bluuebunny/crossref_metadata_2025_split huggingface dataset:
Refining Convergent Rate Analysis with Topology in Mammalian Longevity and Marine Transitions
Authors: Treaster Stephen , Daane Jacob M. , Harris Matthew P. 
Published: March 2021

AbstractThe quest to map the genetic foundations of phenotypes has been empowered by the modern diversity, quality, and availability of genomic resources. Despite these expanding resources, the abundance of variation within lineages makes the association of genetic change to specific phenotypes improbable. Drawing such connections requires ana priorimeans of isolating the associated changes from background genomic variation. Evolution may provide these means via convergence; i.e., the shared variation that may result from replicate evolutionary experiments across independent trait occurrences. To leverage these opportunities, we developedTRACCER: Topologically Ranked Analysis of Convergence via Comparative Evolutionary Rates. As compared to current methods, this software empowers rate convergence analysis by factoring in topological relationships, because variation between phylogenetically proximate trait changes is more likely to be facilitating the trait. Pairwise comparisons are performed not with singular branches, but in reference to their most recent common ancestors. This ensures that comparisons represent identical genetic contexts and timeframes while obviating the problematic requirement of assigning ancestral states. We applied TRACCER to two case studies: marine mammal transitions, an unambiguous trait which has independently evolved three times, as well as the evolution of mammalian longevity, a less delineated trait but with more instances to compare. TRACCER, by factoring in topology, identifies highly significant, convergent genetic signals in these test cases, with important incongruities and statistical resolution when compared to existing convergence approaches. These improvements in sensitivity and specificity generate refined targets for downstream analysis of convergent evolution and identification of genotype-phenotype relationships.
Elevated N-glycosylation of immunoglobulin G variable regions in myasthenia gravis highlights a commonality across autoantibody-associated diseases
Authors: Mandel-Brehm Caleigh , Fichtner Miriam L. , Jiang Ruoyi , Winton Valerie J. , Vazquez Sara E. , Pham Minh C. , Hoehn Kenneth B. , Kelleher Neil L. , Nowak Richard J. , Kleinstein Steven H. , Wilson Michael R. , DeRisi Joseph L. , O’Connor Kevin C. 
Published: March 2021

AbstractElevated N-linked glycosylation of immunoglobulin G variable regions (IgG-VN-Glyc) is an emerging molecular phenotype associated with autoimmune disorders. To test the broader specificity of elevated IgG-VN-Glyc, we studied patients with distinct subtypes of myasthenia gravis (MG), a B cell-mediated autoimmune disease. Our experimental design included adaptive immune receptor repertoire sequencing to quantify and characterize N-glycosylation sites in the global B cell receptor repertoire, proteomics to examine glycosylation patterns of the circulating IgG, and production of human-derived recombinant autoantibodies, which were studied with mass spectrometry and antigen binding assays to confirm occupation of glycosylation sites and determine whether they alter binding. We found that the frequency of IgG-VN-Glycmotifs was increased in the B cell repertoire of MG patients when compared to healthy donors. Motifs were introduced by both biased V gene segment usage and somatic hypermutation. IgG-VN-Glyccould be observed in the circulating IgG in a subset of MG patients. Autoantigen binding, by patient-derived MG autoantigen-specific monoclonal antibodies with experimentally confirmed presence of IgG-VN-Glyc, was not altered by the glycosylation. Our findings extend prior work on patterns of variable region N-linked glycosylation in autoimmunity to MG subtypes. Although occupied IgG-VN-Glycmotifs are found on MG autoantigen-specific monoclonal antibodies, they are not required for binding to the autoantigen in this disease.
Invasive Earthworms Alter Forest Soil Microbiomes and Nitrogen Cycling
Authors: Jang Jeonghwan , Xiong Xianyi , Liu Chang , Yoo Kyungsoo , Ishii Satoshi 
Published: March 2021

