bluuebunny/crossref_metadata_2025_split huggingface dataset:
(Un)common space in infant neuroimaging studies: a systematic review of infant templates
Authors: Dufford Alexander J. , Hahn C. Alice , Peterson Hannah , Gini Silvia , Mehta Saloni , Alfano Alexis , Scheinost Dustin 
Published: September 2021

AbstractIn neuroimaging, spatial normalization is an important step that maps an individual’s brain onto a template brain permitting downstream statistical analyses. Yet, in infant neuroimaging, there remain several technical challenges that have prevented the establishment of a standardized template for spatial normalization. Thus, many different approaches are used in the literature. To quantify the popularity and variability of these approaches in infant neuroimaging studies, we performed a systematic review of infant MRI studies from 2000 to 2020. Here, we present results from 833 studies meeting inclusion criteria. Studies were classified into 1) processing data in single subject space, 2) using a predefined, or “off the shelf”, template, 3) creating a study specific template or 4) using a hybrid of these methods. We found that across the studies in the systematic review, single subject space was the most used (no common space). This was the most used common space for DWI and structural MRI studies while fMRI studies preferred off the shelf atlases. We found a pattern such that more recently published studies are more commonly using off the shelf atlases. When considering special populations, preterm studies most used single subject space while, when no special populations were being analyzed, an off the shelf template was most common. The most used off the shelf templates were the UNC Infant Atlases (26.1%). Using a systematic review of infant neuroimaging studies, we highlight a lack of an established “standard” template brain in these studies.
Benchmarking of a Bayesian single cell RNAseq differential gene expression test for dose-response study designs
Authors: Nault Rance , Saha Satabdi , Bhattacharya Sudin , Dodson Jack , Sinha Samiran , Maiti Tapabrata , Zacharewski Tim 
Published: September 2021

AbstractThe application of single-cell RNA sequencing (scRNAseq) for the evaluation of chemicals, drugs, and food contaminants presents the opportunity to consider cellular heterogeneity in pharmacological and toxicological responses. Current differential gene expression analysis (DGEA) methods focus primarily on two group comparisons, not multi-group dose-response study designs used in safety assessments. To benchmark DGEA methods for dose-response scRNAseq experiments, we proposed a multiplicity corrected Bayesian testing approach and compare it against 8 other methods including two frequentist fit-for-purpose tests using simulated and experimental data. Our Bayesian test method outperformed all other tests for a broad range of accuracy metrics including control of false positive error rates. Most notable, the fit-for-purpose and standard multiple group DGEA methods were superior to the two group scRNAseq methods for dose-response study designs. Collectively, our benchmarking of DGEA methods demonstrates the importance in considering study design when determining the most appropriate test methods.
Parallel evolution of urban-rural clines in melanism in a widespread mammal
Authors: Cosentino Bradley J. , Gibbs James P. 
Published: September 2021

AbstractUrbanization is the dominant trend of global land use change. The replicated nature of environmental change associated with urbanization should drive parallel evolution, yet insight into the repeatability of evolutionary processes in urban areas has been limited by a lack of multi-city studies. Here we leverage community science data on coat color in >60,000 eastern gray squirrels (Sciurus carolinensis) across 43 North American cities to test for parallel clines in melanism, a genetically based trait associated with thermoregulation and crypsis. We show the prevalence of melanism was positively associated with urbanization as measured by impervious cover. Urban-rural clines in melanism were strongest in the largest cities with extensive forest cover and weakest or absent in cities with warmer winter temperatures, where thermal selection likely limits the prevalence of melanism. Our results suggest that novel traits can evolve in a highly repeatable manner among urban areas, modified by factors intrinsic to individual cities, including their size, land cover, and climate.
In their sister’s footsteps: Taxonomic divergence obscures substantial functional overlap among the metabolically diverse symbiotic gut communities of adult and larval turtle ants
Authors: Béchade Benoît , Hu Yi , Sanders Jon G. , Cabuslay Christian S. , Łukasik Piotr , Williams Bethany R. , Fiers Valerie J. , Lu Richard , Wertz John T. , Russell Jacob A. 
Published: September 2021

