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Data from: The subcortical basis of outcome and cognitive impairment in TBI: a longitudinal cohort study
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Sacramento River winter-run Chinook salmon cohort reconstruction – data and code
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Proteome-wide antigenic profiling in Ugandan cohorts identifies associations between age, exposure intensity, and responses to repeat-containing antigens in Plasmodium falciparum
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A Publicly Available Virtual Cohort of Four-chamber Heart Meshes for Cardiac Electro-mechanics Simulations
<p><strong>Motivation: </strong> Computational models of the heart are increasingly being used in the development of devices, patient diagnosis and therapy guidance. While software techniques have been developed for simulating single hearts, there remain significant challenges in simulating cohorts of virtual hearts from multiple patients.</p> <p><strong>Dataset Description: </strong>We present the first database of four-chamber heart models suitable for electro-mechanical simulations. Our database consists of twenty-four four-chamber heart models generated from end-diastolic CT acquired from heart failure patients recruited for cardiac resynchronization therapy upgrade. We also provide a higher resolution version for each of the twenty-four meshes.</p> <p>We segmented end-diastolic CT. The segmentation was then upsampled and smoothed. The final multi-label segmentation was used to generate a tetrahedral mesh. The resulting meshes had an average edge length of 1.1mm. The elements of all the twenty-four meshes are labelled as follows: 1) Left ventricle myocardium 2) Right ventricle myocardium 3) Left atrium myocardium 4) Right atrium myocardium 5) Aorta wall 6) Pulmonary artery wall 7) Left atrium appendage ring 8) Left superior pulmonary vein ring 9) Left inferior pulmonary vein ring 10) Right inferior pulmonary vein ring 11) Right superior pulmonary vein ring 12) Superior vena cava ring 13) Inferior vena cava ring 14) Mitral valve plane 15) Tricuspid valve plane 16) Aortic valve plane 17) Pulmonary valve plane 18) Left atrial appendage valve plane 19) Left superior pulmonary vein valve plane 20) Left inferior pulmonary vein valve plane 21) Right inferior pulmonary vein valve plane 22) Right superior pulmonary vein valve plane 23) Superior vena cava valve plane 24) Inferior vena cava valve plane.</p> <p>Ventricular fibres were generated using a rule-based method, with a fibre orientation varying transmurally from endocardium to epicardium from 80˚ to -60˚, respectively. We defined a system of universal ventricular coordinates on the meshes, see Figure 1B: an apico-basal coordinate varying continuously from 0 at the apex to 1 at the base; a transmural coordinate varying continuously from 0 at the endocardium to 1 at the epicardium; a rotational coordinate varying continuously from – π at the left ventricular free wall, 0 at the septum and then back to + π at the left ventricular free wall; intra-ventricular coordinate defined at -1 at the left ventricle and +1 at the right ventricle. This coordinate system was assigned to the ventricles in the four-chamber meshes and all the other labels were assigned with -100. </p> <p>We also refined each mesh from 1.1mm resolution down to 0.39mm resolution. Each refined mesh has tags defined on its elements (same numbering as described above) and ventricular fibres.</p> <p><strong>Database format: </strong>We provide a zipped folder for each mesh. Each folder contains the coarse and the finer versions of the same mesh. All twenty-four 1mm-meshes are supplied in case format, readable with paraview. All binary files containing the meshes data (ens and geo formats) are provided within the zipped folder. Points coordinates are given in mm. Element tags are assigned to the elements of the mesh as well as fibres and sheet directions. Fibres and sheet directions are assigned to the ventricles according to a rule-based method, while non-ventricular elements are assigned with default vectors [1; 0; 0] and [0; 1; 0]. UVCs are assigned to the nodes of the meshes. We also provide the location of the cardiac resynchronisation therapy right-ventricular electrode used to initiate ventricular excitation. This is given as a label on the nodes called electrode endo rv, which is 1 at the stimulated nodes. Finer meshes are provided in vtk format, also readable in paraview. For these meshes, we provide element tags, fibres and sheet directions on the ventricles, all in the same file.</p>
