Miracle-dz/UniFAR-FTUs huggingface dataset:
Predictive Models of Fever, ICU Transfer, and Mortality in Hospitalized Patients With Neutropenia

Supplemental Digital Content is available in the text. Objectives: Neutropenia is a common side effect of myelosuppressive chemotherapy and is associated with adverse outcomes. Early Warning Scores are used to identify at-risk patients and facilitate rapid clinical interventions. Since few Early Warning Scores have been validated in patients with neutropenia, we aimed to create predictive models and nomograms of fever, ICU transfer, and mortality in hospitalized neutropenic patients. Design: Development of statistical prediction models and nomograms using data from a retrospective cohort study of hospitalized patients with neutropenia. Setting: University of Virginia Medical Center, a tertiary-care academic medical center in Charlottesville, VA. Patients: The derivation and validation cohorts included hospitalized adult patients with neutropenia who were admitted to the inpatient wards between October 2010 and January 2015, and April 2017 and April 2020, respectively. We defined neutropenia as an absolute neutrophil count of less than 500 cells/mm3. Interventions: None. Measurements and Main Results: The derivation cohort included 1,531 hospital admissions in patients with neutropenia. Fever, ICU transfer, and in-hospital mortality occurred in 955 admissions (62%), 297 admissions (19%), and 147 admissions (10%), respectively. In the derivation cohort, the internally validated area under the curves with 95% CI for the fever, ICU transfer, and mortality models were HYPERLINK “callto:0.74%20(0.67-0.84),%200.77”0.74 (0.67–0.84), 0.77 (0.67–0.86), and HYPERLINK “callto:0.95%20(0.0.87-1.0”0.95 (0.0.87–1.0), respectively. The validation cohort included 1,250 admissions in patients with neutropenia. In the validation cohort, the area under the curve (95% CI) for the fever, ICU transfer, and mortality models were HYPERLINK “callto:0.70%20(0.67-0.73),%200.78”0.70 (0.67–0.73), 0.78 (0.72–0.84), and HYPERLINK “callto:0.91%20(0.88-0.94”0.91 (0.88–0.94), respectively. Using these models, we developed clinically applicable nomograms which detected adverse events a median of 4.0–11.4 hours prior to onset. Conclusions: We created predictive models and nomograms for fever, ICU transfer, and mortality in patients with neutropenia. These models could be prospectively validated to detect high-risk patients and facilitate early clinical intervention to improve patient outcomes.
Effects of differing withdrawal times from ractopamine hydrochloride on residue concentrations of beef muscle, adipose tissue, rendered tallow, and large intestine

Ractopamine hydrochloride (RAC) is a beta-agonist approved by the U.S. Food and Drug Administration (FDA) as a medicated feed ingredient for cattle during the final days of finishing to improve feed efficiency and growth. Maximum residue limits and U.S. FDA residue tolerances for target tissues have defined management practices around RAC usage in the U.S. However, many countries have adopted zero tolerance policies and testing of off-target tissues, presenting a major challenge for international export. Therefore, the objective this study was to determine the necessary withdrawal time among cattle group-fed RAC to achieve residue concentrations below tolerance levels in muscle and off-target tissues. Specifically, both total and parent RAC residues were quantified in muscle, adipose tissue, rendered tallow, and large intestines from animals group-fed RAC and subjected to withdrawal 2, 4, or 7 days before harvest. Ractopamine (parent and total) residues were below the assay limit of detection (< 0.12 ng/g) in all muscle and adipose tissue samples from animals in control groups (no RAC). However, RAC residues were detectable, but below the limit of quantitation, in 40% of tallow and 17% of large intestine samples from control animals. As expected, mean RAC residue concentrations in muscle, adipose tissue, and large intestine samples decreased (P < 0.05) as the RAC withdrawal duration (days) was extended. Irrespective of RAC withdrawal duration, mean parent RAC residue concentrations in muscle, adipose tissue, and large intestine ranged from 0.33 to 0.76 ng/g, 0.16 to 0.26 ng/g, 3.97 to 7.44 ng/g, respectively and all tallow samples were > 0.14 ng/g (detectable but below the limit of quantitation). Results of this study provide a baseline for the development of management protocol recommendations associated with withdrawal following group-feeding of RAC to beef cattle in countries that allow RAC use and intend to export to global markets which may be subject to zero tolerance policies and off-target tissue testing.
Gut Microbiome Composition and Metabolomic Pro�les of Wild and Captive Chinese Monals (Lophophorus Lhuysii)

