Miracle-dz/UniFAR-FTUs huggingface dataset:
Volunteering and its association with participation and life satisfaction following traumatic brain injury

ABSTRACT Background: Volunteering has been found to improve life satisfaction and participation in the general population, but its impact has not been thoroughly studied among those with traumatic brain injury (TBI). It is important to investigate whether volunteering is helpful in addressing participation and life satisfaction to inform future treatment. Objective: To characterize those who volunteer after moderate-severe TBI and to investigate the association of volunteering with participation and life satisfaction after TBI. Methods: Using data from a single site contributing to the TBI Model Systems National Database, a retrospective analysis of 725 individuals with TBI was conducted. General Linear Models were used to compare outcomes of those who volunteer and those who do not after controlling for important covariates. Results: Volunteers were more likely to be employed/students, have better current functioning, be further post-injury, non-Hispanic white, and have more education. Significant relationships, after controlling for covariates, were found between volunteering and higher life satisfaction, more frequent community engagement, and greater social relations. No significant relationship between volunteering and productivity emerged. Conclusions: Given the positive relationship between volunteer status with life satisfaction and aspects of participation, future research should investigate the barriers/facilitators of volunteering to improve well-being and participation after TBI.
The usefulness of short-course prednisolone during the initial phase of an elimination diet trial in dogs with food-induced atopic dermatitis.

BACKGROUND Food allergy is a possible cause of atopic dermatitis (AD) in dogs; it is typically diagnosed following an eight-week elimination diet trial (EDT) and a provocation with the original diet. This lengthy procedure is difficult for owners and its interpretation may be unclear. HYPOTHESIS/OBJECTIVES To test the effect of prednisolone used in the first weeks of an EDT in order to reduce the total time period for diagnosis. The goal was to perform food challenges earlier than after the traditionally recommended eight weeks. ANIMALS Fifty-three dogs with AD were included in the study. METHODS AND MATERIALS All dogs were fed a commercially available extensively hydrolyzed protein-based commercial pet food and treated with prednisolone for at least two weeks to control pruritus and inflammation. Dogs were challenged two weeks after prednisolone finished, provided that no flare had occurred. Dogs with relapsing signs were fed the hydrolyzate for at least eight weeks with or without further prednisolone treatment. RESULTS Ten of 53 dogs (19%) had no relapse after two weeks off prednisolone: they were subsequently challenged with their regular food, had a relapse of signs and were diagnosed with a food-induced AD within four to six weeks of starting the EDT. In the other dogs, signs remained uncontrolled without prednisolone or relapsed rapidly after its discontinuation: they were considered nonfood-allergic after an eight week EDT. CONCLUSION AND CLINICAL IMPORTANCE This study demonstrates that a shorter EDT is possible if the allergic pruritus and inflammation are initially controlled with a short course of glucocorticoids. This shortened trial is likely to improve owner adherence and facilitate the diagnosis of food allergy.
Computationally predicted gene regulatory networks in molluscan biomineralization identify extracellular matrix production and ion transportation pathways

Abstract Motivation The molecular processes regulating molluscan shell production remain relatively uncharacterized, despite the clear evolutionary and societal importance of biomineralization. Results Here we built the first computationally predicted gene regulatory network (GRN) for molluscan biomineralization using Antarctic clam (Laternula elliptica) mantle gene expression data produced over an age-categorized shell damage-repair time-course. We used previously published in vivo in situ hybridization expression data to ground truth gene interactions predicted by the GRN and show that candidate biomineralization genes from different shell layers, and hence microstructures, were connected in unique modules. We characterized two biomineralization modules of the GRN and hypothesize that one module is responsible for translating the extracellular proteins required for growing, repairing or remodelling the nacreous shell layer, whereas the second module orchestrates the transport of both ions and proteins to the shell secretion site, which are required during normal shell growth, and repair. Our findings demonstrate that unbiased computational methods are particularly valuable for studying fundamental biological processes and gene interactions in non-model species where rich sources of gene expression data exist, but annotation rates are poor and the ability to carry out true functional tests are still lacking. Availability and implementation The raw RNA-Seq data is freely available for download from NCBI SRA (Accession: PRJNA398984), the assembled and annotated transcriptome can be viewed and downloaded from molluscDB (ensembl.molluscdb.org) and in addition, the assembled transcripts, reconstructed GRN, modules and detailed annotations are all available as Supplementary Files. Supplementary information Supplementary data are available at Bioinformatics online.
Greater genetic and regulatory plasticity of retained duplicates in Epichloë endophytic fungi