AbstractNorthern hardwood forests in formerly glaciated areas had been free of earthworms until exotic European earthworms were introduced by human activities. The invasion of exotic earthworms is known to dramatically alter soil physical, geochemical, and biological properties, but its impacts on soil microbiomes are still unclear. Here we show that the invasive earthworms alter soil microbiomes and ecosystem functioning, especially for nitrogen cycling. We collected soil samples at different depths from three sites across an active earthworm invasion chronosequence in a hardwood forest in Minnesota, USA. We analyzed the structures and the functional potentials of the soil microbiomes by using amplicon sequencing, high-throughput nitrogen cycle gene quantification (NiCE chip), and shotgun metagenomics. Both the levels of earthworm invasion and soil depth influenced the microbiome structures. In the most recently and minimally invaded soils,NitrososphaeraandNitrospiraas well as the genes related to nitrification were more abundant than in the heavily invaded soils. By contrast, genes related to denitrification and nitrogen fixation were more abundant in the heavily invaded than the minimally invaded soils. Our results suggest that the N cycling in forest soils is mostly nitrification driven before earthworm invasion, whereas it becomes denitrification driven after earthworm invasion.
Event-Related Variability is Modulated by Task and Development
Authors: Naik Shruti , Adibpour Parvaneh , Dubois Jessica , Dehaene-Lambertz Ghislaine , Battaglia Demian 
Published: March 2021

ABSTRACTIn carefully designed experiments, cognitive scientists interpret the mean event-related potentials (ERP) in terms of cognitive operations. However, the huge signal variability from one trial to the next, questions the representability of such mean events. We explored here whether this variability is an unwanted noise, or an informative part of the neural response. We took advantage of the rapid changes in the visual system during human infancy and analyzed the variability of visual responses to central and lateralized faces in 2-to 6-month-old infants and adults using high-density electroencephalography (EEG). We observed that neural trajectories of individual trials always remain very far from ERP components, only moderately bending their direction with a substantial temporal jitter across trials. However, single trial trajectories displayed characteristic patterns of acceleration and deceleration when approaching ERP components, as if they were under the active influence of steering forces causing transient attraction and stabilization. These dynamic events could only partly be accounted for by induced microstate transitions or phase reset phenomena. Furthermore, these structured modulations of response variability, both between and within trials, had a rich sequential organization, which, in infants, was modulated by the task difficulty. Our approaches to characterize Event Related Variability (ERV) expand and reinterpret classic ERP analyses, making them compliant with pervasive neural variability and providing a more faithful description of neural events following stimulus presentation.
GraphBreak: Network Community detection and annotation in biomedical regulatory informatics context
Authors: Singh Abhishek Narain 
Published: March 2021

AbstractGraph network science is becoming increasingly popular, notably in big-data perspective where understanding individual entities for individual functional roles is complex and time consuming. It is likely when a set of genes are regulated by a set of genetic variants, the genes set is recruited for a common or related functional purpose. Grouping and extracting communities from network of associations becomes critical to understand system complexity, thus prioritizing genes for disease and functional associations. Workload is reduced when studying entities one at a time. For this, we present GraphBreak, a suite of tools for community detection application, such as for gene co-expression, protein interaction, regulation network, etc.Although developed for use case of eQTLs regulatory genomic network community study- results shown with our analysis with sample eQTL data-Graphbreak can be deployed for other studies if input data has been fed in requisite format, including but not limited to gene co-expression networks, protein-protein interaction network, signaling pathway and metabolic network. GraphBreak showed critical use case value in its downstream analysis for disease association of communities detected. If all independent steps of community detection and analysis are a step-by-step sub-part of the algorithm, GraphBreak can be considered a new algorithm for community based functional characterization. Combination of various algorithmic implementation modules into a single script for this purpose illustrates GraphBreak’s novelty. Compared to other similar tools, with GraphBreak we can better detect communities with overrepresentation of its member genes for statistical association with diseases, therefore target genes which can be prioritized for drug-positioning or drug-repositioning as the case be.
A global multiregional proteomic map of the human cerebral cortex
Authors: Guo Zhengguang , Shao Chen , Zhang Yang , Qiu Wenying , Li Wenting , Zhu Weimin , Yang Qian , Huang Yin , Pan Lili , Dong Yuepan , Sun Haidan , Xiao Xiaoping , Sun Wei , Ma Chao , Zhang Liwei 
Published: March 2021

