bluuebunny/crossref_metadata_2025_split huggingface dataset:
The effect of variable inertial resistance on force, velocity, power and muscle activation during a chest press exercise
Authors: Zoffoli Luca , Biscarini Andrea , Zanuso Silvano 
Published: December 2023

AbstractThis study investigated the effect of the inertial component of the resistance (INERTIA) at different intensity levels (LOAD) on force (FORCE), velocity (VELOCITY), power (POWER), and the muscle activity of the pectoralis major (EMGPM), anterior deltoid (EMGDA) and triceps brachii (EMGTB) muscles during a chest press exercise.A motor-driven exercise apparatus was programmed to offer resistance with different inertial profiles over the range of movement (ROM): gravitational-type constant inertia (IFULL); no-inertia (IZERO); linearly descending inertia along theROM(IVAR). Nine healthy adults performed five, maximal-effort, explosive movements with each inertial profile at 30, 50 and 70% of their 1 repetition maximum. Meanwhile, theEMGPM,EMGDAandEMGTBsignals were obtained jointly with theFORCE, VELOCITYandPOWERreadings returned by the exercise apparatus.One-dimensional statistical non-parametric maps based on 2-way repeated measures ANOVA (SnPM) were employed to evaluate the effect ofLOADandINERTIAon the collected timeseries. Paired t-tests were then used as post-hoc tests on the portions of theROMdenoting significant differences in theSnPM.HigherLOADresulted in elevated outcomes over large portions of theROMin all the investigated timeseries. Compared toIFULL,IZEROallowed greaterVELOCITYat the cost of lowerFORCEthroughout theROM, whileIVAR, despite the lowerVELOCITYthanIZERO, resulted in higherFORCEandPOWERoutput. In addition,IZEROandIVARelevatedEMGTBat the end of theROMwith respect toIFULL.IVARovercame bothIFULLandIZEROin terms ofFORCEandPOWER, which indicates that variable inertial profiles might be effectively integrated into resistance exercise programs. Ultimately, this study suggested thatINERTIAacts independently to the imposedLOADon theFORCE, VELOCITYandPOWERproduction. Coaches and therapists are encouraged to account for the type ofINERTIAas one of the parameters considered during the exercise selection for their athletes or patients.
Open Soil Spectral Library (OSSL): Building reproducible soil calibration models through open development and community engagement
Authors: Safanelli José L. , Hengl Tomislav , Parente Leandro , Minarik Robert , Bloom Dellena E. , Todd-Brown Katherine , Gholizadeh Asa , Mendes Wanderson de Sousa , Sanderman Jonathan 
Published: December 2023

AbstractSoil spectroscopy is a widely used method for estimating soil properties that are important to environmental and agricultural monitoring. However, a bottleneck to its more widespread adoption is the need for establishing large reference datasets for training machine learning (ML) models, which are called soil spectral libraries (SSLs). Similarly, the prediction capacity of new samples is also subject to the number and diversity of soil types and conditions represented in the SSLs. To help bridge this gap and enable hundreds of stakeholders to collect more affordable soil data by leveraging a centralized open resource, the Soil Spectroscopy for Global Good has created the Open Soil Spectral Library (OSSL). In this paper, we describe the procedures for collecting and harmonizing several SSLs that are incorporated into the OSSL, followed by exploratory analysis and predictive modeling. The results of 10-fold cross-validation with refitting show that, in general, mid-infrared (MIR)-based models are significantly more accurate than visible and near-infrared (VisNIR) or near-infrared (NIR) models. From independent model evaluation, we found that Cubist comes out as the best-performing ML algorithm for the calibration and delivery of reliable outputs (prediction uncertainty and representation flag). Although many soil properties are well predicted, total sulfur, extractable sodium, and electrical conductivity performed poorly in all spectral regions, with some other extractable nutrients and physical soil properties also performing poorly in one or two spectral regions (VisNIR or Neospectra NIR). Hence, the use of predictive models based solely on spectral variations has limitations. This study also presents and discusses several other open resources that were developed from the OSSL, aspects of opening data, current limitations, and future development. With this genuinely open science project, we hope that OSSL becomes the driver of the soil spectroscopy community to accelerate the pace of scientific discovery and innovation.
Macrophages control pathological interferon responses during viral respiratory infection
Authors: Hoagland Daisy A. , Rodríguez-Morales Patricia , Mann Alexander O. , Yu Shuang , Lai Alicia , Vazquez Alan Baez , Pope Scott D. , Lim Jaechul , Li Shun , Zhang Xian , Li Ming O. , Medzhitov Ruslan , Franklin Ruth A. 
Published: December 2023