Background (cid:0) The Chinese monal (Lophophorus lhuysii) is an endangered bird species, with a wild population restricted to the mountains of southwest China, and only one known captive population in the world. We investigated the fecal microbiota and metabolomics of wild and captive Chinese monals to explore differences and similarities in nutritional status and digestive characteristics. An integrated approach combining 16S ribosomal rRNA (16S rRNA) gene sequencing and ultra-high performance liquid chromatograph (UHPLC) based metabolomics were used to examine the fecal microbiome composition and the metabolomic pro�le of Chinese monals. Results: The results showed that the alpha diversity of gut microbes in the wild group were signi�cantly higher than that in the captive group and the core bacterial species in the two groups showed remarkable differences at all levels. Metabolomic pro�ling revealed a concurrent difference, mainly related to galactose, starch and sucrose metabolism, fatty acid, bile acid biosynthesis and bile secretion. Furthermore, these metabolites in difference are have a strong correlation with the main microbe in genus level. Conclusions: Various factors related to diet and environmental conditions played a crucial role in shaping the gut microbiome composition and metabolomic pro�le. Through this study, we have established a baseline for a normal gut microbiome and metabolomic pro�le for wild Chinese monals, thus allowing us to evaluate if differences seen in captive specimens has an impact on their overall health and reproduction.
An inventory of biodiversity data sources for conservation monitoring

Many conservation managers, policy makers, businesses and local communities cannot access the biodiversity data they need for informed decision-making on natural resource management. A handful of databases are used to monitor indicators against global biodiversity goals but there is no openly available consolidated list of global data sets to help managers, especially those in high-biodiversity countries. We therefore conducted an inventory of global databases of potential use in monitoring biodiversity states, pressures and conservation responses at multiple levels. We uncovered 145 global data sources, as well as a selection of global data reports, links to which we will make available on an open-access website. We describe trends in data availability and actions needed to improve data sharing. If the conservation and science community made a greater effort to publicise data sources, and make the data openly and freely available for the people who most need it, we might be able to mainstream biodiversity data into decision-making and help stop biodiversity loss.
Noninvasive assessment of peripheral skeletal muscle weakness in idiopathic pulmonary fibrosis: a pilot study with multiparametric MRI of the rectus femoris muscle

Background To investigate differences in magnetic resonance imaging (MRI) features of rectus femoris muscle between idiopathic pulmonary fibrosis (IPF) patients and healthy volunteers. Methods Thirteen IPF patients with GAP Index stage II disease were subjected to pulmonary function tests, 6-minute walk test (6MWT), quadriceps femoris muscle strength measurement and MRI of the thigh at rest. At MRI, muscle cross-sectional areas, T2 and T2* relaxometry, and 3-point Dixon fat fraction were measured. The results were compared to those of eight healthy sedentary volunteers. Results IPF patients had significantly lower %predicted FVC, FEV1 and DLCO (p<0.001 for the three variables) and walked significantly less in the 6MWT (p=0.008). Mean quadriceps femoris muscle strength also was significantly lower in IPF patients (p=0.041). Rectus femoris muscle T2* measurements were significantly shorter in IPF patients (p=0.027). No significant intergroup difference was found regarding average muscle cross-sectional areas (p=0.790 for quadriceps and p=0.816 for rectus femoris) or rectus femoris fat fraction (p=0.901). Rectus femoris T2 values showed a non-significant trend to be shorter in IPF patients (p=0.055). Conclusions Our preliminary findings suggest that, besides disuse atrophy, other factors such as hypoxia (but not inflammation) may play a role in the peripheral skeletal muscle dysfunction observed in IPF patients. This might impact the rehabilitation strategies for IPF patients and warrants further investigation.
Digital Image Analysis of Picrosirius Red Staining: A Robust Method for Multi-Organ Fibrosis Quantification and Characterization