AbstractGut bacterial symbionts can support animal nutrition by facilitating digestion and providing valuable metabolites. While the composition of gut symbiont communities shifts with host development in holometabolous insects, changes in symbiotic roles between immature and adult stages are not well documented, especially in ants. Here, we explored the metabolic capabilities of microbiomes sampled from herbivorous turtle ant (Cephalotessp.) larvae and adult workers through genomic and metagenomic screenings and targetedin vitrometabolic assays. We reveal that larval guts harbor bacterial symbionts from the Enterobacteriales, Lactobacillales and Rhizobiales orders, with impressive metabolic capabilities, including catabolism of plant and fungal recalcitrant fibers common in turtle ant diets, and energy-generating fermentation. Additionally, several members of the specialized turtle ant adult gut microbiome, sampled downstream of an anatomical barrier that dams large food particles, show a conserved potential to depolymerize many dietary fibers and other carbohydrates. Symbionts from both life stages have the genomic capacity to recycle nitrogen, synthesize amino acids and B-vitamins, and perform several key aspects of sulfur metabolism. We also document, for the first time in ants, an adult-associated Campylobacterales symbiont with an apparent capacity to anaerobically oxidize sulfide, reduce nitrate, and fix carbon dioxide. With help of their gut symbionts, including several bacteria likely acquired from the environment, turtle ant larvae appear as an important component of turtle ant colony digestion and nutrition. In addition, the conserved nature of the digestive, energy-generating, and nutritive capacities among adult-enriched symbionts suggests that nutritional ecology of turtle ant colonies has long been shaped by specialized, behaviorally-transferred gut bacteria with over 46 million years of residency.
Modular multilevel TMS device with wide output range and ultrabrief pulse capability for sound reduction
Authors: Zeng Zhiyong , Koponen Lari M. , Hamdan Rena , Li Zhongxi , Goetz Stefan M. , Peterchev Angel V. 
Published: September 2021

AbstractObjectiveThis article presents a novel transcranial magnetic stimulation (TMS) pulse generator with a wide range of pulse shape, amplitude, and width.ApproachBased on a modular multilevel TMS (MM-TMS) topology we had proposed previously, we realized the first such device operating at full TMS energy levels. It consists of ten cascaded H-bridge modules, each implemented with insulated-gate bipolar transistors, enabling both novel high-amplitude ultrabrief pulses as well as pulses with conventional amplitude and duration. The MM-TMS device can output pulses including up to 21 voltage levels with a step size of up to 1100 V, allowing relatively flexible generation of various pulse waveforms and sequences. The circuit further allows charging the energy storage capacitor on each of the ten cascaded modules with a conventional TMS power supply.Main resultsThe MM-TMS device can output peak coil voltages and currents of 11 kV and 10 kA, respectively, enabling suprathreshold ultrabrief pulses (> 8.25 μs active electric field phase). Further, the MM-TMS device can generate a wide range of near-rectangular monophasic and biphasic pulses, as well as more complex staircase-approximated sinusoidal, polyphasic, and amplitude-modulated pulses. At matched estimated stimulation strength, briefer pulses emit less sound, which could enable quieter TMS. Finally, the MM-TMS device can instantaneously increase or decrease the amplitude from one pulse to the next in discrete steps by adding or removing modules in series, which enables rapid pulse sequences and paired-pulse protocols with variable pulse shapes and amplitudes.SignificanceThe MM-TMS device allows unprecedented control of the pulse characteristics which could enable novel protocols and quieter pulses.
Children with amblyaudia show less flexibility in auditory cortical entrainment to periodic non-speech sounds
Authors: Momtaz Sara , Moncrieff Deborah , Ray Meredith A. , Bidelman Gavin M. 
Published: September 2021

