bluuebunny/crossref_metadata_2025_split huggingface dataset:
Life-course social participation and physical activity in midlife: Longitudinal associations in the 1970 British Cohort Study (BCS70)
Authors: Tsoli Stergiani , Fancourt Daisy , Sullivan Alice , Hamer Mark , Ploubidis George B. , Kawachi Ichiro 
Published: October 2022

AbstractBackgroundA hypothesized benefit of social participation is that it encourages people to be more physically active. However, limited evidence exists on the association between social participation over the life-course and physical activity in midlife. We sought to apply a life-course framework to examine the association of social participation and device measured physical activity in midlife in the UK.MethodsWe used the 1970 British Birth Cohort Study (BCS70), which includes all people born in Britain during a single week in 1970. Social participation was assessed at ages 16, 30, 34 and 42. Physical activity was measured by accelerometery at age 46, as mean daily step count and time spent in Moderate to Vigorous Physical Activity (MVPA). The associations of social participation and physical activity were tested using two different life-course models: the sensitive period model and the accumulation model.ResultsIndividuals with medium and high participation compared to no social participation over their life-course had higher mean daily step count and MVPA in midlife, supporting the accumulation model. In the sensitive period model, only those that actively participated at age 42 had higher mean daily steps and MVPA compared to those who did not participate.ConclusionOur study provides empirical evidence on the importance of sustaining social participation at all ages over the life-course rather than at a particular timepoint of someone’s life. Interventions to promote social participation throughout the life-course could be an avenue to promote physical activity in middle life.
Viral load of SARS-CoV-2 Omicron BA.5 is lower than that of BA.2 despite the higher infectivity of BA.5
Authors: Takatsuki Yuna , Takahashi Yuta , Nakajima Jun , Iwasaki Yumi , Nagano Katsutoshi , Tani-Sassa Chihiro , Yuasa Sonoka , Kanehira Saki , Sonobe Kazunari , Nukui Yoko , Takeuchi Hiroaki , Tanimoto Kousuke , Tanaka Yukie , Kimura Akinori , Ichimura Naoya , Tohda Shuji 
Published: October 2022

AbstractSublineage BA.5 of the SARS-CoV-2 Omicron variant rapidly spread and replaced BA.2 in July 2022 in Tokyo. A high viral load can be a possible cause of high transmissibility. Therefore, the copy numbers of SARS-CoV-2 in nasopharyngeal swab samples obtained from all patients visiting the hospital where this research was conducted were measured using quantitative polymerase chain reaction (qPCR). Viral genotypes were determined using PCR-based melting curve analysis. Next, whole-genome sequencing was performed using approximately one-fifth of the samples to verify the viral genotypes determined using PCR. Then, the copy numbers of the BA.1, BA.2, and BA.5 cases were compared. Contrary to expectations, the copy numbers of the BA.5 cases (median 4.7 × 104copies/μL,n= 290) were significantly (p= 0.001) lower than those of BA.2 cases (median 1.1 × 105copies/μL,n= 184). There was no significant difference between the BA.5 and BA.1 cases (median, 3.1 × 104copies/μL;n= 215). The results presented here suggest that the increased infectivity of BA.5 is not caused by higher viral loads, but presumably by other factors such as increased affinity to human cell receptors or immune escape due to its L452R mutation.
Characterising indel diversity in a largeMycobacterium tuberculosisoutbreak – implications for transmission reconstruction
Authors: Sobkowiak Benjamin , Colijn Caroline 
Published: October 2022

