bluuebunny/crossref_metadata_2025_split huggingface dataset:
Emergence of CC17 vancomycin variable Enterococcus faecium in India
Authors: Sugumar Madhan , Peela Sreeram Chandra Murthy , Viswanath Lakshmi Shree , Walia Kamini , Sistla Sujatha 
Published: August 2022

AbstractVancomycin variable enterococci (VVE) are those isolates that are susceptible to glycopeptide like vancomycin but harbour the resistance determinants like vanA gene. Globally the emergence of such strains was reported, and from India our centre was the first to report them. The present study focussed on analysing genome content of these strains from India to assess their genetic diversity. While the five isolates belonged to three sequence types, all the isolates were of clonal complex CC17. This supports that VVE from India are genetically closely related and are emerging from a single clone.
The molecular foundation of proprioceptor muscle-type identity
Authors: Dietrich Stephan , Company Carlos , Song Kun , Lowenstein Elijah David , Riedel Levin , Birchmeier Carmen , Gargiulo Gaetano , Zampieri Niccolò 
Published: August 2022

AbstractThe precise execution of coordinated movements depends on proprioception, the sense of body position in space. However, the molecular underpinnings of proprioceptive neuron subtype identities are not clear yet. In this study, we searched for molecular correlates of proprioceptor subtypes defined according to the identity of the muscle they innervate. We identified and validated signatures for subtypes monitoring the activity of back, abdominal, and hindlimb muscles. We found that proprioceptor muscle identity is acquired early in development and comprise programs controlling wiring specificity. Altogether this work paves the way for defining the mechanisms underlying the development of proprioceptor subtypes to the single muscle level and dissect their contributions to motor control.
Age-related differences in ocular features of a naturalistic free-ranging population of rhesus macaques
Authors: Fernandes Arthur G , Alexopoulos Palaiologos , Burgos-Rodriguez Armando , Martinez Melween I ,   Cayo Biobank Research Unit, Ghassibi Mark , Leskov Ilya , Brent Lauren J N , Snyder-Mackler Noah , Danias John , Wollstein Gadi , Higham James P , Melin Amanda D 
Published: August 2022

ABSTRACTPurposeRhesus macaques (Macaca mulatta) are the premier nonhuman primate model for studying human health and disease. We aimed to investigate if age was associated with ocular features of clinical relevance in a large cohort of free-ranging rhesus macaques from Cayo Santiago, Puerto Rico.MethodsWe evaluated 120 rhesus macaques (73 males, 47 females) aged from 0 to 29 years old (mean±SD: 12.6±6.4) from September to December, 2021. The ophthalmic evaluation included IOP assessment, corneal pachymetry, anterior segment biomicroscopy, A-Scan biometry, automated refraction, and fundus photography after pupil dilation. The effects of age on the outcome variables were investigated through multilevel mixed-effects models adjusted for sex and weight.ResultsOn average, IOP, pachymetry, axial length, and automated refraction spherical equivalent were 15.47±2.47 mmHg, 474.43±32.21 μm, 19.49±1.24 mm, and 0.30±1.70 D, respectively. Age was significantly associated with pachymetry (Coef.= -1.20; 95%CI: -2.27 to -0.14; p=0.026), axial length (Coef.= 0.03; 95%CI: 0.01 to 0.05; p=0.002), and spherical equivalent (Coef.= -0.12; 95%CI: -0.22 to -0.02; p=0.015). No association was detected between age and IOP. The prevalence of cataracts in either eye was 10.83% (95% CI: 6.34 – 17.89%) and was significantly associated with age (OR= 1.20; 95%CI: 1.06 – 1.36; p=0.004). Retinal drusen in either eye was observed in 15.00% (95% CI: 9.60 – 22.68%) of the animals, which was also significantly associated with age (OR=1.14; 95%CI: 1.02 – 1.27; p=0.020).ConclusionsRhesus macaques exhibit age-related ocular associations similar to those observed in human aging, including decreased corneal thickness, increased axial length, myopic shift, and higher occurrence of cataract and retinal drusen.
Boolean dynamic modeling of TNFR1 signaling predicts a nested feedback loop regulating the apoptotic response at single-cell level
Authors: Sherekar Shubhank , Viswanathan Ganesh 
Published: August 2022