AbstractAntiviral immune mediators, including interferons and their downstream effectors, are critical for host defense yet can become detrimental when uncontrolled. Here, we identify a macrophage-mediated anti-inflammatory mechanism that limits type I interferon (IFN-I) responses. Specifically, we found that cellular stress and pathogen recognition induce Oncostatin M (OSM) production by macrophages. OSM-deficient mice succumbed to challenge with influenza or a viral mimic due to heightened IFN-I activation. Macrophage-derived OSM restricted excessive IFN-I production by lung epithelial cells following viral stimulation. Furthermore, reconstitution of OSM in the respiratory tract was sufficient to protect mice lacking macrophage-derived OSM against morbidity, indicating the importance of local OSM production. This work reveals a host strategy to dampen inflammation in the lung through the negative regulation of IFN-I by macrophages.One-Sentence SummaryType I interferons induced by viral stimuli are negatively regulated by macrophage-derived Oncostatin M.
Microbial communities living inside plant leaves or on the leaf surface are differently shaped by environmental cues
Authors: Mahmoudi Maryam , Almario Juliana , Lutap Katrina , Nieselt Kay , Kemen Eric 
Published: December 2023

AbstractLeaf-associated microbial communities can promote plant health and resistance to biotic and abiotic stresses. However, the importance of environmental cues in the assembly of the leaf endo- and epi-microbiota remains elusive. Here we aimed to investigate the impact of seasonal environmental variations, on the establishment of the leaf microbiome, focusing on long-term changes (five years) in bacterial, fungal, and non-fungal eukaryotic communities colonizing the surface and endosphere of six wildArabidopsis thalianapopulations. While leaf-microbial communities were found to be highly stochastic, the leaf niche had a predominant importance with endophytic microbial communities consistently exhibiting a lower diversity and variability. Furthermore, our analyses revealed that among environmental factors, radiation and humidity-related factors are the most important drivers of diversity paderns in the leaf, albeit with stronger effects on epiphytic communities. Using linear models, we further identified 30 important genera whose relative abundance in leaf compartments could be modeled from environmental variables, suggesting specific niche preferences for these taxa. With the hypothesis that these environmental factors could impact interactions within microbial communities, we analyzed the seasonal paderns of microbial interaction networks across leaf compartments. We showed that epiphytic networks are more complex than endophytic, and that the complexity and connectivity of these networks are partially correlated with the mentioned environmental cues. Our results indicate that humidity and solar radiation function as major environmental cues shaping the phyllosphere microbiome at the micro-scale (leaf compartment) and macro-scale (site). These findings could have practical implications for selecting and developing field-adapted microbes in the face of, and for predicting microbial invasions in response to global change.
Unbiased Complete Estimation of Chloroplast Number in Plant Cells Using Deep Learning Methods
Authors: Su Qun , Liu Le , Hu Zhengsheng , Wang Tao , Wang Huaying , Guo Qiuqi , Liao Xinyi , Dong Zhao , Yang Shaokai , Liu Ningjing , Zhao Qiong 
Published: December 2023

