bluuebunny/crossref_metadata_2025_split huggingface dataset:
An algorithm for the identification of indicator taxonomic units and their use in analyses of ecosystem state
Authors: de la Vega Hernán , Falco Liliana , Saravia Leonardo , Sandler Rosana , Duhour Andrés , Velazco Víctor N , Coviella Carlos 
Published: May 2022

AbstractBiological community structure can be used as an ecological state descriptor, and the sensitivity of some taxonomic groups or biological entities to environmental conditions allows for their use as ecological state indicators. This work describes a mathematical methodology developed for the identification of such taxonomic units when comparing environments or ecosystems under different anthropic impacts. Based on this methodology, a freely downloadable R package for easy use was developed, (Ecoindicators, DOI: 10.5281/zenodo.5772829). Based solely on presence or absence information, the method identifies indicator taxonomic units for each environment, estimates the belonging of any additional samples to a given environment, approximates the ecological niche of any taxonomic unit based on two or more selected environmental factors, and returns the frequency of any taxonomic unit in a selected combination of environmental factors. By using the approximation to the ecological niche of species present, given a new sample, the physicochemical parameters can be estimated by the species present in the sample. These analyses can be performed simultaneously for two or more taxonomic units. This paper provides a mathematical description of how the mathematical method was developed. One of the advantages of this method, and the referred R-package is that it can be used for any ecosystem for which there is a suitable biological dataset associated with environmental factors. In addition, both this mathematical procedure and the package referred to, can be tailored by other researchers to fit their own needs. We also expect other developers to further improve it.
Combined reference-free and multi-reference approaches uncover cryptic variation underlying rapid adaptation in microbial pathogens
Authors: Dutta Anik , McDonald Bruce A. , Croll Daniel 
Published: May 2022

AbstractBackgroundMicrobial species often harbor substantial functional diversity driven by structural genetic variation. Rapid adaptation from such standing variation in pathogens threatens global food security and human health. Genome wide association studies (GWAS) provide a powerful approach to identify genetic variants underlying recent pathogen evolution. However, the reliance on single reference genomes and single nucleotide polymorphisms (SNPs) obscures the true extent of adaptive genetic variation. Here, we show quantitatively how a combination of multiple reference genomes and reference-free approaches captures substantially more relevant genetic variation compared to single reference mapping.ResultsWe performed reference-genome based association mapping across 19 reference-quality genomes covering the diversity of the species. We contrasted the results with a reference-free (i.e., K-mer) approach using raw whole genome sequencing data. We assessed the relative power of these GWAS approaches in a panel of 145 strains collected across the global distribution range of the fungal wheat pathogen Zymoseptoria tritici. We mapped the genetic architecture of 49 life history traits including virulence, reproduction and growth in multiple stressful environments. The inclusion of additional reference genome SNP datasets provides a nearly linear increase in additional loci mapped through GWAS. Variants detected through the K-mer approach explained a higher proportion of phenotypic variation than a reference genome based approach, illustrating the benefits of including genetic variants beyond SNPs.ConclusionsOur study demonstrates how the power of GWAS in microbial species can be significantly enhanced by comprehensively capturing functional genetic variation. Our approach is generalizable to a large number of microbial species and will uncover novel mechanisms driving rapid adaptation in microbial populations.
Focal electrical stimulation on an alcohol disorder model using MRI-compatible chronic neural monopolar carbon fiber electrodes
Authors: Lopez-Castro Alejandra , Angeles-Valdez Diego , Rojas-Piloni Gerardo , Garza-Villarreal Eduardo A. 
Published: May 2022

