bluuebunny/crossref_metadata_2025_split huggingface dataset:
DNA binding analysis of rare variants in homeodomains reveals homeodomain specificity-determining residues
Authors: Kock Kian Hong , Kimes Patrick K. , Gisselbrecht Stephen S. , Inukai Sachi , Phanor Sabrina K. , Anderson James T. , Ramakrishnan Gayatri , Lipper Colin H. , Song Dongyuan , Kurland Jesse V. , Rogers Julia M. , Jeong Raehoon , Blacklow Stephen C. , Irizarry Rafael A. , Bulyk Martha L. 
Published: April 2024

AbstractHomeodomains (HDs) are the second largest class of DNA binding domains (DBDs) among eukaryotic sequence-specific transcription factors (TFs) and are the TF structural class with the largest number of disease-associated mutations in the Human Gene Mutation Database (HGMD). Despite numerous structural studies and large-scale analyses of HD DNA binding specificity, HD-DNA recognition is still not fully understood. Here, we analyze 92 human HD mutants, including disease-associated variants and variants of uncertain significance (VUS), for their effects on DNA binding activity. Many of the variants alter DNA binding affinity and/or specificity. Detailed biochemical analysis and structural modeling identifies 14 previously unknown specificity-determining positions, 5 of which do not contact DNA. The same missense substitution at analogous positions within different HDs often exhibits different effects on DNA binding activity. Variant effect prediction tools perform moderately well in distinguishing variants with altered DNA binding affinity, but poorly in identifying those with altered binding specificity. Our results highlight the need for biochemical assays of TF coding variants and prioritize dozens of variants for further investigations into their pathogenicity and the development of clinical diagnostics and precision therapies.
Early-life exercise induces immunometabolic epigenetic modification enhancing anti-inflammatory immunity in middle-aged male mice
Authors: Zhang Nini , Wang Xinpei , Feng Mengya , Li Min , Wang Jing , Yang Hongyan , He Siyu , Xia Ziqi , Shang Lei , Jiang Xun , Sun Mao , Wu Yuanming , Ren Chaoxue , Zhang Xing , Li Jia , Gao Feng 
Published: April 2024

AbstractExercise is usually regarded to have short-term beneficial effects on immune health. Here we show that early-life regular exercise exerts long-term beneficial effects on inflammatory immunity. Swimming training for 3 months in male mice starting from 1-month-old curbs cytokine response and mitigates sepsis when exposed to lipopolysaccharide challenge, even after an 11-month interval of detraining. Metabolomics analysis of serum and liver identifies pipecolic acid, a non-encoded amino acid, as a pivotal metabolite responding to early-life regular exercise. Importantly, pipecolic acid reduces inflammatory cytokines in bone marrow-derived macrophages and alleviates sepsis via inhibiting mTOR complex 1 signaling. Moreover, early-life exercise increases histone 3 lysine 4 trimethylation at the promoter of Crym in the liver, an enzyme responsible for catalyzing pipecolic acid production. Liver-specific knockdown of Crym in adult mice abolishes this early exercise-induced protective effects. Our findings demonstrate that early-life regular exercise enhances anti-inflammatory immunity during middle-aged phase in male mice via epigenetic immunometabolic modulation, in which hepatic pipecolic acid production has a pivotal function.
Charge transfer and spin-valley locking in 4Hb-TaS2
Authors: Almoalem Avior , Gofman Roni , Nitzav Yuval , Mangel Ilay , Feldman Irena , Koo Jahyun , Mazzola Federico , Fujii Jun , Vobornik Ivana , S´anchez-Barriga J. , Clark Oliver J. , Plumb Nicholas Clark , Shi Ming , Yan Binghai , Kanigel Amit 
Published: April 2024