Data from: Sleep duration, midday napping and sleep quality and incident stroke: the Dongfeng-Tongji cohort
Objective: To investigate the associations of sleep duration, midday napping and sleep quality, and change in sleep duration with risk of incident stroke and stroke subtypes. Methods: Among 31750 participants aged 61.7 years on average at baseline from the Dongfeng-Tongji cohort, we used Cox regression models to estimate hazard ratios (HRs) and 95% confidence intervals (CIs) for incident stroke. Results: Compared with sleeping 7-<8 h/night, those reporting longer sleep duration (≥9 h/night) had a greater risk of total stroke (HR, 1.23; 95% CI, 1.07-1.41), while shorter sleep (<6 h/night) had no significant effect on stroke risk. The HR (95% CI) of total stroke was 1.25 (1.03-1.53) for midday napping >90 min vs 1-30 min. The results were similar for ischemic stroke. Compared with good sleep quality, those with poor sleep quality showed a 29%, 28% and 56% higher risk of total, ischemic, and hemorrhagic stroke, respectively. Moreover, we observed significant joint effects of sleeping ≥9 h/night and midday napping >90 min (HR, 1.85; 95% CI, 1.28-2.66), and sleeping ≥9 h/night and poor sleep quality (HR, 1.82; 95% CI, 1.33-2.48) on risks of total stroke. Furthermore, compared with persistently sleeping 7-9 h/night, those persistently slept ≥9 h/night or switched from 7-9 h to ≥9 h/night had a higher risk of total stroke. Conclusions: Long sleep duration, long midday napping and poor sleep quality were independently and jointly associated with higher risks of incident stroke. Persistently long sleep duration or switch from average to long sleep duration increased the risk of stroke.
Data from: ApoE is a correlate of phenotypic heterogeneity in Alzheimer's disease in a national cohort
Objective: To compare the proportion of APOEε4 genotype carriers in aphasic versus amnestic variants of Alzheimer's disease (AD). Method: The proportion of APOEε4 carriers was compared among 3 groups. 1) Forty-two patients with primary progressive aphasia (PPA) and AD pathology (PPA/AD) enrolled in the Northwestern Alzheimer Disease Center Clinical Core. 2) 1,418 patients with autopsy confirmed AD and amnestic dementia of the Alzheimer-type (DAT/AD); 3) 2,608 cognitively normal controls (NC). The latter two groups were compiled from the National Alzheimer Coordinating Center (NACC) database. Logistic regression models analyzed the relationship between groups and APOEε4 carrier status, adjusting for age of onset and sex as needed. Results: Using NC as the reference and adjusting for sex and age, the DAT/AD group was 3.97 times more likely to be APOEε4 carriers. Adjusting for sex and age at symptom onset, the DAT/AD group was 2.46 times as likely to be carriers compared to PPA/AD. There was no significant difference in the proportion of APOEε4 carriers for PPA/AD compared to NC. PPA subtypes included 24 logopenic, 10 agrammatic nonfluent, and eight either mixed (n=5) or too severe (n=3) to subtype. The proportion of carriers and non carriers was similar for logopenic and agrammatic subtypes, both having fewer carriers. Conclusion: The proportion of APOEε4 carriers was elevated in amnestic but not aphasic manifestations of AD. These results suggest that APOEε4 is an anatomically selective risk factor that preferentially increases the vulnerability to AD pathology of memory-related medial temporal areas rather that language-related neocortices.
