bluuebunny/crossref_metadata_2025_split huggingface dataset:
The transcription factor ZmbZIP75 promotes both grain filling and kernel dehydration in maize
Authors: Long Tiandan , Wang Yayun , Yang Jin , Liu Zhou , Mao Changqing , Hu Yufeng , Zhang Junjie , Liu Hanmei , Liu Yinghong , Fan Xiujun , Gao Lei , Huang Huanhuan , Xie Ying , Zhao Daqiu , Huang Yubi , Li Yangping 
Published: September 2024

AbstractSelecting both high-yield and low-kernel-moisture varieties is essential for modern maize production, but relevant breeding efforts are hindered by a lack of valuable regulatory genes. Here, we demonstrate that the transcription factor (TF) basic leucine zipper 75 (ZmbZIP75) promotes grain yield and reduces kernel moisture in maize. Knockout of ZmbZIP75 results in defective grain filling and kernel dehydration, whereas ZmbZIP75 overexpression confers increased grain yield per plant and decreased kernel moisture without altering plant architecture. Mechanistically, during the grain filling stage, ZmbZIP75 is transcriptionally induced by maternal-derived basal abscisic acid (ABA) and directly activates multiple core starch synthesis-related genes and key TFs, thereby promoting grain filling and final yield. In the late stage of kernel development, high concentrations of zygotic ABA enhance ZmbZIP75 phosphorylation through SnRK2.10. The phosphorylated ZmbZIP75 subsequently transactivates and interacts with TF VP1 to synergistically promote kernel dehydration. This study thus highlights the potential of ZmbZIP75 for engineering both high-yield and low-kernel-moisture varieties to meet the demands of high-efficient maize production.IN A NUTSHELLBackgroundHigh grain yield in maize is generally associated with elevated kernel moisture at harvest, which is the main limiting factor for modern maize production. Therefore, it is of importance to select varieties with both high-yield and low-kernel-moisture. These traits are largely controlled by grain filling and kernel dehydration, two tightly connected processes during maize kernel development. Abscisic acid (ABA) is well-documented for its vital role in grain filling and dehydration maturation. However, the molecular mechanisms by which ABA coordinates these two processes remain unclear.QuestionWhat are the regulatory factors involved, and how do they mediate ABA signaling to coordinate grain filling and dehydration maturation in maize?FindingsZmbZIP75 is transcriptionally induced by ABA and directly activates multiple core starch synthesis-related genes and key TFs in developing maize endosperm, thereby promoting grain filling. In developing embryo, ABA enhances ZmbZIP75 phosphorylation via SnRK2.10. The phosphorylated ZmbZIP75 then transactivates and interacts with VP1 to synergistically promote kernel dehydration. Moreover,ZmbZIP75overexpression confers increased grain yield and reduced kernel moisture in maize.Next stepsWhile ZmbZIP75 is directly phosphorylated to mediate ABA signaling during dehydration maturation,ZmbZIP75is transcriptionally induced by ABA during grain filling. We plan to identify upstream factors that mediate ABA signaling to regulateZmbZIP75expression, thereby enhancing our understanding of ABA-promoted grain filling in maize.
DeOri 10.0: An Updated Database of Experimentally Identified Eukaryotic Replication Origins
Authors: Zeng Yu-Hao , Yin Zhen-Ning , Luo Hao , Gao Feng 
Published: September 2024

AbstractDNA replication is a complex and crucial biological process in eukaryotes. To facilitate the study of eukaryotic replication events, we present database of eukaryotic DNA replication origins (DeOri), a database that collects scattered data and integrates extensive sequencing data on eukaryotic DNA replication origins. With continuous updates of DeOri, the number of datasets in the new release increased from 10 to 151 and the number of sequences increased from 16,145 to 9,742,396. Besides nucleotide sequences and bed files, corresponding annotation files, such as coding sequences (CDS), mRNA, and other biological elements within replication origins, are also provided. The experimental techniques used for each dataset, as well as other statistical data, are also presented on web page. Differences in experimental methods, cell lines, and sequencing technologies have resulted in distinct replication origins, making it challenging to differentiate between cell-specific and non-specific replication. We combined multiple replication origins at the species level, scored them, and screened them. The screened regions were considered as species-conservative origins. They are integrated and presented as reference replication origins (rORIs), includingHomo sapiens,Gallus gallus,Mus musculus,Drosophila melanogaster, andCaenorhabditis elegans. Additionally, we analyzed the distribution of relevant genomic elements associated with replication origins at the genome level, such as CpG island (CGI), transcription start site (TSS), and G-quadruplex (G4). These analysis results allow users to select the required data based on it. DeOri is available athttp://tubic.tju.edu.cn/deori10/.
Growth Analysis ofTrichomonas vaginalisin Different Culture Media: Leveraging Large Language Models (LLMs) to Predict and OptimizeIn VitroGrowth Conditions
Authors: Ferguson Shernica L. , Gordon Loria Brown 
Published: September 2024