AbstractChloroplasts are essential organelles in plants that are involved in plant development and photosynthesis. Accurate quantification of chloroplast numbers is important for understanding the status and type of plant cells, as well as assessing photosynthetic potential and efficiency. Traditional methods of counting chloroplasts using microscopy are time-consuming and face challenges such as the possibility of missing out-of-focus samples or double counting when adjusting the focal position. Here, we developed an innovative approach called Detecting- and-Counting-chloroplasts (D&Cchl) for automated detection and counting of chloroplasts. This approach utilizes a deep-learning-based object detection algorithm called You-Only-Look-Once (YOLO), along with the Intersection Over Union (IOU) strategy. The application of D&Cchl has shown excellent performance in accurately identifying and quantifying chloroplasts. This holds true when applied to both a single image and a three-dimensional (3D) structure composed of a series of images. Furthermore, by integrating Cellpose, a cell-segmentation tool, we were able to successfully perform single-cell 3D chloroplast counting. Compared to manual counting methods, this approach improved the accuracy of detection and counting to over 95%. Together, our work not only provides an efficient and reliable tool for accurately analyzing the status of chloroplasts, enhancing our understanding of plant photosynthetic cells and growth characteristics, but also makes a significant contribution to the convergence of botany and deep learning.One-sentence summaryThis deep learning-based approach enables the accurate complete detection and counting of chloroplasts in 3D single cells using microscopic image stacks, and showcases a successful example of utilizing deep learning methods to analyze subcellular spatial information in plant cells.The authors responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (https://academic.oup.com/plcell/) is: Zhao Dong (dongzhao@hebeu.edu.cn), Shaokai Yang, (shaokai1@ualberta.ca), Ningjing Liu (liuningjing1@yeah.net), and Qiong Zhao (qzhao@bio.ecnu.edu.cn).
Iron promotes copper entry inStreptococcus pneumoniae
Authors: Sanchez-Rosario Yamil , Johnson Michael D.L. 
Published: December 2023

AbstractMetals serve an important function at the host-pathogen interface, being used to leverage bacterial survival. To reduce bacterial viability in the host, some metals such as iron, are sequestered by the host, while others, such as copper are used to intoxicate bacteria. During infection, this serves the dual purpose of starving the bacteria of valuable resources while providing it with a toxic substance. By growingStreptococcus pneumoniae,a causative agent of multiple diseases including pneumonia, middle ear infections and sepsis, in the medium RPMI 1640 with a nanomolar concentration of iron, followed by exposure to a higher concentration of iron and copper, we observed an iron-dependent increase in copper association. This process was specific for iron and conserved in otherS. pneumoniaeserotypes. We performed single and double knockouts in selected iron transport systems and observed that under the same experimental conditions as wild-type strain, there was significantly less copper associated with the iron transport knockout bacteria. Taken together, we conclude that copper is inadvertently imported into the bacterial cell during iron acquisition.
COMPUTATIONAL IDENTIFICATION OF ANTIBODY-BINDING EPITOPES FROM MIMOTOPE DATASETS
Authors: Li Rang , Wilderotter Sabrina , Stoddard Madison , Van Egeren Debra , Chakravarty Arijit , Joseph-McCarthy Diane 
Published: December 2023

AbstractA fundamental challenge in computational vaccinology is that most B-cell epitopes are conformational and therefore hard to predict from sequence alone. Another significant challenge is that a great deal of the amino acid sequence of a viral surface protein might not in fact be antigenic. Thus, identifying the regions of a protein that are most promising for vaccine design based on the degree of surface exposure may not lead to a clinically relevant immune response. Linear peptides selected by phage display experiments that have high affinity to the monoclonal antibody of interest (“mimotopes”) usually have similar physicochemical properties to the antigen epitope corresponding to that antibody. The sequences of these linear peptides can be used to find possible epitopes on the surface of the antigen structure or a homology model of the antigen in the absence of an antigen-antibody complex structure. Herein we describe two novel methods for mapping mimotopes to epitopes. The first is an ensemble approach, which combines the prediction results from two existing methods. The second is a novel algorithm named MimoTree, that allows for gaps in the mimotopes and epitopes on the antigen. More specifically, a mimotope may have a gap that does not match to the epitope to allow it to adopt a conformation relevant for binding to an antibody and residues may similarly be discontinuous in conformational epitopes. MimoTree is a fully automated epitope detection algorithm suitable for the identification of conformational as well as linear epitopes.
Effects of aging on glucose and lipid metabolism in mice
Authors: Lien Evan C. , Vu Ngoc , Westermark Anna M. , Danai Laura V. , Lau Allison N. , Gültekin Yetiş , Kukurugya Matthew A. , Bennett Bryson D. , Vander Heiden Matthew G. 
Published: December 2023

