bluuebunny/crossref_metadata_2025_split huggingface dataset:
Early signs of plant community responses to climate warming along mountain roads in Switzerland
Authors: Iseli Evelin , Zeugin Nathan Diaz , Brioschi Camille , Alexander Jake , Lenoir Jonathan 
Published: July 2024

ABSTRACTGlobal warming is pushing species to shift their ranges towards higher latitudes and elevations, causing a reassembly of plant communities potentially accompanied by community thermophilization (i.e., an increasing number or cover of thermophilic species, sometimes at the expense of mesic or cold-adapted species). Given the large variation typically observed in the magnitude and direction of range shifts, quantifying community thermophilization might provide a sensitive method to detect range shifts within short time periods and across limited spatial extents. Assessing changes in plant community composition as a whole might integrate early signs of range shifts across co-occurring species while accounting for changes in both occurrence and abundance.Here, we combine an assessment of (i) species-level range shifts, (ii) changes in species richness and (iii) changes in community-inferred temperatures along three mountain roads in Switzerland to ask whether plant communities have responded to warming climate over a 10 year period, and whether community thermophilization is an appropriate metric for early detection of these changes.We found a community thermophilization signal of +0.13°C over the 10-year study period based on presence-absence data only. Despite significant upward shifts of species’ upper range limits in the lower part of the studied elevational gradient and a decrease in species richness at high elevations, significant thermophilization was not detectable if community- inferred temperatures were weighted by species’ covers. Low cover values of species that were gained or lost over the study period and their similar species-specific temperatures to resident species explained the discrepancy between the thermophilization detected in either cover-weighted or unweighted models.Synthesis.Our work shows that plant species are shifting to higher elevations along roadsides in the western Swiss Alps and that this translates into a detectable warming signal of plant communities within 10 years. However, the species-level range shifts and the community-level warming effect are mostly based on low cover values of gained/lost species, preventing the detection of community thermophilization signals when incorporating cover changes. We therefore recommend using unweighted approaches for early detection of community-level responses to changing climate, ideally set into context by also assessing species-level range shifts.
Dysregulation of gene expression during gastrulation results in impaired primitive erythropoiesis and vascular development in Trim71-KO embryos
Authors: Beckröge Tobias , Jux Bettina , Seifert Hannah , Theobald Hannah , De Domenico Elena , Paulusch Stefan , Beyer Marc , Schlitzer Andreas , Mass Elvira , Kolanus Waldemar 
Published: July 2024

AbstractThe transition of an embryo from gastrulation to organogenesis requires precisely coordinated changes in gene expression. The RNA-binding protein Trim71 is essential for embryonic survival, but its exact role in mammalian developmentin vivoremains poorly defined. Here we show that murineTrim71-KO embryos appear normal until embryonic day (E)8.5 but display severe defects in primitive erythropoiesis, yolk sac vasculature and heart function during the onset of organogenesis at E9.5 and E10.5. This led to an impaired vascular translocation of yolk sac-derived macrophage progenitors to the embryo head, independent of Trim71 expression in erythro-myeloid progenitors. The cardiovascular and erythropoiesis defects explain the embryonic lethality upon globalTrim71-KO. TargetingTrim71in hematoendothelial progenitors did not induce strong developmental defects, indicating an earlier developmental origin of these phenotypes inTrim71-KO embryos. ScRNA-seq of E7.5Trim71-KO embryos revealed that transcriptomic changes arise already at gastrulation, showing a strong upregulation of the transcription factor Eomes. We identify Eomes as a direct target of Trim71-mediated mRNA repression via the NHL domain, demonstrating a functional link of Trim71 to a key regulator of mesodermal development. Taken together, our data suggest that Trim71-dependent control of gene expression at gastrulation establishes a framework for proper development during organogenesis.
Long-term population dynamics of an endangered butterfly are influenced by hurricane-mediated disturbance
Authors: Steele Cabrera Sarah R. , Belitz Michael , Emmel Thomas C. , Khazan Emily S. , Standridge Matthew J. , Rossetti Kristin , Daniels Jaret C. 
Published: July 2024

