The Brain Imaging Data Structure (BIDS) is a specification accompanied by a software ecosystem that was designed to create reproducible and automated workflows for processing neuroimaging data. BIDS ...Apps flexibly build workflows based on the metadata detected in a dataset. However, even BIDS valid metadata can include incorrect values or omissions that result in inconsistent processing across sessions. Additionally, in large-scale, heterogeneous neuroimaging datasets, hidden variability in metadata is difficult to detect and classify. To address these challenges, we created a Python-based software package titled “Curation of BIDS” (CuBIDS), which provides an intuitive workflow that helps users validate and manage the curation of their neuroimaging datasets. CuBIDS includes a robust implementation of BIDS validation that scales to large samples and incorporates DataLad––a version control software package for data––as an optional dependency to ensure reproducibility and provenance tracking throughout the entire curation process. CuBIDS provides tools to help users perform quality control on their images’ metadata and identify unique combinations of imaging parameters. Users can then execute BIDS Apps on a subset of participants that represent the full range of acquisition parameters that are present, accelerating pipeline testing on large datasets.
•CuBIDS is a workflow and software package for curating MRI BIDS data.•CuBIDS summarizes the heterogeneity in a MRI BIDS dataset.•CuBIDS prepares BIDS data for successful preprocessing pipeline runs.•CuBIDS helps users perform metadata-based quality control on MRI BIDS data.
Individual differences in cognition during childhood are associated with important social, physical, and mental health outcomes in adolescence and adulthood. Given that cortical surface arealization ...during development reflects the brain's functional prioritization, quantifying variation in the topography of functional brain networks across the developing cortex may provide insight regarding individual differences in cognition. We test this idea by defining personalized functional networks (PFNs) that account for interindividual heterogeneity in functional brain network topography in 9-10 year olds from the Adolescent Brain Cognitive Development℠ Study. Across matched discovery (n = 3525) and replication (n = 3447) samples, the total cortical representation of fronto-parietal PFNs positively correlates with general cognition. Cross-validated ridge regressions trained on PFN topography predict cognition in unseen data across domains, with prediction accuracy increasing along the cortex's sensorimotor-association organizational axis. These results establish that functional network topography heterogeneity is associated with individual differences in cognition before the critical transition into adolescence.
Abstract
Grazing of cool-season cover crops has been shown to be a viable tool in extending the grazing season while mitigating environmental risks associated with row crop farming systems. While ...there is a vast amount of research available on cover crops in relation to soil health, a more novel approach would be to focus on forage production and animal performance when grazing cover crops. Therefore, our objective was to evaluate the effects of cattle removal date on forage yield, forage quality, and steer performance when grazing cool-season cover crops. A cool-season forage mix consisting of ‘Cosaque’ oats (Avena strigose), ‘FL401’ cereal rye (Secale cereal), ‘AU Sunrise’ crimson clover (Trifolium incarnatum), and ‘T-raptor’ brassica (Brassica napus × B. rapa) was established in twelve, 0.62 ha paddocks in Headland, AL. Each paddock was then randomly allocated to one of four cattle removal treatments: 1) no grazing (CON); 2) February removal (FEB); 3) March removal (MAR); or 4) April removal (APR). Three tester steers were randomly allotted, based on body weight (BW), to each of the grazing treatments, excluding CON. The tester steers were weighed every 30 d for calculation of initial BW, final BW, and average daily gain (ADG). At inception and every subsequent two weeks, forage was harvested to analyze average forage yield, neutral detergent fiber (NDF), acid detergent fiber (ADF), and crude protein (CP). All data were analyzed using GLIMMIX procedure of SAS version 9.4 (SAS Inst., Cary, NC). Significant differences in forage yield were detected between CON and FEB (3,913 vs. 2,261 kg/ha; P < 0.001), CON and MAR (3,913 vs. 1,790 kg/ha; P < 0.001), and CON and APR (3,913 vs. 1,810 kg/ha; P < 0.001). There were no differences found for ADG (1.2 kg/day; P = 0.56), NDF (50.94%; P = 0.46), or ADF (30.34%; P = 0.25) among treatments. Results indicate that grazing of cool-season annual cover crops will reduce forage yield, but removal date of cattle will not further affect forage yield, quality, or individual cattle performance. Thus, we can reduce winter supplementation needs for cattle by increasing grazing days; however, under continuous grazing for stocker cattle production, forage availability may inevitably be the limiting factor.
