bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development and validation of total and regional body composition prediction equations from anthropometry and single frequency segmental bioelectrical impedance with DEXA
Authors: Powell Richard , De Lucia Rolfe Emanuella , Day Felix R. , Perry John R.B. , Griffin Simon J. , Forouhi Nita G. , Brage Soren , Wareham Nicholas J. , Langenberg Claudia , Ong Ken K. 
Published: December 2020

AbstractAimsSingle-frequency segmental Bioelectrical Impedance Analysis (BIA) is commonly used to estimate body composition. To enhance the value of information derived from BIA, especially for use in large-scale epidemiological studies, we developed and validated equations to predict total and regional (arms, legs, trunk, android, gynoid, visceral) body composition parameters (lean mass and fat mass) from anthropometry and single-frequency (50 kHz) segmental BIA variables, using Dual Energy X-ray Absorptiometry (DEXA) as the criterion method.MethodsThe 11,559 adults (age 30 to 65) from the UK population-based Fenland Study with data on DEXA, BIA and anthropometry were randomly assigned to a Derivation sample (4,827 men; 5,732 women) or a Validation sample (500 men; 500 women). Prediction equations based on anthropometry and BIA variables were derived using forward stepwise multiple linear regression in the Fenland Derivation sample. These were validated in the Fenland Validation sample and also in the UK Biobank Imaging Study (2,392 men; 2,606 women) using Pearson correlations and Bland–Altman models.Results and ConclusionsBland Altman analyses revealed no significant mean bias for any predicted DEXA parameter (all P>0.05) for the fenland population. Bias expressed as % of the mean was between -0.6% and 0.5% for all parameters in both men and women, except for visceral FM and subcutaneous abdominal FM (range -3.6 to 1.1%). However, in UK Biobank most predicted parameters showed significant bias: % mean bias was <2% in both sexes only for total fat mass and total lean mass, and was >10% for leg and visceral fat mass in both sexes. In conclusion, new equations based on anthropometry and BIA variables predicted DEXA parameters with sufficient accuracy to assess relative differences between individuals, and were sufficiently accurate to predict absolute values for total body but not regional fat and lean mass.
RAD51AP1 mediates RAD51 activity through nucleosome interaction
Authors: Pires Elena , Sharma Neelam , Selemenakis Platon , Wu Bo , Huang Yuxin , Alimbetov Dauren S. , Zhao Weixing , Wiese Claudia 
Published: December 2020

AbstractRAD51 Associated Protein 1 (RAD51AP1) is a key protein in the homologous recombination DNA repair pathway (HR). Loss of RAD51AP1 leads to defective HR, genome instability and telomere erosion. RAD51AP1 physically interacts with the RAD51 recombinase and promotes RAD51-mediated capture of the donor DNA, synaptic complex assembly and displacement-loop formation when tested with synthetic, nucleosome-free DNA substratesin vitro. In cells, however, DNA is packaged into chromatin, posing an additional barrier to the complexities of the HR reaction. How RAD51AP1 functions as an HR activator in the context of chromatin has remained unclear.In this study, we show that RAD51AP1 binds to Nucleosome Core Particles (NCPs). We identified a C-terminal region in RAD51AP1 and its previously mapped DNA binding domain as critical for mediating the association between RAD51AP1 and both the NCP and the histone octamer. We show that RAD51AP1 is capable of promoting duplex DNA capture and initiating joint-molecule formation with the NCP and chromatinized template DNA, respectively. Together, our results suggest that RAD51AP1directlyassists the RAD51-mediated search of donor DNA in chromatin. We present a model, in which RAD51AP1 anchors the DNA template through affinity for its nucleosomes to the RAD51-ssDNA nucleoprotein filament.
Biotic and abiotic factors shaping the genome of cockle (Cerastoderma edule) in the Northeast Atlantic: a baseline for sustainable management of its wild resources
Authors: Vera Manuel , Maroso Francesco , Wilmes Sophie-B. , Hermida Miguel , Blanco Andrés , Fernández Carlos , Groves Emily , Malham Shelagh K , Bouza Carmen ,   The Cockle’s Consortium, Robins Peter E. , Martínez Paulino 
Published: December 2020