Predictors of abnormal computed tomography findings for paediatric head injury: a retrospective cohort study
<p class="MDPI17abstract"><b>Objectives:</b> Head injuries in children are common causes for visits to the emergency department (ED). Computed tomography<b> (</b>CT) scans are useful for confirming head injury diagnoses. However, radiation exposure from CT scans might cause lethal malignancies. We aimed to examine predictors for the indication of performing CT scans necessary for diagnosis.</p> <p class="MDPI17abstract"><b>Design:</b> Retrospective cohort study.</p> <p class="MDPI17abstract"><b>Setting:</b> Three EDs in Japan</p> <p class="MDPI17abstract"><b>Participants</b>: Patients aged <16 years with head trauma who underwent CT.</p> <p class="MDPI17abstract"><b>Primary and Secondary Outcome Measures</b>: The primary outcome measure was abnormal CT findings that were evaluated using the area under the receiver-operating characteristic curve (AUC). We derived predictors from three existing CDRs: Canadian Assessment of Tomography for Childhood Head Injury (CATCH), Children's Head Injury Algorithm for the Prediction of Important Clinical Events (CHALICE), and Paediatric Emergency Care Applied Research Network (PECARN).</p> <p class="MDPI17abstract"><b>Results:</b> Of 1,103 eligible patients, 410 were included in this study. There were 283 (68%) boys, and the median age was 2 years. In total, 35 (9%) patients showed an abnormality, 73 (18%) were admitted, and 3 (0.7%) underwent neurosurgery. We developed a CDR consisting of 6 predictors for identifying children with abnormal CT findings: (1) severe or worsening headache; (2) GCS <15; (3) signs of skull fracture; (4) hematoma; (5) loss of consciousness; and (6) altered mental status. Our CDR had a sensitivity of 74.3%, a specificity of 75.2%, a negative predictive value of 96.9%, and a positive predictive value of 21.8%. The AUC for our rule was not inferior to those for CATCH, CHALICE, and PECARN {0.75 (95% confidence interval [CI], 0.67-0.81) versus 0.64 (95% CI, 0.56-0.73; p<0.05), 0.68 (95% CI, 0.60–0.76; p=0.28), and 0.67 (95% CI, 0.60-0.74); p=0.10}.</p> <p class="MDPI17abstract"><b>Conclusions:</b> Our findings suggest that a CDR, which lowers the frequency of CT in children with head injuries, must be developed and validated.</p>
Aetiology and prognostic risk factors of mortality in pneumonia patients receiving glucocorticoids alone or glucocorticoids and other immunosuppressants: a retrospective cohort study
<p><b>Objectives:</b> Long-term use of high-dose glucocorticoids can lead to severe immunosuppression and increased risk of treatment-resistant pneumonia and mortality. We investigated the aetiology and prognostic risk factors of mortality in hospitalised patients who developed pneumonia while receiving glucocorticoid therapy alone or glucocorticoid and other immunosuppressant therapies.</p> <p><b>Design:</b> Retrospective cohort study</p> <p><b>Setting: </b>Six secondary and tertiary academic hospitals in China</p> <p><b>Participants: </b>Patients receiving glucocorticoids who were hospitalised with pneumonia between 1<sup>st</sup> January 2013 and 31<sup>st</sup> December 2019.</p> <p><b>Main Outcomes: </b>We analysed<b> </b>the prevalence of comorbidities, microbiology, antibiotic susceptibility patterns, 30-day and 90-day mortality rates, and prognostic risk factors.</p> <p><b>Results</b>: A total of 716 patients were included, with pneumonia pathogens identified in 69.8% of patients. Significant morbidities occurred, including respiratory failure (50.8%), intensive care unit (ICU) transfer (40.8%), and mechanical ventilation (36%), with a 90-day mortality rate of 26.0%. Diagnosis of pneumonia occurred within 6 months of glucocorticoid initiation for 69.7% of patients with <i>Cytomegalovirus</i> (CMV) pneumonia and 79.0% of patients with <i>Pneumocystis jirovecii</i> pneumonia (PCP). Pathogens, including <i>Pneumocystis</i>, CMV, and multidrug-resistant bacteria, were identified more frequently in patients with persistent lymphocytopenia and high-dose glucocorticoid treatment (≥ 30 mg/day of prednisolone or equivalent within 30 days before admission). The 90-day mortality rate was significantly lower for non-CMV viral pneumonias than for PCP (<i>P</i> < 0.05), with a similar mortality rate as CMV pneumonias (24.2% vs 38.1% vs 27.4%, respectively).Cox regression analysis indicated <a name="_Hlk30339725"></a><a name="_Hlk31278800">several independent negative predictors for mortality in this patient population, including septic shock, respiratory failure, </a>persistent lymphocytopenia, interstitial lung disease, and high-dose glucocorticoid use.</p> <p><b>Conclusions</b>: Patients who developed pneumonia while receiving glucocorticoid therapy experienced high rates of opportunistic infections, with significant morbidity and mortality. These findings should be carefully considered when determining treatment strategies for this patient population.</p>