► We tracked seabirds of the tropical Indian Ocean to identify major foraging hotspots. ► Five large oceanic areas have both high seabird densities and high seabird diversity. ► All of them overlap ...with potential threats showing that seabirds may be at risk when foraging. ► These information are crucial to identify potential Marine Protected Areas in the Indian Ocean.
We conducted a regional tracking program on seabirds in order to identify major forging hotspots and potential Marine Protected Areas in the tropical western Indian Ocean. Thirty-one species of seabirds breed in the region, totaling 7.4 million pairs. The main breeding grounds are in the Seychelles, in the Mozambique Channel and in the Mascarene. Seven pelagic species have been tracked so far from eight different islands of the region. Using count per sector analysis we identified five major oceanic foraging hotspots, among which three include the breeding colonies and two are oceanic areas not connected to a breeding island. We found important overlaps between most of these seabird foraging hotspots and potential threats (industrial fishery targeting surface dwelling tunas and marine pollution due to maritime routes) suggesting that in these regions seabirds may be at risk when foraging. Although this analysis is based on a limited number of tracking studies, the knowledge on seabird distribution at sea has increased tremendously in the last 6years in the tropical western Indian Ocean, and this trend will continue, as research is ongoing. The data, we present here for the first time in a single synthesis show clear spatial patterns that identify high priority locations for designation as Marine Protected Areas in the tropical western Indian Ocean.
The genetic and molecular basis of flagellar motility has been investigated for several decades, with innovative research strategies propelling advances at a steady pace. Furthermore, as the ...phenomenon is examined in diverse bacteria, new taxon-specific regulatory and structural features are being elucidated. Motility is also a straightforward bacterial phenotype that can allow undergraduate researchers to explore the palette of molecular genetic tools available to microbiologists. This study, driven primarily by undergraduate researchers, evaluated hundreds of flagellar motility mutants in the Gram-negative plant-associated bacterium Agrobacterium fabrum. The nearly saturating screen implicates a total of 37 genes in flagellar biosynthesis, including genes of previously unknown function.
First-phase ejection fraction (EF1) is a novel measure of early left ventricular systolic dysfunction. We investigated determinants of EF1 and its prognostic value in aortic stenosis.
EF1 was ...measured retrospectively in participants of an echocardiography/cardiovascular magnetic resonance cohort study which recruited patients with aortic stenosis (peak aortic velocity of ≥2 m/s) between 2012 and 2014. Linear regression models were constructed to examine variables associated with EF1. Cox proportional hazards were used to determine the prognostic power of EF1 for aortic valve replacement (AVR, performed as part of clinical care in accordance with international guidelines) or death.
Total follow-up of the 149 participants (69.8% male, 70 (65-76) years, mean gradient 33 (21-42) mm Hg) was 238 029 person-days. Sixty-seven participants (45%) had a low baseline EF1 (<25%) despite normal ejection fraction (67% (62%-71%)). Patients with low EF1 had more severe aortic stenosis (mean gradient 39 (34-45) mm Hg vs 24 (16-35) mm Hg, p<0.001) and more myocardial fibrosis (indexed extracellular volume (iECV) (24.2 (19.6-28.7) mL/m
vs 20.6 (16.8-24.3) mL/m
, p=0.002; late gadolinium enhancement (LGE) prevalence 52% vs 20%, p<0.001). Zva, iECV and infarct LGE were independent predictors of EF1. EF1 improved post-AVR (n=57 with post-AVR EF1 available, baseline 16 (12-24) vs follow-up 27% (22%-31%); p<0.001). Low baseline EF1 was an independent predictor of AVR/death (HR 5.6, 95% CI 3.4 to 9.4), driven by AVR.
EF1 quantifies early, potentially reversible systolic dysfunction in aortic stenosis, is associated with global afterload and myocardial fibrosis, and is an independent predictor of AVR.
Abstract
CRISPR/Cas9 is a powerful tool for editing genomes, but design decisions are generally made with respect to a single reference genome. With population genomic data becoming available for an ...increasing number of model organisms, researchers are interested in manipulating multiple strains and lines. CRISpy-pop is a web application that generates and filters guide RNA sequences for CRISPR/Cas9 genome editing for diverse yeast and bacterial strains. The current implementation designs and predicts the activity of guide RNAs against more than 1000 Saccharomyces cerevisiae genomes, including 167 strains frequently used in bioenergy research. Zymomonas mobilis, an increasingly popular bacterial bioenergy research model, is also supported. CRISpy-pop is available as a web application (https://CRISpy-pop.glbrc.org/) with an intuitive graphical user interface. CRISpy-pop also cross-references the human genome to allow users to avoid the selection of guide RNAs with potential biosafety concerns. Additionally, CRISpy-pop predicts the strain coverage of each guide RNA within the supported strain sets, which aids in functional population genetic studies. Finally, we validate how CRISpy-pop can accurately predict the activity of guide RNAs across strains using population genomic data.