Abstract4Hb-TaS2 is a superconductor that exhibits unique characteristics such as time-reversal symmetry breaking, hidden magnetic memory, and topological edge modes. It is a naturally occurring heterostructure comprising of alternating layers of 1H-TaS2 and 1T-TaS2. The former is a well-known superconductor, while the latter is a correlated insulator with a possible non- trivial magnetic ground state. In this study, we use angle resolved photoemission spectroscopy to investigate the normal state electronic structure of this unconventional superconductor. Our findings reveal that the band structure of 4Hb-TaS2 fundamentally differs from that of its constituent materials. Specifically, we observe a significant charge transfer from the 1T layers to the 1H layers that drives the 1T layers away from half-filling. In addition, we find a substantial reduction in inter-layer coupling in 4Hb-TaS2 compared to the coupling in 2H-TaS2 that results in a pronounced spin-valley locking within 4Hb-TaS2.
Distal colonocytes targeted by C. rodentium recruit T-cell help for barrier defence
Authors: Zindl Carlene L. , Wilson C. Garrett , Chadha Awalpreet S. , Duck Lennard W. , Cai Baiyi , Harbour Stacey N. , Nagaoka-Kamata Yoshiko , Hatton Robin D. , Gao Min , Figge David A. , Weaver Casey T. 
Published: April 2024

AbstractInterleukin 22 (IL-22) has a non-redundant role in immune defence of the intestinal barrier1–3. T cells, but not innate lymphoid cells, have an indispensable role in sustaining the IL-22 signalling that is required for the protection of colonic crypts against invasion during infection by the enteropathogen Citrobacter rodentium4 (Cr). However, the intestinal epithelial cell (IEC) subsets targeted by T cell-derived IL-22, and how T cell-derived IL-22 sustains activation in IECs, remain undefined. Here we identify a subset of absorptive IECs in the mid–distal colon that are specifically targeted by Cr and are differentially responsive to IL-22 signalling. Major histocompatibility complex class II (MHCII) expression by these colonocytes was required to elicit sustained IL-22 signalling from Cr-specific T cells, which was required to restrain Cr invasion. Our findings explain the basis for the regionalization of the host response to Cr and demonstrate that epithelial cells must elicit MHCII-dependent help from IL-22–producing T cells to orchestrate immune protection in the intestine.
Messenger RNA transport on lysosomal vesicles maintains axonal mitochondrial homeostasis and prevents axonal degeneration
Authors: De Pace Raffaella , Ghosh Saikat , Ryan Veronica H. , Sohn Mira , Jarnik Michal , Rezvan Sangsari Paniz , Morgan Nicole Y. , Dale Ryan K. , Ward Michael E. , Bonifacino Juan S. 
Published: April 2024

AbstractIn neurons, RNA granules are transported along the axon for local translation away from the soma. Recent studies indicate that some of this transport involves hitchhiking of RNA granules on lysosome-related vesicles. In the present study, we leveraged the ability to prevent transport of these vesicles into the axon by knockout of the lysosome–kinesin adaptor BLOC-one-related complex (BORC) to identify a subset of axonal mRNAs that depend on lysosome-related vesicles for transport. We found that BORC knockout causes depletion of a large group of axonal mRNAs mainly encoding ribosomal and mitochondrial/oxidative phosphorylation proteins. This depletion results in mitochondrial defects and eventually leads to axonal degeneration in human induced pluripotent stem cell (iPSC)-derived and mouse neurons. Pathway analyses of the depleted mRNAs revealed a mechanistic connection of BORC deficiency with common neurodegenerative disorders. These results demonstrate that mRNA transport on lysosome-related vesicles is critical for the maintenance of axonal homeostasis and that its failure causes axonal degeneration.
Fisheries Inspection in Portuguese Waters from 2015 to 2023
Authors: Moura Ricardo , Pessanha Santos Nuno , Vala Alexandra , Mendes Leonor , Simões Paula , de Castro Neto Miguel , Lobo Victor 
Published: April 2024

AbstractAs a coastal state, Portugal must ensure active surveillance over its maritime area, ensuring its proper control and inspection. One of the most critical inspection activities is the fishery inspection. To protect biodiversity, we must ensure that all the ships comply with the existing safety regulations and respect the current fishing quotas. This georeferenced dataset describes the fisheries inspections done in Portuguese waters between 2015 and 2023. Since we are dealing with occurrences that may have originated some legal process to the ship’s owner, we have ensured data anonymization by pre-processing the dataset to maintain its accuracy while guaranteeing no unique identifiers exist. All the pre-processing performed to ensure data consistency and accuracy is described in detail to allow a quick analysis and implementation of new algorithms. The data containing the results of these inspections can be easily analyzed to implement data mining algorithms that can efficiently retrieve more knowledge and, e.g., suggest new areas of actuation or new strategies.
Numerical subgrid Bi-cubic methods of partial differential equations in image segmentation
Authors: Kim Dongyung 
Published: April 2024

