bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tumour necrosis factor blockade after asphyxia in foetal sheep ameliorates cystic white matter injury
Authors: Lear Christopher A , Lear Benjamin A , Davidson Joanne O , Sae-Jiw Jialin , Lloyd Johanna M , Dhillon Simerdeep K , Gunn Alistair J , Bennet Laura 
Published: September 2022

Abstract
Cystic white matter injury is highly associated with severe neurodevelopmental disability and cerebral palsy in preterm infants, yet its pathogenesis remains poorly understood and there is no established treatment. In the present study, we tested the hypothesis that slowly evolving cystic white matter injury after hypoxia-ischaemia is mediated by programmed necrosis initiated by tumour necrosis factor. Tumour necrosis factor blockade was begun 3 days after hypoxia-ischaemia to target the tertiary phase of injury, when most secondary cell death is thought to be complete.
Chronically instrumented preterm foetal sheep (0.7 gestation) received 25 min of hypoxia-ischaemia induced by complete umbilical cord occlusion or sham-umbilical cord occlusion (controls, n = 10), followed by intracerebroventricular infusion of the soluble TNF inhibitor, Etanercept, at 3, 8 and 13 days after umbilical cord occlusion (n = 9) or vehicle (n = 9). Foetal brains were processed for histology at 21 days after umbilical cord occlusion.
Umbilical cord occlusion with vehicle was associated with a spectrum of macroscopic white matter degeneration, including white matter atrophy, ventriculomegaly and overt temporal lobe cystic white matter injury. Oligodendrocyte maturational arrest and impaired labelling of myelin proteins, characteristic of diffuse white matter injury, was observed in the parietal lobe and surrounding the cystic lesions in the temporal lobe. Etanercept markedly attenuated cystic white matter injury on the side of the intracerebroventricular infusion, with partial contralateral protection. Further, Etanercept improved oligodendrocyte maturation and labelling of myelin proteins in the temporal and parietal lobes.
The present study shows that cystic white matter injury reflects late-onset tertiary cell death mediated by delayed neuroinflammation through the tumour necrosis factor pathway. Delayed tumour necrosis factor blockade markedly attenuated cystic white matter injury and restored oligodendrocyte maturation and deficits in myelin protein expression. These data suggest that delayed tumour necrosis factor blockade may represent a viable therapeutic strategy to reduce the risk of cystic and diffuse white matter injury and potentially cerebral palsy after preterm birth, with a surprisingly wide therapeutic window.
Polygenic Risk Scores for Prediction of Subclinical Coronary Artery Disease in Persons With Human Immunodeficiency Virus (HIV): The Swiss HIV Cohort Study
Authors: Schoepf Isabella C , Thorball Christian W , Kovari Helen , Ledergerber Bruno , Buechel Ronny R , Calmy Alexandra , Weber Rainer , Kaufmann Philipp A , Nkoulou René , Schwenke Johannes M , Braun Dominique L , Fellay Jacques , Tarr Philip E ,   for the Swiss HIV Cohort Study, Abela I , Aebi-Popp K , Anagnostopoulos A , Battegay M , Bernasconi E , Braun D L , Bucher H C , Calmy A , Cavassini M , Ciuffi A , Dollenmaier G , Egger M , Elzi L , Fehr J , Fellay J , Furrer H , Fux C A , Günthard H F , Hachfeld A , Haerry D , Hasse B , Hirsch H H , Hoffmann M , Hösli I , Huber M , Kahlert C R , Kaiser L , Keiser O , Klimkait T , Kouyos R D , Kovari H , Kusejko K , Martinetti G , Martinez de Tejada B , Marzolini C , Metzner K J , Müller N , Nemeth J , Nicca D , Paioni P , Pantaleo G , Perreau M , Rauch A , Schmid P , Speck R , Stöckle M , Tarr P , Trkola A , Wandeler G , Yerly S 
Published: September 2022

Abstract

Background
In people with human immunodeficiency virus (HIV) (PWH), individual polygenic risk scores (PRSs) are associated with coronary artery disease (CAD) events. Whether PRSs are associated with subclinical CAD is unknown.

Methods
In Swiss HIV Cohort Study participants of European descent, we defined subclinical CAD as presence of soft, mixed, or high-risk plaque (SMHRP) on coronary computed tomography (CT) angiography, or as participants in the top tertile of the study population's coronary artery calcium (CAC) score, using noncontrast CT. We obtained univariable and multivariable odds ratios (ORs) for subclinical CAD endpoints based on nongenetic risk factors, and validated genome-wide PRSs built from single nucleotide polymorphisms associated with CAD, carotid intima-media thickness (IMT), or longevity in the general population.