Current understanding of fibrosis remains incomplete despite the increasing burden of related diseases. Preclinical models are used to dissect the pathogenesis and dynamics of fibrosis, and to evaluate anti-fibrotic therapies. These studies require objective and accurate measurements of fibrosis. Existing histological quantification methods are operator-dependent, organ-specific, and/or need advanced equipment. Therefore, we developed a robust, minimally operator-dependent, and tissue-transposable digital method for fibrosis quantification. The proposed method involves a novel algorithm for more specific and more sensitive detection of collagen fibers stained by picrosirius red (PSR), a computer-assisted segmentation of histological structures, and a new automated morphological classification of fibers according to their compactness. The new algorithm proved more accurate than classical filtering using principal color component (red-green-blue; RGB) for PSR detection. We applied this new method on established mouse models of liver, lung, and kidney fibrosis and demonstrated its validity by evidencing topological collagen accumulation in relevant histological compartments. Our data also showed an overall accumulation of compact fibers concomitant with worsening fibrosis and evidenced topological changes in fiber compactness proper to each model. In conclusion, we describe here a robust digital method for fibrosis analysis allowing accurate quantification, pattern recognition, and multi-organ comparisons useful to understand fibrosis dynamics.
An examination of validity and reliability of the Parental Stress Scale in a population based sample of Norwegian parents

The parental stress scale (PSS) is a widely used instrument that assesses stress related to child rearing. Even though several studies have investigated the construct validity and reliability of the PSS, no consensus has been reached regarding which and how many of the original eighteen items that should be included, or a robust factor structure with satisfactory reliability. The present study tested the psychometric properties of the Norwegian version of the PSS and used the advantages of complementary exploratory and confirmatory factor analyses to investigate the underlying factor structure of the PSS items. Data stem from a community sample of 1096 parents from five counties in Norway with a one-year-old child. The sample was randomly split (N = 553/543), and exploratory and confirmatory analyses were performed on each of the samples. Using predefined criteria for the selection of robust items, results revealed a two-dimensional structure (Parental stressors and Lack of rewards) across 13 PSS items, displaying satisfactory reliability. Network analyses revealed differential associations within item constellations and with covariates. Implications of the findings and study limitations are discussed.
Clinical symptoms, comorbidities and complications features in severe and non-severe patients with COVID-19: a systematic review and meta-analysis without cases duplication

Background: The pandemic of COVID-19 posed a challenge to global healthcare. The mortality rates of severe cases range from 8.1% to 31.8%, and it is particularly important to identify risk factors that aggravate the disease.Methods: We performed a systematic review of the literature with meta-analysis, using 7 databases to assess clinical characteristics, comorbidities and complications in severe and non-severe patients with COVID-19. All the observational studies were included. We performed a random or fixed effects model meta-analysis to calculate the pooled proportion and 95% CI. Measure of heterogeneity was estimated by Cochran’s Q statistic, I2 index and P value.Results: 4881 cases from 25 studies related to COVID-19 were included. The most prevalent comorbidity was hypertension (severe: 33.4%, 95% CI: 25.4% - 41.4%; non-severe 21.6%, 95% CI: 9.9% - 33.3%), followed by diabetes (severe: 14.4%, 95% CI: 11.5% - 17.3%; non-severe: 8.5%, 95% CI: 6.1% - 11.0%). The prevalence of ARDS, AKI and shock were all higher in severe cases, with 41.1% (95% CI: 14.1% - 68.2%), 16.4% (95% CI: 3.4% - 29.5%) and 19.9% (95% CI: 5.5% - 34.4%), rather than 3.0% (95% CI: 0.6% - 5.5%), 2.2% (95% CI: 0.1% - 4.2%) and 4.1% (95% CI -4.8% - 13.1%) in non-severe patients, respectively. The death rate was higher in severe cases (30.3%, 95% CI: 13.8% - 46.8%) than non-severe cases (1.5%, 95% CI: 0.1% - 2.8%). Conclusions: Hypertension, diabetes and cardiovascular diseases may be risk factors for COVID-19 patients to develop into severe cases.
Viscoelasticity of concentrated isotropic solutions of semiflexible polymers. 2. Linear response