AbstractEffective species conservation requires understanding an organism’s population dynamics and natural history, but long-term data are challenging to collect and maintain. As a result, conservation management decisions are frequently made using short-term data, which are insufficient to accurately assess population trends in most species. For less-studied taxa, including most invertebrates, inadequate understanding of life and natural history also impedes conservation efforts. Long-term studies are highly valuable for improving conservation decisions for target species as they serve as a model for other understudied species. We use mark-recapture data collected over 35 years to examine weather drivers of population patterns for an endangered butterfly, Schaus’ swallowtail (Heraclides ponceana), and to enhance our understanding of its natural history. We show that the population size of Schaus’ swallowtail butterfly was highly variable, ranging from under 100 to over 10,000 individuals. Population size is influenced by weather events and population size in the previous year. Population size was lower immediately following high wind events but was positively influenced by high wind events four years prior, with notable population increases following tropical cyclone events. Precipitation during the dry season preceding the adult flight period was also associated with higher population sizes. This study reveals the potentially beneficial role of hurricane-mediated disturbance on Schaus’ swallowtail populations potentially due to increased treefall gaps and the resulting shifts in plant communities. This remarkable data set represents one of the longest-term studies on a tropical insect.
Tracking changes in functionality and morphology of repopulated microglia in young and old mice
Authors: Luczak-Sobotkowska Zuzanna M. , Rosa Patrycja , Banqueri Lopez Maria , Ochocka Natalia , Kiryk Anna , Lenkiewicz Anna M. , Furhmann Martin , Jankowski Aleksander , Kaminska Bozena 
Published: July 2024

ABSTRACTMicroglia (MG) are myeloid cells of the central nervous system supporting its homeostasis and instigating neuroinflammation in pathologies. Single-cell RNA sequencing (scRNA-seq) revealed the functional heterogeneity of MG in mice brains. Inhibition of colony-stimulating factor 1 receptor (CSF1R) signaling with inhibitors deplete microglia which rapidly repopulate. Functionalities of repopulated microglia are poorly known. We combined scRNA-seq, bulk RNA-seq, immunofluorescence and confocal imaging to study functionalities and morphology of repopulated microglia. CSRF1R inhibitor (BLZ-945) depleted MG in 21 days and their numbers were restored 7 days later as evidenced by TMEM119 staining and flow cytometry. ScRNA-seq and computational analyses demonstrate that repopulated MG originate from preexisting MG progenitors and reconstitute functional clusters but upregulate inflammatory genes. Percentages of proliferating, immature MG displaying inflammatory gene expression increase in aging mice. Morphometric analysis of MG cell body and branching shows distinct morphology of repopulated MG, particularly in old mouse brains. We demonstrate that with aging some repopulated MG fail to reach the homeostatic phenotype. These differences microglia may contribute to the deterioration of microglia protective functions with age.
A moderate water deficit induces profound changes in the proteome of developing maize ovaries
Authors: Ashenafi Mariamawit , Balliau Thierry , Blein-Nicolas Mélisande , Turc Olivier , Zivy Michel , Marchadier Elodie 
Published: July 2024

AbstractWater deficit is a major cause of yield loss for maize (Zea mays), leading to ovary abortion when applied at flowering time. To help understand the mechanisms involved in this phenomenon, the proteome response to water deficit has been analysed in developing ovaries at silk emergence stage and five days later. Differential analysis, abundance pattern clustering and coexpressions networks were performed in order to draw a general picture of the proteome changes all along ovary development and under the effect of water deficit. The results show that, even mild, water deficit has a major impact on ovary proteome, but that this impact is very different from a response to a stress. A part of the changes can be related to a slowdown of ovary development, while another part cannot. In particular, ovaries submitted to water deficit show an increase in proteins involved in protein biosynthesis and in vesicle transport together with a decrease in proteins involved in amino acid metabolism and proteolysis. According to the functions of increased proteins, the changes may be linked to auxin, brassinosteroids and jasmonate signalling, but not abscisic acid.
A new alignment-free method: Subsequence Correlation Coefficient Vector(SCCFV) for influenza A comparison using virus genomes
Authors: He Lily , Yu Zhenglong , Wu Xinrui , Zhu Yi 
Published: July 2024