AbstractKnowledge on how environmental factors shape the genome of marine species is crucial for sustainable management of fisheries and wild populations. The edible cockle (Cerastoderma edule) is a marine bivalve distributed along the Northeast Atlantic coast of Europe and is an important resource from both commercial and ecological perspectives. We performed a population genomics screening using 2b-RAD genotyping on 9,309 SNPs localised in the cockle’s genome on a sample of 536 specimens pertaining to 14 beds in the Northeast Atlantic to ascertain its genetic structure regarding environmental variation. Larval dispersal modelling considering species behaviour and interannual variability in ocean conditions was carried out, as an essential background to compare genetic information with. Cockle populations in the Northeast Atlantic were shown to be panmictic and displayed low but significant geographical differentiation across populations (FST= 0.0240; P < 0.001), albeit not across generations. We identified 441 outlier SNPs related to divergent selection, sea surface temperature being the main environmental driver following a latitudinal axis. Two main genetic groups were identified, northwards and southwards of French Brittany, in accordance with our modelling, which demonstrated a barrier for larval dispersal linked to the Ushant front. Further genetic subdivision was observed using outlier loci and considering larval behaviour. The northern group was divided into the Irish/Celtic Seas and the English Channel/North Sea, while the southern group was divided into three subgroups. This information represents the baseline for management of cockles, designing conservation strategies, founding broodstock for depleted beds, and producing suitable seed for aquaculture production.
A MYT1L Syndrome mouse model recapitulates patient phenotypes and reveals altered brain development due to disrupted neuronal maturation
Authors: Chen Jiayang , Lambo Mary E. , Ge Xia , Dearborn Joshua T. , Liu Yating , McCullough Katherine B. , Swift Raylynn G. , Tabachnick Dora R. , Tian Lucy , Noguchi Kevin , Garbow Joel R. , Constantino John N. , Gabel Harrison W. , Hengen Keith B. , Maloney Susan E. , Dougherty Joseph D. 
Published: December 2020

AbstractHuman genetics have defined a new autism-associated syndrome caused by loss-of-function mutations inMYT1L, a transcription factor known for enabling fibroblast-to-neuron conversions. However, howMYT1Lmutation causes autism, ADHD, intellectual disability, obesity, and brain anomalies is unknown. Here, we develop a mouse model of this syndrome. Physically,Myt1lhaploinsufficiency causes obesity, white-matter thinning, and microcephaly in the mice, mimicking clinical phenotypes. During brain development we discovered disrupted gene expression, mediated in part by loss ofMyt1lgene target activation, and identified precocious neuronal differentiation as the mechanism for microcephaly. In contrast, in adults we discovered that mutation results in failure of transcriptional and chromatin maturation, echoed in disruptions in baseline physiological properties of neurons. This results in behavioral anomalies including hyperactivity, muscle weakness and fatigue, and social alterations with more severe phenotypes in males. Overall, our findings provide insight into the mechanistic underpinnings of this disorder and enable future preclinical studies.
Myosin V regulates spatial localization of different forms of neurotransmitter release in central synapses
Authors: Maschi Dario , Gramlich Michael W. , Klyachko Vitaly A. 
Published: December 2020

SUMMARYSynaptic active zone (AZ) contains multiple specialized release sites for vesicle fusion. The utilization of release sites is regulated to determine spatiotemporal organization of the two main forms of synchronous release, uni-vesicluar (UVR) and multi-vesicular (MVR). We previously found that the vesicle-associated molecular motor myosin V regulates temporal utilization of release sites by controlling vesicle anchoring at release sites (Maschi et al, 2018). Here we show that acute inhibition of myosin V shifts preferential location of vesicle docking away from AZ center towards periphery, and results in a corresponding spatial shift in utilization of release sites during UVR. Similarly, inhibition of myosin V also reduces preferential utilization of central release sites during MVR, leading to more spatially distributed and temporally uniform MVR that occurs farther away from the AZ center. Thus myosin V regulates both temporal and spatial utilization of release sites during two main forms of synchronous release.
Waterbird abundance and diversity along a stretch of Ganga River, India modified by construction of a barrage
Authors: Vasudeva Vaishali , Garg J.K. , Badola Ruchi , Hussain Syed Ainul 
Published: December 2020