AbstractCell-to-cell variability during Tumor Necrosis Factor Receptor 1 (TNFR1) signaling triggered by the pleiotropic cytokine TNFα can lead to pro-survival and apoptotic phenotypic responses at single-cell level. Harnessing the ability to modulate the signal flow responsible for the balance between these two phenotypes and make cells favour apoptosis have been considered in cancer therapies. We show that a 6-node nested feedback loop facilitates the crucial crosstalk regulation modulating the signal flow between these two responses. We identify this by systematically analysing the partial state transition graph (pSTG) underlying a Boolean dynamic model of the TNFR1 signaling network that accounts for signal flow path variability. We demonstrate a novel approach “Boolean Modeling based Prediction of Steady-state probability of Phenotype Reachability (BM-ProSPR)” that enables constructing a reliable pSTG in a computationally efficient manner and predicting accurately the network’s ability to settle into different phenotypes. We deduce that knocking-off Comp1 – IKK* complex tweaks the signal flow paths leading to a 62% increase in the steady state probability of TNFR1 signaling culminating in apoptosis and thereby favours phenotype switching from pro-survival to apoptosis. Priming cancerous cells with inhibitors targeting the interaction involving Comp1 and IKK* prior to TNFα exposure could be a potential therapeutic strategy.
Complement-dependent loss of inhibitory synapses on pyramidal neurons followingToxoplasma gondiiinfection
Authors: Carrillo Gabriela L. , Su Jianmin , Cawley Mikel L. , Wei Derek , Gill Simran K. , Blader Ira J. , Fox Michael A. 
Published: August 2022

AbstractThe apicomplexan parasiteToxoplasma gondiihas developed mechanisms to establish a central nervous system infection in virtually all warm-blooded animals. AcuteT. gondiiinfection can cause neuroinflammation, encephalitis, and seizures. Meanwhile, studies in humans, non-human primates, and rodents have linked chronicT. gondiiinfection with altered behavior and increased risk for neuropsychiatric disorders, including schizophrenia. We previously demonstrated thatT. gondiiinfection triggers the loss of perisomatic inhibitory synapses, an important source of inhibition on excitatory pyramidal cells, and a type of synapse that is disrupted in neurological and neuropsychiatric disorders. Similar to other instances of inflammation and neurodegeneration, we showed that phagocytic cells (including microglia and infiltrating monocytes) contribute to the loss of these inhibitory synapses. However, in the case ofT. gondii-induced synapse loss, phagocytic cells target and ensheath the cell bodies of telencephalic neurons. Here, we show that these phagocytic cells specifically ensheath excitatory pyramidal neurons, leading to the preferential loss of perisomatic synapses on these neurons. In contrast, inhibitory cortical interneuron subtypes are not extensively ensheathed by phagocytic cells following infection. Moreover, we show that infection induces expression of complement C3 protein by these excitatory neurons and that C3 is required for the loss of perisomatic inhibitory synapses, albeit not through activation of the classical complement pathway. Together, these findings provide evidence thatT. gondiiinfection induces changes in excitatory pyramidal neurons that trigger selective removal of inhibitory perisomatic synapses in the infected neocortex and provide a novel role for complement in remodeling of inhibitory circuits in the infected brain.
Imaging the columnar functional organization of human area MT+ to axis-of-motion stimuli using VASO at 7 Tesla
Authors: Pizzuti Alessandra , Huber Laurentius (Renzo) , Gulban Omer Faruk , Benitez-Andonegui Amaia , Peters Judith , Goebel Rainer 
Published: August 2022

AbstractCortical columns of direction-selective neurons in the motion sensitive area (MT) have been successfully established as a microscopic feature of the neocortex in animals. The same property has been investigated at mesoscale (<1 mm) in the homologous brain area (hMT+, V5) in living humans by using ultra-high field functional magnetic resonance imaging (fMRI). Despite the reproducibility of the selective response to axis-of-motion stimuli, clear quantitative evidence for the columnar organization of hMT+ is still lacking. Using cerebral blood volume (CBV)-sensitive fMRI at 7 Tesla with submillimeter resolution and high spatial specificity to microvasculature, we investigate the columnar functional organization of hMT+ in 5 participants perceiving axis-of-motion stimuli for both blood oxygenation level dependent (BOLD) and vascular space occupancy (VASO) contrast mechanisms provided by the used Slab-Selective Slice Inversion (SS-SI)-VASO sequence. With the development of a new searchlight algorithm for column detection, we provide the first quantitative columnarity map that characterizes the entire 3D hMT+ volume. Using voxel-wise measures of sensitivity and specificity, we demonstrate the advantage of using CBV-sensitive fMRI to detect mesoscopic cortical features by revealing higher specificity of axis-of-motion cortical columns for VASO as compared to BOLD contrast. These voxel-wise metrics also provide further insights on how to mitigate the highly debated draining veins effect. We conclude that using CBV-VASO fMRI together with voxel-wise measurements of sensitivity, specificity and columnarity offers a promising avenue to quantify the mesoscopic organization of hMT+ with respect to axis-of-motion stimuli. Furthermore, our approach and methodological developments are generalizable and applicable to other human brain areas where similar mesoscopic research questions are addressed.
Insecticides, more than herbicides, land use, and climate, are associated with declines in butterfly species richness and abundance in the American Midwest
Authors: Deynze Braeden Van , Swinton Scott M. , Hennessy David A. , Haddad Nick M. , Ries Leslie 
Published: August 2022