AbstractNeuromodulation interventions, such as Deep Brain Stimulation (DBS) and repeated transcranial magnetic stimulation (rTMS), are proposed as possible new complementary therapies to treat substance use disorders (SUD) such as alcohol use disorder (AUD). It is hypothesized that neuromodulation may induce neural plasticity in the reward and frontostriatal systems via electrical field induction, possibly reducing symptoms. Preclinical self-administration rodent models of AUD may help us gain insight into the effects of neuromodulation therapies on different pathology, as well as the neural mechanisms behind the positive effects. DBS, or any type of brain stimulation using intracranial electrodes in rodents, would benefit from the use of MRI to study the longitudinal effects and mechanisms of stimulation as well as novel targets, as it is a non-invasive technique that allows the analysis of structural and functional changes in the brain. To do this, there is a need for MRI-compatible electrodes that allow for MRI acquisition with minimal distortion of the magnetic field. In this protocol, we present a method for the construction and surgery of chronically implantable monopolar carbon electrodes for use in rats. Unlike conventional electrodes, carbon electrodes are resistant to high temperatures, flexible, and generate fewer artifacts in MRI compared to conventional ones. We validated its use by using a focal electrical stimulation high-frequency (20 Hz) protocol that lasted ~10 sessions. We propose that this technique can also be used for the research of the neurophysiological bases of the neuromodulatory treatment in other preclinical substance use disorders (SUD) models.
Evaluation of the DBA/2J mouse as a potential background strain for genetic models of cardiomyopathy
Authors: Hart Cora C. , Lee Young il , Hammers David W. , Sweeney H. Lee 
Published: May 2022

ABSTRACTThe potential use of the D2.mdx mouse (the mdx mutation on the DBA/2J genetic background) as a preclinical model of the cardiac aspects of Duchenne muscular dystrophy (DMD) has been criticized based on speculation that the DBA/2J genetic background displays an inherent hypertrophic cardiomyopathy phenotype. Accordingly, the goal of the current study was to further examine the cardiac status of this mouse strain over a 12-month period. DBA/2J mice have been scrutinized for the presence of cardiac lesions, however, in the current study we find that DBA/2J mice contain equivalent amounts of left ventricular collagen as healthy canine and human samples. In a longitudinal echocardiography study, neither sedentary or exercised DBA/2J mice demonstrated left ventricular wall thickening or cardiac functional deficits. In summary, we find no evidence of hypertrophic cardiomyopathy, or any other cardiac pathology, and thus propose that it is an appropriate background strain for genetic modeling of cardiac diseases, including the cardiomyopathy associated with DMD.
Botrytis cinerea infection accelerates ripening and cell wall disassembly to promote disease in tomato fruit
Authors: Silva Christian , Adaskaveg Jaclyn A. , Mesquida-Pesci Saskia D. , Ortega-Salazar Isabel B. , Pattathil Sivakumar , Zhang Lisha , Hahn Michael G. , van Kan Jan A.L. , Cantu Dario , Powell Ann L.T. , Blanco-Ulate Barbara 
Published: May 2022

AbstractPostharvest fungal pathogens benefit from the increased host susceptibility that occurs during fruit ripening. In unripe fruit, pathogens often remain quiescent and unable to cause disease until ripening begins, emerging at this point into destructive necrotrophic lifestyles that quickly result in fruit decay. Here, we demonstrate that one such pathogen, Botrytis cinerea, actively induces ripening processes to facilitate infections and promote disease. Assessments of ripening progression revealed that B. cinerea accelerated external coloration, ethylene production, and softening in unripe fruit, while mRNA sequencing of inoculated unripe fruit confirmed the corresponding upregulation of host genes involved in ripening processes, such as ethylene biosynthesis and cell wall degradation. Furthermore, an ELISA-based glycomics technique to assess fruit cell wall polysaccharides revealed remarkable similarities in the cell wall polysaccharide changes caused by both infections of unripe fruit and ripening of healthy fruit, particularly in the increased accessibility of pectic polysaccharides. Virulence and additional ripening assessment experiments with B. cinerea knockout mutants showed that induction of ripening is dependent on the ability to infect the host and break down pectin. The B. cinerea double knockout Δbcpg1Δbcpg2 lacking two critical pectin degrading enzymes was found to be incapable of emerging from quiescence even long after the fruit had ripened at its own pace, suggesting that the failure to accelerate ripening severely inhibits fungal survival on unripe fruit. These findings demonstrate that active induction of ripening in unripe tomato fruit is an important infection strategy for B. cinerea.One-Sentence SummaryPhysiological, transcriptional, and glycomic evidence indicates Botrytis cinerea hastens tomato fruit ripening to facilitate infection by a mechanism dependent on the fungal enzymes Bcpg1 and Bcpg2.
Protective geometry and reproductive anatomy as candidate determinants of clutch size variation in pentatomid bugs
Authors: Abram Paul K. , Guerra-Grenier Eric , Brodeur Jacques , Capko Clarissa , Aquino Michely Ferreira Santos , Beers Elizabeth H. , Blassioli-Moraes Maria Carolina , Borges Miguel , Cingolani M. Fernanda , Cusumano Antonino , De Clercq Patrick , Fernandez Celina A. , Gariepy Tara D. , Haye Tim , Hoelmer Kim , Laumann Raul Alberto , Lietti Marcela , McPherson J.E. , Punschke Eduardo , Saunders Thomas E. , Zhang Jin Ping , Hardy Ian C.W. 
Published: May 2022

