bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of probiotic supplementation on exercise endurance among non-elite athletes: study protocol for a randomized, placebo-controlled, double-blind, clinical trial
Authors: McDermott Caitlin E. , Vincent Heather K. , Mathews Anne E. , Cautela Brunella Gonzalez , Sandoval Mariana , Tremblay Annie , Langkamp-Henken Bobbi 
Published: July 2022

AbstractBackgroundSome probiotics appear to improve athletic performance, endurance, and recovery after intense exercise. Other formulations may provide performance-related benefits via immune and gastrointestinal functions in athletic individuals. However, few formulations have been studied for both types of effects among non-elite athletes. The primary objective of this study is to assess the ergogenic effects of a probiotic on high-intensity endurance running performance in non-elite runners. Secondary objectives include assessment of perceived exertion, blood chemistry, immune and stress biomarkers, cold and flu symptoms, and gastrointestinal health after the probiotic intervention.MethodsThis 9-week randomized, placebo-controlled, double-blind, parallel trial will assess the ergogenic effects of a probiotic (5 billion colony-forming units/day, for 6 weeks) in healthy, non-elite runners (N=32; 18–45 years). Participants will be monitored via daily and weekly questionnaires during the 2-week pre-baseline, 6-week intervention, and 1-week washout. Questionnaires will inquire about activity, muscle soreness, gastrointestinal symptoms, cold and flu symptoms, stool form and frequency, and adverse events. During the pre-baseline visit, maximal oxygen uptake (V̇O2max) is assessed to set appropriate individualized workload settings for the treadmill time-to-exhaustion endurance tests. These time-to-exhaustion endurance running tests will be completed at an intensity of 85% VO2max at baseline and final visits. During these tests, self-perceived exercise effort will be rated via the Borg Rating of Perceived Exertion scale and finger sticks assessing capillary blood glucose and lactate concentrations will be collected every 3 min. Additional questionnaires will assess diet and motivation to exercise. Body composition will be assessed using air displacement plethysmography at the baseline and final visits. Hypotheses will be tested using two-sided tests, and a linear model and with a type I error rate ofα=0.05. Primary and secondary outcomes will be tested by comparing results between the intervention groups, adjusting for baseline values.DiscussionThese results will build evidence documenting the role of probiotics on running endurance performance and physiological responses to exercise in non-elite athletes. Understanding the potential mechanisms of probiotic effects and how they mitigate the intestinal or immune discomforts caused by running could provide additional strategy means to help runners improve their performance.Trial registration numberClinicalTrials.govNCT04588142. Posted on October 19, 2020.Protocol version: July 2, 2021, version 1.2
A fat body transcriptome analysis of the immune responses of Rhodnius prolixus to artificial infections with bacteria
Authors: Salcedo-Porras Nicolas , Oliveira Pedro Lagerblad , Guarneri Alessandra Aparecida , Lowenberger Carl 
Published: July 2022

Abstract
Background
Rhodnius prolixus is an important vector of Trypanosoma cruzi, the causal agent of Chagas disease in humans. Despite the medical importance of this and other triatomine vectors, the study of their immune responses has been limited to a few molecular pathways and processes. Insect immunity studies were first described for holometabolous insects such as Drosophila melanogaster, and it was assumed that their immune responses were conserved in all insects. However, study of the immune responses of triatomines and other hemimetabolous insects has revealed discrepancies between these and the Drosophila model.

Methods
To expand our understanding of innate immune responses of triatomines to pathogens, we injected fifth instar nymphs of R. prolixus with the Gram-negative (Gr−) bacterium Enterobacter cloacae, the Gram-positive (Gr+) bacterium Staphylococcus aureus, or phosphate-buffered saline (PBS), and evaluated transcript expression in the fat body 8 and 24 h post-injection (hpi). We analyzed the differential expression of transcripts at each time point, and across time, for each treatment.