The effects of palliative care (PC) consultation on patient costs and hospitalization metrics in the adult trauma population are unclear.
We interrogated our Level I trauma center databases from ...1/1/19 to 3/31/21 for patients age ≥18 admitted to the trauma service. Patients undergoing PC consult were matched using propensity scoring to those without PC consultation based on age, admission Glasgow Coma Scale score, Injury Severity Score and Head Abbreviated Injury Scale. Total costs, total cost per day, hospital length of stay (LOS), ICU LOS, intubation days, discharge disposition, and rates of nephrology consultation and tracheostomy/feeding tube placements were compared.
140 unique patients underwent PC consultation and were matched to a group not receiving PC consult during the same period. Median total costs in the PC cohort were $39,532 compared to $70,330 in the controls (p<0.01). Median costs per day in the PC cohort were $3,495 vs $17,970 in the controls (p<0.01). Median costs per ICU day in the PC cohort were $3,774 vs $17,127 in the controls (p<0.01). Mean hospital LOS (15.7 vs 7 days), ICU LOS (7.9 vs 2.9 days), and ventilator days (5.1 vs 1.5) were significantly higher in the PC cohort (all p<0.01). Rates of nephrology consultation (8.6 vs 2.1%, p = 0.03) and tracheostomy/feeding tube placements (12.1 vs 1.4%, p<0.01) were also higher in the PC group. Patients were more likely to discharge to hospice if they received a PC consult (33.6 vs 2.1%, p<0.01). Mean time to PC consult was 7.2 days (range 1 hour to 45 days). LOS post-consult correlated positively with time to PC consultation (r = 0.27, p<0.01).
Expert PC services are known to alleviate suffering and avert patient goal- and value-incongruent care. While trauma patients demand significant resources, PC consultation offered in concordance with life-sustaining interventions is associated with significant savings to patients and the healthcare system. Given the correlation between LOS following PC consult and time to PC consult, savings may be amplified by earlier PC consultation in appropriate patients.
The Human respiratory syncytial virus (RSV) is one of the most important viral pathogens, causing epidemics of acute respiratory infection (ARI), especially bronchiolitis and pneumonia, in children ...worldwide. To investigate the RSV burden in Laos, we conducted a one-year study in children <5 years old admitted to Mahosot Hospital, Vientiane Capital, to describe clinical and epidemiological characteristics and predictive factors for severity of RSV-associated ARI. Pooled nasal and throat swabs were tested using multiplex real-time PCR for 33 respiratory pathogens (FTD
kit). A total of 383 patients were included, 277 (72.3%) of whom presented with pneumonia. 377 (98.4%) patients were positive for at least one microorganism, of which RSV was the most common virus (41.0%), with a peak observed between June and September, corresponding to the rainy season. Most RSV inpatients had pneumonia (84.1%), of whom 35% had severe pneumonia. Children <3-months old were a high-risk group for severe pneumonia, independently of RSV infection. Our study suggests that RSV infection is frequent in Laos and commonly associated with pneumonia in hospitalized young children. Further investigations are required to provide a better overall view of the Lao nationwide epidemiology and public health burden of RSV infection over time.
Carbonaceous meteorites are thought to be fragments of C-type (carbonaceous) asteroids. Samples of the C-type asteroid (162173) Ryugu were retrieved by the Hayabusa2 spacecraft. We measured the ...mineralogy and bulk chemical and isotopic compositions of Ryugu samples. The samples are mainly composed of materials similar to those of carbonaceous chondrite meteorites, particularly the CI (Ivuna-type) group. The samples consist predominantly of minerals formed in aqueous fluid on a parent planetesimal. The primary minerals were altered by fluids at a temperature of 37° ± 10°C, about Formula: see text million (statistical) or Formula: see text million (systematic) years after the formation of the first solids in the Solar System. After aqueous alteration, the Ryugu samples were likely never heated above ~100°C. The samples have a chemical composition that more closely resembles that of the Sun's photosphere than other natural samples do.
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