ABSTRACTObjectiveWe investigated auditory temporal processing in children with amblyaudia (AMB), a subtype of auditory processing disorder, via cortical neural entrainment.Design and study samplesEvoked responses were recorded to click-trains at slow vs. fast (8.5 vs. 14.9/sec) rates in n=14 children with AMB and n=11 age-matched controls. Source and time-frequency analyses decomposed EEGs into oscillations (reflecting neural entrainment) stemming from the bilateral auditory cortex.ResultsPhase-locking strength in AMB depended critically on the speed of auditory stimuli. In contrast to age-matched peers, AMB responses were largely insensitive to rate manipulations. This rate resistance was seen regardless of the ear of presentation and in both cortical hemispheres.ConclusionChildren with AMB show a stark inflexibility in auditory cortical entrainment to rapid sounds. In addition to reduced capacity to integrate information between the ears, we identify more rigid tagging of external auditory stimuli. Our neurophysiological findings may account for certain temporal processing deficits commonly observed in AMB and related auditory processing disorders (APDs) behaviorally. More broadly, our findings may inform communication strategies and future rehabilitation programs; increasing the rate of stimuli above a normal (slow) speech rate is likely to make stimulus processing more challenging for individuals with AMB/APD.
Phosphatidylglycerol synthesis facilitates plastid gene expression and light induction of nuclear photosynthetic genes
Authors: Fujii Sho , Kobayashi Koichi , Lin Ying-Chen , Liu Yu-chi , Nakamura Yuki , Wada Hajime 
Published: September 2021

AbstractPhosphatidylglycerol (PG) is the only major phospholipid in the thylakoid membrane of chloroplasts. PG is essential for photosynthesis and loss of PG in Arabidopsis thaliana results in severe defects of growth and chloroplast development with decreased chlorophyll accumulation, impaired thylakoid formation, and downregulation of photosynthesis-associated genes encoded in nuclear and plastid genomes. However, how the absence of PG affects the gene expression and plant growth remains unclear. To elucidate this mechanism, we investigated the growth and transcriptional profiles of a PG-deficient Arabidopsis mutant pgp1-2 under various light conditions. Microarray analysis demonstrated that reactive oxygen species-responsive genes were upregulated in pgp1-2. Decreased growth light did not alleviated the impaired leaf development and the downregulation of photosynthesis-associated genes in pgp1-2, indicating limited impacts of photooxidative stress on the defects of pgp1-2. Illumination to dark-adapted pgp1-2 triggered downregulation of photosynthesis-associated nuclear-encoded genes (PhANGs), while plastid-encoded genes were constantly suppressed. Overexpression of GOLDEN2-LIKE1 (GLK1), a transcription factor regulating chloroplast development, in pgp1-2 upregulated PhANGs but not plastid-encoded genes along with chlorophyll accumulation. Our data suggest a broad impact of PG biosynthesis on nuclear-encoded genes partially via GLK1 and a specific involvement of this lipid in the plastid gene expression and plant development.
Weight Pulling: A Novel Mouse Model of Human Progressive Resistance Exercise
Authors: Zhu Wenyuan G. , Hibbert Jamie E. , Lin Kuan-Hung , Steinert Nathaniel D. , Lemens Jake L. , Jorgenson Kent W. , Newman Sarah M. , Lamming Dudley W. , Hornberger Troy A. 
Published: September 2021

AbstractThis study describes a mouse model of progressive resistance exercise that utilizes a full-body/multi-joint exercise (weight pulling) along with a training protocol that mimics a traditional human paradigm (3 training sessions per week, ∼8-12 repetitions per set, 2 minutes of rest between sets, ∼2 maximal-intensity sets per session, last set taken to failure, and a progressive increase in loading that is based on the individual’s performance). We demonstrate that weight pulling can induce an increase in the mass of numerous muscles throughout the body. The relative increase in muscle mass is similar to what has been observed in human studies, and it is associated with the same type of long-term adaptations that occur in humans (e.g., fiber hypertrophy, myonuclear accretion, and in some instances a fast-to-slow transition in Type II fiber composition). Moreover, we demonstrate that weight pulling can induce the same type of acute responses that are thought to drive these long-term adaptations (e.g., the activation of signaling through mTORC1 and the induction of protein synthesis at 1 hr post-exercise). Collectively, the results of this study indicate that weight pulling can serve as a highly translatable mouse model of progressive resistance exercise.
Strong and specific connections between retinal axon mosaics and midbrain neurons revealed by large scale paired recordings
Authors: Sibille Jérémie , Gehr Carolin , Benichov Jonathan I. , Balasubramanian Hymavathy , Teh Kai Lun , Lupashina Tatiana , Vallentin Daniela , Kremkow Jens 
Published: September 2021