Linear rheological properties of tightly-entangled isotropic solutions of semi-flexible polymers are calculated using a tube model, and qualitative predictions are given for the response of more dilute solutions. The linear complex modulus of a solution of long, tightly-entangled chains is dominated at low frequencies by a curvature contribution, analogous to the elastic stress of entangled flexible chains, that relaxes by reptation and gives rise to a broad elastic plateau. The modulus is dominated at higher frequencies by a larger tension contribution, whose frequency dependence is controlled at intermediate frequencies by the diffusion of excess length along the tube and at very high frequencies by the unhindered transverse motion of the chain within the tube. This high-frequency regime yields a complex modulus that varies as G*(ω) ∝ (iω)3/4 with frequency ω. Solutions of shorter, rod-like chains also exhibit a slowly-decaying orientational contribution analogous to the elastic stress found in solution.
Soil water storage in an upland forest after selective logging in Central Amazonia

Soil water storage of Central Amazonian soil profiles in upland forest plots subjected to selective logging (in average, 8 trees or 34, 3 m3 of timber per hectare were removed) was measured in four layers, down to a depth of 70 cm. The study lasted 27-months and was divided in two phases: measurements were carried out nearly every week during the first 15 months; in the following year, five intensive periods of measurements were performed. Five damage levels were compared: (a) control (undisturbed forest plot); (b) centre of the clearing/gap; (c) edge of the gap; (d) edge of the remaining forest; and (e) remaining forest. The lowest values for water storage were found in the control (296 ± 19.1 mm), while the highest were observed (333 ± 25.8 mm) in the centre of the gap, during the dry period. In the older gaps (7.5-8.5 year old), soil water storage was similar to the remaining and the control forest, indicating a recovery of hydric soil properties to nearly the levels prior to selective logging.
The Many Roads to Generality in Ecology

ABSTRACT:The variety of nature presents a challenge for ecologists. Individual organisms differ from one another in ways both obvious and subtle, even if they're members of the same species living in the same location. Different populations, species, communities, ecosystems, biomes, habitats, food webs, etc. also differ from another. What, if anything, can be said in general about ecological systems and how they work? If there are generalities in ecology, do they take the form of exceptionless "laws of nature" analogous to the laws of physics? Or do they take some other form? Should ecologists even try to identify ecological generalities? If so, how? The variety of nature is matched by the variety of ecologists' answers to those questions. I will suggest that all of their answers are right—sometimes. Here I propose a taxonomy of the many different "roads to generality" in ecology: the various different kinds of "generality" that ecologists seek. I argue that each road to generality is valuable in its own way, but that different roads are useful in different contexts and for different purposes. Different roads to generality thus can be complementary to one another, and it would be a mistake for the field of ecology as a whole to focus exclusively on any one of them.
Brain transcriptomic changes in Japanese quail reveal a role for neurotensin in avian parental care

For many species, parental care critically affects offspring survival. But what drives animals to display parental behaviours towards young? In mammals, pregnancy-induced physiological transformations seem key in preparing the neural circuits that lead towards attraction (and reduced-aggression) to young. Beyond mammalian maternal behaviour, knowledge of the neural mechanisms that underlie parental care is severely lacking. We took advantage of a domesticated bird species, the Japanese quail, for which parental behaviour towards chicks can be induced through a sensitization procedure, a process that is not effective in all animals. We used the variation in parental responses to study neural transcriptomic changes associated with the sensitization procedure itself, with the outcome of the procedure (i.e., presence of parental behaviours) and with spontaneous parental care (i.e., in the absence of sensitization). Out of the brain regions studied, we found that most differences in gene expression were located in the hypothalamus. Our results highlight several molecular pathways that may contribute to the modulation of avian parental care. We identified one gene, neurotensin, that was previously only demonstrated to be causally associated with parental care in mammals. Our work opens new avenues of research into understanding the neural basis of parental care in non-mammalian species.
Separase cleaves the kinetochore protein Meikin to direct the meiosis I/II transition