AbstractInfluenza viruses remain a formidable threat to global public health due to their high mutability and infectivity. Accurate prediction of influenza virus subtypes is crucial for clinical treatment and disease prevention. In recent years, machine learning methods have played an important role in studying influenza viruses. This study proposes a new alignment-free method based on the correlation of k-grams called Subsequence Correlation Coefficient Vector (SCCFV) to subtype hemagglutinin (HA) and neuraminidase (NA) of influenza virus. In the method, each influenza virus sequence is converted to four time series and the correlation coefficients of time series are utilized to extract the features of sequences. Then the supervised learning methods are used for the subtype classification of influenza viruses. We compare the effectiveness of the random forest, decision tree and support vector machine classifiers. Experimental results show that the random forest method achieves the best performance with an accuracy of 0.99979, an precision of 0.99996 and a recall of 0.99997. All prediction indicators of our method are significantly higher than traditional methods.
Visual system structural and functional connections during face viewing in body dysmorphic disorder
Authors: Wong Wan-wa , Peel Hayden , Cabeen Ryan , Diaz-Fong Joel P. , Feusner Jamie D. 
Published: July 2024

AbstractBackgroundIndividuals with body dysmorphic disorder (BDD) perceive distortions in their appearance, which could be due to imbalances in global and local visual processing. The vertical occipital fasciculus connects dorsal and ventral visual stream regions, integrating global and local information, yet the role of this structural connection in BDD has not been explored. Here, we investigated the vertical occipital fasciculus’s white matter microstructure in those with BDD and healthy controls and tested associations with psychometric measures and effective connectivity while viewing their face during fMRI.MethodsWe analyzed diffusion MRI and fMRI data in 17 unmedicated adults with BDD and 21 healthy controls. For diffusion MRI, bundle-specific analysis was performed, enabling quantitative estimation of neurite density and orientation dispersion of the vertical occipital fasciculus. For task fMRI, participants naturalistically viewed photos of their own face, from which we computed effective connectivity from dorsal to ventral visual regions.ResultsIn BDD, neurite density was negatively correlated with appearance dissatisfaction and negatively correlated with effective connectivity. Further, those with weaker effective connectivity while viewing their face had worse BDD symptoms and worse insight. In controls, no significant relationships were found between any of the measures. There were no significant group differences in neurite density or orientation dispersion.ConclusionThose with BDD with worse appearance dissatisfaction have a lower fraction of tissue having axons or dendrites along the vertical occipital fasciculus bundle, possibly reflecting impacting the degree of integration of global and local visual information between the dorsal and ventral visual streams. These results provide early insights into how the vertical occipital fasciculus’s microstructure relates to the subjective experience of one’s appearance, as well as the possibility of distinct functional-structural relationships in BDD.
Macrophage-derived CCL24 promotes fibrosis and worsens cardiac dysfunction during heart failure
Authors: Parthiban Preethy , Barrow Fanta , Nguyen Huy , Neto Fernando , Florczak Kira , Wang Haiguang , Yucel Dogacan , Liu Hong , Draxler Micah , Ciske Erin , Fredrickson Gavin , Herman Adam , Rothenberg Marc E. , Dudley Samuel , van Berlo Jop , Revelo Xavier S. 
Published: July 2024