AbstractMany animals lay their eggs in clusters. Eggs on the periphery of clusters can be at higher risk of mortality. We asked whether the most commonly occurring clutch sizes in pentatomid bugs could result from geometrical arrangements that maximize the proportion of eggs in the cluster’s interior. Although the most common clutch sizes do not correspond with geometric optimality, stink bugs do tend to lay clusters of eggs in shapes that protect increasing proportions of their offspring as clutch sizes increase. We also considered whether ovariole number, an aspect of reproductive anatomy that may be a fixed trait across many pentatomids, could explain observed distributions of clutch sizes. The most common clutch sizes across many species correspond with multiples of ovariole number. However, there are species with the same number of ovarioles that lay clutches of widely varying size, among which multiples of ovariole number are not over-represented. In pentatomid bugs, reproductive anatomy appears to be more important than egg mass geometry in determining clutch size uniformity. In addition, within this group of animals that has lost most of its variation in ovariole number, clutches with a broad range of shapes and sizes may still be laid.
Gradient-based parameter optimization to determine membrane ionic current composition of human induced pluripotent stem cell-derived cardiomyocytes
Authors: Kohjitani Hirohiko , Koda Shigeya , Himeno Yukiko , Makiyama Takeru , Yamamoto Yuta , Yoshinaga Daisuke , Wuriyanghai Yimin , Kashiwa Asami , Toyoda Futoshi , Zhang Yixin , Amano Akira , Noma Akinori , Kimura Takeshi 
Published: May 2022

1.AbstractPremature cardiac myocytes derived from human-induced pluripotent stem cells (hiPSC-CMs) show heterogeneous action potentials (APs), most probably because of different expression patterns of membrane ionic currents. We aim to develop a method of determining expression patterns of functional channels in terms of the whole-cell ionic conductances (Gx) using individual spontaneous AP configurations. However, it has been suggested that apparently identical AP configurations were obtained by different sets of ionic currents in a mathematical model of cardiac membrane excitation. If so, the inverse problem of Gx estimation might not be solved. We computationally tested the feasibility of the gradient-based optimization method. For realistic examination, conventional ‘cell-specific models’ were prepared by superimposing the model output of AP on each experimental AP record by the conventional manual adjustment of Gxs of the baseline model. Then, Gxs of 4 ~ 6 major ionic currents of the ‘cell-specific models’ were randomized within a range of ±5 ~ 15% and were used as initial parameter sets for the gradient-based automatic Gxs recovery by decreasing the mean square error (MSE) between the target and model output. When plotted all data points of MSE - Gx relation during the optimization, we found that the randomized population of Gxs progressively converged to the original value of the cell-specific model with decreasing MSE. To confirm the absence of any other local minimum in the global search space, we mapped the MSE by randomizing Gxs over a range of 0.1 ~ 10 times the control. No additional local minimum of MSE was obvious in the whole parameter space besides the global minimum of MSE at the default model parameter.
Tracking and perceiving diverse motion signals: Directional biases in human smooth pursuit and perception
Authors: Wu Xiuyun , Spering Miriam 
Published: May 2022