Results
We included 345 genotyped participants (median age, 53 years; 89% male; 96% suppressed HIV RNA); 172 and 127 participants had SMHRP and CAC, respectively. CAD-associated PRS and IMT-associated PRS were associated with SMHRP and CAC (all P &lt; .01), but longevity PRS was not. Participants with unfavorable CAD-PRS (top quintile) had an adjusted SMHRP OR = 2.58 (95% confidence interval [CI], 1.18–5.67), and a CAC OR = 3.95 (95% CI, 1.45–10.77) vs. bottom quintile. Unfavorable nongenetic risk (top vs. bottom quintile) was associated with adjusted SMHRP OR = 24.01 (95% CI, 9.75–59.11), and a CAC-OR = 65.07 (95% CI, 18.48–229.15). Area under the receiver operating characteristic curve increased when we added CAD-PRS to nongenetic risk factors (SMHRP: 0.75 and 0.78, respectively; CAC: 0.80 and 0.83, respectively).

Conclusions
In Swiss PWH, subclinical CAD is independently associated with an individual CAD-associated PRS. Combining nongenetic and genetic cardiovascular risk factors provided the most powerful subclinical CAD prediction.
Long-term variation in psoas muscle mass index is affected by short-term loss after esophagectomy in survivors of esophageal cancer
Authors: Nishimura Erica , Kawakubo Hirofumi , Matsuda Satoru , Fukuda Kazumasa , Nakamura Rieko , Kitagawa Yuko 
Published: September 2022

SummaryChanges in muscle mass may be an objective approach toward measuring the quality of life after surgery, but long-term changes due to surgery without the effect of cachexia remain unclear. Patients with esophageal cancer who underwent esophagectomy and did not experience cancer recurrence for 3 years were analyzed. The psoas muscle mass index (PMI) was assessed before surgery and 7 days, 1 year, and 3 years after surgery. Patients with no change or increased PMI within 7 days after surgery were categorized into the Nondecreasing-PMI group, whereas those with decreased PMI were categorized into the Decreasing-PMI group. Eighty-four and 51 patients were categorized into the Nondecreasing- and Decreasing-PMI groups, respectively. The Decreasing-PMI group had a higher incidence rate of anastomotic leakage than the Nondecreasing-PMI group (25% vs. 12%, respectively; P = 0.042). Moreover, the Decreasing-PMI group showed a significantly greater decrease in the PMI 1 year after surgery than the Nondecreasing-PMI group (−9.2% vs. −4.0%, respectively; P = 0.048). However, although the Decreasing-PMI group had a greater decrease in the PMI than the Nondecreasing-PMI group, no significant difference was observed 3 years after surgery (−9.8% vs. −5.3%, respectively; P = 0.115). A decrease in PMI in the acute phase after esophagectomy may contribute to a long-term decrease in the PMI. Intensive interventions may be beneficial for these patients to improve their long-term quality of life.
Incidence, Prevalence, Disease Course, and Treatment Strategy of Crohn’s Disease Patients from the Veszprem Cohort, Western Hungary: A Population-based Inception Cohort Study Between 2007 and 2018
Authors: Gonczi Lorant , Lakatos Laszlo , Kurti Zsuzsanna , Golovics Petra A , Pandur Tunde , David Gyula , Erdelyi Zsuzsanna , Szita Istvan , Lakatos Peter L 
Published: September 2022

