bluuebunny/crossref_metadata_2025_split huggingface dataset:
Muscle mass, strength, power and physical performance and their association with quality of life in older adults, the Study of Muscle, Mobility and Aging (SOMMA)
Authors: Petnehazy Nora , Barnes Haley N. , Newman Anne B. , Kritchevsky Stephen B. , Cummings Steven R. , Hepple Russel T. , Cawthon Peggy M. 
Published: November 2023

AbstractBackgroundSarcopenia negatively impacts quality of life. It is unclear whether different measures of muscle size, strength, physical performance, and fitness have similar associations with quality of life.ObjectiveTo describe associations of sarcopenia metrics with quality of life outcomes.ParticipantsCommunity-dwelling adults aged 70+ years participating in the SOMMA (Study of Muscle, Mobility and Aging) study.Design and settingsTwo academic medical centers.MeasurementsMeasures included muscle size (MRI-muscle volume. D3Cr muscle mass); strength and power (grip strength, leg extension power and strength); walking and physical performance (4m and 400m walk, SPPB (Short Physical Performance Battery), stair climb, chair stand); fitness (VO2peak); health related quality of life (EQ-5D); and anthropometrics (weight, height, and body mass index).Results were stratified by sex. Correlations, scatterplots and linear regression models described the association between various measures of sarcopenia and fitness with overall quality of life score (EQ5D VAS) as a continuous variable. We also quantified differences between sarcopenia and fitness measures by overall QOL (Quality of Life) as a categorical variable (low, medium, high) and by QOL subcomponents (pain and discomfort, problems with usual activities, mobility, anxiety and depression, and problems with self-care) using distributionally appropriate methods.ResultsWalking tests and physical performance were most consistently (but modestly) associated with overall quality of life (r∼0.2, p<.001) and its subcomponents. Both men and women several sarcopenia and fitness measures were more strongly associated with pain and usual activity than other QOL components.ConclusionsPoor performance, lower fitness and lower strength are related to worse quality of life, particularly pain, in older adults. Future studies should quantify these relationships longitudinally.
Human mobility impacts the transmission of common respiratory viruses: A modeling study of the Seattle metropolitan area
Authors: Perofsky Amanda C. , Hansen Chelsea , Burstein Roy , Boyle Shanda , Prentice Robin , Marshall Cooper , Reinhart David , Capodanno Ben , Truong Melissa , Schwabe-Fry Kristen , Kuchta Kayla , Pfau Brian , Acker Zack , Lee Jover , Sibley Thomas R. , McDermot Evan , Rodriguez-Salas Leslie , Stone Jeremy , Gamboa Luis , Han Peter D. , Adler Amanda , Waghmare Alpana , Jackson Michael L. , Famulare Mike , Shendure Jay , Bedford Trevor , Chu Helen Y. , Englund Janet A. , Starita Lea M. , Viboud Cécile 
Published: November 2023

AbstractMany studies have used mobile device location data to model SARS-CoV-2 dynamics, yet relationships between mobility behavior and endemic respiratory pathogens are less understood. We studied the impacts of human mobility on the transmission of SARS-CoV-2 and 16 endemic viruses in Seattle over a 4-year period, 2018-2022. Before 2020, school-related foot traffic and large-scale population movements preceded seasonal outbreaks of endemic viruses. Pathogen circulation dropped substantially after the initiation of stay-at-home orders in March 2020. During this period, mobility was a positive, leading indicator of transmission of all endemic viruses and lagged SARS-CoV-2 activity. Mobility was briefly predictive of SARS-CoV-2 transmission when restrictions relaxed in summer 2020 but associations weakened in subsequent waves. The rebound of endemic viruses was heterogeneously timed but exhibited stronger relationships with mobility than SARS-CoV-2. Mobility is most predictive of respiratory virus transmission during periods of dramatic behavioral change, and, to a lesser extent, at the beginning of epidemic waves.Teaser:Human mobility patterns predict the transmission dynamics of common respiratory viruses in pre- and post-pandemic years.
Breathing exercises for the management of gastrointestinal conditions: protocol for a scoping review
Authors: Gholamrezaei Ali , Guadagnoli Livia , Teugels Anouk , Peluso Natalie , Fung Asta , Van Oudenhove Lukas , Van Diest Ilse , Vlaeyen Johan , Tack Jan , Vanuytsel Tim , Aziz Qasim , Talley Nicholas J , Keefer Laurie 
Published: November 2023