ABSTRACTInflammation is a significant risk factor and contributes to cardiovascular disease by driving both adaptive and maladaptive processes. Macrophages are the most abundant immune cells in the heart and play an important role in the remodeling of cardiac tissue. We have previously shown an overall protective function of resident cardiac macrophages after pressure-overloaded injury. However, a subpopulation of resident macrophages also expresses high levels of the profibrotic CC motif chemokine ligand 24 (CCL24), suggesting a dichotomous role in pressure overload-induced cardiac remodeling. Here, we report that following transverse aortic constriction CCL24 knockout (CCL24 KO) mice have improved systolic function, cardiac wall enlargement, as well as increased myocyte surface area and hypertrophy, suggesting that CCL24 disrupts compensatory hypertrophy. TAC-operated CCL24 KO mice also displayed reduced fibrosis and diminished expression of fibrotic genes, implying a pro-fibrotic role for CCL24. Indeed, CCL24 induced the proliferation and activation of primary mouse fibroblasts in a process that required CCR3, the sole G protein-coupled receptor for CCL24. Correspondingly, selective ablation of CCR3 in fibroblasts improved cardiac function and ameliorated fibrosis following pressure overload. Administration of a CCL24 blocking antibody or a CCR3 antagonist both improved cardiac function in pressure-overloaded mice, highlighting the CCL24-CCR3 axis as a potential therapeutic target for heart failure. Finally, CCL24 deficiency improved cardiac function and ameliorated fibrosis during physiological aging. Overall, these results show that macrophage-derived CCL24 aggravates fibrosis via the CCR3 receptor, leading to impaired cardiac function in acute and chronic heart failure.
Highly quantitative measurement of differential protein-genome binding with PerCell chromatin sequencing
Authors: Tallan Alexi , Kucinski Jack , Sunkel Benjamin , Taslim Cenny , LaHaye Stephanie , Liu Qi , Qi Jun , Wang Meng , Kendall Genevieve C. , Stanton Benjamin Z. 
Published: July 2024

AbstractWe report a universal strategy for 2D chromatin sequencing, to increase uniform data analyses and sharing across labs, and to facilitate highly quantitative comparisons across experimental conditions. Within our system, we provide wetlab and drylab tools for researchers to establish and analyze protein-genome binding data with PerCell ChIP-seq. Our methodology is virtually no cost and flexible, enabling rapid, quantitative, internally normalized chromatin sequencing to catalyze project development in a variety of systems, including in vivo zebrafish epigenomics and cancer cell epigenomics. While we highlight utility in these key areas, our methodology is flexible enough such that rapid comparisons of cellular spike-in versus non spike-in are possible, and generalizability to nuclease-based 2D chromatin sequencing would also be possible within the framework of our pipeline. Through the use of well-defined cellular ratios containing orthologous species’ chromatin, we enable cross-species comparative epigenomics and highly quantitative low-cost chromatin sequencing with utility across a range of disciplines.
A Novel Registration Framework for Aligning Longitudinal Infant Brain Tensor Images
Authors: Duan Kuaikuai , Li Longchuan , Calhoun Vince D. , Shultz Sarah 
Published: July 2024

AbstractRegistering longitudinal infant brain images is challenging, as the infant brain undergoes rapid changes in size, shape and tissue contrast in the first months and years of life. Diffusion tensor images (DTI) have relatively consistent tissue properties over the course of infancy compared to commonly used T1 or T2- weighted images, presenting great potential for infant brain registration. Moreover, groupwise registration has been widely used in infant neuroimaging studies to reduce bias introduced by predefined atlases that may not be well representative of samples under study. To date, however, no methods have been developed for groupwise registration of tensor-based images. Here, we propose a novel registration approach to groupwise align longitudinal infant DTI images to a sample-specific common space. Longitudinal infant DTI images are first clustered into more homogenous subgroups based on image similarity using Louvain clustering. DTI scans are then aligned within each subgroup using standard tensor-based registration. The resulting images from all subgroups are then further aligned onto a sample-specific common space. Results show that our approach significantly improved registration accuracy both globally and locally compared to standard tensor-based registration and standard fractional anisotropy-based registration. Additionally, clustering based on image similarity yielded significantly higher registration accuracy compared to no clustering, but comparable registration accuracy compared to clustering based on chronological age. By registering images groupwise to reduce registration bias and capitalizing on the consistency of features in tensor maps across early infancy, our groupwise registration framework facilitates more accurate alignment of longitudinal infant brain images.
Modeling plant-microbe interactions with species distribution models
Authors: Wang Zihui , Piché-Choquette Sarah , Lauzon Jocelyn , Ishak Sarah , Kembel Steven W. 
Published: July 2024