AbstractHuman smooth pursuit eye movements and motion perception behave similarly when observers track and judge the motion of simple objects, such as dots. But moving objects in our natural environment are complex and contain internal motion. We ask how pursuit and perception integrate the motion of objects with motion that is internal to the object. Observers (n = 20) tracked a moving random-dot kinematogram with their eyes and reported the object’s perceived direction. Objects moved horizontally with vertical shifts of 0, ±3, ±6, or ±9° and contained internal dots that were static or moved ±90° up/down. Results show that whereas pursuit direction was consistently biased in the direction of the internal dot motion, perceptual biases differed between observers. Interestingly, the perceptual bias was related to the magnitude of the pursuit bias (r = 0.75): perceptual and pursuit biases were directionally aligned in observers that showed a large pursuit bias, but went in opposite directions in observers with a smaller pursuit bias. Dissociations between perception and pursuit might reflect different functional demands of the two systems. Pursuit integrates all available motion signals in order to maximize the ability to monitor and collect information from the whole scene. Perception needs to recognize and classify visual information, thus segregating the target from its context. Ambiguity in whether internal motion is part of the scene or contributes to object motion might have resulted in individual differences in perception. The perception-pursuit correlation suggests shared early-stage motion processing or perception-pursuit interactions.
Detecting cell type from single cell RNA sequencing based on deep bi-stochastic graph regularized matrix factorization
Authors: Lan Wei , Chen Jianwei , Chen Qingfeng , Liu Jin , Wang Jianxin , Chen Yi-Ping Phoebe 
Published: May 2022

AbstractThe application of fruitful achievement of single-cell RNA-sequencing (scRNA-seq) technology has generated huge amount of gene transcriptome data. It has provided a whole new perspective to analyze the transcriptome at single-cell level. Cluster analysis of scRNA-seq is an efficient approach to reveal unknown heterogeneity and functional diversity of cell populations, which could further assist researchers to explore pathogenesis and biomarkers of diseases. In this paper, we propose a new cluster method (DSINMF) based on deep matrix factorization to detect cell type in the scRNA-seq data. In our method, the feature selection is used to reduce redundant features. Then, the imputation method is utilized to impute dropout events. Further, the dimension reduction is utilized to reduce the impact of noise. Finally, the deep matrix factorization with bi-stochastic graph regularization is employed to cluster scRNA-seq data. To evaluate the performance of DSINMF, eight datasets are used as test sets in the experiment. The experimental results show DSINMF outperformances than other state-of-the-art methods in clustering performance.
Quantifying Visual Acuity for Pre-Clinical Testing of Visual Prostheses
Authors: Spencer Martin , Kameneva Tatiana , Grayden David B. , Burkitt Anthony N. , Meffin Hamish 
Published: May 2022

AbstractVisual prostheses currently restore only limited vision. More research and pre-clinical work are required to improve the devices and stimulation strategies that are used to induce neural activity that results in visual perception. Evaluation of candidate strategies and devices requires an objective way to convert measured and modelled patterns of neural activity into a quantitative measure of visual acuity.This study presents an approach that compares evoked patterns of neural activation with target and reference patterns. A d-prime measure of discriminability determines whether the evoked neural activation pattern is sufficient to discriminate between the target and reference patterns and thus provide a quantified level of visual perception in the clinical Snellen and MAR scales. The measure was accurate in providing an estimate of the perceivable feature sizes in scaled standardized “C” and “E” optotypes.The approach was used to assess the visual acuity provided by two alternative stimulation strategies applied to simulated retinal implants with different phosphene sizes and electrode pitch configurations. It was found that when there is substantial overlap in neural activity generated by different electrodes, an estimate of acuity based only upon electrode pitch is incorrect; our proposed method gives an accurate result in these circumstances.Quantification of visual acuity using this approach in pre-clinical development will allow for more rapid and accurate prototyping of improved devices and neural stimulation strategies.
TOB is an effector of the hippocampus-mediated acute stress response
Authors: Youssef Mohieldin , Hamada Hiro Taiyo , Lai Esther Suk King , Kiyama Yuji , Eltabbal Mohamed , Kiyonari Hiroshi , Nakano Kohei , Kuhn Bernd , Yamamoto Tadashi 
Published: May 2022

