bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mapping Contributions of the Anterior Temporal Semantic Hub to the Processing of Abstract and Concrete Verbs
Authors: Muraki Emiko J. , Pexman Penny M. , Binney Richard J. 
Published: September 2024

AbstractMultiple representation theories of semantic processing propose that word meaning is supported by simulated sensorimotor experience in modality-specific neural regions, as well as in cognitive systems that involve processing of linguistic, emotional, and introspective information. According to the Hub and Spoke Model of Semantic Memory, activity from these distributed cortical areas feeds into a primary semantic hub located in the ventral anterior temporal lobe (vATL). Though a substantial amount of research has tested this model in terms of concrete noun representation, there is less known about how this model can account for the representation of verb meaning, and in particular the meaning of abstract verbs which convey important information, for example, about socioemotional dynamics. In the present pre-registered study, we examined whether different types of abstract verbs (mental, emotional, nonembodied) and concrete (embodied) verbs all engage the vATL, and also whether they differentially recruit a broader set of distributed neurocognitive systems (consistent with multiple representation theories). Finally, we investigated whether there is information about different verb types distributed across the broader ATL region, consistent with a Graded Semantic Hub Hypothesis. We collected data from 30 participants who completed a syntactic classification task (is it a verb? Yes or no) and a numerical judgement task which served as an active but less semantic baseline task. Whole brain univariate analyses revealed consistent BOLD signal throughout the canonical semantic network, including the left inferior frontal gyrus, left middle temporal gyrus, and the vATL. All types of abstract verbs engaged the vATL except for mental state verbs. Finally, a multivariate pattern analysis revealed clusters within the ATL that were differentially engaged when processing each type of abstract verb. Our findings extend previous research and suggest that the hub-and-spoke hypothesis and the graded semantic hub hypothesis provide a neurobiologically constrained model of semantics that can account for abstract verb representation and processing.
CAR-T cells targeting CCR9 and CD1a for the treatment of T cell acute lymphoblastic leukemia
Authors: Tirado Néstor , Mansilla María José , Martínez-Moreno Alba , Alcain Juan , García-Peydró Marina , Roca-Ho Heleia , Fernandez-Fuentes Narcis , Garcia-Perez Alba , Guerrero-Murillo Mercedes , Falgàs Aïda , Velasco-Hernandez Talia , Vinyoles Meritxell , Bueno Clara , Engel Pablo , González E Azucena , Vick Binje , Jeremias Irmela , Caye-Eude Aurélie , Baruchel André , Cavé Hélène , Genescà Eulàlia , Ribera Jordi , Díaz-Beyá Marina , Ramírez-Orellana Manuel , Torrebadell Montserrat , Díaz Víctor M , Toribio María L , Sánchez-Martínez Diego , Menéndez Pablo 
Published: September 2024

ABSTRACTT cell acute lymphoblastic leukemia (T-ALL) is an aggressive malignancy characterized by high rates of induction failure and relapse, and effective targeted immunotherapies are lacking. Despite promising clinical progress with genome-edited CD7-directed CAR-T cells, which present significant logistical and regulatory issues, CAR-T cell therapy in T-ALL remains challenging due to the shared antigen expression between malignant and healthy T cells. This can result in CAR-T cell fratricide, T cell aplasia, and the potential for blast contamination during CAR-T cell manufacturing. Recently, CAR-T cells have been described that target non-pan-T antigens, absent on healthy T cells but expressed on specific T-ALL subsets. These antigens include CD1a (NCT05679895), which is expressed in cortical T-ALL, and CCR9. We show that CCR9 is expressed on >70% of T-ALL patients (132/180) and is maintained at relapse, with a safe expression profile in healthy hematopoietic and non-hematopoietic tissues. Further analyses showed that dual targeting of CCR9 and CD1a could benefit ∼86% of patients with T-ALL, with a greater blast coverage than single CAR-T cell treatments. We therefore developed, characterized, and preclinically validated a novel humanized CCR9-specific CAR with robust and specific antileukemic activity as a monotherapyin vitroandin vivoagainst cell lines, primary T-ALL samples, and patient-derived xenografts. Importantly, CCR9/CD1a dual-targeting CAR-T cells showed higher efficacy than single-targeting CAR-T cells, particularly in T-ALL cases with phenotypically heterogeneous leukemic populations. Dual CCR9/CD1a CAR-T therapy may prevent T cell aplasia and obviate the need for allogeneic transplantation and regulatory-challenging genome engineering approaches in T-ALL.
Does transcutaneous vagus nerve stimulation alter pupil dilation? A living Bayesian meta-analysis
Authors: Pervaz Ipek , Thurn Lilly , Vezzani Cecilia , Kaluza Luisa , Kühnel Anne , Kroemer Nils B. 
Published: September 2024