AbstractAging is accompanied by multiple molecular changes that contribute to aging-associated pathologies, such as accumulation of cellular damage and mitochondrial dysfunction. Tissue metabolism can also change with age, in part because mitochondria are central to cellular metabolism. Moreover, the co-factor NAD+, which is reported to decline across multiple tissue types during aging, plays a central role in metabolic pathways such as glycolysis, the tricarboxylic acid cycle, and the oxidative synthesis of nucleotides, amino acids, and lipids. To further characterize how tissue metabolism changes with age, we intravenously infused [U-13C]-glucose into young and old C57BL/6J, WSB/EiJ, and Diversity Outbred mice to trace glucose fate into downstream metabolites within plasma, liver, gastrocnemius muscle, and brain tissues. We found that glucose incorporation into central carbon and amino acid metabolism was robust during healthy aging across these different strains of mice. We also observed that levels of NAD+, NADH, and the NAD+/NADH ratio were unchanged in these tissues with healthy aging. However, aging tissues, particularly brain, exhibited evidence of up-regulated fatty acid and sphingolipid metabolism reactions that regenerate NAD+from NADH. Because mitochondrial respiration, a major source of NAD+regeneration, is reported to decline with age, our data supports a model where NAD+-generating lipid metabolism reactions may buffer against changes in NAD+/NADH during healthy aging.
A genome and tissue-specific transcriptomes of the large-polyp coral,Fimbriaphyllia(Euphyllia)ancora: Recipe for a coral polyp
Authors: Shikina Shinya , Yoshioka Yuki , Chiu Yi-Ling , Uchida Taiga , Chen Emma , Cheng Yin-Chu , Lin Tzu-Chieh , Chu Yu-Ling , Kanda Miyuki , Kawamitsu Mayumi , Fujie Manabu , Takeuchi Takeshi , Zayasu Yuna , Satoh Noriyuki , Shinzato Chuya 
Published: December 2023

AbstractCoral “polyps” are composed of several tissues; however, their characteristics are largely unexplored. Here we report biological characteristics of the four tissues that comprise polyps: tentacle (Te), mesenterial filament (Me), body wall (Bo), and mouth with pharynx (MP), using comparative genomic, morpho-histological, and transcriptomic analyses of the large-polyp coral,Fimbriaphyllia ancora. A draftF. ancoragenome assembly of 434 Mbp was created. Morpho-histological and transcriptomic characterization of the four tissues showed that they have distinct differences in structure, primary cellular composition, and transcriptional profiles. Tissue-specific, highly expressed genes (HEGs) ofTeare related to biological defense, predation, and coral-algal symbiosis.Meexpresses multiple digestive enzymes, whereasBoexpresses innate immunity and biomineralization-related molecules. Many receptors for neuropeptides and neurotransmitters are expressed inMP. The established dataset and new insights into tissue functions will facilitate a deeper understanding of coral biology.
Orbitofrontal Cortex Modulates Auditory Cortical Sensitivity and Sound Perception
Authors: Macedo-Lima Matheus , Hamlette Lashaka Sierra , Caras Melissa L. 
Published: December 2023

