bluuebunny/crossref_metadata_2025_split huggingface dataset:
Neuroglia in cognitive reserve
Authors: Verkhratsky Alexei , Zorec Robert 
Published: July 2024

AbstractThe concept of cognitive reserve was born to account for the disjunction between the objective extent of brain damage in pathology and its clinical and intellectual outcome. The cognitive reserve comprises structural (brain reserve) and functional (brain maintenance, resilience, compensation) aspects of the nervous tissue reflecting exposome-driven life-long plasticity, which defines the ability of the brain to withstand aging and pathology. The mechanistic background of this concept was primarily focused on adaptive changes in neurones and neuronal networks. We present arguments favoring the more inclusive view, positing that neuroglia are fundamental for defining the cognitive reserve through homeostatic, neuroprotective, and neurodegenerative mechanisms. Neuroglia are critical for the life-long shaping of synaptically connected neuronal circuits as well as the brain connectome thus defining cognitive reserve. Neuroglial homeostatic and protective physiological responses define brain maintenance and resilience, while neuroglia regenerative capabilities are critical for brain compensation in pathology. Targeting neuroglia may represent an untrodden path for prolonging cognitive longevity.
Sex differences in the association between vitamin D and prediabetes in adults: A cross-sectional study
Authors: Ziyab Ali H. , Mohammad Anwar , Almousa Zainab , Mohammad Talal 
Published: July 2024

Abstract
Background/Objectives
Vitamin D status has been shown to be associated with prediabetes risk. However, epidemiologic evidence on whether sex modulates the association between vitamin D and prediabetes is limited. The present study investigated sex-specific associations between vitamin D and prediabetes.

Subjects/Methods
The Kuwait Wellbeing Study, a population-based cross-sectional study, enrolled nondiabetic adults. Prediabetes was defined as 5.7 ≤ HbA1c% ≤6.4; 25-hydroxyvitamin D (25(OH)D) was measured in venous blood and analyzed as a continuous, dichotomous (deficiency: <50 nmol/L vs. insufficiency/sufficiency ≥50 nmol/L), and categorical (tertiles) variable. Associations were evaluated by estimating adjusted prevalence ratios (aPRs) and 95% confidence intervals (CIs), while stratifying by sex.

Results
A total of 384 participants (214 males and 170 females) were included in the current analysis, with a median age of 40.5 (interquartile range: 33.0–48.0) years. The prevalence of prediabetes was 35.2%, and 63.0% of participants had vitamin D deficiency. Assessments of statistical interaction between sex and 25(OH)D status were statistically significant (PSex × 25(OH)D Interaction < 0.05). In the sex-stratified analysis, after adjustment for confounding factors, decreased 25(OH)D levels were associated with increased prevalence of prediabetes in males (aPRDeficiency vs. In-/Sufficiency: 2.35, 95% CI: 1.36–4.07), but not in females (aPRDeficiency vs. In-/Sufficiency: 1.03, 95% CI: 0.60–1.77). Moreover, the prevalence of prediabetes differed between males and females at 25(OH)D levels of ≤35 nmol/L, with a higher prevalence of prediabetes in males compared to females. Such a sex-specific difference was not observed at 25(OH)D levels of >35 nmol/L.

Conclusions
Sex modified the association between vitamin D levels and prediabetes, with an inverse association observed among males, but not among females. Moreover, the observed sex-disparity in the prevalence of prediabetes was only pronounced at 25(OH)D levels of ≤35 nmol/L.
Development and optimization of expected cross value for mate selection problems
Authors: Ahadi Pouya , Balasundaram Balabhaskar , Borrero Juan S. , Chen Charles 
Published: July 2024