1.AbstractObjectivesThis scoping review will identify and map the literature on breathing exercises for the management of gastrointestinal conditions.IntroductionEmerging evidence suggests the potential benefits of breathing exercises for gastrointestinal conditions. However, there is a lack of a comprehensive review to systematically map the research done in this area, as well as to identify existing gaps in knowledge and guide future research.Inclusion criteriaThe review will consider any study that describes or evaluates a breathing exercise to manage a gastrointestinal condition or symptom in a patient population. Original studies including controlled clinical trials and observational studies (e.g., on patient’s experience), systematic reviews, scoping reviews, meta-analyses or any other form of systematic evidence synthesis, and case series will be sourced from published literature, gray literature, and the references of retrieved articles. Case reports, narrative reviews, letters, comments, editorials, and experimental studies including a healthy population only will be excluded.MethodsThe review will follow the Joanna Briggs Institute Reviewer’s Manual for the conduct and reporting of scoping reviews. Databases to be searched will include PubMed, EMBASE, PsycINFO, Web of Science, Scopus, Cochrane Database of Systematic Reviews, CINAHL, JBI Evidence Synthesis, and databases for gray literature. All databases will be searched from inception till the present. Retrieved citations will be independently reviewed, relevant studies will be included, and data will be extracted using a data extraction form. The results will be presented in tabular format, accompanied by a narrative summary and figures.
A STING-CASM-GABARAP Pathway Activates LRRK2 at Lysosomes
Authors: Bentley-DeSousa Amanda , Roczniak-Ferguson Agnes , Ferguson Shawn M. 
Published: November 2023

AbstractMutations that increase LRRK2 kinase activity have been linked to Parkinson’s disease and Crohn’s disease. LRRK2 is also activated by lysosome damage. However, the endogenous cellular mechanisms that control LRRK2 kinase activity are not well understood. In this study, we identify signaling through Stimulator of Interferon Genes (STING) as an activator of LRRK2 via the Conjugation of ATG8 to Single Membranes (CASM) pathway. We furthermore establish that multiple chemical stimuli that perturb lysosomal homeostasis also converge on CASM to activate LRRK2. Although CASM results in the lipidation of multiple ATG8 protein family members, we establish that LRRK2 lysosome recruitment and kinase activation is highly dependent on interactions with the GABARAP member of this family. Collectively these results define a pathway that integrates multiple stimuli at lysosomes to control the kinase activity of LRRK2. Aberrant activation of LRRK2 via this pathway may be of relevance in both Parkinson’s and Crohn’s diseases.
Chloroplasts lacking class I glutaredoxins are functional but show a delayed recovery of protein cysteinyl redox state after oxidative challenge
Authors: Bohle Finja , Rossi Jacopo , Tamanna Sadia S. , Jansohn Hannah , Schlosser Marlene , Reinhardt Frank , Brox Alexa , Bethmann Stephanie , Kopriva Stanislav , Trentmann Oliver , Jahns Peter , Deponte Marcel , Schwarzländer Markus , Trost Paolo , Zaffagnini Mirko , Meyer Andreas J. , Müller-Schüssele Stefanie J. 
Published: November 2023