AbstractMounting evidence shows overall insect abundances are in decline globally. Habitat loss, climate change, and pesticides have all been implicated, but their relative effects have never been evaluated in a comprehensive large-scale study. We harmonized 17 years of land use, climate, multiple classes of pesticides, and butterfly survey data across 81 counties in five states in the US Midwest. We find community-wide declines in total butterfly abundance and species richness to be most strongly associated with pesticides in general, and for butterflies species richness the use of neonicotinoid-treated seeds in particular. This included the abundance of the migratory monarch (Danaus plexippus), whose decline is the focus of intensive debate and public concern. Insect declines cannot be understood without comprehensive data on all putative drivers, and the 2015 cessation of neonicotinoid data releases in the US will impede future research.One Sentence SummaryShifts in insecticide use towards neonicotinoid-treated seeds are associated with an 8 percent decline in butterfly species diversity across the American Corn Belt.
Lectocyte secrete novel leukolectinsin ovofor first-line innate immunity defence
Authors: Miftari Mirushe H. , Walther Bernt T. 
Published: August 2022

ABSTRACTAtlantic salmon hatching fluid (HF) contains numerous polypeptides. A component unidentified by proteomics, was cloned from tryptic peptides and characterized as lectin-like (LL-) proteins in the tectonin-family. Purified salmon LL-proteins elicited high-titre, LL-specific polyclonal antibodies. This study aims to delineate the cellular and genetic basis of fish embryonic LL-expression. LL-proteins were detected in salmon, cod, rainbow trout and zebrafish HFs. LL-immunoreactive cells were numerous in salmon and rainbow trout embryos, but fewer in zebrafish, cod and halibut. Peridermal salmon LL-positive cells (lectocytes) corresponded to non-eosinophilic cells stained by PAS-reagent. Northern blots revealed two transcripts in salmon and zebrafish embryos, and LL-transcripts were detected specifically in lectocytes. Dualin situhybridization distinguished lectocytes from hatching glands. BAC-library screening yielded salmon Leukolectin’s gene-structure with 4 introns, 5 exons, TATA-box, multiple upstream putative transcription-factor binding-sites, and polyadenylation site. Sequence-analysis indicated zebrafish LL’s conserved nt-sequences and gene-structure, which exhibited mature and truncated LL-transcripts. Zebrafish LL-expression was detected at 6 hpf (yolk syncytium) and 19 hpf (lectocytes and PVF). In dermal mucus, Leukolectins with TECPR-domains may function as pathogen-recognition receptors in first-line innate immunity defence.SUMMARY STATEMENT:At hatching, embryos lose maternal chorions, their first-line innate immuno-protection. Novel leukolectin-genes specifically expressed in non-eosinophilic peridermal cells (lectocytes) help explain how embryos develop innate immuno-competency to survive as larvae.
HiFi chromosome-scale diploid assemblies of the grape rootstocks 110R, Kober 5BB, and 101-14 Mgt
Authors: Minio Andrea , Cochetel Noé , Massonnet Mélanie , Figueroa-Balderas Rosa , Cantu Dario 
Published: August 2022

ABSTRACTCultivated grapevines are commonly grafted on closely related species to cope with specific biotic and abiotic stress conditions. The three North American Vitis species V. riparia, V. rupestris, and V. berlandieri, are the main species used for breeding grape rootstocks. Here, we report the diploid chromosome-scale assembly of three widely used rootstocks derived from these species: Richter 110 (110R), Kober 5BB, and 101-14 Millardet et de Grasset (Mgt). Draft genomes of the three hybrids were assembled using PacBio HiFi sequences at an average coverage of 53.1 X-fold. Using the tool suite HaploSync, we reconstructed the two sets of nineteen chromosome-scale pseudomolecules for each genome with an average haploid genome size of 494.5 Mbp. Residual haplotype switches were resolved using shared-haplotype information. These three reference genomes represent a valuable resource for studying the genetic basis of grape adaption to biotic and abiotic stresses, and designing trait-associated markers for rootstock breeding programs.
Deducing genotypes for loci of interest from SNP array data via haplotype sharing, demonstrated for apple and cherry
Authors: Schaller Alexander , Vanderzande Stijn , Peace Cameron 
Published: August 2022