AbstractDamming and diverting river water alters the channel characteristics and natural flow regime. The change in biotic and abiotic factors results in dissimilar habitat conditions upstream and downstream of the barrage. Given the habitat dissimilarity and therefore resource availability, we hypothesized the dissimilarity in waterbird abundance and species diversity in the river habitat upstream and downstream of the barrage. The study was conducted on a 24 km stretch of Ganga River at Narora, Uttar Pradesh, India. This stretch overlaps with a Ramsar site as well as an Important Bird and Biodiversity Area (IBA). Bird sampling was done using transect count method for summer and winter season in 2017. The abundance was studied in relation to three habitat variablesviz. channel depth, channel width and anthropogenic disturbances using Generalized Linear Model. A total of 140 species of birds were recorded. There was statistically significant difference in the abundance of waterbirds between upstream and downstream stretch in winter season (Mann-Whitney U,p< 0.05). During winters, migratory waterbirds especially ducks and geese occupied the deep water upstream of barrage, while the downstream was mostly occupied by terns and cormorants. Waterbird species diversity was higher in downstream during winters (Effective Number of Species=28; Shannon’s Index= 3.35) and higher in upstream during summer (Effective Number of Species=25, Shannon’s Index=2.87). Channel width, channel depth and anthropogenic disturbance influenced waterbird abundance in both the seasons (Generalized Linear Model;p< 0.05). The influence of channel depth varied with season for the upstream stretch.
Existence and Features of the Myodural Bridge in Gentoo Penguins: a morphological study
Authors: Chen Cheng , Yu Sheng-bo , Chi Yan-yan , Tan Guang-yuan , Yan Bao-cheng , Zheng Nan , Sui Hong-Jin 
Published: December 2020

AbstractRecent studies have evidenced that the anatomical structure now known as the myodural bridge (MDB) connects the suboccipital musculature to the cervical spinal dura mater (SDM). In humans, the MDB passes through both the posterior atlanto-occipital and the posterior atlanto-axial interspaces. The present authors suggest that the MDB has important physiological functions in humans. The existence of the MDB in various mammals, including flying birds (Rock pigeons and Gallus domesticus) has been previously validated. Gentoo penguins are marine birds, able to make 450 dives per day, reaching depths of up to 660 feet. Gentoo penguins are also the world’s fastest diving birds. The present study was therefore carried out to investigate the existence and characteristics of the MDB in Gentoo penguin (Pygoscelis papua), a non-flying, marine bird that can dive. While foraging, this penguin is able to reach speeds of up to 22 miles per hour. For this study, six Gentoo penguin specimens were dissected to observe the existence and composition of their MDB. Histological staining was also performed to analyze the anatomic relationships and characteristic of the MDB in the Gentoo penguin. In this study, it was found that the suboccipital musculature in the Gentoo penguin consists of the rectus capitis dorsalis minor (RCDmi) muscle and rectus capitis dorsalis major (RCDma) muscle. Dense connective tissue fibers were observed connecting these two suboccipital muscles to the spinal dura mater (SDM). This dense connective tissue bridge consists of primarily type I collagen fibers. Thus, this penguin’s MDB appears to be analogous to the MDB previously observed in humans. The present study evidences that the MDB not only exists in penguins but it also has unique features that distinguishes it from that of flying birds. Thus, this study advances the understanding of the morphological characteristics of the MDB in flightless, marine birds.
Evaluation of the tyrosine and dopamine serum level in experimental infected BALB/c mice with chronic toxoplasmosis
Authors: Mirzaeipour Mehdi , Mikaeili Fattaneh , Asgari Qasem , Nohtani Mohammad , Rashidi Sajad , Bahreini Mohammad Saleh 
Published: December 2020