Data from: Metabolically similar cohorts of bacteria exhibit strong co-occurrence patterns with diet items and eukaryotic microbes in lizard guts
Gut microbiomes perform essential services for their hosts, including helping them to digest food and manage pathogens and parasites. Performing these services requires a diverse and constantly changing set of metabolic functions from the bacteria in the microbiome. The metabolic repertoire of the microbiome is ultimately dependent on the outcomes of the ecological interactions of its member microbes, as these interactions in part determine the taxonomic composition of the microbiome. The ecological processes that underpin the microbiome's ability to handle a variety of metabolic challenges might involve rapid turnover of the gut microbiome in response to new metabolic challenges, or it might entail maintaining sufficient diversity in the microbiome that any new metabolic demands can be met from an existing set of bacteria. To differentiate between these scenarios, we examine the gut bacteria and resident eukaryotes of two generalist-insectivore lizards, while simultaneously identifying the arthropod prey each lizard was digesting at the time of sampling. We find that the cohorts of bacteria that occur significantly more or less often than expected with arthropod diet items or eukaryotes include bacteria species that are highly similar to each other metabolically. This pattern in the bacteria microbiome could represent an early step in the taxonomic shifts in bacteria microbiome that occur when host lineages change their in diet niche over evolutionary timescales.
data set related to article Linking Sleep to Externalizing Behavioral Difficulties: A Longitudinal Psychometric Survey in a Cohort of Italian School-Age Children
<pre>This record contains raw data related to article Linking Sleep to Externalizing Behavioral Difficulties: A Longitudinal Psychometric Survey in a Cohort of Italian School-Age Children</pre>
Data from: Vegetarian diet and incidence of total, ischemic and hemorrhagic stroke in two cohorts in Taiwan
<p><span><b>Objectives <i>–</i></b> To determine how a vegetarian diet affects stroke incidence in two prospective cohorts, and to explore whether the association is modified by dietary vitamin B12 intakes. </span></p> <p><b>Methods</b><i> –</i>Participants without stroke in the Tzu Chi Health study (Cohort1, n=5,050, recruited in 2007-2009) and the Tzu Chi Vegetarian Study (Cohort2, n=8,302, recruited in 2005) were followed until end of 2014. Diet was assessed through food frequency questionnaires in both cohorts at baseline. Stroke events and baseline comorbidities were identified through the National Health Insurance Database. A subgroup of 1528 participants in Cohort1 were assessed for serum homocysteine, vitamin B12, and folate. Associations between vegetarian diet and stroke incidences were estimated by Cox regression with age as time scale, adjusted for sex, education, smoking, alcohol, physical activities, BMI (only in Cohort1), hypertension, diabetes, dyslipidemia, and ischemic heart diseases.</p> <p><b>Results <i>–</i></b> Vegetarians had lower serum vitamin B12 and higher folate and homocysteine than nonvegetarians. In Cohort1, 54 events occurred in 30,797 person-years follow-up. Vegetarians (vs. nonvegetarians) experienced lower risk of ischemic stroke (HR: 0.26, 95% CI: 0.08-0.88). In Cohort2, 121 events occurred in 76,797 person-years follow-up. Vegetarians (vs. nonvegetarians) experienced lower risk of overall stroke (HR: 0.52, 95% CI: 0.33-0.82), ischemic stroke (HR: 0.41, 0.19-0.88), and hemorrhagic stroke (HR: 034, 95%CI: 0.12-1.00). Our explorative analysis showed that vitamin B12 intake may modify the association between vegetarian diet and overall stroke (<i>p</i>-interaction = 0.046).</p> <p><b><i>Conclusion</i></b> –Taiwanese vegetarian diet is associated with a lower risk of ischemic and hemorrhagic strokes.</p>
Data from: Vaginal host immune-microbiome interactions in a cohort of primarily African-American women who ultimately underwent spontaneous preterm birth or delivered at term