AbstractBackground and AimsThe number of prospective population-based studies on Crohn’s disease[CD] is still limited from Eastern Europe. The present study is a continuation of the Veszprem IBD cohort. Our aim was to analyse incidence, prevalence, disease phenotype, treatment strategy, disease course, and surgical outcomes in a prospective population-based inception cohort including CD patients diagnosed between 2007 and 2018.MethodsA total of 421 consecutive inception patients were included [male/female:237/184; mean age at diagnosis: 33.3 ± 16.2years]. Both in-hospital and outpatient records were collected and comprehensively reviewed. Demographic data were derived from the Hungarian Central Statistical Office.ResultsMean incidence rate was 9.9 [95% CI: 9.0-10.9]/105 person-years in this 12-year period. Prevalence rate was 236.8 [95% CI: 220.8-252.8] in 2015; 17.6% and 20.0% of the patients had stenosing[B2] and penetrating[B3] disease behavior at diagnosis,respectively. The probability of disease behaviour progression from luminal to B2/B3 phenotype was 14.7% (standard error [SE]: 2.2) at 5 years after diagnosis. Distribution of maximal therapeutic steps during the total follow-up (8.5 years [8.5y], standard deviation [SD]: 3.3) was 5-aminosalicylic acid [5-ASA] in 15.7%, corticosteroids in 14.3%, immunosuppressives in 42.5%, and biologic therapy in 26.2%. The probability of receiving biologictherapy after diagnosis was 20.9% [SE: 2.0] at 5 years. The probability of first resective surgery was 20.7% [SE: 2.0] at 1 year, 26.1% [SE: 2.2] at 5 years, and 30.7% [SE: 2.4] at 10 years. The perianal surgery rate was 31.3% among patients with perianal involvement.ConclusionsThe incidence of CD in Hungary was high, similar to high-incidence areas in Western Europe. Treatment strategies are reflecting the biologic era. Disease behaviour progression was lower, as well as long-term [10y] surgery rates decreasing compared with data from previous decades.
Beyond the White Pill: Advocating for Racial Diversity in IBD Trials
Authors: Wong Emily C L , Moayyedi Paul , Narula Neeraj 
Published: September 2022

AbstractAlthough inflammatory bowel disease [IBD] affects an increasingly diverse patient population, most patients in IBD clinical trials are White. Acknowledging current barriers and taking meaningful action is required at multiple levels to improve racial diversity across clinical trials in IBD. Ultimately, improving racial diversity in trials can in turn improve the care received by the diverse patients seen in clinical practice.
Econometric Issues in Prospective Economic Evaluations Alongside Clinical Trials: Combining the Nonparametric Bootstrap With Methods That Address Missing Data
Authors: Jalali Ali , Tamimi Rulla M , McPherson Sterling M , Murphy Sean M 
Published: September 2022

AbstractProspective economic evaluations conducted alongside clinical trials have become an increasingly popular approach in evaluating the cost-effectiveness of a public health initiative or treatment intervention. These types of economic studies provide improved internal validity and accuracy of cost and effectiveness estimates of health interventions and, compared with simulation or decision-analytic models, have the advantage of jointly observing health and economics outcomes of trial participants. However, missing data due to incomplete response or patient attrition, and sampling uncertainty are common concerns in econometric analysis of clinical trials. Missing data are a particular problem for comparative effectiveness trials of substance use disorder interventions. Multiple imputation and inverse probability weighting are 2 widely recommended methods to address missing data bias, and the nonparametric bootstrap is recommended to address uncertainty in predicted mean cost and effectiveness between trial interventions. Although these methods have been studied extensively by themselves, little is known about how to appropriately combine them and about the potential pitfalls and advantages of different approaches. We provide a review of statistical methods used in 29 economic evaluations of substance use disorder intervention identified from 4 published systematic reviews and a targeted search of the literature. We evaluate how each study addressed missing data bias, whether the recommended nonparametric bootstrap was used, how these 2 methods were combined, and conclude with recommendations for future research.
Antimicrobial volatiles emitted by members of the nest microbiome of social spiders
Authors: Lammers Alexander , Nazipi Seven , Zweers Hans , Bilde Trine , Schramm Andreas , Garbeva Paolina , Lalk Michael 
Published: September 2022

Abstract
Microbes produce and respond to a range of structurally and functionally diverse volatiles. Many microbial volatiles have antimicrobial properties. Since volatiles can diffuse through complex 3D systems like spider nests, they are promising pathogen protection for social arthropods. Here, we analyzed the volatilomes of five nest microbiome members of the Namibian, social spider Stegodyphus dumicola, namely the bacteria Massilia sp. IC2-278, Massilia sp. IC2-477, Sphingomonas sp. IC-11, Streptomyces sp. IC-207, and the fungus Aureobasidium sp. CE_32, and tested their antimicrobial activity against two putative spider pathogens, namely Bacillus thuringiensis and Purpureocillium lilacinum. Most nest microbiome members released volatilomes with antibacterial and/or antifungal activities under in vitro conditions. The analysis of their volatilomes using GC/Q-TOF revealed that they include numerous antimicrobial volatiles. We tested the antimicrobial activity of five pure volatile compounds found in the volatilomes and revealed that all of them were antibacterial and/or antifungal. We could not identify the same antimicrobial volatiles as in a previous in situ study, but our results indicate that social spider-associated microorganisms as a source of antimicrobial volatiles are important for pathogen inhibition. Additionally, we showed the influence of the volatilomes on the antibiotic sensitivity of B. thuringiensis offering novel approaches to counter antibiotic resistance.
Using GPS Technologies to Examine Community Mobility in Older Adults
Authors: Crane Breanna M , Moored Kyle D , Rosso Andrea L , Carlson Michelle C 
Published: September 2022