AbstractBreeders, collection curators, and other germplasm users require genetic information, both genome-wide and locus-specific, to effectively manage their genetically diverse plant material. SNP arrays have become the preferred platform to provide genome-wide genetic profiles for elite germplasm and could also provide locus-specific genotypic information. However, genotypic information for loci of interest such as those within PCR-based DNA fingerprinting panels and trait-predictive DNA tests is not readily extracted from SNP array data, thus creating a disconnect between historic and new data sets. This study aimed to establish a method for deducing genotypes at loci of interest from their associated SNP haplotypes, demonstrated for two fruit crops and three locus types: quantitative trait loci Ma and Ma3 for acidity in apple, apple fingerprinting microsatellite marker GD12, and Mendelian trait locus Rf for sweet cherry fruit color. Using phased data from an apple 8K SNP array and sweet cherry 6K SNP array, unique haplotypes spanning each target locus were associated with alleles of important breeding parents. These haplotypes were compared via identity-by-descent (IBD) or identity-by-state (IBS) to haplotypes present in germplasm important to U.S. apple and cherry breeding programs to deduce target locus alleles in this germplasm. While IBD segments were confidently tracked through pedigrees, confidence in allele identity among IBS segments used a shared length threshold. At least one allele per locus was deduced for 64–93% of the 181 individuals. Successful validation compared deduced Rf and GD12 genotypes with reported and newly obtained genotypes. Our approach can efficiently merge and expand genotypic data sets, deducing missing data and identifying errors, and is appropriate for any crop with SNP array data and historic genotypic data sets, especially where linkage disequilibrium is high. Locus-specific genotypic information extracted from genome-wide SNP data is expected to enhance confidence in management of genetic resources.
Sensitivity analysis of genome-scale metabolic flux prediction
Authors: Niu Puhua , Soto Maria J. , Huang Shuai , Yoon Byung-Jun , Dougherty Edward R. , Alexander Francis J. , Blaby Ian , Qian Xiaoning 
Published: August 2022

ABSTRACTTRIMER, Transcription Regulation Integrated with MEtabolic Regulation, is a genome-scale modeling pipeline targeting at metabolic engineering applications. Using TRIMER, regulated metabolic reactions can be effectively predicted by integrative modeling of metabolic reactions with Transcription Factor (TF)-gene regulatory network (TRN), where the TRN is modeled via Bayesian network (BN). In this paper, we focus on sensitivity analysis of metabolic flux prediction considering potential model uncertainty in TRIMER. We propose a computational strategy to construct the uncertainty class of TRN models based on the inferred regulatory order uncertainty when learning from given transcriptomic expression data and analyze the prediction sensitivity of the TRIMER pipeline for the metabolite yield of interest. The obtained sensitivity analyses can provide a useful guidance for Optimal Experimental Design (OED) to help acquire new data that can enhance TRN modeling and effectively achieve specific metabolic engineering objectives, including metabolite yield alterations. We have performed simulation experiments to demonstrate the effectiveness of our developed sensitivity analysis strategy and its potential to effectively guide OED.ACM Reference FormatPuhua Niu, Maria J. Soto, Shuai Huang, Byung-Jun Yoon, Edward R. Dougherty,, Francis J. Alexander, Ian Blaby, Xiaoning Qian. 2018. Sensitivity analysis of genome-scale metabolic flux prediction. InProceedings of Make sure to enter the correct conference title from your rights confirmation email (CNB-MAC 2022). ACM, New York, NY, USA, 9 pages.https://doi.org/XXXXXXX.XXXXXXX
Standing balance in aging is robust against head rotation during visual tracking
Authors: Georgiadis Petros , Chatzinikolaou Konstantinos , Voudouris Dimitrios , Van Dieen Jaap , Hatzitaki Vassilia 
Published: August 2022