AbstractIn this study, we address the mate selection problem in the hybridization stage of a breeding pipeline, which constitutes the multi-objective breeding goal key to the performance of a variety development program. The solution framework we formulate seeks to ensure that individuals with the most desirable genomic characteristics are selected to cross in order to maximize the likelihood of the inheritance of desirable genetic materials to the progeny. Unlike approaches that use phenotypic values for parental selection and evaluate individuals separately, we use a criterion that relies on the genetic architecture of traits and evaluates combinations of genomic information of the pairs of individuals. We introduce the expected cross value (ECV) criterion that measures the expected number of desirable alleles for gametes produced by pairs of individuals sampled from a population of potential parents. We use the ECV criterion to develop an integer linear programming formulation for the parental selection problem. The formulation is capable of controlling the inbreeding level between selected mates. We evaluate the approach or two applications: (i) improving multiple target traits simultaneously, and (ii) finding a multi-parental solution to design crossing blocks. We evaluate the performance of the ECV criterion using a simulation study. Finally, we discuss how the ECV criterion and the proposed integer linear programming techniques can be applied to improve breeding efficiency while maintaining genetic diversity in a breeding program.
Ligand-enabled ruthenium-catalyzed meta-C−H alkylation of (hetero)aromatic carboxylic acids
Authors: Luo Xianglin , Hou Peichao , Shen Jiayi , Kuang Yifeng , Sun Fengchao , Jiang Huanfeng , Gooßen Lukas J. , Huang Liangbin 
Published: July 2024

AbstractCarboxylates are ideal directing groups because they are widely available, readily cleavable and excellent linchpins for diverse follow-up reactions. However, their use in meta-selective C−H functionalizations remains a substantial unmet catalytic challenge. Herein, we report the ruthenium-catalyzed meta-C–H alkylation of aromatic carboxylic acids with various functionalized alkyl halides. A bidentate N-ligand increases the electron density at the metal center of ortho-benzoate ruthenacycles to the extent that single-electron reductions of alkyl halides can take place. The subsequent addition of alkyl radicals is exclusively directed to the position para to the CAr–Ru bond, i.e., meta to the carboxylate group. The resulting catalytic meta-C−H alkylation extends to a wide range of (hetero)aromatic carboxylic acids including benzofused five-membered ring heteroarenes but no pyridine derivatives in combination with secondary/tertiary alkyl halides, including fluorinated derivatives. It also allows site-selective C5−H alkylation of 1-naphthoic acids. The products are shown to be synthetic hubs en route to meta-alkylated aryl ketones, nitriles, amides, esters and other functionalized products.
RNA-guided RNA silencing by an Asgard archaeal Argonaute
Authors: Bastiaanssen Carolien , Bobadilla Ugarte Pilar , Kim Kijun , Finocchio Giada , Feng Yanlei , Anzelon Todd A. , Köstlbacher Stephan , Tamarit Daniel , Ettema Thijs J. G. , Jinek Martin , MacRae Ian J. , Joo Chirlmin , Swarts Daan C. , Wu Fabai 
Published: July 2024

AbstractArgonaute proteins are the central effectors of RNA-guided RNA silencing pathways in eukaryotes, playing crucial roles in gene repression and defense against viruses and transposons. Eukaryotic Argonautes are subdivided into two clades: AGOs generally facilitate miRNA- or siRNA-mediated silencing, while PIWIs generally facilitate piRNA-mediated silencing. It is currently unclear when and how Argonaute-based RNA silencing mechanisms arose and diverged during the emergence and early evolution of eukaryotes. Here, we show that in Asgard archaea, the closest prokaryotic relatives of eukaryotes, an evolutionary expansion of Argonaute proteins took place. In particular, a deep-branching PIWI protein (HrAgo1) encoded by the genome of the Lokiarchaeon ‘Candidatus Harpocratesius repetitus’ shares a common origin with eukaryotic PIWI proteins. Contrasting known prokaryotic Argonautes that use single-stranded DNA as guides and/or targets, HrAgo1 mediates RNA-guided RNA cleavage, and facilitates gene silencing when expressed in human cells and supplied with miRNA precursors. A cryo-EM structure of HrAgo1, combined with quantitative single-molecule experiments, reveals that the protein displays structural features and target-binding modes that are a mix of those of eukaryotic AGO and PIWI proteins. Thus, this deep-branching archaeal PIWI may have retained an ancestral molecular architecture that preceded the functional and mechanistic divergence of eukaryotic AGOs and PIWIs.
Light-driven C–H activation mediated by 2D transition metal dichalcogenides
Authors: Li Jingang , Zhang Di , Guo Zhongyuan , Chen Zhihan , Jiang Xi , Larson Jonathan M. , Zhu Haoyue , Zhang Tianyi , Gu Yuqian , Blankenship Brian W. , Chen Min , Wu Zilong , Huang Suichu , Kostecki Robert , Minor Andrew M. , Grigoropoulos Costas P. , Akinwande Deji , Terrones Mauricio , Redwing Joan M. , Li Hao , Zheng Yuebing 
Published: July 2024