AbstractGenomic sequencing ofMycobacterium tuberculosis (Mtb), the primary aetiological agent of tuberculosis (TB) in humans, has been used to understand transmission dynamics and reconstruct past outbreaks. Putative transmission events between hosts can be predicted by linking cases with low genomic variation between pathogen strains, though typically only variation in single nucleotide polymorphisms (SNPs) is used to calculate divergence. In highly clonalMtbpopulations there can be many strains that appear identical by SNPs, reducing the utility of genomic data to disentangle potential transmission routes in these settings. Small insertions and deletions (indels) are found in high numbers across theMtbgenome and can be an important source of variation to increase the observed diversity in outbreaks. Here, we examine the value of including indels in the transmission reconstruction of a largeMtboutbreak in London, UK, characterised by low levels of SNP diversity between 1998 and 2013. Our results show that including indel polymorphism decreases the number of strains in the outbreak with at least one other identical sequence by 43% compared to using only SNP variation and reduces the size of largest clonal cluster by 53%. Considering both SNPs and indel polymorphisms alters the reconstructed transmission network and decreases likelihood of direct transmission between hosts with variation in indels. This work demonstrates the importance of incorporating indels intoMtbtransmission reconstruction and we provide recommendations for further work to optimise the inclusion of indel diversity in such analyses.
A deficiency screen of the 3rdchromosome for dominant modifiers of the Drosophila ER integral membrane protein, Jagunal
Authors: Ascencio Gerson , de Cruz Matthew A. , Abuel Judy , Alvardo Sydney , Arriaga Yuma , Conrad Emily , Castro Alonso , Eichelberger Katharine , Galvan Laura , Gundy Grace , Inojoza Garcia Jorge Alberto , Jimenez Alyssa , Lu Nhein Tuyet , Lugar Catharine , Marania Ronnie , Mendsaikhan Tserendavaa , Ortega Jose , Nand Natasha , Rodrigues Nicole S. , Shabazz Khayla , Tam Cynnie , Valenciano Emannuel , Hayzelden Clive , Eritano Anthony S. , Riggs Blake 
Published: October 2022

AbstractThe mechanism surrounding chromosome inheritance during cell division has been well documented, however, organelle inheritance during mitosis is less understood. Recently, the Endoplasmic Reticulum (ER) has been shown to reorganize during mitosis, dividing asymmetrically in proneuronal cells prior to cell fate selection, indicating a programmed mechanism of inheritance. ER asymmetric partitioning in proneural cells relies on the highly conserved ER integral membrane protein, Jagunal (Jagn). Knockdown of Jagn in the compoundDrosophilaeye displays a pleotropic rough eye phenotype in 48% of the progeny. To identify genes involved in Jagn dependent ER partitioning pathway, we performed a dominant modifier screen of the 3rdchromosome for enhancers and suppressors of this Jagn RNAi-induced rough eye phenotype. We screened through 181 deficiency lines covering the 3L and 3R chromosomes and identified 12 suppressors and 10 enhancers of the Jagn RNAi phenotype. Based on the functions of the genes covered by the deficiencies, we identified genes that displayed a suppression or enhancement of the Jagn RNAi phenotype. These include Division Abnormally Delayed (Dally), an heparan sulfate proteoglycan, the γ-secretase subunit Presenilin, and the ER resident protein Sec63. Based on our understanding of the function of these targets, there is a connection between Jagn and the Notch signaling pathway. Further studies will elucidate the role of Jagn and identified interactors within the mechanisms of ER partitioning during mitosis.
A mind-body interface alternates with effector-specific regions in motor cortex
Authors: Gordon Evan M. , Chauvin Roselyne J. , Van Andrew N. , Rajesh Aishwarya , Nielsen Ashley , Newbold Dillan J. , Lynch Charles J. , Seider Nicole A. , Krimmel Samuel R. , Scheidter Kristen M. , Monk Julia , Miller Ryland L. , Metoki Athanasia , Montez David F. , Zheng Annie , Elbau Immanuel , Madison Thomas , Nishino Tomoyuki , Myers Michael J. , Kaplan Sydney , D’Andrea Carolina Badke , Demeter Damion V. , Feigelis Matthew , Barch Deanna M. , Smyser Christopher D. , Rogers Cynthia E. , Zimmermann Jan , Botteron Kelly N. , Pruett John R. , Willie Jon T. , Brunner Peter , Shimony Joshua S. , Kay Benjamin P. , Marek Scott , Norris Scott A. , Gratton Caterina , Sylvester Chad M. , Power Jonathan D. , Liston Conor , Greene Deanna J. , Roland Jarod L. , Petersen Steven E. , Raichle Marcus E. , Laumann Timothy O. , Fair Damien A. , Dosenbach Nico U.F. 
Published: October 2022