AbstractPlants interact with diverse microorganisms that play a crucial role in plant growth and development. The diversity and distribution of plant microbiota are altered by anthropogenic environmental change, leading to subsequent impacts on ecosystems. Modeling the distribution of plant-associated microbes is critical for predicting and managing future changes in microbial function, but there remain challenges and open questions when developing these models. We present a conceptual framework for process-oriented predictive modeling of the distribution of plant-associated microbiota. We first describe different approaches to incorporating host plants into modeling microbial distributions, namely by including them as static variables, nesting them within microbial distribution models or incorporating them simultaneously via joint species distribution models. Additionally, we discuss issues associated with collecting and analyzing sequencing-based microbial data, emphasizing the importance of data normalization and careful interpretation of species distribution models. We further discuss how to incorporate evolutionary history into microbial distribution modeling. Finally, we present a case study demonstrating how incorporating host information can improve the prediction of microbial distributions. This study provides insights for predicting future distributions of plant-associated microbes under climate change and plant species redistribution, which can be generalized to other host-associated microbial systems.
Effects of leg immobilization and recovery resistance training on skeletal muscle-molecular markers in previously resistance trained versus untrained adults
Authors: Michel J. Max , Godwin Joshua S. , Plotkin Daniel L. , McIntosh Mason C. , Mattingly Madison L. , Agostinelli Philip J. , Mueller Breanna J. , Anglin Derick A. , Berry Alexander C. , Vega Marina Meyer , Pipkin Autumn A. , Stock Matt S. , Graham Zachary A. , Baweja Harsimran S. , Mobley C. Brooks , Bamman Marcas M. , Roberts Michael D. 
Published: July 2024

ABSTRACTWe sought to examine how resistance training (RT) status in young healthy individuals, either well-trained (T, n=10 (8 males)) or untrained (UT, n=11 (8 males)), affected muscle size and molecular markers with leg immobilization followed by recovery RT. All participants underwent two weeks of left leg immobilization via the use of crutches and a locking leg brace. After this two-week period, all participants underwent eight weeks (3 d/week) of knee extensor focused progressive RT. Vastus lateralis (VL) ultrasound-derived thickness and muscle cross-sectional area were measured at baseline (PRE), immediately after disuse (MID), and after RT (POST) with VL muscle biopsies collected at these time points. T and UT presented lower ultrasound derived VL size (cross-sectional area and thickness) values at MID versus PRE (p≤0.001), and values increased in both groups from MID to POST (p<0.05); however, VL size increased from PRE to POST in UT only (p<0.001). Mean and type II myofiber cross-sectional area (fCSA) values demonstrated a main effect of time where PRE and POST were greater than MID (p<0.05) and main effect of training status where T was greater than UT (P≤0.012). In both groups, satellite cell number was not affected by leg immobilization but increased in response to RT (p≤0.014), with T being greater than UT across all time points (p=0.004). Additionally, ribosome content (total RNA) decreased (p=0.010) from PRE to MID while the endoplasmic reticulum stress proteins (BiP, Xbp1s, and CHOP) increased from MID to POST regardless of training status. Finally, the phosphorylation states of mechanistic target of rapamycin complex-1 signaling proteins were not significantly altered for either group throughout the intervention. In conclusion, immobilization-induced muscle atrophy and recovery RT hypertrophy outcomes are similar between UT and T participants, and the lack of molecular signature differences between groups supports these findings. However, these data are limited to younger adults undergoing non-complicated disuse. Thus, further investigation to determine the impact of training status on prolonged leg immobilization models mirroring current medical protocols (e.g., following orthopedic injury and surgery) is warranted.