AbstractStress affects behavior and involves critical dynamic changes at multiple levels ranging from molecular pathways to neural circuits and behavior. Abnormalities at any of these levels lead to decreased stress resilience and pathological behavior. However, temporal modulation of molecular pathways underlying stress response remains poorly understood. Transducer of ErbB2.1, known as TOB, (TOB1) is involved in different physiological functions, including cellular stress and immediate response to stimulation. In this study, we investigated the role of TOB in the brain’s stress machinery at molecular, neural circuit, and behavioral levels. Interestingly, TOB protein levels increased after mice were exposed to acute stress. At the neural circuit level, functional magnetic resonance imaging (fMRI) suggested that intra-hippocampal and hippocampal-prefrontal connectivity were dysregulated in Tob knockout (Tob-KO) mice. Electrophysiological recordings in hippocampal slices showed increased postsynaptic AMPAR-mediated neurotransmission, accompanied by decreased GABA neurotransmission and subsequently altered Excitatory/Inhibitory balance after Tob deletion. At the behavioral level, Tob-KO mice show abnormal, hippocampus-dependent, contextual fear conditioning and extinction, and depression-like behaviors. On the other hand, increased anxiety observed in Tob-KO mice is hippocampus-independent. At the molecular level, we observed decreased stress-induced LCN2 expression and ERK phosphorylation, as well as increased MKP-1 expression. This study suggests that TOB serves as an important modulator in hippocampal stress signaling machinery. In summary, we show a molecular pathway and neural circuit mechanism by which TOB deletion contributes to expression of pathological stress-related behavior.
3D-multiple immunoimaging using whole male organs in rice
Authors: Araki Saori , Tamotsu Hinako , Komiya Reina 
Published: May 2022

AbstractThe spatiotemporal regulation of proteins and RNAs is essential for the precise development of reproductive tissues in many organisms. The anther, a significant part of the male reproductive organ in plants, contains the somatic cell layers named the anther wall and germ cells located inside. The cell-to-cell communication between the soma and germ cells in the development of male and female tissues is reported, although the mechanism remains unknown in plants. Here, we successfully developed a simple 3D-organ-immunoimaging technique, which distinguishes each single cell from the four somatic cell layers and germ cells without the need for transformation, embedding, sectioning, or clearing in rice. The 3D-immunostaining method is also applicable to the intracellular localization of meiosis-specific proteins in meiocytes—namely MEL1, a germ cell-specific Argonaute in the cytoplasm, and ZEP1, a pachytene marker on meiotic chromosomes. Our study suggests that the 3D-multiple immunostaining method with single-cell and intracellular resolution will contribute to the organ-level elucidation of comprehensive molecular mechanisms and non-cell-autonomous systems.
Actin limits egg aneuploidies associated with female reproductive aging
Authors: Dunkley Sam , Mogessie Binyam 
Published: May 2022

AbstractAging-related centromeric cohesion loss underlies premature separation of sister chromatids (PSSC) and egg aneuploidy in reproductively older females. Here we show that F-actin maintains chromatid association after cohesion deterioration in aged eggs. F-actin disruption in aged mouse eggs exacerbated PSSC, while its removal in young eggs induced extensive chromatid separation events generally only seen in advanced reproductive ages. In young eggs containing experimentally reduced cohesion, F-actin removal accelerated PSSC in a microtubule dynamics-dependent manner, suggesting that actin counteracts chromatid-pulling spindle forces. Consistently, F-actin stabilization restricted PSSC even when cohesion was acutely depleted by targeted protein degradation. We conclude that actin mitigates PSSCs arising from age-related cohesion depletion by limiting microtubule-driven chromatid separation. This is supported by a spindle-specific disruption of F-actin in aged mammalian eggs.One-Sentence SummaryActin counteracts microtubule-based pulling forces to reduce the effects of chromosome cohesion loss in aged mammalian eggs.