AbstractTranscutaneous vagus nerve stimulation (tVNS) has emerged as a promising technique to modulate autonomic functions, and pupil dilation has been recognized as a promising biomarker for tVNS-induced monoaminergic release. Nevertheless, studies on the effectiveness of various tVNS protocols have produced heterogeneous results on pupil dilatation to date. Here, we synthesize the existing evidence and compare conventional continuous and pulsed stimulation protocols using Bayesian meta-analysis. To maintain a living version, we developed a Shiny App with the possibility to incorporate newly published studies in the future. Based on a systematic review, we included 18 studies (N = 771) applying either continuous or pulsed stimulation protocols. Across studies, we found anecdotal evidence for the alternative hypothesis that tVNS increases pupil size (g= 0.14, 95% CI = [0.001, 0.29], BF01 = 2.5). Separating studies according to continuous vs. pulsed protocols revealed that results were driven by studies using pulsed taVNS (strong evidence for the alternative hypothesis:g= 0.34, 95% CI = [0.15, 0.53], BF10 = 14.15) while continuous tVNS provided strong evidence for the null hypothesis (g= 0.01, CI = [-0.15, 0.16], BF01= 20.7). In conclusion, our meta-analysis highlights differential effects of continuous and pulsed tVNS protocols on pupil dilation. These findings underscore the relevance of tVNS protocols in optimizing its use for specific applications that may require modulation of tonic vs. phasic monoaminergic responses.
Long-term Tolerance to Islet Transplantation via Targeted Reduction of beta cell-specific T cells
Authors: Kotliar Michael , Cianciolo Eileen E. , Pham Duc Hung , Carroll Kaitlin R. , Barski Artem , Jordan Michael B. , Katz Jonathan D. 
Published: September 2024

AbstractType 1 diabetes (T1D) results from insulin insufficiency due to the loss or dysfunction of pancreatic beta cells following T cell-mediated autoimmune attack. Currently the only long-term therapy is daily exogenous insulin replacement. The ideal curative approach is the durable restoration of functional islets via transplantation. To date the limiting factors impeding realization of this goal is the lack of a cost effective and limitless source of high-quality islets suitable for transplantation and the ability to provide long-term islet graft acceptance without prolonged need for deleterious immunosuppression. Ongoing clinical trials are testing islets derived from human induced pluripotent stem cells (iPSC); however, long-term acceptance of islet graft will require a effective therapeutic strategy to prevent engrafted islet destruction by pre-existing islet-antigen specific T cells. Here we demonstrate in the NOD mouse model for T1D that autologous islet graft acceptance can be achieved by the targeted elimination of (re)-activated islet-reactive CD4+and CD8+T effector (Teff) cells in the initial post-transplantation period by using a short-acting, combination therapy that results in the elimination of islet-reactive Teff cells by exacerbation of their natural DNA damage response (DDR) to drive apoptosis while at the same time maintaining endogenous Treg cells.Article HighlightsActivated beta-cell reactive CD4+and CD8+T effector cells undergo a profound DNA-damage response which is targetable by small molecule inhibitors of the p53 and cell cycle pathways that lead to apoptosis.The use of a combination of MDM2 and WEE1 inhibitors, which termed “p53 potentiation with checkpoint abrogation” (PPCA), conferred significant therapeutic efficacy in treating mouse models of new onset T1D.Specific targeting of these T effector cells by PPCA results in a loss of inflammatory T cell subsets, notably proliferation CD4+Th0 and Th1 subsets and CD8+T effector memory cells, as determined by single cell RNA-seq studies with the preservation of T regulatory cells.When autologous islet grafts are given to established diabetic NOD mice, a single course of PPCA results in long-term islet graft acceptance, restoration of normoglycemia and loss of beta cell specific CD4+and CD8+T cells.PPCA shows promise as a potential means of estimating islet graft tolerance in T1D recipients of islet graft transplantation.
Architecture of the ATP-driven motor for protein import into chloroplasts
Authors: Wang Ning , Xing Jiale , Su Xiaodong , Pan Junting , Chen Hui , Shi Lifang , Si Long , Yang Wenqiang , Li Mei 
Published: September 2024