SUMMARYThe superior colliculus (SC) is a midbrain structure that plays important roles in visually guided behaviors. Neurons in the SC receive afferent inputs from retinal ganglion cells (RGC), the output cells of the retina, but how SC neurons integrate RGC activityin vivois unknown. SC neurons might be driven by strong but sparse retinal inputs, thereby reliably transmitting specific retinal functional channels. Alternatively, SC neurons could sum numerous but weak inputs, thereby extracting new features by combining a diversity of retinal signals. Here, we discovered that high-density electrodes simultaneously capture the activity and the location of large populations of retinal axons and their postsynaptic SC target neurons, permitting us to investigate the retinocollicular circuit on a structural and functional levelin vivo. We show that RGC axons in the mouse are organized in mosaics that provide a single cell precise representation of the retina as input to SC. This isomorphic mapping between retina and SC builds the scaffold for highly specific wiring in the retinocollicular circuit which we show is characterized by strong connections and limited functional convergence, established in log-normally distributed connection strength. Because our novel method of large-scale paired recordings is broadly applicable for investigating functional connectivity across brain regions, we were also able to identify retinal inputs to the avian optic tectum of the zebra finch. We found common wiring rules in mammals and birds that provide a precise and reliable representation of the visual world encoded in RGCs to neurons in retinorecipient areas.HIGHLIGHTSHigh-density electrodes capture the activity of afferent axons and target neuronsin vivoRetinal ganglion cells axons are organized in mosaicsSingle cell precise isomorphism between dendritic and axonal RGC mosaicsMidbrain neurons are driven by sparse but strong retinal inputsFunctional wiring of the retinotectal circuit is similar in mammals and birds
Joint Registration of Multiple Point Clouds for Fast Particle Fusion in Localization Microscopy
Authors: Wang Wenxiu , Heydarian Hamidreza , Huijben Teun A.P.M. , Stallinga Sjoerd , Rieger Bernd 
Published: September 2021

AbstractWe present a fast particle fusion method for particles imaged with single-molecule localization microscopy. The state-of-the-art approach based on all-to-all registration has proven to work well but its computational cost scales unfavourably with the number of particles N, namely as N2. Our method overcomes this problem and achieves a linear scaling of computational cost with N by making use of the Joint Registration of Multiple Point Clouds (JRMPC) method. Straightforward application of JRMPC fails as mostly locally optimal solutions are found. These usually contain several overlapping clusters, that each consist of well-aligned particles, but that have different poses. We solve this issue by repeated runs of JRMPC for different initial conditions, followed by a classification step to identify the clusters, and a connection step to link the different clusters obtained for different initializations. In this way a single well-aligned structure is obtained containing the majority of the particles.We achieve reconstructions of experimental DNA-origami datasets consisting of close to 400 particles within only 10 min on a CPU, with an image resolution of 3.2 nm. In addition, we show artifact-free reconstructions of symmetric structures without making any use of the symmetry. We also demonstrate that the method works well for poor data with a low density of labelling and for 3D data.
Differential antibody dynamics to SARS-CoV-2 infection and vaccination
Authors: Chen Yuezhou , Tong Pei , Whiteman Noah B. , Moghaddam Ali Sanjari , Zuiani Adam , Habibi Shaghayegh , Gautam Avneesh , Xiao Tianshu , Cai Yongfei , Chen Bing , Wesemann Duane R. 
Published: September 2021

ABSTRACTOptimal immune responses furnish long-lasting (durable) antibodies protective across dynamically mutating viral variants (broad). To assess robustness of mRNA vaccine-induced immunity, we compared antibody durability and breadth after SARS-CoV-2 infection and vaccination. While vaccination delivered robust initial virus-specific antibodies with some cross-variant coverage, pre-variant SARS-CoV-2 infection-induced antibodies, while modest in magnitude, showed highly stable long-term antibody dynamics. Vaccination after infection induced maximal antibody magnitudes with enhanced longitudinal stability while infection-naïve vaccinee antibodies fell with time to post-infection-alone levels. The composition of antibody neutralizing activity to variant relative to original virus also differed between groups, with infection-induced antibodies demonstrating greater relative breadth. Differential antibody durability trajectories favored COVID-19-recovered subjects with dual memory B cell features of greater early antibody somatic mutation and cross-coronavirus reactivity. By illuminating an infection-mediated antibody breadth advantage and an anti-SARS-CoV-2 antibody durability-enhancing function conferred by recalled immunity, these findings may serve as guides for ongoing vaccine strategy improvement.
Mechanical and possible auxetic properties of human Achilles tendon during in vitro testing to failure
Authors: Nagelli Christopher V. , Hooke Alexander , Quirk Nicholas , De Padilla Consuelo Lopez , Hewett Timothy E. , van Griensven Martijn , Coenen Michael , Berglund Lawrence , Evans Christopher H. , Müller Sebastian A. 
Published: September 2021