AbstractImage segmentation is a core research in the image processing and computer vision. In this paper, we suggest a Bi-cubic spline phase transition potential and elaborate a Bi-Cubic spline phase transition potential development. In the image segmentation, we develop the new approach to apply the novel computational fluid dynamics in the boundary with subgrid. The numerical subgrid Bi-cubic method with Bi-Cubic spline for minimizing the piecewise constant energy functional is very efficient, robust and fast in the image segmentation with a multispecies multiphase segmentation models. The subgrid Bi-cubic spline is applied on the boundary with subgrid and the regular grid is applied on the non-boundary. The model generates a multispecies multiphase distribution with Bi-Cubic spline and we can extract the image segments with multispecies multiphase. Finally, we analyze the models and show the numerical results. Numerical results are presented with OCR (Optical Character Recognition) and the medical image.
Spindle oscillations in communicating axons within a reconstituted hippocampal formation are strongest in CA3 without thalamus
Authors: Wang Mengke , Lassers Samuel B. , Vakilna Yash S. , Mander Bryce A. , Tang William C. , Brewer Gregory J. 
Published: April 2024

AbstractSpindle-shaped waves of oscillations emerge in EEG scalp recordings during human and rodent non-REM sleep. The association of these 10–16 Hz oscillations with events during prior wakefulness suggests a role in memory consolidation. Human and rodent depth electrodes in the brain record strong spindles throughout the cortex and hippocampus, with possible origins in the thalamus. However, the source and targets of the spindle oscillations from the hippocampus are unclear. Here, we employed an in vitro reconstruction of four subregions of the hippocampal formation with separate microfluidic tunnels for single axon communication between subregions assembled on top of a microelectrode array. We recorded spontaneous 400–1000 ms long spindle waves at 10–16 Hz in single axons passing between subregions as well as from individual neurons in those subregions. Spindles were nested within slow waves. The highest amplitudes and most frequent occurrence suggest origins in CA3 neurons that send feed-forward axons into CA1 and feedback axons into DG. Spindles had 50–70% slower conduction velocities than spikes and were not phase-locked to spikes suggesting that spindle mechanisms are independent of action potentials. Therefore, consolidation of declarative-cognitive memories in the hippocampus may be separate from the more easily accessible consolidation of memories related to thalamic motor function.
Welfare of invertebrates: a pilot study on a new land snail stunning technique
Authors: Fossati Paola , Stefanini Federico M. , Ravasio Giuliano , Coerezza Umberto 
Published: April 2024

AbstractThe almost complete absence of regulations to protect invertebrates is a common condition in legal systems, including the European one, especially when it comes to invertebrates intended for human consumption. Thus, in the vast majority of cases, edible invertebrates do not receive even the most basic protection at slaughter. Despite recent research indicating that invertebrates are capable of feeling pain and stress, the humane step of stunning is not used on them. This is also the case for land snails, which are gastropod invertebrates whose consumption has now reached significant levels, already involving tonnes and that is expected to increase significantly as edible snail farming becomes more popular as a relatively low-cost, easy-to-perform, and sustainable alternative animal husbandry, thereby making land snails an increasingly economically important species. This paper presents and investigates a proposed stunning method based on the immersion of mollusks in CO2-supplemented and refrigerated water that could be used in the snail meat production chain to reduce the slaughter suffering of millions of these invertebrates. To this end, body condition descriptors (hemolymph parameters) in snails were determined before and after CO2 treatment in cold water, while generating useful data for defining a preliminary set of reference intervals for basal values.
Response times are affected by mispredictions in a stochastic game
Authors: Cabral-Passos Paulo Roberto , Galves Antonio , Garcia Jesus Enrique , Vargas Claudia D. 
Published: April 2024

AbstractActing as a goalkeeper in a video-game, a participant is asked to predict the successive choices of the penalty taker. The sequence of choices of the penalty taker is generated by a stochastic chain with memory of variable length. It has been conjectured that the probability distribution of the response times is a function of the specific sequence of past choices governing the algorithm used by the penalty taker to make his choice at each step. We found empirical evidence that besides this dependence, the distribution of the response times depends also on the success or failure of the previous prediction made by the participant. Moreover, we found statistical evidence that this dependence propagates up to two steps forward after the prediction failure.
Traffic coordination by reducing jamming attackers in VANET using probabilistic Manhattan Grid Topology for automobile applications
Authors: Santhi G. B. , Jacob Suma Sira , Sheela D. , Kumaran P. 
Published: April 2024