AbstractThe Brodmann area (BA)-based map is one of the most widely used cortical maps for studies of human brain functions and in clinical practice; however, the molecular architecture of BAs remain unknown. The present study provided a global multiregional proteomic map of the human cerebral cortex by analyzing 29 BAs. These 29 BAs were grouped into 6 clusters based on similarities in proteomic patterns: the motor and sensory cluster, vision cluster, auditory cluster and Broca’s area, Wernicke’s area cluster, cingulate cortex cluster, and heterogeneous function cluster. We identified 474 cluster-specific and 134 BA-specific signature proteins whose functions are closely associated with specialized functions and disease vulnerability of the corresponding cluster or BA. The findings of the present study could provide explanations for the functional connections between the anterior cingulate cortex and sensorimotor cortex and for anxiety-related function in the sensorimotor cortex. The brain transcriptomic and proteomic comparison indicated that they both could reflect the function of cerebral cortex, but showed different characteristics. These proteomic data are publicly available at the Human Brain Proteome Atlas (www.brain-omics.com). Our results may enhance our understanding of the molecular basis of brain functions and provide an important resource to support human brain research.
Impact of isolation method on cellular activation and presence of specific tendon cell subpopulations duringin vitroculture
Authors: Nichols Anne E.C. , Miller Sarah E. , Green Luke J. , Richards Michael S. , Loiselle Alayna E. 
Published: March 2021

AbstractTendon injuries are common and heal poorly, due in part to a lack of understanding of fundamental tendon cell biology. A major impediment to the study of tendon cells is the absence of robust, well-characterizedin vitromodels. Unlike other tissue systems, current tendon cell models do not account for how differences in isolation methodology may affect the activation state of tendon cells or the presence of various tendon cell sub-populations. The objective of this study was to characterize how common isolation methods affect the behavior, fate, and lineage composition of tendon cell cultures. Tendon cells isolated by explant exhibited reduced proliferative capacity, decreased expression of tendon marker genes, and increased expression of genes associated with fibroblast activation compared to digested cells. Consistently, explanted cells also displayed an increased propensity to differentiate to myofibroblasts compared to digested cells. Explanted cultures from multiple different tendons were substantially enriched for the presence of scleraxis-lineage (Scx-lin+) cells compared to digested cultures, while the overall percentage of S100a4-lineage (S100a4-lin+) cells was dependent on both isolation method and tendon of origin. Neither isolation method preserved the ratios of Scx-lin+ or S100a4-lin+ to non-lineage cells seen in tendonsin vivo. Combined, these data indicate that further refinement ofin vitrocultures models is required in order to more accurately understand the effects of various stimuli on tendon cell behavior.Statement of clinical significanceThe development of informedin vitrotendon cell models will facilitate enhanced screening of potential therapeutic candidates to improve tendon healing.
Multiple bouts of high-intensity interval exercise reverse age-related functional connectivity disruptions without affecting motor learning in older adults
Authors: Greeley Brian , Chau Briana , Jones Christina B. , Neva Jason L. , Kraeutner Sarah N. , Campbell Kristin L. , Boyd Lara A. 
Published: March 2021

AbstractExercise has emerged as an intervention that may mitigate age-related resting state functional connectivity and sensorimotor declines. Here, 42 healthy older adults rested or completed 3 sets of high-intensity interval exercise for a total of 23 minutes, then immediately practiced an implicit motor task with their non-dominant hand across five separate sessions. Participants completed resting stage functional MRI before the first and after the fifth day of practice; they also returned 24-hours and 35-days later to complete short- and long-term retention. Independent component analysis of resting state functional MRI revealed increased connectivity in the frontoparietal, the dorsal attentional, and cerebellar networks and group. seed-based analysis showed strengthened connectivity between the limbic system and right cerebellum, and between the right cerebellum and bilateral middle temporal gyri in the exercise group. There was no motor learning advantage for the exercise group. Our data suggest that exercise paired with an implicit motor learning task in older adults can augment resting state functional connectivity without enhancing behaviour beyond that stimulated by skilled motor practice.Impact statementFive separate bouts of exercise paired with skilled motor practice strengthens resting state networks in brain regions that are susceptible to declines in older adults without affecting motor acquisition or learning.
A comparative recombination analysis of human coronaviruses and implications for the SARS-CoV-2 pandemic
Authors: Pollett Simon , Conte Matthew A , Sanborn Mark , Jarman Richard G , Lidl Grace M. , Modjarrad Kayvon , Berry Irina Maljkovic 
Published: March 2021