<p><strong>Background</strong>: Recent studies suggest that alterations in the vaginal microbiome allow for the assessment of the risk for spontaneous preterm birth (PTB), the leading cause of neonatal morbidity and mortality worldwide. However, the associations between the local immune response and the vaginal microbiome are still poorly understood. Herein, we characterize the vaginal host immune-microbiome interactions in women who ultimately underwent PTB and in those who delivered at term.</p> <p><strong>Methods</strong>: Vaginal fluid samples from 52 pregnant women (of whom 18 underwent PTB and 34 delivered at term) were collected from 10-32 weeks in a case-control study. Concentrations of 33 immune mediators were determined using sensitive and specific immunoassays. The previously published 16S rRNA gene sequence and bacterial phylotype data of these subjects were utilized in this study. Linear mixed effects models were utilized to test associations between vaginal immune mediator concentrations and bacterial phylotype relative abundances.</p> <p><strong>Results</strong>: 1) Specific immune mediators (β-defensins 2 and 3, IL-1β, CXCL10, CCL2, CCL3, SLPI, and VEGF) correlated with 18 different vaginal bacterial phylotypes in the overall study population; 2) vaginal concentrations of CXCL10, CCL2, CCL3, SLP1 and VEGF negatively correlated with non-Lactobacillus members of the vaginal microbiome; 3) vaginal concentrations of CXCL10 were negatively correlated with 15 bacterial phylotypes, most of which are typical members of Community State Type IV of the vaginal microbiome, such as Gardnerella vaginalis, Megasphaera sp. type 1, and Atopobium vaginae; 4) Gemella spp. were negatively correlated with vaginal concentrations of VEGF, CCL2, CCL3, SLPI, and CXCL10; 5) when comparing PTB cases to term controls, five soluble immune mediators (CCL26, CCL22 and CCL2, CXCL10 and IL-16), and especially CCL26, were negatively correlated with five typical members of Community State Type IV: Sneathia sanguinegens, Parvimonas micra, Veillonellaceae, BVAB2, and Gemella spp; and 6) Sneathia sanguinegens had stronger negative associations with all five soluble immune mediators (CCL26, CCL22 and CCL2, CXCL10 and IL-16) in PTB cases than in term controls.</p> <p><strong>Conclusions</strong>: The assessment of vaginal host immune-microbiome interactions revealed that specific soluble immune mediators, mainly CXCL10, negatively correlated with typical members of Community State Type IV of the vaginal microbiome. In addition, this assessment particularly showed that Sneathia sanguinegens had stronger negative associations with different immune mediators, including CXCL10 and CCL26, in women who ultimately had a PTB compared to those who delivered at term. These findings provide insight into the vaginal host immune-microbiome interactions in normal and complicated pregnancies.</p>
Data from: Acute febrile illness and influenza disease burden in a rural cohort dedicated to malaria in Senegal, 2012-2013
Background: African populations are considered to be particularly vulnerable to fever illnesses, including malaria, and acute respiratory disease, owing to limited resources and overcrowding. However, the overall burden of influenza in this context is poorly defined and incidence data for African countries are scarce. We therefore studied the fever syndrome incidence and more specifically influenza incidence in a cohort of inhabitants of Dielmo and Ndiop in Sokone district, Senegal. Methods: Daily febrile-illness data were prospectively obtained from January 2012 to December 2013 from the cohort of the villages of Dielmo and Ndiop, initially dedicated to the study of malaria. Nasopharyngeal swabs were collected from, and malaria diagnosis tests (thick blood smears) carried out on, every febrile individual during clinical visits; reverse transcriptase-polymerase chain reaction was used to identify influenza viruses in the samples. Binomial negative regression analysis was used to study the relationship between the monthly incidence rate and various covariates. Results: In Dielmo and Ndiop, the incidence of malaria has decreased, but fever syndromes remain frequent. Among the 1036 inhabitants included in the cohort, a total of 1,129 episodes of fever were reported. Influenza was present all year round with peaks in October-December 2012 and August 2013. The fever, ILI and influenza incidence density rates differed significantly between age groups. At both sites, the adjusted incidence relative risks for fever syndromes and ILI were significantly higher in the [6–24 months) than other age groups: 7.3 (95%CI: [5.7–9.3]) and 16.1 (95%CI: [11.1–23.3]) respectively. The adjusted incidence relative risk for influenza was significantly higher for the [0–6 months) than other age groups: 9.9 (95%CI: [2.9–33.6]). At both sites, incidence density rates were lowest among adults > = 50 years. Conclusions: In this rural setting in Senegal, influenza was most frequent among the youngest children. Preventive strategies targeting this population should be implemented.