SummaryThousands of nuclear-encoded proteins are transported into chloroplasts through the TOC-TIC translocon spanning the chloroplast envelope membranes. A motor complex pulls the translocated proteins out of the TOC-TIC complex into the chloroplast stroma by hydrolyzing ATP. The Orf2971-FtsHi complex was suggested to serve as the ATP-hydrolyzing motor inChlamydomonas reinhardtii, but little is known about its architecture and assembly. Here, we report the 3.2-Å resolution structure of theChlamydomonasOrf2971-FtsHi complex. The 20-subunit complex spans the chloroplast inner envelope with two bulky modules protruding into the intermembrane space and stromal matrix. Six subunits form a hetero-hexamer potentially providing the pulling force through ATP hydrolysis. The remaining subunits, including potential enzymes/chaperones, likely facilitate the complex assembly and regulate its proper function. Our results provide the structural foundation for mechanistic understanding of chloroplast protein translocation.
Conserved variation across scales unveils dialectical relationships of micro- and macroevolution
Authors: Saito Keita , Tsuboi Masahito , Takahashi Yuma 
Published: September 2024

AbstractVariation enables short-term evolution (microevolution), but its role in long-term evolution (macroevolution) is debated. Here, we analyzed a dataset ofDrosophilawing variation across six levels of biological organization to demonstrate that microevolutionary variation and macroevolutionary divergence are positively correlated at all levels from variation within an individual to 40 million years of macroevolution. Surprisingly, the strongest relationship was between developmental noise and macroevolutionary divergence—levels thought to be the most distant—whereas the relationship between standing genetic variation and population divergence was modest, despite established theoretical predictions. Our results indicate that the congruence of developmental system with long-term history of fluctuation in adaptive peaks creates dialectical relationships between microevolution and macroevolution.
Constructing a Draft Indian Cattle Pangenome Using Short-Read Sequencing
Authors: Azam Sarwar , Sahu Abhisek , Pandey Naveen Kumar , Neupane Mahesh , Van Tassell Curtis P , Rosen Benjamin D , Gandham Ravi Kumar , Rath Subha Narayan , Majumdar Subeer S 
Published: September 2024

AbstractBackgroundIndian cattle known asdesicattle, renowned for their adaptability to harsh environments and diverse phenotypic traits, represent a valuable genetic resource. While reference genome assemblies have been instrumental in advancing cattle genomics, they often fail to capture the full spectrum of genetic variation present within diverse populations. To address this limitation, we aimed to construct a pangenome fordesicattle by identifying and characterizing Non-Reference Novel Sequences (NRNS).FindingsWe sequenced 68desicattle genomes representing seven distinct breeds, generating 48.35 billion short reads. A PanGenome Analysis (PanGA) pipeline was developed in Bash scripts to process these data to identify NRNS missing in the reference genome. A total of 13,065 NRNS with a cumulative length of ∼41 Mbp were identified that exhibited substantial variation across the population. These NRNS were found to be exclusive to Indiandesicattle, matching only 4.1% with the Chinese indicine pangenome. However, a significant proportion (∼40%) of NRNS displayed ancestral origins within the Bos genus. These sequences were enriched in genic regions, suggesting functional roles, and were associated with quantitative trait loci (QTLs), particularly for milk production. Compared to a single reference genome, the pangenome approach significantly enhanced read mapping accuracy, reduced spurious SNP calls, and facilitated the discovery of novel genetic variants.ConclusionsThis study has successfully established a within-species cattle pangenome specifically focused ondesicattle breeds from India. Our findings highlight the importance of pangenome based analyses for understanding the complex genetic architecture ofdesicattle.
Histone serves as an eat-me signal to induce RAGE-mediated phagocytosis
Authors: Li Yuqing , Zhou Xiaoman , Yang Yan , Du Congcong , Liu Yi-shi , Li Zijie , Nakanishi Hideki 
Published: September 2024