To generate haploid gametes, germ cells undergo two consecutive meiotic divisions requiring key changes to the cell division machinery. Here, we explore the regulatory mechanisms that differentially control meiotic events. We demonstrate that the protease Separase rewires key cell division processes at the meiosis I/II transition by cleaving the meiosis-specific protein Meikin. In contrast to cohesin, which is inactivated by Separase proteolysis, cleaved Meikin remains functional, but results in a distinct activity state. Full-length Meikin and the C-terminal Meikin Separase-cleavage product both localize to kinetochores, bind to Plk1 kinase, and promote Rec8 cleavage, but our results reveal distinct roles for these proteins in controlling meiosis. Mutations that prevent Meikin cleavage or that conditionally inactivate Meikin at anaphase I both result in defective meiosis II chromosome alignment. Thus, Separase cleavage of Meikin creates an irreversible molecular switch to rewire the cell division machinery at the meiosis I/II transition.
Modality-specific frequency band activity during neural entrainment to auditory and visual rhythms

Rhythm perception depends on the ability to predict the onset of rhythmic events. Previous studies indicate beta band modulation is involved in predicting the onset of auditory rhythmic events (Snyder & Large, 2005; Fujioka et al., 2009, 2012). We sought to determine if similar processes are recruited for prediction of visual rhythms by investigating whether beta band activity plays a role in a modality dependent manner for rhythm perception. We looked at source-level EEG time-frequency neural correlates of prediction using an omission paradigm with auditory and visual rhythms. By using omissions, we can separate out predictive timing activity from stimulus driven activity. We hypothesized that there would be modality specific markers of rhythm prediction in induced beta band oscillatory activity, characterized primarily by activation in the motor system specific to auditory rhythm processing. Our findings suggest the existence of overlapping networks of predictive beta activity based on common activation in the parietal and right frontal regions, auditory specific predictive beta in bilateral sensorimotor regions, and visually specific predictive beta in midline central, and bilateral temporal/parietal regions. We also found evidence for evoked predictive beta activity in the left sensorimotor region specific to auditory rhythms. These findings implicate modality dependent networks for auditory and visual rhythm perception. The results further suggest that auditory rhythm perception may have left hemispheric specific mechanisms.
Rare Genetic Variation Underlying Human Diseases and Traits: Results from 200,000 Individuals in the UK Biobank

Background Many human diseases are known to have a genetic contribution. While genome-wide studies have identified many disease-associated loci, it remains challenging to elucidate causal genes. In contrast, exome sequencing provides an opportunity to identify new disease genes and large-effect variants of clinical relevance. We therefore sought to determine the contribution of rare genetic variation in a curated set of human diseases and traits using a unique resource of 200,000 individuals with exome sequencing data from the UK Biobank. Methods and Results We included 199,832 participants with a mean age of 68 at follow-up. Exome-wide gene-based tests were performed for 64 diseases and 23 quantitative traits using a mixed-effects model, testing rare loss-of-function and damaging missense variants. We identified 51 known and 23 novel associations with 26 diseases and traits at a false-discovery-rate of 1%. There was a striking risk associated with many Mendelian disease genes including: MYPBC3 with over a 100-fold increased odds of hypertrophic cardiomyopathy, PKD1 with a greater than 25-fold increased odds of chronic kidney disease, and BRCA2, BRCA1, ATM and PALB2 with 3 to 10-fold increased odds of breast cancer. Notable novel findings included an association between GIGYF1 and type 2 diabetes (OR 5.6, P=5.35×10−8), elevated blood glucose, and lower insulin-like-growth-factor-1 levels. Rare variants in CCAR2 were also associated with diabetes risk (OR 13, P=8.5×10−8), while COL9A3 was associated with cataract (OR 3.4, P=6.7×10−8). Notable associations for blood lipids and hypercholesterolemia included NR1H3, RRBP1, GIGYF1, SCGN, APH1A, PDE3B and ANGPTL8. A number of novel genes were associated with height, including DTL, PIEZO1, SCUBE3, PAPPA and ADAMTS6, while BSN was associated with body-mass-index. We further assessed putatively pathogenic variants in known Mendelian cardiovascular disease genes and found that between 1.3 and 2.3% of the population carried likely pathogenic variants in known cardiomyopathy, arrhythmia or hypercholesterolemia genes. Conclusions Large-scale population sequencing identifies known and novel genes harboring high-impact variation for human traits and diseases. A number of novel findings, including GIGYF1,represent interesting potential therapeutic targets. Exome sequencing at scale can identify a meaningful proportion of the population that carries a pathogenic variant underlying cardiovascular disease.