SUMMARYPrimary motor cortex (M1) has been thought to form a continuous somatotopic homunculus extending down precentral gyrus from foot to face representations1,2. The motor homunculus has remained a textbook pillar of functional neuroanatomy, despite evidence for concentric functional zones3and maps of complex actions4. Using our highest precision functional magnetic resonance imaging (fMRI) data and methods, we discovered that the classic homunculus is interrupted by regions with sharpy distinct connectivity, structure, and function, alternating with effector-specific (foot, hand, mouth) areas. These inter-effector regions exhibit decreased cortical thickness and strong functional connectivity to each other, and to prefrontal, insular, and subcortical regions of the Cingulo-opercular network (CON), critical for executive action5and physiological control6, arousal7, and processing of errors8and pain9. This interdigitation of action control-linked and motor effector regions was independently verified in the three largest fMRI datasets. Macaque and pediatric (newborn, infant, child) precision fMRI revealed potential cross-species analogues and developmental precursors of the inter-effector system. An extensive battery of motor and action fMRI tasks documented concentric somatotopies for each effector, separated by the CON-linked inter-effector regions. The inter-effector regions lacked movement specificity and co-activated during action planning (coordination of hands and feet), and axial body movement (e.g., abdomen, eyebrows). These results, together with prior work demonstrating stimulation-evoked complex actions4and connectivity to internal organs (e.g., adrenal medulla)10, suggest that M1 is punctuated by an integrative system for implementing whole-body action plans. Thus, two parallel systems intertwine in motor cortex to form an integrate-isolate pattern: effector-specific regions (foot, hand, mouth) for isolating fine motor control, and a mind-body interface (MBI) for the integrative whole-organism coordination of goals, physiology, and body movement.
Can Harvesting Flowers Reduce the Amount of Atmospheric Carbon Dioxide? : The Case of Cherry Blossoms
Authors: Zo Hannah , Appleyard Stephen J. 
Published: October 2022

AbstractCherry blossoms are popular as street trees in East Asia, providing an attractive backdrop to urban architecture, however their fallen petals can create a waste problem. These petals are likely to contain a significant proportion of fixed carbon so it is suggested that harvesting them may be a solution to both the waste problem and a means of quenching atmospheric CO2concomitantly. This study investigated the feasibility of flower harvesting for reducing atmospheric CO2. In particular, the total carbon (TC) stored in all cherry blossoms on streets was quantified in the geographic area of South Korea and compared to various CO2emission rates or amounts quenched by other methods. Branches with flowers were collected from different locations; the TC stored in them ranged between 41.5% - 44.8% of flower dry weights, resulting a mean flower TC per a metre of branch as 0.851±0.070 gC/m. A functional relationship of the sum of the two most apical branch lengths against crown diameter was developed to obtain an estimate of total flowering branch length from the crown diameter of a typical tree on street. The product of flowering branch length and flower TC per a metre of branch indicated that TC stored in all flowers of a tree summed to 336±163 g of carbon, equivalent to 1.23±0.60 kg CO2per tree, on average. The nationwide flower TC in each spring was calculated to be 1,900±920 tonnes of CO2, equivalent to the yearly carbon capture of 176 hectares of mature pine trees and carbon emissions from 0.24 million car operations each day. As compounds from cherry blossoms can be used extensively for pharmaceutical and cosmetic products, harvesting can be cost effective. Yet, its environmental costs and disposal after component extraction need to be considered altogether in a more complete life cycle analysis of diverting this product from landfill or decomposition.
Nucleoside-driven specificity of DNA Methyltransferase
Authors: Gade Madhuri , Gardner Jasmine M. , Jain Prashant , Laurino Paola 
Published: October 2022

AbstractWe have studied adenosine binding specificities of two bacterial DNA methyltransferase Taq methyltransferase (M.TaqI), and HhaI methyltransferase (M.HhaI). While these DNA methyltransferases have similar cofactor binding pocket interactions, experimental data showed different specificity for novel cofactors ((SNM) (S-guanosyl-L-methionine (SGM), S-cytidyl-L-methionine (SCM), S-uridyl-L-methionine (SUM)). Protein dynamics corroborate the experimental data on the cofactor specificities. For M.TaqI the specificity for S-adenosyl-L-methionine (SAM) is governed by the tight binding on the nucleoside part of the cofactor, while for M.HhaI the degree of freedom of the nucleoside chain allows the acceptance of other bases. The experimental data proves a catalytically productive methylation by M.HhaI binding pocket for all the SNM. Our results suggest a new route for successful design of unnatural SNM analogues for methyltransferases as a tool for cofactor engineering.Table of ContentTOC: Methylation by DNA methyltransferase is nucleobase dependent. While M.Taq1 is specific for SAM, M.HhaI is promiscuous for other SAM analogs
Higher habitual FODMAP intake is associated with lower body mass index, lower insulin resistance and higher short-chain fatty acid-producing microbiota in people with prediabetes
Authors: Chu NHS , He J , Ling J , Leung K , Ma RCW , Lee J , Varney J , Chan JCN , Muir JG , Chow E 
Published: October 2022