Gene duplicates can act as a source of genetic material from which new functions arise. Most duplicated genes revert to single copy genes and only a small proportion are retained. However, it remains unclear why some duplicate genes persist in the genome for an extended time. We investigate this question by analysing retained gene duplicates in the fungal genus Epichloë, ascomycete fungi that form close endophytic symbioses with their host grasses. Retained duplicates within this genus have two independent origins, but both long pre‐date the origin and diversification of the genus Epichloë. We find that loss of retained duplicates within the genus is frequent and often associated with speciation. Retained duplicates have faster evolutionary rates (Ka) and show relaxed selection (Ka/Ks) compared to single copy genes. Both features are time‐dependent. Through comparison of conspecific strains, we find greater evolutionary rates in coding regions and sequence divergence in regulatory regions of retained duplicates than single copy genes, with this pattern more pronounced for strains adapted to different grass host species. Consistent with this sequence divergence in regulatory regions, transcriptome analyses show greater expression variation of retained duplicates than single copy genes. This suggest that cis‐regulatory changes make important contributions to the expression patterns of retained duplicates. Coupled with supporting observations from the model yeast Saccharomyces cerevisiae, these data suggest that genetic robustness and regulatory plasticity are common drivers behind the retention of duplicated genes in fungi.
High Dose of Dietary Nicotinamide Riboside Induces Glucose Intolerance and White Adipose Tissue Dysfunction in Mice Fed a Mildly Obesogenic Diet

Nicotinamide riboside (NR) is a nicotinamide adenine dinucleotide (NAD+) precursor vitamin. The scarce reports on the adverse effects on metabolic health of supplementation with high-dose NR warrant substantiation. Here, we aimed to examine the physiological responses to high-dose NR supplementation in the context of a mildly obesogenic diet and to substantiate this with molecular data. An 18-week dietary intervention was conducted in male C57BL/6JRccHsd mice, in which a diet with 9000 mg NR per kg diet (high NR) was compared to a diet with NR at the recommended vitamin B3 level (control NR). Both diets were mildly obesogenic (40 en% fat). Metabolic flexibility and glucose tolerance were analyzed and immunoblotting, qRT-PCR and histology of epididymal white adipose tissue (eWAT) were performed. Mice fed with high NR showed a reduced metabolic flexibility, a lower glucose clearance rate and aggravated systemic insulin resistance. This was consistent with molecular and morphological changes in eWAT, including sirtuin 1 (SIRT1)-mediated PPARγ (proliferator-activated receptor γ) repression, downregulated AKT/glucose transporter type 4 (GLUT4) signaling, an increased number of crown-like structures and macrophages, and an upregulation of pro-inflammatory gene markers. In conclusion, high-dose NR induces the onset of WAT dysfunction, which may in part explain the deterioration of metabolic health.
Effects of Different Growth Stages of Amaranth Silage on the Rumen Degradation of Dairy Cows