AbstractSensory perception is dynamic, quickly adapting to sudden shifts in environmental or behavioral context. Though decades of work have established that these dynamics are mediated by rapid fluctuations in sensory cortical activity, we have a limited understanding of the brain regions and pathways that orchestrate these changes. Neurons in the orbitofrontal cortex (OFC) encode contextual information, and recent data suggest that some of these signals are transmitted to sensory cortices. Whether and how these signals shape sensory encoding and perceptual sensitivity remains uncertain. Here, we asked whether the OFC mediates context-dependent changes in auditory cortical sensitivity and sound perception by monitoring and manipulating OFC activity in freely moving animals under two behavioral contexts: passive sound exposure and engagement in an amplitude modulation (AM) detection task. We found that the majority of OFC neurons, including the specific subset that innervate the auditory cortex, were strongly modulated by task engagement. Pharmacological inactivation of the OFC prevented rapid context-dependent changes in auditory cortical firing, and significantly impaired behavioral AM detection. Our findings suggest that contextual information from the OFC mediates rapid plasticity in the auditory cortex and facilitates the perception of behaviorally relevant sounds.Significance StatementSensory perception depends on the context in which stimuli are presented. For example, perception is enhanced when stimuli are informative, such as when they are important to solve a task. Perceptual enhancements result from an increase in the sensitivity of sensory cortical neurons; however, we do not fully understand how such changes are initiated in the brain. Here, we tested the role of the orbitofrontal cortex (OFC) in controlling auditory cortical sensitivity and sound perception. We found that OFC neurons change their activity when animals perform a sound detection task. Inactivating OFC impairs sound detection and prevents task-dependent increases in auditory cortical sensitivity. Our findings suggest that the OFC controls contextual modulations of the auditory cortex and sound perception.
EFEMP1 contributes to light-dependent ocular growth in zebrafish
Authors: Xie Jiaheng , Bui Bang V. , Goodbourn Patrick T. , Jusuf Patricia R. 
Published: December 2023

AbstractMyopia (short-sightedness) is the most common ocular disorder. It generally develops after over-exposure to aberrant visual environments, disrupting emmetropization mechanisms that should match eye growth with optical power. A pre-screening of strongly associated myopia-risk genes identified through human genome-wide association studies implicatesefemp1in myopia development, but how this gene impacts ocular growth remains unclear. Here, we modifyefemp1expression specifically in the retina of zebrafish. We found that under normal lighting,efemp1mutants developed axial myopia, enlarged eyes, reduced spatial vision and altered retinal function. However, under myopia-inducing dark-rearing, compared to control fish, mutants remained emmetropic and showed changes in retinal function.Efemp1modification changed the expression ofefemp1,egr1,tgfb1a,vegfabandrbp3genes in the eye, and changes the inner retinal distributions of myopia-associated EFEMP1, TIMP2 and MMP2 proteins.Efemp1modification also impacted dark-rearing-induced responses ofvegfabandwnt2bgenes and above-mentioned myopia-associated proteins. Together, we provided robust evidence that light-dependent ocular growth is regulated byefemp1.SummaryThis study shows that retina-specific modification ofefemp1expression in zebrafish results in myopic eye, and impacts responses to myopia-inducing dark-rearing in eye growth, retinal function, and myopia-associated molecular expression and distribution, implicating light-dependent regulation ofefemp1in ocular development.
Long-read sequencing of extrachromosomal circular DNA and genome assembly of aSolanum lycopersicumbreeding line revealed active LTR retrotransposons originating fromS. peruvianumL. introgressions
Authors: Merkulov Pavel , Serganova Melania , Petrov Georgy , Mityukov Vladislav , Kirov Ilya 
Published: December 2023

AbstractTransposable elements (TEs) are a major force in the evolution of plant genomes. Differences in the transposition activities and landscapes of TEs can vary substantially, even in closely related species. Interspecific hybridization, a widely employed technique in tomato breeding, results in the creation of novel combinations of TEs from distinct species. The implications of this process for TE transposition activity have not been studied in modern cultivars. In this study, we used nanopore sequencing of extrachromosomal circular DNA (eccDNA) and identified two highly active Ty1/CopiaLTR retrotransposon families of tomato (Solanum lycopersicum), calledSalsaandKetchup. Elements of these families produce thousands of eccDNAs under controlled conditions and epigenetic stress. EccDNA sequence analysis revealed that the major parts of eccDNA produced byKetchupandSalsaexhibited low similarity to theS. lycopersicumgenomic sequence. To trace the origin of these TEs, whole-genome nanopore sequencing and de novo genome assembly were performed. We found that these TEs occurred in a tomato breeding line via interspecific introgression fromS. peruvianum. Our findings collectively show that interspecific introgressions can contribute to both genetic and phenotypic diversity not only by introducing novel genetic variants, but also by importing active transposable elements from other species.