ABSTRACTThe SARS-CoV-2 pandemic prompts evaluation of recombination in human coronavirus (hCoV) evolution. We undertook recombination analyses of 158,118 public seasonal hCoV, SARS-CoV-1, SARS-CoV-2 and MERS-CoV genome sequences using the RDP4 software. We found moderate evidence for 8 SARS-CoV-2 recombination events, two of which involved the spike gene, and low evidence for one SARS-CoV-1 recombination event. Within MERS-CoV, 229E, OC43, NL63 and HKU1 datasets, we noted 7, 1, 9, 14, and 1 high-confidence recombination events, respectively. There was propensity for recombination breakpoints in structural genes, and recombination severely skewed the temporal structure of these data, especially for NL63 and OC43. Bayesian time-scaled analyses on recombinant-free data indicated the sampled diversity of seasonal CoVs emerged in the last 70 years, with 229E displaying continuous lineage replacements. These findings emphasize the importance of genomic based surveillance to detect recombination in SARS-CoV-2, particularly if recombination may lead to immune evasion.
Multichromatic Near-Infrared Imaging to Assess Interstitial Lymphatic and Venous UptakeIn Vivo
Authors: Bernard Fabrice C. , Kaiser Jarred , Raval Sarvgna K. , Nepiyushchikh Zhanna V. , Doan Thanh N. , Willett Nick J. , Dixon J. Brandon 
Published: March 2021

AbstractSignificanceChanges in interstitial fluid clearance are implicated in many diseases. Using NIR imaging with properly sized tracers could enhance our understanding of how venous and lymphatic drainage are involved in disease progression or enhance drug delivery strategies.AimWe investigated multichromatic NIR imaging with multiple tracers to assessin vivomicrovascular clearance kinetics and pathways in different tissue spaces.ApproachWe used a chemically inert IR Dye 800CW (free dye) to target venous capillaries and a purified conjugate of IR Dye 680RD with a 40 kDa PEG (PEG) to target lymphatic capillariesin vivo. Optical imaging settings were validated and tunedin vitrousing tissue phantoms. We investigated multichromatic NIR imaging’s utility in twoin vivotissue beds – the mouse tail and rat knee joint. We then tested the ability of the approach to detect interstitial fluid perturbations due to exercise.ResultsIn anin vitrosimulated tissue environment, free dye and PEG mixture allowed for simultaneous detection without interference. Co-injected NIR tracers cleared from the interstitial space via distinct routes allowed assessment lymphatic and venous uptake in the mouse tail. We determined that exercise after injection transiently increased lymphatic drainage as measured by lower normalized intensity immediately after exercise, while exercise pre-injection exhibited a transient delay in clearance from the jointConclusionsNIR imaging enables of simultaneous imaging of lymphatic and venous-mediated fluid clearance with great sensitivity and can be used to measure transient changes in clearance rates and pathways.
Differential Roles of Positive and Negative Valence Systems in the Development of Post-Traumatic Stress Psychopathology
Authors: Ben-Zion Ziv , Shany Ofir , Admon Roee , Keynan Nimrod Jackob , Avisdris Netanell , Balter Shira Reznik , Shalev Arieh Y. , Liberzon Israel , Hendler Talma 
Published: March 2021