AbstractIn recent years Intelligent Transportation System (ITS) has been growing interest in the development of vehicular communication technology. The traffic in India shows considerable fluctuations owing to the static and dynamic characteristics of road vehicles in VANET (Vehicular Adhoc Network). These vehicles take up a convenient side lane position on the road, disregarding lane discipline. They utilize the opposing lane to overtake slower-moving vehicles, even when there are oncoming vehicles approaching. The primary objective of this study is to minimize injuries resulting from vehicle interactions in mixed traffic conditions on undivided roads. This is achieved through the implementation of the Modified Manhattan grid topology, which primarily serves to guide drivers in the correct path when navigating undivided roads. Furthermore, the Fuzzy C-Means algorithm (FCM) is applied to detect potential jamming attackers, while the Modified Fisheye State Routing (MFSR) Algorithm is employed to minimize the amount of information exchanged among vehicles. Subsequently, the Particle Swarm Optimization (PSO) algorithm is developed to enhance the accuracy of determining the coordinates of jamming attackers within individual clusters. The effectiveness of the outcomes is affirmed through the utilization of the Fuzzy C-Means algorithm, showcasing a notable 30% reduction in the number of attackers, along with the attainment of a 70% accuracy rate in this research endeavor.
Plasma metabolites and physical function in patients undergoing hemodialysis
Authors: Moorthi Ranjani N. , Moe Sharon M. , O’Connell Thomas , Dickinson Stephanie , Kalim Sahir , Thadhani Ravi , Clish Clary B. , Shafi Tariq , Rhee Eugene P. , Avin Keith G. 
Published: April 2024

AbstractImpaired physical function contributes to falls, fractures, and mortality among patients undergoing dialysis. Using a metabolomic approach, we identified metabolite alterations and effect size-based composite scores for constructs of impaired gait speed and grip strength. 108 participants incident to dialysis had targeted plasma metabolomics via liquid chromatography-mass spectrometry and physical function assessed (i.e., 4 m walk, handgrip strength). Physical function measures were categorized as above/ below median, with grip utilizing sex-based medians. To develop composite scores, metabolites were identified via Wilcoxon uncorrected p < 0.05 and effect size > 0.40. Receiver operating characteristic analyses tested whether scores differentiated between above/below function groups. Participants were 54% male, 77% Black and 53 ± 14 y with dialysis vintage of 101 ± 50 days. Median (IQR) grip strength was 35.5 (11.1) kg (males) and 20 (8.4) kg (females); median gait speed was 0.82 (0.34) m/s. Of 246 measured metabolites, composite scores were composed of 22 and 12 metabolites for grip strength and gait speed, respectively. Area under the curve for metabolite composite was 0.88 (gait) and 0.911 (grip). Composite scores of physical function performed better than clinical parameters alone in patients on dialysis. These results provide potential pathways for interventions and needed validation in an independent cohort.
Modeling the influence of bacteria concentration on the mechanical properties of self-healing concrete (SHC) for sustainable bio-concrete structures
Authors: Onyelowe Kennedy C. , Adam Ali F. H. , Ulloa Nestor , Garcia Cesar , Andrade Valle Alexis Ivan , Zúñiga Rodríguez María Gabriela , Zarate Villacres Andrea Natali , Shakeri Jamshid , Anyaogu Lewechi , Alimoradijazi Mohammadreza , Ganasen Nakkeeran 
Published: April 2024