AbstractRedox status of protein cysteinyl residues is mediated via glutathione (GSH)/glutaredoxin (GRX) and thioredoxin (TRX)-dependent redox cascades. An oxidative challenge can induce post-translational protein modifications on thiols, such as proteinS-glutathionylation. Class I GRX are small thiol-disulfide oxidoreductases that reversibly catalyseS-glutathionylation and protein disulfide formation. TRX and GSH/GRX redox systems can provide partial backup for each other in several subcellular compartments, but not in the plastid stroma where TRX/light-dependent redox regulation of primary metabolism takes place. While the stromal TRX system has been studied at detail, the role of class I GRX on plastid redox processesin vivois still unknown. We generate knockout lines ofGRXC5as the only chloroplast class I GRX of the mossPhyscomitrium patens.While we find that class I PpGRXC5 has high activities in glutathione-dependent oxidoreductase assays using hydroxyethyl disulfide or redox-sensitive GFP2 (roGFP2) as substratesin vitro, Δgrxc5plants show no detectable growth defect or stress sensitivity, in contrast to mutants with a less negative stromalEGSH(Δgr1). Using stroma-targeted roGFP2, we show increased protein Cys oxidation and decreased reduction rates after oxidative challenge in Δgrxc5plantsin vivo, indicating kinetic uncoupling of the protein Cys redox state from glutathione redox potential. Protein Cys disulfide andS-glutathionylation formation rates after H2O2treatment remained unchanged. Lack of class I GRX function in the stroma did not result in impaired carbon fixation.Our observations suggest specific roles for class I GRX in the efficient redox equilibration betweenEGSHand protein Cys in the plastid stroma as well as negligible cross-talk with metabolic regulation via the TRX system. We propose a model for stromal class I GRX function as efficient kinetic couplers of protein Cys redox state to the dynamic stromalEGSHand highlight the importance of identifyingin vivotarget proteins of GRXC5.One sentence summaryRemoval of class I GRX activity in the chloroplast stroma ofP. patenskinetically uncouples GRX-dependent cysteine redox changes from the local glutathione redox potential, without an effect on NPQ or photosynthetic carbon reactions.
Nanometer-scale views of visual cortex reveal anatomical features of primary cilia poised to detect synaptic spillover
Authors: Ott Carolyn M. , Torres Russel , Kuan Tung-Sheng , Kuan Aaron , Buchanan JoAnn , Elabbady Leila , Seshamani Sharmishtaa , Bodor Agnes L. , Collman Forrest , Bock Davi D. , Lee Wei Chung , Maçarico da Costa Nuno , Lippincott-Schwartz Jennifer 
Published: November 2023

AbstractA primary cilium is a thin membrane-bound extension off a cell surface that contains receptors for perceiving and transmitting signals that modulate cell state and activity. While many cell types have a primary cilium, little is known about primary cilia in the brain, where they are less accessible than cilia on cultured cells or epithelial tissues and protrude from cell bodies into a deep, dense network of glial and neuronal processes. Here, we investigated cilia frequency, internal structure, shape, and position in large, high-resolution transmission electron microscopy volumes of mouse primary visual cortex. Cilia extended from the cell bodies of nearly all excitatory and inhibitory neurons, astrocytes, and oligodendrocyte precursor cells (OPCs), but were absent from oligodendrocytes and microglia. Structural comparisons revealed that the membrane structure at the base of the cilium and the microtubule organization differed between neurons and glia. OPC cilia were distinct in that they were the shortest and contained pervasive internal vesicles only occasionally observed in neuron and astrocyte cilia. Investigating cilia-proximal features revealed that many cilia were directly adjacent to synapses, suggesting cilia are well poised to encounter locally released signaling molecules. Cilia proximity to synapses was random, not enriched, in the synapse-rich neuropil. The internal anatomy, including microtubule changes and centriole location, defined key structural features including cilium placement and shape. Together, the anatomical insights both within and around neuron and glia cilia provide new insights into cilia formation and function across cell types in the brain.
Semantic composition in experimental and naturalistic paradigms
Authors: Li Jixing , Lai Marco , Pylkkänen Liina 
Published: November 2023

AbstractNaturalistic paradigms using movies or audiobooks have become increasingly popular in cognitive neuroscience, but connecting them to findings from controlled experiments remains rare. Here, we aim to bridge this gap in the context of semantic composition in language processing, which is typically examined using a “minimal” two-word paradigm. Using magnetoencephalography (MEG), we investigated whether the neural signatures of semantic composition observed in an auditory two-word paradigm can extend to naturalistic story listening, and vice versa. Our results demonstrate consistent differentiation between phrases and single nouns in the left anterior and middle temporal lobe, regardless of the context. Notably, this distinction emerged later during naturalistic listening. Yet this latency difference disappeared when accounting for various factors in the naturalistic data, such as prosody, word rate, word frequency, surprisal, and emotional content. These findings suggest the presence of a unified compositional process underlying both isolated and connected speech comprehension.
Chromosome-scale assembly of the African yam bean genome
Authors: Waweru Bernice , Njaci Isaac , Murungi Edwin , Paliwal Rajneesh , Mulli Collins , Maranga Mary , Kaimenyi Davies , Lyimo Beatus , Nigussie Helen , Ahadi Bwihangane Birindwa , Assefa Ermias , Ishag Hassan , Olomitutu Oluwaseyi , Abberton Michael , Darby Christopher , Uauy Cristobal , Yao Nasser , Adewale Daniel , Emmrich Peter , Domelevo Entfellner Jean-Baka , Shorinola Oluwaseyi 
Published: November 2023