Results
At 8 hpi, the Gr− bacteria-injected group had a large number of differentially expressed (DE) transcripts, and most of the changes in transcript expression were maintained at 24 hpi. In the Gr+ bacteria treatment, few DE transcripts were detected at 8 hpi, but a large number of transcripts were DE at 24 hpi. Unexpectedly, the PBS control also had a large number of DE transcripts at 24 hpi. Very few DE transcripts were common to the different treatments and time points, indicating a high specificity of the immune responses of R. prolixus to different pathogens. Antimicrobial peptides known to be induced by the immune deficiency pathway were induced upon Gr− bacterial infection. Many transcripts of genes from the Toll pathway that are thought to participate in responses to Gr+ bacteria and fungi were induced by both bacteria and PBS treatment. Pathogen recognition receptors and serine protease cascade transcripts were also overexpressed after Gr− bacteria and PBS injections. Gr- injection also upregulated transcripts involved in the metabolism of tyrosine, a major substrate involved in the melanotic encapsulation response to pathogens.

Conclusions
These results reveal time-dependent pathogen-specific regulation of immune responses in triatomines, and hint at strong interactions between the immune deficiency and Toll pathways.

Graphical abstract
Association between serum lipid profile and liver fibrosis in patients infected with Schistosoma japonicum
Authors: Liu Yang , Zhang PengPeng , Li JunHui , Li Hao , Zhou Chen , Zhang Yu , Ming YingZi 
Published: July 2022

Abstract
Background
Liver fibrosis is thought to have a close relationship with lipid profile. The possible association between lipids and liver fibrosis of different etiologies has been widely explored. However, the association between lipids and liver fibrosis in patients infected with Schistosoma japonicum remains unclear. In the present study we undertook a preliminary exploration of the association between lipid profile and liver fibrosis, and developed a new predictive index for liver fibrosis in S. japonicum-infected patients.

Methods
A total of 1503 patients diagnosed with S. japonicum at Xiangyue Hospital, China were enrolled in this retrospective study. The patients were divided into two groups, i.e., those with and those without liver fibrosis, by two experienced schistosomiasis specialists, according to the results of liver ultrasound examination. Demographic, clinical, and laboratory data were collected. Multivariable logistic models were used to estimate the independent associations between lipid profile and liver fibrosis. Receiver operating characteristic (ROC) curves were used to assess the discriminative ability of the new index in predicting liver fibrosis in patients with schistosomiasis.

Results
Logistic regression analysis showed that high-density lipoprotein (HDL) [adjusted odds ratio (aOR), 95% confidence interval (CI) 7.334, 5.051–10.649; P < 0.001], low-density lipoprotein (LDL) (aOR, 95% CI 0.434, 0.370–0.509; P < 0.001), hemoglobin (HB) (aOR, 95% CI 0.979, 0.971–0.987; P < 0.001) and platelets (PLT) (aOR, 95% CI 0.996, 0.994–0.999; P < 0.001) were independently associated with liver fibrosis in patients with schistosomiasis. ROC analysis indicated that the combination of HDL, LDL and HB levels [(HDL × 100)/(LDL × HB)] had a higher area under the ROC curve (AUC = 0.773), and thus may better predict liver fibrosis than the aspartate transaminase-to-platelet ratio index (AUC = 0.608) and fibrosis index based on four factors (AUC = 0.624).

Conclusions
To the best of our knowledge, this is the first study to report that HDL, LDL, HB and PLT levels are independently associated with liver fibrosis in patients with schistosomiasis. (HDL × 100)/(LDL × HB) outperformed the aspartate transaminase-to-platelet ratio index and fibrosis index based on four factors in terms of ROC, and thus could be a new predictive index for liver fibrosis. These findings may help clinicians to more easily and effectively diagnose liver fibrosis in patients with schistosomiasis.

Graphical abstract
Investigation of urine metabolome of BALB/c mouse infected with an avirulent strain of Toxoplasma gondii
Authors: Zhou Chun-Xue , Li Ling-Yu , Huang Cui-Qin , Guo Xu-Dong , An Xu-Dian , Luo Fang-Fang , Cong Wei 
Published: July 2022

Abstract
Background
The protozoan parasite Toxoplasma gondii is a major concern for human and animal health. Although the metabolic understanding of toxoplasmosis has increased in recent years, the analysis of metabolic alterations through noninvasive methodologies in biofluids remains limited.