Simple Summary The production of some crops is limited in parts of the world because of the shortage of water resources. Therefore, it is an irresistible trend to make full use of roughage resources. Amaranth is one of the crops which can grow in the poor soils and areas with high temperature and limited rainfall. In addition, the quality and yield of forage depend on harvest stage, and the appropriate growth stage is an important influencing factor of forage quality. The purpose of this study was to investigate the rumen degradation characteristic of amaranth silage including four kinds of growing stages. The results showed that with the extension of the growing period, the crude protein contents decreased gradually, and the contents of dry matter, neutral detergent fiber, and acid detergent fiber exhibited an opposite trend. Besides, the ruminal dry matter, crude protein, neutral detergent fiber, and acid detergent fiber degradability was significantly affected by growth stage. Our result suggested that amaranth silage can be used as a roughage in the diet of dairy cow. However, growth stage is an essential factor to influence the ruminal degradability, thus the growth stage of amaranth should be taken into consideration when making silage. Abstract The purpose of this study was to investigate the rumen degradation characteristic of amaranth silage (Amaranthus hypochondriacus) including four kinds of growing stages (budding stage (BS), 50 d after planting (DAP); early flowering stage (ES), 58 DAP; peak flowering stage (PS), 70 DAP; heading stage (HS), 90 DAP). Four Holstein dairy cows with permanent ruminal cannulas were used as experimental animals. Nylon-bag method was used to assess the ruminal degradability of dry matter (DM), crude protein (CP), neutral detergent fiber (NDF), and acid detergent fiber (ADF). The results showed that the concentration of DM in HS was significantly higher than other stages (p < 0.05), whereas the contents of CP, were lower than in other stages (p < 0.05). With the extension of the growing period, the DM effective degradability of amaranth silage decreased gradually, and the difference was significant (p < 0.05). The ruminal CP degradation of 72 h was more than 80%, and compared with ES and HS, the degradation rate of BS and PS was significantly increased (p < 0.05). Compared to BS, the effective degradability of CP was increased (p < 0.05) in ES and HS. For ruminal NDF degradability, the effective degradability of HS was minimum, and it had a noticeable difference with BS and ES (p < 0.05). Thus, the different quality of amaranth growth stage including chemical contents and rumen degradation should be taken into consideration when making amaranth silage. In the present study, the optimal growth stage of amaranth was from the peak flowering stage to heading stage for ensiling.
Maximum Value of End-Tidal Carbon Dioxide Concentrations during Resuscitation as an Indicator of Return of Spontaneous Circulation in out-of-Hospital Cardiac Arrest

Abstract Background: The end-tidal carbon dioxide (ETCO2) concentration during resuscitation (CPR) of an out-of-hospital cardiac arrest (OHCA) has an increasingly well-known prognostic value. Nevertheless, few studies have investigated its maximum value in different etiologies. Methods: It was a retrospective, observational, multicentre study from the French OHCA Registry. All adult OHCA with a known maximum value of ETCO2 during CPR were included. The primary end-point was to determine the area under the receiver operating characteristic curve (AUROC) of the maximum value of ETCO2 during resuscitation for the return of spontaneous circulation (ROSC). Results: Of the 53,048 eligible subjects from 2011 to 2018, ETCO2 was known in 32,249 subjects (61%). Among them, there were 9.2% of traumatic OHCA, 37.7% of suspected cardiac etiology and 16.4% of suspected respiratory etiology. The AUROC of maximum value of ETCO2 during CPR to achieve ROSC was 0.887 95CI [0.875–0.898] in traumatic OHCA, 0.772 95CI [0.765–0.780] in suspected cardiac etiology and 0.802 95CI [0.791–0.812] in suspected respiratory etiology. The threshold with no survivors at d-30 was <10 mmHg for traumatic etiologies and <6 mmHg for suspected cardiac and respiratory causes. The probability of ROSC increased with the value of ETCO2 in the 3 etiologies studied. Conclusions: The maximum value of ETCO2 during OHCA resuscitation was strongly associated with ROSC, especially in the case of a traumatic cause. This suggests that a single elevated ETCO2 value, regardless of time, could help to predict the outcome.
Exosomes: Versatile Nano Mediators of Immune Regulation

One of many types of extracellular vesicles (EVs), exosomes are nanovesicle structures that are released by almost all living cells that can perform a wide range of critical biological functions. Exosomes play important roles in both normal and pathological conditions by regulating cell-cell communication in cancer, angiogenesis, cellular differentiation, osteogenesis, and inflammation. Exosomes are stable in vivo and they can regulate biological processes by transferring lipids, proteins, nucleic acids, and even entire signaling pathways through the circulation to cells at distal sites. Recent advances in the identification, production, and purification of exosomes have created opportunities to exploit these structures as novel drug delivery systems, modulators of cell signaling, mediators of antigen presentation, as well as biological targeting agents and diagnostic tools in cancer therapy. This review will examine the functions of immunocyte-derived exosomes and their roles in the immune response under physiological and pathological conditions. The use of immunocyte exosomes in immunotherapy and vaccine development is discussed.
Capturing Maize Stand Heterogeneity Across Yield-Stability Zones Using Unmanned Aerial Vehicles (UAV)