AbstractThe receptor for advanced glycation end products (RAGE) is a multiligand receptor that can induce phagocytosis in both professional and nonprofessional phagocytes. We found that histones are another ligand for RAGE. Binding between histones and RAGE is increased when DNA is attached to histones. While histones are chromosomal proteins in healthy cells, they are exposed to the cell surface as a complex with DNA when cells undergo apoptosis. The phagocytosis of apoptotic cells by either professional or nonprofessional phagocytes is enhanced when histones are present on the surface of apoptotic cells. Thus, histones serve as eat-me signals. InRAGEknockout cells, the phagocytosis of apoptotic cells was not influenced by the removal of histones, indicating that RAGE is required for the removal of histones from histone-presenting cells. In RAGE knockout mice, wound healing and removal of apoptotic cells from wound sites are delayed, suggesting that RAGE-mediated phagocytosis functions under physiological conditions.
Neural population dynamics during sleep in a songbird vocal circuit resemble sharp wave ripple activity
Authors: Lorenz Corinna , Das Anindita , Centeno Eduarda Gervini Zampieri , Yeganegi Hamed , Duvoisin Robin , Ursu Roman , Retailleau Aude , Giret Nicolas , Leblois Arthur , Hahnloser Richard H. R. , Ondracek Janie M. 
Published: September 2024

AbstractDuring vocal learning, juvenile songbirds use auditory feedback and trial-and-error motor learning to transition from acoustically simple, highly variable songs to complex and stereotypical adult songs. Similar to motor skill learning in mammals, vocal learning in songbirds requires a set of interconnected brain areas that make up an analogous basal ganglia-thalamocortical circuit known as the anterior forebrain pathway (AFP). Although neural activity in the AFP has been extensively investigated during awake singing, very little is known about its neural activity patterns during offline sleep periods.In this work, we used chronically implanted Neuropixels probes to investigate neural activity in the AFP during offline periods of natural sleep. We found that neurons in the pallial region LMAN (lateral magnocellular nucleus of the nidopallium) transitioned from sparse synchronous firing to asynchronous firing during sleep, which corresponded to slow wave sleep (SWS) and rapid eye movement (REM) sleep, respectively. SWS periods were associated with increased spiking variability for LMAN neurons, but not for neurons in the striatal region Area X (proper name). Coinciding with the increased spiking variability, we observed that populations of LMAN neurons were co-activated at specific time points during sleep in bursting events that were characterized by a negative deflection in the local field potential (LFP) and a transient increase in gamma power. Overall, the LMAN population bursting events were highly reminiscent of sharp-wave ripple (SWR) activity observed in rodent hippocampus.Contrary to our expectations, we did not observe strong cross-area field coherence between LMAN and Area X, although individual LMAN-Area X LFP pairs did show coherence > 0.5. These results provide the first description of cross-area dynamics within the AFP during sleep. Furthermore, the observation of SWR-like events during sleep in LMAN suggests that large-scale population events have diverse functions across vertebrates.
Novel Role of Endothelial CD45 in Regulating Endothelial-to-Mesenchymal Transition in Atherosclerosis
Authors: Peng Qianman , Arulsamy Kulandaisamy , Lu Yao Wei , Wu Hao , Zhu Bo , Singh Bandana , Cui Kui , Wylie-Sears Jill , Li Kathryn , Wong Scott , Cowan Douglas B. , Aikawa Masanori , Wang Da-Zhi , Bischoff Joyce , Chen Kaifu , Chen Hong 
Published: September 2024