ABSTRACTTrichomonas vagnalisis a tiny protozoan universally known to have one of the highest prevalance rates of any common sexually transmitted disease. Its popularity in HIV transmission and preterm labor highlights its importance in clinical, biological, and epidemiological investigations worldwide. Propagation of Tvaginalisin vitro uses modified Diamonds media in commercial and clinical culture environments. Several modifications of this medium exist, but a more recent modification proved the most efficient. Our study aimed to investigate media modifications that could optimize the growth ofT. vaginalisin routine laboratory cultivation. RSMT media enriched with quantitated media components was compared to modified Diamond’s, Oxoid, and In Pouch culture mediums. Several growth studies were employed to select eight isolates (n=8) ofT. vaginalis, including an ATCC reference isolate. These isolates were examined for several days at 37 degrees C in an anaerobic environment. Tests revealed that isolates in RSMT media had over 85% higher concentrations of Tvaginalisgrowth than our testing mediums, with a maximum growth increase of 250%. The composite counts ofT. vaginalisin RSMT showed a significant difference (p <0.05) from those ofT. vaginalisin the standard Diamonds media Oxoid or In Pouch mediums. This data suggests that more efficient culturing and growth ofT. vaginalisrequires more vitamins and other growth factors beyond what would conventionally be expended in standard Trichomonas culture mediums.Author’s SummaryIn this study, we explored the growth conditions ofTrichomonas vaginalis, a common sexually transmitted parasite, to find ways to improve its cultivation in the laboratory. By comparing a new growth medium we developed, called RSMT, with existing methods, we identified the best conditions for sustaining this parasite’s growth. Our results showed that RSMT, which includes higher concentrations of essential nutrients, significantly enhanced the growth ofTrichomonas vaginaliscompared to standard media. This advancement is crucial for developing more reliable lab cultures, essential for diagnosing infections and researching new treatments. Additionally, our work demonstrates how innovation in lab practices can optimize clinical procedures and potentially influence public health strategies by improving the management and treatment of infections caused by this parasite.
Multifocal cutaneous neoplastic vascular proliferations in a rainbow boa (Epicrates cenchria) collection with boid inclusion body disease
Authors: Broering Ferreira Anthony , Fonteque Joandes Henrique , Withoeft Jéssica Aline , Casagrande Renata Assis , Maciel da Costa Ubirajara , Imkamp Frank , Göller Pauline , Baggio Francesca , Hepojoki Jussi , Hetzel Udo , Kipar Anja 
Published: September 2024

AbstractReports on neoplastic processes in snakes are sparse regardless of their location, origin or behavior. Here, we describe the occurrence of multifocal cutaneous neoplastic processes consistent with hemangioma and hemangioendothelioma, with a differential diagnosis of angiomatosis, in a colony of native Brazilian rainbow boas (Epicrates cenchria) which also included animals affected by boid inclusion body disease (BIBD). Thirteen snakes were affected; seven of these had been introduced from other Brazilian sites years earlier, the others had been bred in house but were not offspring of knowingly affected animals. The breeding regime allowed contact between all female and male animals over the years. The cutaneous lesions were first observed over eight years ago, with additional cases detected during the three following years, but no new cases in the last five years. Two affected animals were subjected to a post mortem examination and were found to suffer from peliosis hepatis as one of the additional pathological changes. BIBD was confirmed in five of the eight examined animals, by histology, immunohistology for reptarenavirus nucleoprotein, and multiplex RT-PCR targeting the reptarenavirus S segment. Reptarenavirus infection was also detected in cells in the cutaneous neoplastic processes. PCRs forBartonella henselaeandB. quintanaas well as bacterial DNA in general, performed on a pool of six skin lesions, yielded negative results, ruling out ongoing bacterial infection, like bacillary angiomatosis in humans, of the lesions. The results hint towards an association of reptarenavirus infection and BIBD with neoplastic processes which is worth further investigations.
Novel regulator Fpr2 controls immune homeostasis via CCL4-dependent neutrophils
Authors: Sun Zeyu , Mei Song , Xu Shenglong , Yi Jiaxuan , Zhang Shengwei , Wang Yuhang , Liu Peng , Liu Hui , Lv Qingyu , Huang Wenhua , Kong Decong , Li Qian , Ren Yuhao , Jiang Yongqiang , Zhang Peng , Jiang Hua 
Published: September 2024