Data from: Size-mediated priority and temperature effects on intra-cohort competition and cannibalism in a damselfly
1. A shift in the relative arrival of offspring, e.g., a shift in hatching time, can affect competition at the intraspecific level through size-mediated priority effects, where the larger individuals gain more resources. These priority effects are likely to be affected by climate warming and the rate of intraspecific predation, i.e., cannibalism. 2. In a laboratory experiment, we examined size-mediated priority effects in larvae of the univoltine damselfly, Lestes sponsa, at two different temperatures (21°C and 23°C). We created three size groups of larvae by manipulating hatching time: early hatched with a large size (extra-advanced), intermediate hatched with an intermediate size (advanced) and late hatched with a small size (non-advanced). Thereafter we reared the larvae from these groups in non-mixed and mixed groups of 12 larvae. 3. We found strong priority and temperature effects. First, extra-advanced larvae most often had higher survival, growth and development rates than non-advanced larvae in mixed groups, compared to groups that consisted of only extra-advanced larvae. Second, temperature increased growth and development rates and cannibalism. 4. However, the strength of priority effects did not differ between the two experimental temperatures, because there was no statistical interaction between temperature and treatments. That is, the mixed and non-mixed groups of non-advanced, advanced and extra-advanced larvae showed the same relative change in life history traits across the two temperatures. 5. Non-advanced and advanced larvae had similar or higher growth rate and mass in mixed groups compared to non-mixed groups, suggesting that predation from advanced larvae in the mixed group released resources for the non-advanced and advanced larvae that survived despite cannibalism risk. Thus, a thinning effect occurred due to cannibalism caused by priority effects. 6. The results suggest that a shift in the relative arrival of offspring can cause temperature-dependent priority effects, mediated through cannibalism, growth and development, which may change the size distribution and abundance of emerging aquatic insects.
Data from: Repurposing population genetics data to discern genomic architecture: a case study of linkage cohort detection in mountain pine beetle (Dendroctonus ponderosae)
Genetic surveys of the population structure of species can be used as resources for exploring their genomic architecture. By adjusting filtering assumptions, genome-wide single nucleotide polymorphism (SNP) datasets can be reused to give new insights into the genetic basis of divergence and speciation without targeted re-sampling of specimens. Filtering only for missing data and minor allele frequency, we used a combination of principle components analysis and linkage disequilibrium network analysis to distinguish three cohorts of variable SNPs in the mountain pine beetle in western Canada, including one that was sex-linked and one that was geographically associated. These marker cohorts indicate genomically localized differentiation, and their detection demonstrates an accessible and intuitive method for discovering potential islands of genomic divergence without a priori knowledge of a species' genomic architecture. Thus, this method has utility for directly addressing the genomic architecture of species and generating new hypotheses for functional research.