AbstractBackgroundToxoplasmaparasite alters the transduction of neurotransmitter signals and leads to changes in the level of brain neurotransmitters including tyrosine and dopamine, so, behavior changes can occur in infected hosts. Based on this concept, this study was conducted for evaluation of the tyrosine and dopamine serum level in infected mice with chronic toxoplasmosis.Materials and methodsToxoplasma gondii(Prugniaud strain II) was injected intra-peritoneal into BALB/c mice to induce chronic toxoplasmosis. Modified agglutination test (MAT), polymerase chain reaction (PCR), and microscopic methods were conducted to confirm the induction of chronic toxoplasmosis. The infected mice sera were separated at days 40, 50, 60, 70, and 80 for evaluation of tyrosine and dopamine serum level using High-performance Liquid Chromatography (HPLC).ResultsMicroscopic methods confirmed the formation of theToxoplasmacysts in mice tissues. Inducing chronic toxoplasmosis is also confirmed by MAT, PCR and histological methods. HPLC results indicated a decrease in serum tyrosine level at days 40 in infected mice in comparison to control and the levels were too low to be measured at other times. However, a significantly high serum dopamine level was observed that gradually increased after parasite inoculation.ConclusionsNo detection of tyrosine level in most of the sample groups is probably related to the very low concentration of tyrosine in sera. However, low concentration of tyrosine at days 40 and increase of dopamine in most of the sample groups suggests the production of dopamine from tyrosine due to the presence ofToxoplasmain infected mice.
Higher-order structures of the foot-and-mouth disease virus RNA-dependent RNA polymerase required for dynamic inter-molecular interactions involved in viral genome replication
Authors: Loundras Eleni-Anna , Streetley James , Herod Morgan R. , Thompson Rebecca F. , Harris Mark , Bhella David , Stonehouse Nicola J. 
Published: December 2020

AbstractReplication of many positive-sense RNA viruses occurs within intracellular membrane-associated compartments. These are believed to provide a favourable environment for replication to occur, concentrating essential viral structural and non-structural components, as well as protecting these components from host-cell pathogen recognition and innate immune responses. However, the details of the molecular interactions and dynamics within these structures is very limited. One of the key components of the replication machinery is the RNA-dependent RNA polymerase, RdRp. This enzyme has been shown to form higher-order fibrilsin vitro. Here, using the RdRp from foot-and-mouth disease virus (termed 3Dpol), we report fibril structures, solved at ~7-9 Å resolution by cryo-EM, revealing multiple conformations of a flexible assembly. Fitting high-resolution coordinates led to the definition of potential intermolecular interactions. We employed mutagenesis using a sub-genomic replicon system to probe the importance of these interactions for replication. We use these data to propose models for the role of higher order 3Dpolcomplexes as a dynamic scaffold within which RNA replication can occur.
NetGenes: A database of essential genes predicted using features from interaction networks
Authors: Senthamizhan Vimaladhasan , Ravindran Balaraman , Raman Karthik 
Published: December 2020

AbstractEssential gene prediction models built so far are heavily reliant on sequence-based features and the scope of network-based features has been narrow. Previous work from our group demonstrated the importance of using network-based features for predicting essential genes with high accuracy. Here, we applied our approach for the prediction of essential genes to organisms from the STRING database and hosted the results in a standalone website. Our database, NetGenes, contains essential gene predictions for 2700+ bacteria predicted using features derived from STRING protein-protein functional association networks. Housing a total of 3.5M+ genes, NetGenes offers various features like essentiality scores, annotations and feature vectors for each gene. NetGenes is available athttps://rbc-dsai-iitm.github.io/NetGenes/
Induced Cognitive Impairments Reversed by Grafts of Neural Precursors: a Longitudinal Study in a Macaque Model of Parkinson’s Disease
Authors: Wianny Florence , Dzahini Kwamivi , Fifel Karim , Wilson Charles R.E. , Bernat Agnieszka , Dolmazon Virginie , Misery Pierre , Lamy Camille , Cooper Howard M. , Procyk Emmanuel , Kennedy Henry , Savatier Pierre , Dehay Colette , Vezoli Julien 
Published: December 2020