AbstractAims/hypothesisThe quantity and quality of FODMAPs can alter the relative abundance of gut microbiota with metabolic consequences although similar data are lacking in people with prediabetes. We investigated associations between habitual FODMAP contents, gut microbiota and glucose/insulin responses in subjects with prediabetes.MethodsIn this prospective cross-sectional study, ninety-eight subjects with impaired glucose tolerance (IGT) (mean age: 57±7 years, 43 % men) had assessment of body composition, 6-point oral glucose tolerance tests (OGTT), Homeostatic Model Assessment of Insulin Resistance (HOMA-IR) and 3-day dietary intake. We analysed faecal samples in a sub-group of 20 subjects with IGT and 10 subjects with normal glucose tolerance by 16S rRNA microbiome analysis.ResultsObese subjects with IGT had the lowest daily FODMAP intake compared with their non-overweight and non-obese counterparts (5.7 (3.9-7.9) vs 7.1 (5.0-11.3) vs 9.9 (4.1-22.4) g/day, p=0.024) despite having similar total daily energy intake. Total content of FODMAPs was negatively correlated with body fat. After adjustment for age and gender, total FODMAPs were negatively associated with BMI and HOMA-IR. This remained significant after adjustment for macronutrients and physical activity (p=0.032 and p=0.036 respectively). FODMAP contents were strongly associated with short-chain fatty acid (SCFA)-producing bacteria, such asLactobacillus(p=0.011),Akkermansia muciniphila(p=0.012), andBifidobacterium longum(p=0.010), the abundance of which were negatively correlated with 2-hr plasma glucose (r = -0.524, p =0.003).ConclusionIn individuals with IGT, higher habitual FODMAP intake was associated with lower body fat and insulin resistance and increased abundance of SCFA-producing bacteria, calling for interventional studies to evaluate the effects of FODMAP intake in prediabetes.
Effects of development and parental care on Hamilton’s force of selection
Authors: Netz Christoph 
Published: October 2022

AbstractThe force of selection describes the sensitivity of population growth to changes in life history parameters, with a focus usually on the survival probabilities from one age class to the next. Importantly, according to Hamilton the force of selection generally decreases after the onset of reproduction, thereby providing a possible explanation for patterns of senescence. A second characteristic feature is that the force of selection remains constant up to the age of first reproduction. This latter observation, however, rests on the assumption that offspring become independent from their parents right after birth. I show here in a minimal model that if offspring are reliant on their parents, either during early embryonal development or via parental care at later stages, the force of selection on offspring survival generally increases up until the age at which offspring become independent. This provides a possible explanation for the commonly observed pattern of decreasing mortality during early ontogeny. Further, genes acting during recurrent life stages are observed to experience a heightened force of selection compared to genes that act strictly age-specifically, demonstrating the need to develop a mechanistic understanding of gene activation patterns through which to consider life history evolution.
Spectrum preserving tilings enable sparse and modular reference indexing
Authors: Fan Jason , Khan Jamshed , Pibiri Giulio Ermanno , Patro Rob 
Published: October 2022

AbstractThe reference indexing problem fork-mers is to pre-process a collection of reference genomic sequencesℛso that the position of all occurrences of any queriedk-mer can be rapidly identified. An efficient and scalable solution to this problem is fundamental for many tasks in bioinformatics.In this work, we introduce thespectrum preserving tiling(SPT), a general representation ofℛthat specifies how a set oftilesrepeatedly occur tospellout the constituent reference sequences inℛ. By encoding the order and positions wheretilesoccur, SPTs enable the implementation and analysis of a general class of modular indexes. An index over an SPT decomposes the reference indexing problem fork-mers into: (1) ak-mer-to-tile mapping; and (2) a tile-to-occurrence mapping. Recently introduced work to construct and compactly indexk-mer sets can be used to efficiently implement thek-mer-to-tile mapping. However, implementing the tile-to-occurrence mapping remains prohibitively costly in terms of space. As reference collections become large, the space requirements of the tile-to-occurrence mapping dominates that of thek-mer-to-tile mapping since the former depends on the amount of total sequence while the latter depends on the number of uniquek-mers inℛ.To address this, we introduce a class of sampling schemes for SPTs that trade off speed to reduce the size of the tile-to-reference mapping. We implement a practical index with these sampling schemes in the toolpufferfish2. When indexing over 30,000 bacterial genomes,pufferfish2reduces the size of the tile-to-occurrence mapping from 86.3GB to 34.6GB while incurring only a 3.6× slowdown when queryingk-mers from a sequenced readset.Supplementary materialsSections S.1 to S.8 available online athttps://doi.org/10.5281/zenodo.7504717Availabilitypufferfish2is implemented in Rust and available athttps://github.com/COMBINE-lab/pufferfish2.
Neurotrophic and immunomodulatory lanostane triterpenoids from wood-inhabiting Basidiomycota
Authors: Hassan Khadija , Kemkuignou Blondelle Matio , Kirchenwitz Marco , Wittstein Kathrin , Rascher Monique , Chepkirui Clara , Matasyoh Josphat C. , Decock Cony , Köster Reinhard , Stradal Theresia E. B. , Stadler Marc 
Published: October 2022