Despite the new equipment capabilities, uneven crop stands are still common occurrences in crop fields, mainly due to spatial heterogeneity in soil conditions, seedling mortality due to herbivore predation and disease, or human error. Non-uniform plant stands may reduce grain yield in crops like maize. Thus, detecting signs of variability in crop stand density early in the season provides critical information for management decisions and crop yield forecasts. Processing techniques applied on images captured by unmanned aerial vehicles (UAVs) has been used successfully to identify crop rows and estimate stand density and, most recently, to estimate plant-to-plant interval distance. Here, we further test and apply an image processing algorithm on UAV images collected from yield-stability zones in a commercial crop field. Our objective was to implement the algorithm to compare variation of plant-spacing intervals to test whether yield differences within these zones are related to differences in crop stand characteristics. Our analysis indicates that the algorithm can be reliably used to estimate plant counts (precision >95% and recall >97%) and plant distance interval (R2 ~0.9 and relative error <10%). Analysis of the collected data indicated that plant spacing variability differences were small among plots with large yield differences, suggesting that it was not a major cause of yield variability across zones with distinct yield history. This analysis provides an example of how plant-detection algorithms can be applied to improve the understanding of patterns of spatial and temporal yield variability.
Quantifying Actual and Perceived Inaccuracy When Estimating the Sugar, Energy Content and Portion Size of Foods

In order to adhere to dietary guidelines and manage health risks, consumers need to be able to estimate with some accuracy the sugar and energy content of foods. The present study compared how well participants could estimate the sugar and energy content of foods, the weight of foods, and approximate portion size (using a hand measure estimation aid). The study had three aims. First, it aimed to investigate differences in accuracy across the four measures. Second, it aimed to examine whether these differences in accuracy between estimation measures were accurately perceived by the participants. Third, it aimed to test if estimation accuracy was related to food journaling experience, body-mass index or gender. One hundred and ninety-seven participants took part in an estimation task and filled in a questionnaire. While the participants were inaccurate when using all four estimation measures, inaccuracy was most pronounced for sugar content (ds ≥ 0.39), which was consistently overestimated by between 62.1% and 98.5% of the sample. None of the other measures showed a consistent pattern of under- or overestimation. Participants’ perceived accuracy did not match their actual accuracy (rs ≤ |0.20|, ps ≥ 0.005). Actual accuracy showed only marginal covariation with food journaling experience (ts ≤ 2.01, ps ≥ 0.049, ds ≤ 0.14), body-mass index (rs ≤ |0.15|, ps ≥ 0.041) or gender (ts ≤ 3.17, ps ≥ 0.002, ds ≤ 0.46). It is particularly challenging for consumers to estimate the sugar content of food, which might have negative consequences for health and well-being. Thus, more education about sugar content and misperceptions is needed to support consumers so that they can make healthy food choices.
Plasma pentraxin 3 is associated with progression of radiographic joint damage, but not carotid atherosclerosis, in female rheumatoid arthritis patients: 3-year prospective study