AbstractParkinson’s disease (PD) evolves over an extended and variable period in humans; several years prior to the onset of classical motor symptoms, cognitive deficits as well as sleep and biological rhythm disorders develop and worsen with disease progression, significantly impacting the quality of life of patients. The gold standard MPTP macaque model of PD recapitulates the progression of motor and non-motor symptoms over contracted periods of time.Here, this multidisciplinary and multiparametric study follows, in five animals, the steady progression of motor and non-motor symptoms and describes their reversal following bilateral grafts of neural precursors in diverse functional domains of the basal ganglia.Results show unprecedented recovery from cognitive symptoms in addition to a strong clinical motor recuperation. Both motor and cognitive recovery and partial circadian rhythm recovery correlate with the degree of graft integration into the host environment as well as with in-vivo levels of striatal dopaminergic innervation and function.Given inter-individuality of disease progression and recovery the present study underlines the importance of longitudinal multidisciplinary assessments in view of clinical translation and provides empirical evidence that integration of neural precursors following transplantation efficiently restores function at multiple levels in parkinsonian non-human primates.One Sentence SummaryEmpirical evidence that cell therapy efficiently reverts cognitive and clinical motor symptoms in the non-human primate model of Parkinson’s disease.
A human coronavirus evolves antigenically to escape antibody immunity
Authors: Eguia Rachel , Crawford Katharine H. D. , Stevens-Ayers Terry , Kelnhofer-Millevolte Laurel , Greninger Alexander L. , Englund Janet A. , Boeckh Michael J. , Bloom Jesse D. 
Published: December 2020

AbstractThere is intense interest in antibody immunity to coronaviruses. However, it is unknown if coronaviruses evolve to escape such immunity, and if so, how rapidly. Here we address this question by characterizing the historical evolution of human coronavirus 229E. We identify human sera from the 1980s and 1990s that have neutralizing titers against contemporaneous 229E that are comparable to the anti-SARS-CoV-2 titers induced by SARS-CoV-2 infection or vaccination. We test these sera against 229E strains isolated after sera collection, and find that neutralizing titers are lower against these “future” viruses. In some cases, sera that neutralize contemporaneous 229E viral strains with titers >1:100 do not detectably neutralize strains isolated 8–17 years later. The decreased neutralization of “future” viruses is due to antigenic evolution of the viral spike, especially in the receptor-binding domain. If these results extrapolate to other coronaviruses, then it may be advisable to periodically update SARS-CoV-2 vaccines.
Probiotic Supplementation Reduces Inflammatory Profiles But Does Not Prevent Oral Immune Perturbations During SIV Infection
Authors: Jones Rhianna , Kroll Kyle , Broedlow Courtney , Schifanella Luca , Smith Scott , Hueber Brady , Shah Spandan V. , Ram Daniel R. , Manickam Cordelia , Varner Valerie , Klatt Nichole R. , Reeves R. Keith 
Published: December 2020

ABSTRACTHIV/SIV infections lead to massive loss of mucosal CD4+ T cells and breakdown of the epithelial mucosa resulting in severe microbial dysbiosis and chronic immune activation that ultimately drive disease progression. Moreover, disruption of one of the most understudied mucosal environments, the oral cavity, during HIV-induced immunosuppression results in significant microbial and neoplastic co-morbidities and contributes to and predicts distal disease complications. In this study we evaluated the effects of oral probiotic supplementation (Pbx), which can stimulate and augment inflammatory or anti-inflammatory pathways, on early SIV infection of rhesus macaques. Our study revealed that similar to the GI mucosae, oral CD4+ T cells were rapidly depleted, and as one of the first comprehensive analyses of the oral microflora in SIV infection, we also observed significant modulation among two genera,PorphyromonasandActinobacillus,early after infection. Interestingly, although Pbx therapy did not substantially protect against oral dysbiosis or ameliorate cell loss, it did dampen inflammation and T cell activation. Collectively, these data provide one of the most comprehensive evaluations of SIV-induced changes in oral microbiome and CD4+ T cell populations, and also suggest that oral Pbx could be a simple therapy to improve anti-inflammatory states in addition to more traditional antivirals.