AbstractBackgroundProtein-tyrosine-phosphatase CD45 is exclusively expressed in all nucleated cells of the hematopoietic system but is rarely expressed in endothelial cells. Interestingly, our recent study indicated that activation of the endogenous CD45 promoter in human endothelial colony forming cells (ECFCs) induced expression of multiple EndoMT marker genes. However, the detailed molecular mechanisms underlying CD45 that drive EndoMT and the therapeutic potential of manipulation of CD45 expression in atherosclerosis are entirely unknown.MethodWe generated a tamoxifen-inducible EC-specific CD45 deficient mouse strain (EC-iCD45KO) in an ApoE-deficient (ApoE-/-) background and fed with a Western diet (C57BL/6) for atherosclerosis and molecular analyses. We isolated and enriched mouse aortic endothelial cells with CD31 beads to perform single-cell RNA sequencing. Biomedical, cellular, and molecular approaches were utilized to investigate the role of endothelial CD45-specific deletion in the prevention of EndoMT in ApoE-/-model of atherosclerosis.ResultsSingle-cell RNA sequencing revealed that loss of endothelial CD45 inhibits EndoMT marker expression and transforming growth factor-β signaling in atherosclerotic mice. which is associated with the reductions of lesions in the ApoE-/-mouse model. Mechanistically, the loss of endothelial cell CD45 results in increased KLF2 expression, which inhibits transforming growth factor-β signaling and EndoMT. Consistently, endothelial CD45 deficient mice showed reduced lesion development, plaque macrophages, and expression of cell adhesion molecules when compared to ApoE-/-controls.ConclusionsThese findings demonstrate that the loss of endothelial CD45 protects against EndoMT-driven atherosclerosis, promoting KLF2 expression while inhibiting TGFβ signaling and EndoMT markers. Thus, targeting endothelial CD45 may be a novel therapeutic strategy for EndoMT and atherosclerosis.
Are farmers willing to pay for low-carbon agriculture? Evidence from China
Authors: Yang Wanping , Mou Muge , Mu Lan , Zeng Xuanwen 
Published: September 2024

PurposeReducing carbon emissions in agriculture is vital for fostering sustainable agricultural growth and promoting ecological well-being in rural areas. The adoption of Low-Carbon Agriculture (LCA) by farmers holds great potential to accomplish substantial reductions in carbon emissions. The purpose of this study is to explore the farmers' preference and willingness to engage in LCA.Design/methodology/approachThis study employs the Choice Experiment (CE) method to examine farmers' preferences and willingness to adopt LCA, using field survey data of 544 rural farmers in the Weihe River Basin between June and July 2023. We further investigate differences in willingness to pay (WTP) and personal characteristics among different farmer categories.FindingsThe empirical results reveal that farmers prioritize government-led initiatives providing pertinent technical training as a key aspect of the LCA program. Farmers' decisions to participate in LCA are influenced by factors including age, gender, education and the proportion of farm income in household income, with their evaluations further shaped by subjective attitudes and habits. Notably, we discovered that nearly half of the farmers exhibit indifference towards LCA attributes.Originality/valueTo the best of the authors' knowledge, this study is the first to investigate farmers' attitudes toward LCA from their own perspectives and to analyze the factors influencing them from both subjective and objective standpoints. This study presents a fresh perspective for advocating LCA, bolstering rural ecology and nurturing sustainable development in developing nations.
Optimize data association of point cloud to improve the quality of mapping and positioning
Authors: Zhou Guangbing , Quan Letian , Huang Kaixuan , Zhang Shunqing , Xu Shugong 
Published: September 2024

Purpose
Accurate mapping is crucial for the positioning and navigation of mobile robots. Recent advancements in algorithms and the accuracy of LiDAR sensors have led to a gradual improvement in map quality. However, challenges such as lag in closing loops and vignetting at map boundaries persist due to the discrete and sparse nature of raster map data. The purpose of this study is to reduce the error of map construction and improve the timeliness of closed loop.

Design/methodology/approach
In this letter, the authors introduce a method for dynamically adjusting point cloud distance constraints to optimize data association (ODA-d), effectively addressing these issues. The authors propose a dynamic threshold optimization method for matching point clouds to submaps during scan matching.

Findings
Large deviations in LiDAR sensor point cloud data, when incorporated into the submap, can result in irreparable errors in correlation matching and loop closure optimization. By implementing a data association framework with double constraints and dynamically adjusting the matching threshold, the authors significantly enhance submap quality. In addition, the authors introduce a dynamic fusion method that accounts for both submap size and the distance between submaps during the mapping process. ODA-d reduces errors between submaps and facilitates timely loop closure optimization.

Originality/value
The authors validate the localization accuracy of ODA-d by examining translation and rotation errors across three open data sets. Moreover, the authors compare the quality of map construction in a real-world environment, demonstrating the effectiveness of ODA-d.