AbstractStanding balance is relatively more unstable when visually pursuing a moving target than when fixating a stationary one. These effects are common across age groups if the head is restrained during visual task performance. The present study focused on the role of the head motion on standing balance during the pursuit of a moving target as a function of age. Three predictions were tested: a) standing balance is compromised to a greater extent in older than young adults by gaze target pursuit compared to fixation, b) older adults pursue a moving target with greater and more variable head rotation than young adults, and c) greater and more variable head rotation during the gaze pursuit task is associated with greater postural sway. Twenty-two (22) older (age: 71.7±8.1, 12 M / 10 F) and twenty-three (23) young adults (age: 23.6±2.5, 12 M / 11 F) stood on a force plate in front of a 60-inch monitor while performing two visual tasks: fixation at a stationary target and gaze pursuit of a horizontally moving target. Centre of pressure (CoP) and head kinematics were synchronously recorded with the Vicon motion analysis system, while head-unconstrained gaze was captured by the Pupil Labs Invisible mobile tracking system. Postural sway, reflected in the interquartile CoP range and the root mean square (RMS) of CoP velocity increased during the gaze pursuit compared to the fixation task (p<.05), and this effect was more pronounced in older than young participants (p<.05). Older adults pursued the moving target employing more variable (p=.022) head yaw rotation than young participants although the amplitude of head rotation was not systematically different between groups (p=. 077). The amplitude and variance of head yaw rotation did not correlate with postural sway measures. Results suggest that older adults may engage more variable head rotation when tracking a moving target to compensate for age-related deficits in eye smooth pursuit movement. However, this strategy does not seem to compromise standing balance.
High-precision neural stimulation by a highly efficient candle soot fiber optoacoustic emitter
Authors: Chen Guo , Shi Linli , Lan Lu , Wang Runyu , Li Yueming , Du Zhiyi , Hyman Mackenzie , Cheng Ji-Xin , Yang Chen 
Published: August 2022

AbstractHighly precise neuromodulation with a high efficacy poses great importance in neuroscience. Here, we developed a candle soot fiber optoacoustic emitter (CSFOE), capable of generating a high pressure of over 10 MPa, enabling highly efficient neuromodulation in vitro. The design of the fiber optoacoustic emitter, including the choice of the material and the thickness of the layered structure, was optimized in both simulations and experiments. The optoacoustic conversion efficiency of the optimized CSFOE was found to be ten times higher than the other carbon-based fiber optoacoustic emitters. Driven by a single laser, the CSFOE can perform dual-site optoacoustic activation of neurons, confirmed by calcium (Ca) imaging. Our work opens potential avenues for more complex and programmed control in neural circuits using a simple design for multisite neuromodulation in vivo.
The ENCODE Imputation Challenge: A critical assessment of methods for cross-cell type imputation of epigenomic profiles
Authors: Schreiber Jacob , Boix Carles , Lee Jin wook , Li Hongyang , Guan Yuanfang , Chang Chun-Chieh , Chang Jen-Chien , Hawkins-Hooker Alex , Schölkopf Bernhard , Schweikert Gabriele , Carulla Mateo Rojas , Canakoglu Arif , Guzzo Francesco , Nanni Luca , Masseroli Marco , Carman Mark James , Pinoli Pietro , Hong Chenyang , Yip Kevin Y. , Spence Jeffrey P. , Batra Sanjit Singh , Song Yun S. , Mahony Shaun , Zhang Zheng , Tan Wuwei , Shen Yang , Sun Yuanfei , Shi Minyi , Adrian Jessika , Sandstrom Richard , Farrell Nina , Halow Jessica , Lee Kristen , Jiang Lixia , Yang Xinqiong , Epstein Charles , Strattan J. Seth , Snyder Michael , Kellis Manolis , Noble William Stafford , Kundaje Anshul ,   ENCODE Imputation Challenge Participants
Published: August 2022

AbstractFunctional genomics experiments are invaluable for understanding mechanisms of gene regulation. However, comprehensively performing all such experiments, even across a fixed set of sample and assay types, is often infeasible in practice. A promising alternative to performing experiments exhaustively is to, instead, perform a core set of experiments and subsequently use machine learning methods to impute the remaining experiments. However, questions remain as to the quality of the imputations, the best approaches for performing imputations, and even what performance measures meaningfully evaluate performance of such models. In this work, we address these questions by comprehensively analyzing imputations from 23 imputation models submitted to the ENCODE Imputation Challenge. We find that measuring the quality of imputations is significantly more challenging than reported in the literature, and is confounded by three factors: major distributional shifts that arise because of differences in data collection and processing over time, the amount of available data per cell type, and redundancy among performance measures. Our systematic analyses suggest several steps that are necessary, but also simple, for fairly evaluating the performance of such models, as well as promising directions for more robust research in this area.