Abstract

Background
Objective measures of community mobility are advantageous for capturing movement outside the home. Compared with subjective, self-reported techniques, global positioning system (GPS) technologies leverage passive, real-time location data to reduce recall bias and increase measurement precision. We developed methods to quantify community mobility among community-dwelling older adults and assessed how GPS-derived indicators relate to clinical measures of physical and cognitive performance.

Methods
Participants (n = 149; M ± standard deviation [SD] = 77.1 ± 6.5 years) from the program to improve mobility in aging (PRIMA) study, a physical therapy intervention to improve walking ability, carried a GPS device for 7 days. Community mobility was characterized by assessing activity space, shape, duration, and distance. Associations between GPS-derived indicators and cognition and physical function were evaluated using Spearman correlations.

Results
In adjusted models, a larger activity space, greater duration (eg, time out-of-home), and greater distance traveled from home were correlated with better 6-Minute Walk Test performance (ρ = 0.17–0.23, p’s &lt; .05). A more circular activity shape was related to poorer performance on the Trail Making Test, Part A (ρ = 0.18, p &lt; .05). More time out-of-home and a larger activity space were correlated with faster times on the Trail Making Test, Part B (ρ = −0.18 to −0.24, p’s &lt; .05). Community mobility measures were not associated with global cognition, skilled walking, or usual gait speed.

Conclusion
GPS-derived community mobility indicators capture real-world activity among older adults and were correlated with clinical measures of executive function and walking endurance. These findings will guide the design of future interventions to promote community mobility.
Multidisciplinary team directed analysis of whole genome sequencing reveals pathogenic non-coding variants in molecularly undiagnosed inherited retinal dystrophies
Authors: Daich Varela Malena , Bellingham James , Motta Fabiana , Jurkute Neringa , Ellingford Jamie M , Quinodoz Mathieu , Oprych Kathryn , Niblock Michael , Janeschitz-Kriegl Lucas , Kaminska Karolina , Cancellieri Francesca , Scholl Hendrik P N , Lenassi Eva , Schiff Elena , Knight Hannah , Black Graeme , Rivolta Carlo , Cheetham Michael E , Michaelides Michel , Mahroo Omar A , Moore Anthony T , Webster Andrew R , Arno Gavin 
Published: September 2022

Abstract
The purpose of this paper is to identify likely pathogenic non-coding variants in inherited retinal dystrophy (IRD) genes, using genome sequencing (GS). Patients with IRD were recruited to the study and underwent comprehensive ophthalmological evaluation and GS. The results of GS were investigated through virtual gene panel analysis, and plausible pathogenic variants and clinical phenotype evaluated by the multidisciplinary team (MDT) discussion. For unsolved patients in whom a specific gene was suspected to harbor a missed pathogenic variant, targeted re-analysis of non-coding regions was performed on GS data. Candidate variants were functionally tested by messenger RNA analysis, minigene or luciferase reporter assays. Previously unreported, likely pathogenic, non-coding variants in 7 genes (PRPF31, NDP, IFT140, CRB1, USH2A, BBS10 and GUCY2D), were identified in 11 patients. These were shown to lead to mis-splicing (PRPF31, IFT140, CRB1 and USH2A) or altered transcription levels (BBS10 and GUCY2D). MDT-led, phenotype-driven, non-coding variant re-analysis of GS is effective in identifying the missing causative alleles.
Step in Time: Conservation of Circadian Clock Genes in Animal Evolution
Authors: Stanton Daniel , Justin Hannah S , Reitzel Adam M 
Published: September 2022