Data from: Quality of evidence considered by Health Canada in granting full market authorization to new drugs with a conditional approval: a retrospective cohort study
Objectives: This study examines the characteristics of studies that Health Canada uses to grant full marketing authorization for products given a conditional approval between January 1, 1998 and June 30, 2017. Design: Cohort study. Data sources: Journal articles listing drugs that fulfilled their conditions and received full marketing authorization, Notice of Compliance database, Notice of Compliance with conditions web site, Qualifying Notices listing required confirmatory studies, clinicaltrials.gov, PubMed, Embase, companies making products being analyzed, journal articles resulting from confirmatory studies. Interventions: None Primary and secondary outcome measures: Characteristics of studies - study design (randomized controlled trials, observational), primary outcome used (clinical, surrogate), blinding, number of patients in studies, patient median age, number of men and women. Results: Eleven companies confirmed 36 publications for 19 products (21 indications). Twenty-nine out of the 36 studies were randomized controlled trials (RCTs) but only 10 stated if they were blinded. Twenty used surrogate outcomes. The median age of patients was 56 (interquartile range (IQR) 44, 61). The median number of men per study/trial was 184 (IQR 58, 514) versus women - 141 (IQR 46, 263). Conclusions: Postmarket studies required by Health Canada had more rigorous methodology than those required by either the Food and Drug Administration or the European Medicines Agency. There were still deficiencies in these studies. The absence of blinding in the majority of RCTs may introduce bias in their results. The use of surrogate outcomes especially in oncology trials means that improvements in survival are not available. The relatively young age of patients, even for products for cancer, means that predicting how the elderly will respond is often unknown. The almost universal finding that men outnumbered number women may make it hard to differentiate responses by sex. These results raise potential concerns about the quality of evidence that Health Canada accepts.
Effectiveness of steroid therapy on pneumonic chronic obstructive pulmonary disease exacerbation: a multi-centred retrospective cohort study
<p><span>Background</span></p> <p><span>To date, no consensus exists on the effects of steroid use on pneumonic chronic obstructive pulmonary disease (COPD) owing to trial design issues in previous trials involving these conditions. Therefore, we aimed to evaluate steroid effectiveness in pneumonic COPD exacerbation patients.</span></p> <p><span>Methods</span></p> <p><span>This multi-centred, retrospective, observational study was conducted across five acute general hospitals in Japan. We analysed the association between parenteral/oral steroid therapy and time to clinical stability in pneumonic COPD exacerbation. </span></p> <p><span>We used a validated algorithm derived from the 10th revision of the International Classification of Diseases and Related Health Problems (ICD-10) to include pneumonic COPD exacerbation patients. We excluded patients with other hypoxia causes (asthma exacerbation, pneumothorax, heart failure) and complicated pneumonia (obstructive pneumonia, empyema), those who required tracheal intubation/vasopressors, and those who were clinically stable on the admission day. </span></p> <p><span>The primary outcome was time to clinical stability. Multiple imputation was used for missing data. Propensity scores within each imputed dataset were calculated using potential confounding factors. The Fine and Gray model was used within each dataset to account for the competing risk of death and hospital discharge without clinical stability, and we combined the results.</span></p> <p><span>Results</span></p> <p><span>Altogether, 1237 patients were included. The pooled estimated subdistribution hazard ratio of time to clinical stability in steroid versus non-steroid users was 0.89 (95% confidence interval, 0.78<a name="_Hlk33128668"> to</a> 1.03). However, there were potentially unmeasured confounders, and we could not assess longer-term outcomes.</span></p> <p><span>Conclusions</span></p> <p><span>The current study recommends that steroid therapy should not be used routinely for pneumonic COPD exacerbation.</span></p>
Data from: Sputum microbiota and inflammation at stable state and during exacerbations in a cohort of chronic obstructive pulmonary disease (COPD) patients
Background: Exacerbations of chronic obstructive pulmonary disease (COPD) are debilitating events and spur disease progression. Infectious causes are frequent; however, it is unknown to what extent exacerbations are caused by larger shifts in the airways' microbiota. The aim of the current study was to analyse the changes in microbial composition between stable state and during exacerbations, and the corresponding immune response. Methods: The study sample included 36 COPD patients examined at stable state and exacerbation from the Bergen COPD Cohort and Exacerbations studies, and one patient who delivered sputum on 13 different occasions during the three-year study period. A physician examined the patients at all time points, and sputum induction was performed by stringent protocol. Only induced sputum samples were used in the current study, not spontaneously expectorated sputum. Sputum inflammatory markers (IL-6, IL-8, IL-18, IP-10, MIG, TNF-α) and antimicrobial peptides (AMPs, i.e. LL-37/hCAP-18, SLPI) were measured in supernatants, whereas target gene sequencing (16S rRNA) was performed on corresponding cell pellets. The microbiome bioinformatics platform QIIME2TM and the statistics environment R were applied for bioinformatics analyses. Results: Levels of IP-10, MIG, TNF-α and AMPs were significantly different between the two disease states. Of 36 sample pairs, 24 had significant differences in the 12 most abundant genera between disease states. The diversity was significantly different in several individuals, but not when data was analysed on a group level. The one patient case study showed longitudinal dynamics in microbiota unrelated to disease state. Conclusion: Changes in the sputum microbiota with ch anging COPD disease states are common, and are accompanied by changes in inflammatory markers. However, the changes are highly individual and heterogeneous events.