AbstractPolymorphonuclear leukocytes (PMNs) inFpr2-deficient mice have significantly impaired bactericidal activity, yet the precise mechanism remains elusive. Our research unveiled the cellular heterogeneity of peripheral blood PMNs through single-cell RNA-sequencing (scRNA-seq) and identified two new neutrophil clusters related to bacterial infection, including a sterilization cluster named Neu_CSTA and a regulation cluster named Neu_CCL4. The lack ofFpr2leads to an immune regulation imbalance of Neu_CCL4 on other clusters in uninfected conditions, resulting in persistent instability of PMNs in peripheral blood, elevated inflammatory factors, and increased NOX2 expression. Furthermore, our findings corroborate that the regulatory function of Neu_CCL4 on PMNs immune balance is closely tied to its high expression of the anti-inflammatory ligand Anxa1. Regulon analysis inferred by scRNA-seq and ChIP-seq data suggested that a specific transcription factor Elf4, could modulate the expression ofAnxa1, thereby facilitating its regulatory impact on other clusters. In the infection state, there was a noted increase in intercellular interactions across different clusters, leading to a general improvement in the bactericidal activity of PMNs. In summary, our research revealed distinct functional cellular sub-populations of PMNs, discovered the potential regulatory mechanisms, and elucidated the essential roles of Fpr2 in their ability to resist infection.
SIRPα+ PD-L1+ bone marrow macrophages aid AML growth by modulating T cell function
Authors: Birch Flora , Gonzalez-Anton Sara , Haltalli Myriam L.R. , Chakravarty Probir , Bruno Federica , Georgiou Christiana , Mai Cera , Todd Yvette , Payne Beth , Blum Sabine , Pospori Constandina , Arber Caroline , Burt Richard , Tissot Floriane S. , Celso Cristina Lo 
Published: September 2024

AbstractAcute myeloid leukemia (AML) continues to have a poor prognosis due to its ability to relapse following initial response to chemotherapy. While immunotherapies hold the promise to revolutionize cancer treatment, AML has been particularly challenging to target. It is therefore important to better understand the relationship between AML cells and immune cells within the bone marrow (BM) microenvironment, where this disease grows. Here we focus on non-malignant BM macrophages, and using a combination of intravital microscopy, flow cytometry, transcriptomics and functional analyses we identify a subpopulation of immunomodulatory BM macrophages (IMMs) with a unique profile and function during AML progression. While the majority of macrophages are already being lost at early infiltration, IMMs are locally enriched. They are capable of efferocytosis and support AML growth through inhibition of T cells. Enrichment of IMMs in the BM of patients developing early relapse indicates that future development of interventions that target IMMs’ development and function may improve AML patients’ outcome.
Policy complexity suppresses dopamine responses
Authors: Gershman Samuel J. , Lak Armin 
Published: September 2024