Abstract
Over the past few decades, the molecular mechanisms responsible for circadian phenotypes of animals have been studied in increasing detail in mammals, some insects, and other invertebrates. Particular circadian proteins and their interactions are shared across evolutionary distant animals, resulting in a hypothesis for the canonical circadian clock of animals. As the number of species for which the circadian clockwork has been described increases, the circadian clock in animals driving cyclical phenotypes becomes less similar. Our focus in this review is to develop and synthesize the current literature to better understand the antiquity and evolution of the animal circadian clockwork. Here, we provide an updated understanding of circadian clock evolution in animals, largely through the lens of conserved genes characterized in the circadian clock identified in bilaterian species. These comparisons reveal extensive variation within the likely composition of the core clock mechanism, including losses of many genes, and that the ancestral clock of animals does not equate to the bilaterian clock. Despite the loss of these core genes, these species retain circadian behaviors and physiology, suggesting novel clocks have evolved repeatedly. Additionally, we highlight highly conserved cellular processes (e.g., cell division, nutrition) that intersect with the circadian clock of some animals. The conservation of these processes throughout the animal tree remains essentially unknown, but understanding their role in the evolution and maintenance of the circadian clock will provide important areas for future study.
Encountering Cover Versions of Songs Derived from Personal Music-Listening History Data: a Design and Field Trial of Musée in Homes
Authors: Jang Sangu , Lee Woojin , Kim Beom , Odom William , Park Young-Woo 
Published: September 2022

AbstractWe designed and implemented Musée to capture the novel experience of interpreting cover versions of music, which contain both familiar and unfamiliar musical components and are curated based on the user’s music-streaming history data. Musée is a tangible music player that enables users to explore and listen to professional or amateur covers of songs (via YouTube) in two categories: covers of songs from users’ most-liked artists and covers of users’ most-played songs. To investigate its potential value in situ, we conducted field trials of Musée in four households for 1 month. Findings showed that unfamiliar musical elements in cover music provided a sense of ‘freshness’ to past songs and helped the listener appreciate over-consumed music in new ways. In addition, restricting detailed information about cover songs that were playing helped users focus on the sound, thus priming them to infer and reflect on the original song and their memories associated with it. Our findings point to new insights for the design of interfaces that use historical personal data to expand users’ experience beyond solely revisiting prior tastes.
The effects of dietary ellagic acid supplementation on growth performance, immune response, antioxidant activity, digestive enzyme activities, and intestinal functions in yellow-feathered broilers
Authors: Wang Fang , Chen Jiashun , Yin Yexin , Yang Mei , Xiao Yintao , Cheng Ying , Yin Lichen , Fu Chenxing 
Published: September 2022

Abstract
This study was conducted to investigate the effects of dietary supplementation with ellagic acid (EA) on the performance, immune function, antioxidant activity, digestive enzyme activities, and intestinal functions in yellow-feathered broilers. In total, 288 healthy yellow-feathered broilers with an average body weight of 39 ± 0.24 g were randomly divided into four treatment groups. Broilers were given a corn-soybean meal basal diet supplemented with 0 (control group), 100, 200, or 400 mg/kg EA. In the finisher period and the overall period, the inclusion of 100, 200, and 400 mg/kg EA increased the average daily gain (P &lt; 0.05), and the inclusion of 200 or 400 mg/kg EA decreased the feed/gain ratio compared with the control group (P &lt; 0.05). The best immune activity (immunoglobulin G [IgG] and immunoglobulin M [IgM] concentrations) in serum was shown in the 200 mg/kg EA group (P &lt; 0.05). Broilers fed with 200 or 400 mg/kg EA-containing diets exhibited higher serum catalase and glutathione peroxidase activities (P &lt; 0.05) than control broilers. The inclusion of 200 mg/kg EA in the broiler diets increased intestinal chymotrypsin, pepsin, and lipase activities (P &lt; 0.05). Broilers fed 200 mg/kg EA-containing diets had higher villus height in the jejunum and ileum, a higher ratio between villus height and crypt depth in the jejunum, and a deeper crypt in the duodenum compared to control broilers (P &lt; 0.05). EA reduced the diamine oxidase activity and D-lactate concentration in serum. Furthermore, in birds fed EA-containing diets, the abundance of Rikenella and norank_f_norank_o_Clostridia_UCG-014 in cecum were decreased compared with control birds (P &lt; 0.05). Moreover, in birds fed EA-containing diets, the levels of acetate, butyrate, and total short-chain fatty acids in the cecum were higher (P &lt; 0.05) than those in control birds. These findings indicated that dietary EA had ameliorative effects on antioxidant capability, digestive enzyme activity, immune function, and intestinal functions, which led to strengthened growth performance.