AbstractNeurotrophins such as nerve growth factor (ngf) and brain derived neurotrophic factor (bdnf) play important roles in the central nervous system. They are potential therapeutic drugs for treatment of neurodegerative diseases including Alzheimer’s disease and Parkinson’s disease. In this study, we investigated the neurotrophic properties of triterpenes isolated from fruiting bodies ofLaetiporus sulphureusand a mycelial culture ofAntrodiasp. MUCL 56049. The structures of the isolated compounds were elucidated based on nuclear magnetic resonance (NMR) spectroscopy in combination with high-resolution Electrospray mass spectrometry (HR-ESIMS). The secondary metabolites were tested for neurotrophin (ngfandbdnf) expression levels on human astrocytoma 1321N1 cells. Neurite outgrowth activity using rat pheochromocytoma (PC-12) cells was also determined. Twelve triterpenoids were isolated, of which several potently stimulated the expression of neurotrophic factors namely,ngf(sulphurenic acid, 15α-dehydroxytrametenolic acid, fomefficinic acid D and 16α-hydroxyeburicoic acid) andbdnf(sulphurenic acid and 15α- dehydroxytrametenolic acid), respectively. The triterpenes also potentiatedngf-induced neurite outgrowth in PC-12 cells. This is, to the best of our knowledge, the first report on the compound class of lanostanes in direct relation tobdnfandngfenhancement. These compounds are widespread in medicinal mushrooms; hence, they appear promising as starting point for development of drugs and mycopharmaceuticals to combat neurodegenerative diseases. Interestingly, they do not show any pronounced cytotoxicity and may therefore be better suited for therapy than many other neurotrophic compounds that were previously reported.
Game Bird Carcasses are Less Persistent Than Raptor Carcasses, But Can Predict Raptor Persistence Dynamics
Authors: Hallingstad Eric , Riser-Espinoza Daniel , Brown Samantha , Rabie Paul , Haddock Jeanette , Kosciuch Karl 
Published: October 2022

ABSTRACTResearchers conduct post-construction fatality monitoring (PCFM) to determine a wind energy facility’s direct impacts on wildlife. Results of PCFM can be used to evaluate compliance with permitted take, potentially triggering adaptive management measures or offsetting mitigation; reducing uncertainty in fatality rates benefits wind companies, wildlife agencies, and other stakeholders. As part of PCFM, investigators conduct carcass persistence trials to account for imperfect detection during carcass surveys. In most PCFM studies, pen-raised game birds and other non-raptor surrogates have been used to estimate persistence of all large birds, including raptors. However, there is a growing body of evidence showing carcass persistence varies by bird type; raptor fatality estimates based on game bird carcass persistence may therefore be biased high. We conducted raptor and game bird carcass persistence field trials for 1 year at 6 wind energy facilities. Raptor carcass persistence varied by habitat and season, whereas the best-supported game bird model only included habitat. Raptor persistence probabilities were higher than corresponding game bird persistence probabilities for 13 of the 16 habitat and season combinations. Analysis of a meta-dataset showed that raptor carcass persistence varied by season, habitat, and region. The probability of persisting through a 30-day search interval ranged from 0.44 to 0.99 for raptors and from 0.16 to 0.79 for game birds. Raptor persistence was significantly higher than game bird persistence for 95% of the sampled strata. We used these carcass persistence estimates to develop linear mixed-effects models that predict raptor persistence probabilities based on estimated game bird persistence probabilities. Our scaling model provides an important statistical method to address gaps in raptor persistence data at sites in a broad range of landscape contexts in the continental United States and should be used to inform fatality estimation when site-specific raptor persistence data are limited or absent.