AbstractC–H bond activation enables the facile synthesis of new chemicals. While C–H activation in short-chain alkanes has been widely investigated, it remains largely unexplored for long-chain organic molecules. Here, we report light-driven C–H activation in complex organic materials mediated by 2D transition metal dichalcogenides (TMDCs) and the resultant solid-state synthesis of luminescent carbon dots in a spatially-resolved fashion. We unravel the efficient H adsorption and a lowered energy barrier of C–C coupling mediated by 2D TMDCs to promote C–H activation and carbon dots synthesis. Our results shed light on 2D materials for C–H activation in organic compounds for applications in organic chemistry, environmental remediation, and photonic materials.
Baseline levels and longitudinal changes in plasma Aβ42/40 among Black and white individuals
Authors: Xiong Chengjie , Luo Jingqin , Wolk David A. , Shaw Leslie M. , Roberson Erik D. , Murchison Charles F. , Henson Rachel L. , Benzinger Tammie L. S. , Bui Quoc , Agboola Folasade , Grant Elizabeth , Gremminger Emily N. , Moulder Krista L. , Geldmacher David S. , Clay Olivio J. , Babulal Ganesh , Cruchaga Carlos , Holtzman David M. , Bateman Randall J. , Morris John C. , Schindler Suzanne E. 
Published: July 2024

AbstractBlood-based biomarkers of Alzheimer disease (AD) may facilitate testing of historically under-represented groups. The Study of Race to Understand Alzheimer Biomarkers (SORTOUT-AB) is a multi-center longitudinal study to compare AD biomarkers in participants who identify their race as either Black or white. Plasma samples from 324 Black and 1,547 white participants underwent analysis with C2N Diagnostics’ PrecivityAD test for Aβ42 and Aβ40. Compared to white individuals, Black individuals had higher average plasma Aβ42/40 levels at baseline, consistent with a lower average level of amyloid pathology. Interestingly, this difference resulted from lower average levels of plasma Aβ40 in Black participants. Despite the differences, Black and white individuals had similar longitudinal rates of change in Aβ42/40, consistent with a similar rate of amyloid accumulation. Our results agree with multiple recent studies demonstrating a lower prevalence of amyloid pathology in Black individuals, and additionally suggest that amyloid accumulates consistently across both groups.
Dimeric transport mechanism of human vitamin C transporter SVCT1
Authors: Kobayashi Takaaki A. , Shimada Hiroto , Sano Fumiya K. , Itoh Yuzuru , Enoki Sawako , Okada Yasushi , Kusakizako Tsukasa , Nureki Osamu 
Published: July 2024

AbstractVitamin C plays important roles as a cofactor in many enzymatic reactions and as an antioxidant against oxidative stress. As some mammals including humans cannot synthesize vitamin C de novo from glucose, its uptake from dietary sources is essential, and is mediated by the sodium-dependent vitamin C transporter 1 (SVCT1). Despite its physiological significance in maintaining vitamin C homeostasis, the structural basis of the substrate transport mechanism remained unclear. Here, we report the cryo-EM structures of human SVCT1 in different states at 2.5–3.5 Å resolutions. The binding manner of vitamin C together with two sodium ions reveals the counter ion-dependent substrate recognition mechanism. Furthermore, comparisons of the inward-open and occluded structures support a transport mechanism combining elevator and distinct rotational motions. Our results demonstrate the molecular mechanism of vitamin C transport with its underlying conformational cycle, potentially leading to future industrial and medical applications.
Unraveling dislocation-based strengthening in refractory multi-principal element alloys
Authors: Wang Tianyi , Li Jiuyin , Wang Mian , Li Chengzhi , Su Yanqing , Xu Shuozhi , Li Xiang-Guo 
Published: July 2024