Abstract Background: Pentraxin 3 (PTX3) has an important role in inflammation, immunity, and atherosclerosis. Rheumatoid arthritis (RA) is a chronic inflammatory disease featuring both joint damage and atherosclerosis. We investigated whether the plasma PTX3 level was associated with progression of joint destruction and subclinical atherosclerosis in RA patients. Methods: Plasma PTX3 levels were measured in 72 women with RA and 80 female control subjects. In RA patients, we also evaluated clinical characteristics, medications, and at one and three years, joint damage and atherosclerosis. Then we investigated whether PTX3 was associated with progression of joint destruction or an increase of carotid intima-media thickness (IMT). Results: Plasma PTX3 levels were significantly higher in the RA patients than in healthy controls (4.05 ± 2.91 ng/mL vs. 1.61 ± 1.05 ng/mL, p < .001). By multivariate linear regression analysis, the plasma pentraxin 3 level was independently associated with radiographic progression of joint damage for 3 years in the RA patients after adjustment for age, disease duration, body mass index, rheumatoid factor, MMP-3, Disease Activity Score 28-ESR, postmenopausal status, current use of corticosteroids and biologic use. On the other hands, pentraxin 3 was not associated with an increase of carotid intima-media thickness in RA patients. Conclusion: Female RA patients had elevated plasma PTX3 levels compared with control female subjects. PTX3 was independently associated with radiographic progression of joint damage in the RA patients, but not with carotid atherosclerosis.
A Comparison of Four Different Methods of Fixation of Osteochondral Fragments

Summary Fixation methods for osteochondral shell grafts were studied using replace-ment of a femoral trochlear autograft in rabbits as the model. Twenty skeletally mature rabbits were divided into four groups with five rabbits in each. The articular cartilage of the femoral trochlea, including 2.0 mm of subchondral bone, was removed using a sagittal bone saw. The grafts were immediately reattached using either small Kirschner pins (K-pins), polydioxanone pins (PDP), polydioxanone suture (PDS), or polymethylmethacrylate (PMMA) cement. Six months postoperatively the rabbits were killed and the graft sites compared to the contralateral control using radiography, gross examination, Safranin-O and H & E staining, and sulphate-35 radioactive uptake. Mild degenerative joint changes were evident radio-graphically in all of the operated joints. Articular surface defects at the graft sites were common and included small craters and erosions; a few had larger areas devoid of cartilage. Defects associated with the pin entrance sites were common in the K-pin and PD P groups. The PDS group had the least number of animals with articular surface defects. Safranin-O staining was complete in the PDS group, partial or complete in the K-pin and PD P groups, and partial in all of the joints in the PMM A group. H & E preparations of the cartilage sections were graded from 1 (normal cartilage) to 5 (multiple fissures, severe degradation). The PDS group had a mean (SD) score of 1.8 (0.8), the PD P group 2.4 (1.1), the K-pin group 2.5 (1.3), and the PMM A group 4.6 (0.6). The scores for the PMM A group were significantly greater then the scores for the other groups (p <0.05). The mean (SD) for radioactive counts per minute/mg tissue in treated graft sites as a percent of control was PDS: 130 (83); PDP : 115 (14); K-pins: 92 (42); PMMA : 91 (29). The relative percentages for radioactive uptake were not significantly different (P >0.05). Graft fixation using PDS, PDP, or K-pins was technically easy to perform and the results were generally satisfactory. Fixation using PMM A was technically demanding and histological evidence of moderate to severe cartilage degradation was present in all treated joints. Femoral trochlear autografts in rabbits were used to study fixation methods for osteochondral graft fragments. Six months after the operations the graft sites were evaluated using radiographs, gross examination, Safranin-O and H & E staining, and sulphate-35 radioactive uptake. Grafts stabilized using polydioxanone suture had the least number of articular surface defects and the most complete Safranin-O staining.
Neonatal Abstinence Syndrome and Childhood Mental Health Conditions, 2009-2015: Commercial Versus Medicaid Populations.

OBJECTIVE This study aimed to examine mental health conditions of children diagnosed with neonatal abstinence syndrome (NAS) in a commercially insured population and compare them with a multistate Medicaid-insured population identified in prior research. METHODS Data from the IBM MarketScan Commercial Database from January 1, 2009, to September 30, 2015, were used to identify mental health conditions among children ages 1-5 both with and without NAS. Frequency analyses were conducted to ascertain intrapopulation differences and differences between the commercially insured and Medicaid populations. RESULTS The NAS rate in the Medicaid population was 28.7 times higher than in the commercially insured population. Although the sample of children with NAS was small, and the results must be interpreted with caution, elevated rates of childhood mental health conditions observed in the commercially insured population were comparable to the Medicaid population. CONCLUSIONS This analysis emphasizes the difference in rates of NAS between commercially insured and Medicaid populations.