AbstractNegative and positive valence systems (NVS and PVS) pertain to processing of aversive and rewarding stimuli, respectively. Post-Traumatic Stress Disorder (PTSD) has been typically associated with hyper-responsivity of the NVS, and more recently, with deficient PVS functionality. The respective roles of these systems in early PTSD development have yet to be resolved. Here, we assessed neurobehavioral indicators of PVS and NVS longitudinally among 171 adult civilians at 1-, 6-, and 14-months following trauma exposure (TP1, TP2, and TP3). Using the ‘Safe or Risky Domino Choice’ (SRDC) game during fMRI, NVS and PVS functionality (i.e., activity and connectivity) were indicated by the amygdala and ventral striatum (VS) responses to punishments and rewards, respectively. The complementary functionality of these systems was behaviorally assessed as the percentage of risky choices taken during the game. Results revealed that increased amygdala functionality at TP1 was associated with greater PTSD severity at TP1 and TP3, specifically with hyperarousal and intrusion. Decreased VS functionality at TP1 was associated with greater PTSD severity at TP3, specifically with avoidance. Explainable machine learning revealed the primacy of PVS over NVS functionality at TP1 in predicting PTSD severity at TP3. Behaviorally, fewer risky choices were associated with more severe symptoms at TP1, especially with intrusion and avoidance. Overall, these results suggest a differential and potentially complementary involvement of NVS and PVS in PTSD development following trauma. Early therapeutics for PTSD in the immediate aftermath of trauma may thus target both negative and positive valence processing.
The developing brain structural and functional connectome fingerprint
Authors: Ciarrusta Judit , Christiaens Daan , Fitzgibbon Sean P. , Dimitrova Ralica , Hutter Jana , Hughes Emer , Duff Eugene , Price Anthony N , Cordero-Grande Lucilio , Tournier J-Donald , Rueckert Daniel , Hajnal Joseph V , Arichi Tomoki , McAlonan Grainne , Edwards A David , Batalle Dafnis 
Published: March 2021

AbstractIn the mature brain, structural and functional connectivity ‘fingerprints’ can be used to identify the uniqueness of an individual. However, whether the characteristics that make a brain distinguishable from others already exist at birth remains unknown. Here, we used neuroimaging data of preterm born neonates who were scanned twice during the perinatal period to assess the developing brain fingerprint. We found that 62% of the participants could be identified based on the congruence of the later structural connectome to the initial connectivity matrix derived from the earlier timepoint. In contrast, similarity between functional connectomes only allowed to identify 12% of the participants. These suggests that structural connectivity is more stable in early life and can represent a potential connectome fingerprint. Thus, a relatively stable structural connectome appears to support a changing functional connectome at a time when neonates must rapidly acquire new skills to adapt to their new environment.
The influences of Shariah governance mechanisms on Islamic banks performance and Shariah compliance quality
Authors: Alam Md. Kausar , Rahman Mohammad Mizanur , Runy Mahfuza Kamal , Adedeji Babatunji Samuel , Hassan Md. Farjin 
Published: March 2021

PurposeThe purpose of this paper is to examine the influences of Shariah governance (SG) mechanisms on Islamic banks' performance and Shariah compliance quality in the context of Bangladesh.Design/methodology/approachA semi-structured personal interview tactic was applied to accomplish the research objectives. The data were collected from the regulators, Shariah supervisory boards, Shariah department executives and Shariah experts from the Central Bank (Bangladesh Bank) and Islamic banks in Bangladesh.FindingsThe study discovers that the quality of the Board of Directors (BODs), Shariah Supervisory Board (SSB), management and Shariah executives have both positive and negative influences on the Shariah compliance quality, image, goodwill and performance of Islamic banks' in Bangladesh. The compositions, formations and quality of SSB and Shariah officers positively influence the Islamic banks' fatwas, Shariah decisions, compliance quality and firm performance. The study also finds that prevailing banking pressure, current political situation, the willingness of BOD and management and social limitations impact Islamic banks' performance, Shariah compliance quality, image and goodwill.Research limitations/implicationsBased on our findings, if the regulators, BODs and Islamic banks can manage effective and efficient executives, it will create a positive impact on Islamic banks' performance, image, goodwill and quality compliance. As the prevailing banking pressure, current political situation and social limitations hinder the functions and employment system of the Islamic banks as well as result the Islamic banks' image, performance, Shariah implementations and compliance. Thus, the theorist needs to consider these mechanisms in extending the agency, stakeholder and resource dependence theories.Originality/valueThis research extends the literature concerning the influences of Islamic banks' SG mechanisms in Bangladesh. The study also argued not only the efficient and effective mechanisms but also the prevailing banking pressure, current political situation and social limitations impact on Islamic banks' performance and Shariah compliance quality.