AbstractGenomics-informed breeding of locally adapted, nutritious, albeit underutilised African crops can help mitigate food and nutrition insecurity challenges in Africa, particularly against the backdrop of climate change. However, utilisation of modern crop improvement tools including genomic selection and genome editing for many African indigenous crops is hampered by the scarcity of genetic and genomic resources. Here we report on the assembly of the genome of African yam bean (Sphenostylis stenocarpa), a tuberous legume crop that is indigenous to Africa. By combining long and short read sequencing with Hi-C scaffolding, we produced a chromosome-scale assembly with an N50 of 69.5 Mbp and totalling 649 Mbp in length (77 - 81% of the estimated genome size based on flow cytometry). Using transcriptome evidence from Nanopore RNA-Seq and homology evidence from related crops, we annotated 31,614 putative protein coding genes. We further show how this resource improves anchoring of markers, genome-wide association analysis and candidate gene analyses in Africa yam bean. This genome assembly provides a valuable resource for genetic research in Africa yam bean.
A Simple Bias Reduction Algorithm for RNA Sequencing Datasets
Authors: Thron Christopher , Bergom Hannah , Boytim Ella , Roberts Mienie , Hwang Justin , Jafari Farhad 
Published: November 2023

AbstractRNA sequencing (RNA-seq) is the conventional genome-scale approach used to capture the expression levels of all detectable genes in a biological sample. This is now regularly used in the clinical diagnostic space for cancer patients. While the information gained is intended to impact treatment decisions, numerous technical and quality issues remain. This includes inaccuracies in the dissemination of gene-gene relationships. For such reasons, clinical decisions are still mostly driven by DNA biomarkers, such as gene mutations or fusions. In this study, we aimed to correct for systemic bias based on RNA-sequencing platforms in order to improve our understanding of the gene-gene relationships. To do so, we examined standard pre-processed RNA-seq datasets obtained from three studies conducted by two consortium efforts including The Cancer Genome Atlas (TCGA) and Stand Up 2 Cancer (SU2C). We particularly examined the TCGA Bladder Cancer (n = 408) and Prostate Cancer (n = 498) studies as well as the SU2C Prostate Cancer study (n = 208). Using various statistical tests, we detected expression-level dependent, per-sample biases in all datasets. Using simulations, we show that these biases corrupt the results oft-tests designed to identify expression level differences between subpopulations. Importantly, these biases introduce large errors into estimates of gene-gene correlations. To mitigate these biases, we introduceLocal Levelingas a novel mathematical approach that transforms count level data and corrects these observed biases. Local Leveling specifically corrects for the bias due to the inherent differential detection of transcripts that is driven by differential expression levels. Based on standard forms of count data (Raw counts, transcripts per million, fragments per kilobase of exon per million), we demonstrate that local leveling effectively removes the observed per-sample biases, and improves the accuracy in simulated statistical tests. Importantly, this led to systemic changes of gene-gene relationships when examining the correlation of key oncogenes, such as the Androgen Receptor, with all other detectable genes. Altogether, Local Leveling improves our capacity towards understanding gene-gene relationships, which may lead to novel ways to utilize the information derived from clinical tests.
Inferring the proportion of undetected cholera infections from serological and clinical surveillance in an immunologically naive population
Authors: Finger Flavio , Lemaitre Joseph , Juin Stanley , Jackson Brendan , Funk Sebastian , Lessler Justin , Mintz Eric , Dely Patrick , Boncy Jacques , Azman Andrew S 
Published: November 2023