AbstractRefractory multi-principal element alloys (RMPEAs) draw great interest with their superior mechanical properties and extremely high melting points, yet the strengthening mechanism remains unclear. Here, we calculate the critical resolved shear stress (CRSS) for a single dislocation to move in RMPEAs consisting of 4 or 5 elements with or without short-range order (SRO) to represent strength by a machine learning-based interatomic potential. The increased CRSS is then attributed to high lattice distortion, elastic mismatch, and SRO strengthening, all of which originate from the solid solution strengthening theory. After detailed research of the CRSS across many RMPEAs systems with different composition ratios, we construct an XGBoost model to predict the CRSS from a few parameters and rank their importance. We find that lattice distortion strongly influences both dislocation types and reduces the screw-to-edge ratio in CRSS, while the elastic mismatch has a more significant impact on the screw dislocation than the edge one.
Identification of metabolites reproducibly associated with Parkinson’s Disease via meta-analysis and computational modelling
Authors: Luo Xi , Liu Yanjun , Balck Alexander , Klein Christine , Fleming Ronan M. T. 
Published: July 2024

AbstractMany studies have reported metabolomic analysis of different bio-specimens from Parkinson’s disease (PD) patients. However, inconsistencies in reported metabolite concentration changes make it difficult to draw conclusions as to the role of metabolism in the occurrence or development of Parkinson’s disease. We reviewed the literature on metabolomic analysis of PD patients. From 74 studies that passed quality control metrics, 928 metabolites were identified with significant changes in PD patients, but only 190 were replicated with the same changes in more than one study. Of these metabolites, 60 exclusively increased, such as 3-methoxytyrosine and glycine, 54 exclusively decreased, such as pantothenic acid and caffeine, and 76 inconsistently changed in concentration in PD versus control subjects, such as ornithine and tyrosine. A genome-scale metabolic model of PD and corresponding metabolic map linking most of the replicated metabolites enabled a better understanding of the dysfunctional pathways of PD and the prediction of additional potential metabolic markers from pathways with consistent metabolite changes to target in future studies.
A modified mycobacterial growth inhibition assay for the functional assessment of vaccine-mediated immunity
Authors: Vergara Emil Joseph , Tran Andy Cano , Paul Matthew J. , Harrison Thomas , Cooper Andrea , Reljic Rajko 
Published: July 2024

AbstractThe Mycobacterial growth inhibition assay (MGIA) is an ex-vivo assay used to measure the overall functional immune response elicited by infection or vaccination. In tuberculosis (TB) vaccine development, MGIA is a potentially important tool for preclinical evaluation of early-stage vaccine candidates to complement existing assays, and to potentially reduce the need for lengthy and costly pathogenic Mycobacterium tuberculosis (Mtb) animal challenge experiments. The conventional method of MGIA in mice entails directly infecting mixed cell cultures, most commonly splenocytes, from immunised mice with mycobacteria. However, this direct infection of mixed cell populations may yield unreliable results and lacks sufficient sensitivity to discriminate well between different vaccines due to the low number of mycobacteria-permissive cells. Here, we modified the assay by inclusion of mycobacteria-infected congenic murine macrophage cell lines as the target cells, and by measuring the total number of killed cells rather than the relative reduction between different groups. Thus, using splenocytes from Mycobacterium bovis BCG immunised mice, and J774 and MH-S (BALB/c background) or BL/6-M (C57Bl/6 background) macrophage cell lines, we demonstrated that the modified assay resulted in at least 26-fold greater mycobacterial killing per set quantity of splenocytes as compared to the conventional method. This increased sensitivity of measuring mycobacterial killing was confirmed using both the standard culture forming unit (CFU) assay and luminescence readings of luciferase-tagged virulent and avirulent mycobacteria. We propose that the modified MGIA can be used as a highly calibrated tool for quantitating the killing capacity of immune cells in preclinical evaluation of vaccine candidates for TB.
An international, open-access dataset of dental wear patterns and associated broad age classes in archaeological cattle mandibles
Authors: Hill Eden , Albarella Umberto 
Published: July 2024