AbstractLimits on information processing capacity impose limits on task performance. We show that animals achieve performance on a perceptual decision task that is near-optimal given their capacity limits, as measured by policy complexity (the mutual information between states and actions). This behavioral profile could be achieved by reinforcement learning with a penalty on high complexity policies, realized through modulation of dopaminergic learning signals. In support of this hypothesis, we find that policy complexity suppresses midbrain dopamine responses to reward outcomes, thereby reducing behavioral sensitivity to these outcomes. Our results suggest that policy compression shapes basic mechanisms of reinforcement learning in the brain.
Pipeline Olympics: continuable benchmarking of computational workflows for DNA methylation sequencing data against an experimental gold standard
Authors: Lin Yu-Yu , Breuer Kersten , Weichenhan Dieter , Lafrenz Pascal , Wilk Agata , Chepeleva Marina , Mücke Oliver , Schönung Maximilian , Petermann Franziska , Kensche Philipp , Weiser Lena , Thommen Frank , Giacomelli Gideon , Nordstroem Karl , Gonzalez-Avalos Edahi , Merkel Angelika , Kretzmer Helene , Fischer Jonas , Krämer Stephen , Iskar Murat , Wolf Stephan , Buchhalter Ivo , Esteller Manel , Lawerenz Chris , Twardziok Sven , Zapatka Marc , Hovestadt Volker , Schlesner Matthias , Schulz Marcel , Hoffmann Steve , Gerhauser Clarissa , Walter Jörn , Hartmann Mark , Lipka Daniel B. , Assenov Yassen , Bock Christoph , Plass Christoph , Toth Reka , Lutsik Pavlo 
Published: September 2024

AbstractDNA methylation is a widely studied epigenetic mark and a powerful biomarker of cell type, age, environmental exposures, and disease. Whole-genome sequencing following selective conversion of unmethylated cytosines into thymines via bisulfite treatment or enzymatic methods remains the reference method for DNA methylation profiling genome-wide. While numerous software tools facilitate processing of DNA methylation sequencing reads, a comprehensive benchmarking study has been lacking thus far. In this study, we systematically compared complete computational workflows for processing DNA methylation sequencing data using a dedicated benchmarking dataset generated with five genome-wide profiling protocols. As an evaluation reference, we employed highly quantitative locus-specific measurements from our preceding benchmark of targeted DNA methylation assays. Based on this experimental gold-standard assessment and several comprehensive metrics, we identified workflows that consistently demonstrated superior performance and revealed major workflow development trends. To facilitate the sustainability of our benchmark, we implemented an interactive workflow execution and data presentation platform, adaptable to user-defined criteria and seamlessly expandable to future software.
Heritability of movie-evoked brain activity and connectivity
Authors: Gruskin David C. , Vieira Daniel J. , Lee Jessica K. , Patel Gaurav H. 
Published: September 2024

AbstractThe neural bases of sensory processing are conserved across people, but no two individuals experience the same stimulus in exactly the same way. Recent work has established that the idiosyncratic nature of subjective experience is underpinned by individual variability in brain responses to sensory information. However, the fundamental origins of this individual variability have yet to be systematically investigated. Here, we establish a genetic basis for individual differences in sensory processing by quantifying (1) the heritability of high-dimensional brain responses to movies and (2) the extent to which this heritability is grounded in lower-level aspects of brain function. Specifically, we leverage 7T fMRI data collected from a twin sample to first show that movie-evoked brain activity and connectivity patterns are heritable across the cortex. Next, we use hyperalignment to decompose this heritability into genetic similarity inwherevs.howsensory information is processed. Finally, we show that the heritability of brain activity patterns can be partially explained by the heritability of the neural timescale, a one-dimensional measure of local circuit functioning. These results demonstrate that brain responses to complex stimuli are heritable, and that this heritability is due, in part, to genetic control over stable aspects of brain function.
Analysis of coordinated group behavior based on role-sharing: Practical application from an experimental task to a 3-on-3 basketball game as a pilot study
Authors: Ichikawa Jun , Yamada Masatoshi , Fujii Keisuke 
Published: September 2024

AbstractA human group shares a common goal and distributes roles to implement activities that are difficult to accomplish alone and higher performance than an individual. In such coordination, nonverbal behavior among three or more members makes it difficult to explain the mechanism because of complex and dynamic interactions. In cognitive science, a crucial role is indicated, which intervenes moderately with others and adjusts the whole balance without interrupting their main smooth interactions, using an experimental task. It suggests that the third role and related playing supports to coordination. This is similar to off-ball movements in team sports, which are not involved directly with the ball and are focused on mainly in sports science because common statistical data do not reflect. A new perspective for discussing coordination has arisen because existing theories, such as synchronization, cannot explain the mentioned role; however, there is room for its usefulness. Therefore, this study applied the experimental findings to the sports field. We designed a 3-on-3 basketball game in which the relevant offensive role is key and introduced it to the practice of the university team as a pilot study. Participants repeatedly engaged in the mini-game, and the playing on the offensive team was compared before and after receiving tips on this role. Consequently, in the bins of the relatively large distance between the participant required in this role and each defensive player, the frequencies after the tips were significantly higher, and the winning rate on the offensive team improved temporarily. It suggests that the spacing skill, which indicates a reasonable distance for intervening with the other offensive players, emerged. This study may provide findings that satisfy usefulness and ecological validity, and make an educational contribution about giving the tips of off-ball movements.
Predicting Degradation Potential of Protein Targeting Chimeras
Authors: Petrou Andreas , Minhas Fayyaz 
Published: September 2024