Methods
Here, we applied liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based metabolomics and multivariate statistical analysis to analyze BALB/c mouse urine collected from acutely infected, chronically infected and control subjects.

Results
In total, we identified 2065 and 1409 metabolites in the positive electrospray ionization (ESI +) mode and ESI − mode, respectively. Metabolomic patterns generated from principal component analysis (PCA) and partial least squares discriminant analysis (PLS-DA) score plots clearly separated T. gondii-infected from uninfected urine samples. Metabolites with altered levels in urine from T. gondii-infected mice revealed changes in pathways related to amino acid metabolism, fatty acid metabolism, and nicotinate and nicotinamide metabolism.

Conclusions
This is the first study to our knowledge on urine metabolic profiling of BALB/c mouse with T. gondii infection. The urine metabolome of infected mouse is distinctive and has value in the understanding of Toxoplasmosis pathogenesis and improvement of treatment.

Graphical Abstract
X-CAP improves pathogenicity prediction of stopgain variants
Authors: Rastogi Ruchir , Stenson Peter D. , Cooper David N. , Bejerano Gill 
Published: July 2022

AbstractStopgain substitutions are the third-largest class of monogenic human disease mutations and often examined first in patient exomes. Existing computational stopgain pathogenicity predictors, however, exhibit poor performance at the high sensitivity required for clinical use. Here, we introduce a new classifier, termed X-CAP, which uses a novel training methodology and unique feature set to improve the AUROC by 18% and decrease the false-positive rate 4-fold on large variant databases. In patient exomes, X-CAP prioritizes causal stopgains better than existing methods do, further illustrating its clinical utility. X-CAP is available athttps://github.com/bejerano-lab/X-CAP.
Toosendanin activates caspase-1 and induces maturation of IL-1β to inhibit type 2 porcine reproductive and respiratory syndrome virus replication via an IFI16-dependent pathway
Authors: Zhang Mingxin , Lu Chunni , Su Lizhan , Long Feixiang , Yang Xia , Guo Xiaofeng , Song Gaopeng , An Tongqing , Chen Weisan , Chen Jianxin 
Published: July 2022

AbstractPorcine reproductive and respiratory syndrome virus (PRRSV) is a prevalent and endemic swine pathogen which causes significant economic losses in the global swine industry. Multiple vaccines have been developed to prevent PRRSV infection. However, they provide limited protection. Moreover, no effective therapeutic drugs are yet available. Therefore, there is an urgent need to develop novel antiviral strategies to prevent PRRSV infection and transmission. Here we report that Toosendanin (TSN), a tetracyclic triterpene found in the bark or fruits of Melia toosendan Sieb. et Zucc., strongly suppressed type 2 PRRSV replication in vitro in Marc-145 cells and ex vivo in primary porcine alveolar macrophages (PAMs) at sub-micromolar concentrations. The results of transcriptomics revealed that TSN up-regulated the expression of IFI16 in Marc-145 cells. Furthermore, we found that IFI16 silencing enhanced the replication of PRRSV in Marc-145 cells and that the anti-PRRSV activity of TSN was dampened by IFI16 silencing, suggesting that the inhibition of TSN against PRRSV replication is IFI16-dependent. In addition, we showed that TSN activated caspase-1 and induced maturation of IL-1β in an IFI16-dependent pathway. To verify the role of IL-1β in PRRSV infection, we analyzed the effect of exogenous rmIL-1β on PRRSV replication, and the results showed that exogenous IL-1β significantly inhibited PRRSV replication in Marc-145 cells and PAMs in a dose-dependent manner. Altogether, our findings indicate that TSN significantly inhibits PRRSV replication at very low concentrations (EC50: 0.16–0.20 μM) and may provide opportunities for developing novel anti-PRRSV agents.
Susceptibility of different TMEM154 genotypes in three Italian sheep breeds infected by different SRLV genotypes
Authors: Moretti Riccardo , Sartore Stefano , Colitti Barbara , Profiti Margherita , Chessa Stefania , Rosati Sergio , Sacchi Paola 
Published: July 2022