AbstractZooarchaeologists investigate past interactions between animals, humans, and their environments by analyzing the remains of archaeological fauna. Age-at-death distributions are fundamental to faunal analysis and are often estimated by comparing exposed dentine patterns to standardized tooth wear stages that have been associated with relative age classes. We present Bubona, an international dataset of dental wear patterns and associated broad age classes in archaeological cattle mandibles. Our open-access dataset of 1460 data entries from nine counties is being used to create tooth-type specific reference tables of probable age class attribution for cattle mandibles lacking complete dentition. Bubona is a valuable resource for the innovation of new systems of age estimation for cattle and it is the creators hope that researchers will continue to both help expand the dataset by contributing their own data, as well as utilize the data to refine and innovate age-at-death estimation methods.
Tidings from the Tides–De novo transcriptome assembly of the endemic estuarine bivalve Villorita cyprinoides
Authors: Rahuman Summaya , N. S. Jeena , Sebastian Wilson , Varghese Eldho , P. K. Asokan 
Published: July 2024

AbstractThe Indian black clam Villorita cyprinoides Gray, 1825, is an economically valuable estuarine bivalve that faces challenges from multiple stressors and anthropogenic pressures. However, limited genomic resources have hindered molecular investigations into the impact of these stressors on clam populations. Here, we have generated the first transcriptomic reference datasets for V. cyprinoides to address this knowledge gap. A total of 25,040,592 and 22,486,217 million Illumina paired-end reads generated from two individuals were assembled using Trinity and rnaSPAdes. From the 47,607 transcripts identified as Coding Domain Sequences, 37,487 returned positive BLAST hits against six different databases. Additionally, a total of 14,063 Single Sequence Repeats were identified using GMATA. This study significantly enhances the genetic understanding of V. cyprinoides, a potential candidate for aquaculture that supports the livelihoods of many people dependent on small-scale fisheries. The data generated provides insights into broader genealogical connections within the family Cyrenidae through comparative transcriptomics. Furthermore, this transcriptional profile serves as baseline data for future studies in toxicological and conservation genetics.
A high-precision oasis dataset for China from remote sensing images
Authors: Lin Jingwu , Gui Dongwei , Liu Yunfei , Liu Qi , Zhang Siyuan , Liu Chuang 
Published: July 2024

AbstractHigh-resolution oasis maps are imperative for understanding ecological and socio-economic development of arid regions. However, due to the late establishment and relatively niche nature of the oasis discipline, there are no high-precision datasets related to oases in the world to date. To fill this gap, detailed visual interpretation of remote sensing images on Google Earth Professional or Sentinel-2 was conducted in summer 2020, and for the first time, a high-precision dataset of China’s oases (abbreviation HDCO) with a resolution of 1 meter was constructed. HDCO comprises 1,466 oases with a total area of 277,375.56 km2. The kappa coefficient for this dataset validated by the field survey was 0.8686 and the AUC value for the ROC curve was 0.935. In addition, information on the geographic coordinates, climatic conditions, major landforms, and hydrological features of each oasis was added to the attribute table of the dataset. This dataset enables researchers to quantitatively monitor location and area of oases, fosters exploration of the relationship between oases and human under climate change and urbanization.
Urea intercalated encapsulated microalgae composite hydrogels for slow-release fertilizers
Authors: Sarhan Nada , Arafa Esraa G. , Elgiddawy Nada , Elsayed Khaled N. M. , Mohamed Fatma 
Published: July 2024

AbstractIn agriculture, hydrogels can be addressed for effective operation of water and controlled-release fertilizers. Hydrogels have a significant ability for retaining water and improving nutrient availability in soil, enhancing plant growth while reducing water and fertilizer usage. This work aimed to prepare a hydrogel composite based on microalgae and biopolymers including chitosan and starch for use as a soil conditioner. The hydrogel composite was characterized by FTIR, XRD, and SEM. All hydrogel properties were studied including swelling degree, biodegradability, water-holding capacity, water retention, and re-swelling capacity in soil and water. The urea fertilizer loading and releasing behavior of the prepared hydrogels were investigated. The results revealed that the range of the maximal urea loading was between 99 and 440%, and the kinetics of loading was fitted with Freundlich model. The urea release % exhibited 78–95%, after 30 days, and the kinetics of release was fitted with zero-order, Higuchi, and Korsmeyer–Peppas models. Furthermore, the prepared hydrogels obtained a significant water-holding capacity, after blending soil (50 g) with small amount of hydrogels (1 g), the capacity increased in the range of 99.4–101.5%. In sum, the prepared hydrogels have the potential to be applied as a soil conditioner.