plexus injuries cause long-term maiming of patients. The major target function to restore in complex brachial plexus injury is elbow flexion. OBJECTIVE To retrospectively analyze the correlation between the length of the nerve graft and the strength of target muscle recovery in extraplexual and intraplexual nerve transfers. METHODS A total of 51 patients with complete or near-complete brachial plexus injuries were treated with a combination of nerve reconstruction strategies. The phrenic nerve (PN) was used as axon donor in 40 patients and the spinal accessory nerve was used in 11 patients. The recipient nerves were the anterior division of the upper trunk (AD), the musculocutaneous nerve (MC), or the biceps branches of the MC (BBs). An index comparing the strength of elbow flexion between the affected and the healthy arms was correlated with the choice of target nerve recipient and the length of nerve grafts, among other parameters. The mean follow-up was 4 yr. RESULTS Neither the choice of MC or BB as a recipient nor the length of the nerve graft showed a strong correlation with the strength of elbow flexion. The choice of very proximal recipient nerve (AD) led to axonal misrouting in 25% of the patients in whom no graft was employed. CONCLUSION The length of the nerve graft is not a negative factor for obtaining good muscle recovery for elbow flexion when using PN or spinal accessory nerve as axon donors in traumatic brachial plexus injuries.