AbstractSmall ruminant lentiviruses (SRLV) belong to the Retroviridae family and can cause various diseases. One of the most impacting diseases is visna-maedi, a complex disease characterized by long latencies and chronic progressive inflammatory events affecting the nervous system, lungs, mammary gland, and articular joints. A single nucleotide polymorphism (rs408593969, c.103G>A, missense mutation E35K) in the ovine transmembrane protein gene 154 (TMEM154) was identified as protective against small ruminant lentivirus infection in different herds worldwide. However, there is evidence in the scientific literature of a breed-specificity of this protective effect and, furthermore, there are still limited studies regarding the association between the animal genotype and the infecting virus genotype. Thus, the aim of this study was to further investigate the association between the animal genotype for the suggested protective mutation and the infecting virus genotype, in three different sheep breeds reared in northern Italy. The results obtained only partially confirmed the data available in the literature, as the protective effect was confirmed only for SRLV genotype A clusters, while other genotypes (namely B and E) infected AA and GA animals. Further studies with an experimental infection of specific virus genotypes in hosts with specific genotypes are required to confirm the larger number of cases the results obtained in this study.
Identification of the ataxin-1 interaction network and its impact on spinocerebellar ataxia type 1
Authors: Chen Jiu-Ming , Chen Shi-Kai , Jin Pei-Pei , Sun Shun-Chang 
Published: July 2022

Abstract
Background
Spinocerebellar ataxia type 1 (SCA1) is a neurodegenerative disease caused by a polyglutamine expansion in the ataxin-1 protein. The pathogenic mechanism resulting in SCA1 is still unclear. Protein–protein interactions affect the function and stability of ataxin-1.

Methods
Wild-type and mutant ataxin-1 were expressed in HEK-293T cells. The levels of expression were assessed using real-time polymerase chain reaction (PCR) and Western blots. Co-immunoprecipitation was done in HEK-293T cells expressing exogenous wild-type and mutant ataxin-1 using anti-Flag antibody following by tandem affinity purification in order to study protein–protein interactions. The candidate interacting proteins were validated by immunoprecipitation. Chromatin immunoprecipitation and high-throughput sequencing and RNA immunoprecipitation and high-throughput sequencing were performed using HEK-293T cells expressing wild-type or mutant ataxin-1.

Results
In this study using HEK-293T cells, we found that wild-type ataxin-1 interacted with MCM2, GNAS, and TMEM206, while mutant ataxin-1 lost its interaction with MCM2, GNAS, and TMEM206. Two ataxin-1 binding targets containing the core GGAG or AAAT were identified in HEK-293T cells using ChIP-seq. Gene Ontology analysis of the top ataxin-1 binding genes identified SLC6A15, NTF3, KCNC3, and DNAJC6 as functional genes in neurons in vitro. Ataxin-1 also was identified as an RNA-binding protein in HEK-293T cells using RIP-seq, but the polyglutamine expansion in the ataxin-1 had no direct effects on the RNA-binding activity of ataxin-1.

Conclusions
An expanded polyglutamine tract in ataxin-1 might interfere with protein–protein or protein–DNA interactions but had little effect on protein–RNA interactions. This study suggested that the dysfunction of protein–protein or protein–DNA interactions is involved in the pathogenesis of SCA1.
Linking physical activity to personal values: feasibility and acceptability randomized pilot of a behavioral intervention for older adults with osteoarthritis pain
Authors: Plumb Vilardaga Jennifer C. , Kelleher Sarah A. , Diachina Allison , Riley Jennie , Somers Tamara J. 
Published: August 2022

Abstract
Background
Osteoarthritis (OA) pain is common and leads to functional impairment for many older adults. Physical activity can improve OA outcomes for older adults, but few are appropriately active. Behavioral interventions can reduce physical activity barriers. We developed and tested a brief, novel behavioral intervention (i.e., Engage-PA) for older adults combining values to enhance motivation and strategic activity pacing to improve arthritis-related pain and functioning and increase physical activity.