SummaryMost infections with pandemic Vibrio cholerae are thought to result in subclinical disease and are not captured by surveillance. Previous estimates of the ratio of infections to clinical cases have varied widely (2 to 100). Understanding cholera epidemiology and immunity relies on the ability to translate between numbers of clinical cases and the underlying number of infections in the population. We estimated the infection incidence during the first months of an outbreak in a cholera-naive population using a Bayesian vibriocidal antibody titer decay model combining measurements from a representative serosurvey and clinical surveillance data. 3,880 suspected cases were reported in Grande Saline, Haiti, between 20 October 2010 and 6 April 2011 (clinical attack rate 18.4%). We found that more than 52.6% (95% Credible Interval (CrI) 49.4-55.7) of the population ≥2 years showed serologic evidence of infection, with a lower infection rate among children aged 2-4 years (35.5%; 95%CrI 24.2-51.6) compared with people ≥5 years (53.1%; 95%CrI 49.4-56.4). This estimated infection rate, nearly three times the clinical attack rate, with underdetection mainly seen in those ≥5 years, has likely impacted subsequent outbreak dynamics. Our findings show how seroincidence estimates improve understanding of links between cholera burden, transmission dynamics and immunity.Key ResultsWe combine serological and clinical cholera incidence in an outbreak in a naive population in Grande Saline, Haiti.The rate of infection withVibrio choleraewas several times the clinical attack rate.Half of the population ≥2 years showed serological evidence of infection.For every reported clinical case ≥5 years old, 3.2 (95% CrI 3.0-3.4) people were infected.Children 2-4 years old had a lower infection rate, which was not significantly different from the clinical attack rate.
Negative association between higher maternal body mass index and breastfeeding outcomes is not mediated by DNA methylation
Authors: Elliott Hannah R. , Bennett Chloe L. , Caramaschi Doretta , English Sinead 
Published: November 2023

AbstractThe benefits of breastfeeding for the health and wellbeing of both infants and mothers are well documented, yet global breastfeeding rates are low. One factor associated with low breastfeeding is maternal body mass index (BMI), which is used as a measure of obesity. The negative relationship between maternal obesity and breastfeeding is likely caused by a variety of social, psychological, and physiological factors. Maternal obesity may also have a direct biological association with breastfeeding through changes in maternal DNA methylation. Here, we investigate this potential biological association using data from a UK-based cohort study, the Avon Longitudinal Study of Parents and Children (ALSPAC). We find that pre-pregnancy body mass index (BMI) is associated with lower initiation to breastfeed and shorter breastfeeding duration. We conduct epigenome-wide association studies (EWAS) of maternal BMI and breastfeeding outcomes and candidate-gene analysis of methylation sites associated with BMI identified via previous meta-EWAS. We find that DNA methylation at cg11453712, annotated to PHTP1, is associated with maternal BMI. From our results, neither this association nor those at candidate-gene sites are likely to mediate the link between maternal BMI and breastfeeding.
Systemic immune markers and infection risk in preterm infants fed human milk fortified with bovine colostrum or conventional fortifier, a secondary analysis of theFortiColostrial
Authors: Bæk Ole , Muk Tik , Aunsholt Lise , Zachariassen Gitte , Sangild Per Torp , Nguyen Duc Ninh 
Published: November 2023

AbstractBackgroundFor very preterm infants, human milk is often fortified with formula products based on processed bovine milk. Intact bovine colostrum (BC) is rich in anti-inflammatory milk factors and considered an alternative. Our objective was to investigate if BC affects anti-inflammatory/TH2 immunity and infection risk in very preterm infants.MethodsIn a secondary analysis of a multicenter, randomized controlled trial (NCT03537365), very preterm infants (26-31 weeks gestation, 23% small for gestational age, SGA) were randomized to receive BC (ColoDan, Biofiber, Denmark, n=113) or a conventional fortifier (PreNAN, Nestlé, Switzerland, n=116). Infection was defined as antibiotic treatment for five or more consecutive days. Levels of 29 cytokines and chemokines were measured in plasma before and after start of fortification.ResultsInfants fortified with BC showed more infection episodes (20 vs. 12%, P<0.05) and tendency to higher cumulative infection risk (hazard ratio, HR 1.9, P=0.06), particularly for SGA infants (HR 3.6, P<0.05). Additionally, BC-fortified infants had higher levels of TH2 related cytokines and chemokines (IL-10, MDC, MCP4) and reduced levels of cytokines related to TH1/TH17 responses (IL-15, IL-17, GM-CSF). The differences were most pronounced in SGA infants, displaying higher levels of TH2-related IL-4, IL-6, and IL-13, and lower interferon-γ and IL-1α levels in the BC groupConclusionInfants fortified with BC show delayed transition from TH2-to TH1-biased systemic immunity, especially for SGA infants. This was associated with more frequent antibiotic use, indicating elevated sensitivity to infection. Thus, an anti-inflammatory milk supplement like BC may delay systemic immune development in preterm infants with effects depending on weight at birth.