AbstractPRoteolysis TArgeting Chimeras (PROTACs) can inhibit protein activity by utilizing natural proteasomal degradation pathways for the degradation of target proteins. Being able to determine the degradation potential of PROTACs is crucial in drug development as it can lead to time, labor and cost savings. In this paper, we present a novel machine-learning pipeline that utilizes common compound fingerprints and a pre-trained graph neural network for the prediction of half-maximal degradation concentration of PROTACs by benchmarking a variety of protein tertiary structures and chemical features. Based on critical analysis of our cross-validation and independent test results, we have highlighted several key challenges underlying this prediction problem that need to be addressed to improve the generalization of predictive models in this domain. Moreover, we demonstrate the effectiveness of our approach by testing it on two different datasets and show that it performs better than the current state of the art with an AUC-ROC of 0.85 and accuracy of 0.875 on the DeepPROTACs test dataset.
Notch and LIM-homeodomain protein Arrowhead regulate each other in a feedback mechanism to play a role in wing and neuronal development inDrosophila
Authors: Singh Jyoti , Verma Dipti , Sarkar Bappi , Paul Maimuna Sali , Mutsuddi Mousumi , Mukherjee Ashim 
Published: September 2024

AbstractNotch pathway is an evolutionarily conserved signaling system that operates to influence an astonishing array of cell fate decisions in different developmental contexts. To identify novel effectors of Notch signaling, we analyzed the whole transcriptome ofDrosophilawing and eye imaginal discs in which an activated form of Notch was overexpressed. A LIM homeodomain protein Arrowhead (Awh) was identified as a novel candidate which plays a crucial role in Notch mediated developmental events.Awhalleles show strong genetic interaction with Notch pathway components. Awh loss-of-function upregulates Notch targets Cut and Wingless. Awh gain-of-function downregulates Notch targets by reducing the expression of ligand, Delta. Consequently, the expression of Wingless effector molecule Armadillo and its downstream targets, Senseless and Vestigial, also gets downregulated. Awh overexpression leads to ectopicexpression ofengrailed, a segment polarity gene in the anterior region of wing disc, leading to patterning defects. Additionally, Notch gain-of-function mediated neuronal defects get significantly rescued with Awh overexpression. Activated Notch inhibits Awh activity, suggesting a regulatory loop between Awh and Notch. Additionally, the defects caused by Awh gain-of-function were remarkably rescued by Chip, a LIM interaction domain containing transcriptional co-factor. The present study highlights the novel feedback regulation between Awh and Notch.
Auditory Cortex Learns to Discriminate Audiovisual Cues through Selective Multisensory Enhancement
Authors: Chang Song , Zheng Beilin , Keniston Les , Xu Jinghong , Yu Liping 
Published: September 2024

AbstractMultisensory object discrimination is essential in everyday life, yet the neural mechanisms underlying this process remain unclear. In this study, we trained rats to perform a two-alternative forced-choice task using both auditory and visual cues. Our findings reveal that multisensory perceptual learning actively engages auditory cortex (AC) neurons in both visual and audiovisual processing. Importantly, many audiovisual neurons in the AC exhibited experience-dependent associations between their visual and auditory preferences, displaying a unique integration model. This model employed selective multisensory enhancement for the auditory-visual pairing guiding the contralateral choice, which correlated with improved multisensory discrimination. Furthermore, AC neurons effectively distinguished whether a preferred auditory stimulus was paired with its associated visual stimulus using this distinct integrative mechanism. Our results highlight the capability of sensory cortices to develop sophisticated integrative strategies, adapting to task demands to enhance multisensory discrimination abilities.