Methods
A randomized feasibility and acceptability pilot trial compared Engage-PA to treatment-as-usual plus fitness tracker (TAU+) in N = 40 adults age 65+ with OA pain in the knee or hip. Engage-PA involved two 60-min telephone sessions. All participants wore a fitness tracker to collect daily steps throughout the study and completed baseline and post-treatment assessments of secondary outcomes (arthritis-related pain and physical functioning, physical activity, psychological distress, psychological flexibility, and valued living). The impact of COVID-19 on general well-being and physical activity was also assessed. Descriptive statistics were conducted for feasibility and acceptability outcomes. Indicators of improvement in secondary outcomes were examined via change scores from baseline to post-treatment and performing independent samples t-tests to assess for between-group differences.

Results
Feasibility was high; 100% accrual, low (5%) attrition, and 100% completion of study sessions. Acceptability was high, with 89% finding the intervention “mostly” or “very” helpful. Engage-PA participants demonstrated improvements in arthritis pain severity (Mdiff = 1.68, p = 0.044, 95% CI [− 0.26, 3.62]) and self-reported activity (Mdiff = 0.875, p = 0.038, 95% CI [− 1.85, 0.98]) from baseline to post-treatment as compared to TAU+. Due to pandemic-related challenges, there was a high level of missing data (43%) for daily steps, but available data showed no significant change in steps over time or between the groups. COVID-19 added an additional burden to participants, such that 50% were exercising less, 68% were more sedentary, and 72% lost access to spaces and social support to be active.

Conclusions
Engage-PA is a promising brief, novel behavioral intervention with the potential to support older adults in improving arthritis-related pain and functioning and increasing physical activity. The feasibility and acceptability of Engage-PA are particularly notable as most participants reported COVID-19 added more barriers to physical activity.

Trial registration
ClinicalTrials.gov, NCT04490395. Registered on July 29, 2020
Neural net detection of seismic features related to gas hydrates and free gas accumulations on the northern U.S. Atlantic margin
Authors: Majumdar Urmi , Miller Nathaniel C. , Ruppel Carolyn D. 
Published: August 2022

Bottom-simulating reflections (BSRs) that sometimes mark the base of the gas hydrate stability zone in marine sediments are often identified based on the reverse polarity reflections that cut across stratigraphic layering in seismic amplitude data. On the northern U.S. Atlantic margin (USAM) between Cape Hatteras and Hudson Canyon, legacy seismic data have revealed pronounced BSRs south of the deepwater extension of Hudson Canyon and more subtle ones from offshore Delaware south to Cape Hatteras, where the reflections sometimes follow stratigraphic layering. Using high-resolution seismic data acquired during the 2018 Mid-Atlantic Resource Imaging Experiment and a supervised neural net, we identify seismic features associated with gas hydrates and/or the top of gas between Hudson Canyon and Cape Hatteras. Using seismic attributes especially sensitive to the presence of gas, we train a neural network algorithm on seismic data from an area with strong BSRs and then apply the model to the rest of the data set. The results indicate that gas hydrate and/or shallow free gas are significantly more widespread on the northern part of the USAM than previously known. Seismic indicators of gas extend landward from the 2000 m isobath to the upper continental slope in sectors with (offshore Virginia) and, to a lesser extent, without (offshore New Jersey) pervasive upper slope methane seeps. Higher sand content and intermediate sediment thickness, factors related to the container size and gas charge in a petroleum systems framework, are associated with more robust gas indicators.
Time to go: neural crest cell epithelial-to-mesenchymal transition
Authors: Leathers Tess A. , Rogers Crystal D. 
Published: July 2022

ABSTRACT
Neural crest cells (NCCs) are a dynamic, multipotent, vertebrate-specific population of embryonic stem cells. These ectodermally-derived cells contribute to diverse tissue types in developing embryos including craniofacial bone and cartilage, the peripheral and enteric nervous systems and pigment cells, among a host of other cell types. Due to their contribution to a significant number of adult tissue types, the mechanisms that drive their formation, migration and differentiation are highly studied. NCCs have a unique ability to transition from tightly adherent epithelial cells to mesenchymal and migratory cells by altering their polarity, expression of cell-cell adhesion molecules and gaining invasive abilities. In this Review, we discuss classical and emerging factors driving NCC epithelial-to-mesenchymal transition and migration, highlighting the role of signaling and transcription factors, as well as novel modifying factors including chromatin remodelers, small RNAs and post-translational regulators, which control the availability and longevity of major NCC players.