AbstractIn this research paper, the intelligent learning abilities of the gray wolf optimization (GWO), multi-verse optimization (MVO), moth fly optimization, particle swarm optimization (PSO), and whale optimization algorithm (WOA) metaheuristic techniques and the response surface methodology (RSM) has been studied in the prediction of the mechanical properties of self-healing concrete. Bio-concrete technology stimulated by the concentration of bacteria has been utilized as a sustainable structural concrete for the future of the built environment. This is due to the recovery tendency of the concrete structures after noticeable structural failures. However, it requires a somewhat expensive exercise and technology to create the medium for the growth of the bacteria needed for this self-healing ability. The method of data gathering, analysis and intelligent prediction has been adopted to propose parametric relationships between the bacteria usage and the concrete performance in terms of strength and durability. This makes is cheaper to design self-healing concrete structures based on the optimized mathematical relationships and models proposed from this exercise. The performance of the models was tested by using the coefficient of determination (R2), root mean squared errors, mean absolute errors, mean squared errors, variance accounted for and the coefficient of error. At the end of the prediction protocol and model performance evaluation, it was found that the classified metaheuristic techniques outclassed the RSM due their ability to mimic human and animal genetics of mutation. Furthermore, it can be finally remarked that the GWO outclassed the other methods in predicting the concrete slump (Sl) with R2 of 0.998 and 0.989 for the train and test, respectively, the PSO outclassed the rest in predicting the flexural strength with R2 of 0.989 and 0.937 for train and test, respectively and the MVO outclassed the others in predicting the compressive strength with R2 of 0.998 and 0.958 for train and test, respectively.
A histological and diceCT-derived 3D reconstruction of the avian visual thalamofugal pathway
Authors: Straight Parker J. , Gignac Paul M. , Kuenzel Wayne J. 
Published: April 2024

AbstractAmniotes feature two principal visual processing systems: the tectofugal and thalamofugal pathways. In most mammals, the thalamofugal pathway predominates, routing retinal afferents through the dorsolateral geniculate complex to the visual cortex. In most birds, the thalamofugal pathway often plays the lesser role with retinal afferents projecting to the principal optic thalami, a complex of several nuclei that resides in the dorsal thalamus. This thalamic complex sends projections to a forebrain structure called the Wulst, the terminus of the thalamofugal visual system. The thalamofugal pathway in birds serves many functions such as pattern discrimination, spatial memory, and navigation/migration. A comprehensive analysis of avian species has unveiled diverse subdivisions within the thalamic and forebrain structures, contingent on species, age, and techniques utilized. In this study, we documented the thalamofugal system in three dimensions by integrating histological and contrast-enhanced computed tomography imaging of the avian brain. Sections of two-week-old chick brains were cut in either coronal, sagittal, or horizontal planes and stained with Nissl and either Gallyas silver or Luxol Fast Blue. The thalamic principal optic complex and pallial Wulst were subdivided on the basis of cell and fiber density. Additionally, we utilized the technique of diffusible iodine-based contrast-enhanced computed tomography (diceCT) on a 5-week-old chick brain, and right eyeball. By merging diceCT data, stained histological sections, and information from the existing literature, a comprehensive three-dimensional model of the avian thalamofugal pathway was constructed. The use of a 3D model provides a clearer understanding of the structural and spatial organization of the thalamofugal system. The ability to integrate histochemical sections with diceCT 3D modeling is critical to better understanding the anatomical and physiologic organization of complex pathways such as the thalamofugal visual system.
Ablation of Wnt signaling in bone marrow stromal cells overcomes microenvironment-mediated drug resistance in acute myeloid leukemia
Authors: Palani Hamenth Kumar , Ganesan Saravanan , Balasundaram Nithya , Venkatraman Arvind , Korula Anu , Abraham Aby , George Biju , Mathews Vikram 
Published: April 2024

AbstractThe survival of leukemic cells is significantly influenced by the bone marrow microenvironment, where stromal cells play a crucial role. While there has been substantial progress in understanding the mechanisms and pathways involved in this crosstalk, limited data exist regarding the impact of leukemic cells on bone marrow stromal cells and their potential role in drug resistance. In this study, we identify that leukemic cells prime bone marrow stromal cells towards osteoblast lineage and promote drug resistance. This biased differentiation of stroma is accompanied by dysregulation of the canonical Wnt signaling pathway. Inhibition of Wnt signaling in stroma reversed the drug resistance in leukemic cells, which was further validated in leukemic mice models. This study evaluates the critical role of leukemic cells in establishing a drug-resistant niche by influencing the bone marrow stromal cells. Additionally, it highlights the potential of targeting Wnt signaling in the stroma by repurposing an anthelmintic drug to overcome the microenvironment-mediated drug resistance.