Data from: Patient characteristics associated with tuberculosis treatment default: a cohort study in a high-incidence area of Lima, Peru
Background: Although tuberculosis (TB) is usually curable with antibiotics, poor adherence to medication can lead to increased transmission, drug resistance, and death. Prior research has shown several factors to be associated with poor adherence, but this problem remains a substantial barrier to global TB control. We studied patients in a high-incidence district of Lima, Peru to identify factors associated with premature termination of treatment (treatment default). Methods: We conducted a prospective cohort study of adult smear-positive TB patients enrolled between January 2010 and December 2011 with no history of TB disease. Descriptive statistics and multivariable logistic regression analyses were performed to determine risk factors associated with treatment default. Results: Of the 1233 patients studied, 127 (10%) defaulted from treatment. Patients who defaulted were more likely to have used illegal drugs (OR = 4.78, 95% CI: 3.05-7.49), have multidrug-resistant TB (OR = 3.04, 95% CI: 1.58-5.85), not have been tested for HIV (OR = 2.30, 95% CI: 1.50-3.54), drink alcohol at least weekly (OR = 2.22, 95% CI: 1.40-3.52), be underweight (OR = 2.08, 95% CI: 1.21-3.56), or not have completed secondary education (OR = 1.55, 95% CI: 1.03-2.33). Conclusions: Our study identified several factors associated with defaulting from treatment, suggesting a complex set of causes that might lead to default. Addressing these factors individually would be difficult, but they might help to identify certain high-risk patients for supplemental intervention prior to treatment interruption. Treatment adherence remains a barrier to successful TB care and reducing the frequency of default is important for both the patients' health and the health of the community.
Data from: Anthracycline induced cardiotoxicity: prospective cohort study from Pakistan.
Objectives: To identify anthracycline induced acute (within one month) and early onset chronic progressive (within year) cardiotoxicity in children younger than 16 years of age with childhood malignancies at tertiary care center of Pakistan. Design: Prospective Cohort study. Setting: Aga Khan University, Karachi, Pakistan. Participants: 110 children (aged 1 month to 16 years). Intervention: Anthracycline (Doxorubicin and/or Daunorubicin). Outcome measurements: All children who received anthracycline as chemotherapy and three echocardiographic evaluations (baseline, one month and 1 year) between July 2010 and June 2012 were prospectively analyzed for cardiac dysfunction. Statistical analysis including systolic and diastolic functions at baseline, 1 month and 1 year were made by repeated measures analysis of variance (r-ANOVA). Results: Mean age was 74±44 months and 75 (68.2%) were males. Acute lymphoblastic leukemia (ALL) was seen in 70 (64%) patients. Doxorubicin alone was used in 59 (54%) and combination therapy was used in 35(32%). A cumulative dose of anthracycline <300mg/m2 was in 95 (86%). Fifteen (14%) children developed cardiac dysfunction within a month and 28(25%) children within a year. Of these 10/15 (66.6%) and 12/28 (42%) had isolated diastolic dysfunction respectively, while 5/15 (33.3%) and 16/28 (57%) had combined systolic and diastolic dysfunction. Seven (6.4%) patients expired due to severe cardiac dysfunction. 8/59 (13.5%) children receiving doxorubicin showed dysfunction mostly related to higher cumulative dose (p=<0.001). Cardiotoxicity was high where combination of doxorubicin and daunorubicin was used (p=0.004). Conclusion: Anthracycline induced cardiac dysfunction is high. Long term follow-up is essential in children received any dosage of anthracyclines because of its late manifestation.
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.