AbstractThe Achilles tendon is the strongest tendon in the human body, but the basis of its high tensile strength has not been elucidated in detail. Here we have loaded healthy, human, Achilles tendons to failure in an anatomically authentic fashion while studying the local three-dimensional deformation and strains in real time, with very high precision, using digital image correlation (DIC). These studies identified a remarkable degree of anisotropic, medio-lateral auxetic behavior, with Poisson’s ratios not exceeding minus 1 in any part of the tendon at any time; under certain loads, discrete areas within the tendon had a Poisson’s ratio below minus 6. Early in the loading cycle, the proximal region of the tendon accumulated high lateral strains while longitudinal strains remained low. This behavior shielded the mid-substance of the tendon, its weakest part, from high longitudinal strains until immediately before rupture. These new insights are of great relevance to understanding the material basis of tendon injuries, designing improved prosthetic replacements, and developing regenerative strategies.
blupADC: An R package and shiny toolkit for comprehensive genetic data analysis in animal and plant breeding
Authors: Mei Quanshun , Fu Chuanke , Li Jieling , Zhao Shuhong , Xiang Tao 
Published: September 2021

AbstractSummaryGenetic analysis is a systematic and complex procedure in animal and plant breeding. With fast development of high-throughput genotyping techniques and algorithms, animal and plant breeding has entered into a genomic era. However, there is a lack of software, which can be used to process comprehensive genetic analyses, in the routine animal and plant breeding program. To make the whole genetic analysis in animal and plant breeding straightforward, we developed a powerful, robust and fast R package that includes genomic data format conversion, genomic data quality control and genotype imputation, breed composition analysis, pedigree tracing, analysis and visualization, pedigree-based and genomic-based relationship matrix construction, and genomic evaluation. In addition, to simplify the application of this package, we also developed a shiny toolkit for users.Availability and implementationblupADC is developed primarily in R with core functions written in C++. The development version is maintained athttps://github.com/TXiang-lab/blupADC.Supplementary informationSupplementary dataare available online
Visualizing the Costs and Benefits of Correcting P-Values for Multiple Hypothesis Testing in Omics Data
Authors: Shuken Steven R. , McNerney Margaret W. 
Published: September 2021

AbstractThe multiple hypothesis testing problem is inherent in high-throughput quantitative genomic, transcriptomic, proteomic, and other “omic” screens. The correction of p-values for multiple testing is a critical element of quantitative omic data analysis, yet many researchers are unfamiliar with the sensitivity costs and false discovery rate (FDR) benefits of p-value correction. We developed models of quantitative omic experiments, modeled the costs and benefits of p-value correction, and visualized the results with color-coded volcano plots. We developed an R Shiny web application for further exploration of these models which we call the Simulator of P-value Multiple Hypothesis Correction (SIMPLYCORRECT). We modeled experiments in which no analytes were truly differential between the control and test group (all null hypotheses true), all analytes were differential, or a mixture of differential and non-differential analytes were present. We corrected p-values using the Benjamini-Hochberg (BH), Bonferroni, and permutation FDR methods and compared the costs and benefits of each. By manipulating variables in the models, we demonstrated that increasing sample size or decreasing variability can reduce or eliminate the sensitivity cost of p-value correction and that permutation FDR correction can yield more hits than BH-adjusted and even unadjusted p-values in strongly differential data. SIMPLYCORRECT can serve as a tool in education and research to show how p-value adjustment and various parameters affect the results of quantitative omics experiments.