bluuebunny/crossref_metadata_2025_split huggingface dataset:
Autism patient-derived SHANK2BY29X mutation affects the development of ALDH1A1 negative dopamine neuron
Authors: Lai Wanjing , Zhao Yingying , Chen Yalan , Dai Zhenzhu , Chen Ruhai , Niu Yimei , Chen Xiaoxia , Chen Shuting , Huang Guanqun , Shan Ziyun , Zheng Jiajun , Hu Yu , Chen Qingpei , Gong Siyi , Kang Sai , Guo Hui , Ma Xiaokuang , Song Youqiang , Xia Kun , Wang Jie , Zhou Libing , So Kwok-Fai , Wang Kai , Qiu Shenfeng , Zhang Li , Chen Jiekai , Shi Lingling 
Published: May 2024

AbstractAutism spectrum disorder (ASD) encompasses a range of neurodevelopmental conditions. Different mutations on a single ASD gene contribute to heterogeneity of disease phenotypes, possibly due to functional diversity of generated isoforms. SHANK2, a causative gene in ASD, demonstrates this phenomenon, but there is a scarcity of tools for studying endogenous SHANK2 proteins in an isoform-specific manner. Here, we report a point mutation on SHANK2, which is found in a patient with autism, located on exon of the SHANK2B transcript variant (NM_133266.5), hereby SHANK2BY29X. This mutation results in an early stop codon and an aberrant splicing event that impacts SHANK2 transcript variants distinctly. Induced pluripotent stem cells (iPSCs) carrying this mutation, from the patient or isogenic editing, fail to differentiate into functional dopamine (DA) neurons, which can be rescued by genetic correction. Available SMART-Seq single-cell data from human midbrain reveals the abundance of SHANK2B transcript in the ALDH1A1 negative DA neurons. We then show that SHANK2BY29X mutation primarily affects SHANK2B expression and ALDH1A1 negative DA neurons in vitro during early neuronal developmental stage. Mice knocked in with the identical mutation exhibit autistic-like behavior, decreased occupancy of ALDH1A1 negative DA neurons and decreased dopamine release in ventral tegmental area (VTA). Our study provides novel insights on a SHANK2 mutation derived from autism patient and highlights SHANK2B significance in ALDH1A1 negative DA neuron.
Simulated lunar microgravity transiently arrests growth and induces osteocyte-chondrocyte lineage differentiation in human Wharton’s jelly stem cells
Authors: Subramanian Arjunan , IP Chelsea Han Lin , Qin Wei , Liu Xiawen , W.D. Carter Sean , Oguz Gokce , Ramasamy Adaikalavan , E. Illanes Sebastian , Biswas Arijit , G. Perron Gabriel , L. Fee Erin , W. L. Li Sarah , K.Y. Seah Michelle , A. Choolani Mahesh , W. Kemp Matthew 
Published: May 2024

AbstractHuman Wharton’s jelly stem cells (hWJSCs) are multipotent stem cells that are extensively employed in biotechnology applications. However, the impact of simulated lunar microgravity (sμG) on the growth, differentiation, and viability of this cell population is incompletely characterized. We aimed to determine whether acute (72 h) exposure to sμG elicited changes in growth and lineage differentiation in hWJSCs and if putative changes were maintained once exposure to terrestrial gravity (1.0 G) was restored. hWJSCs were cultured under standard 1.0 G conditions prior to being passaged and cultured under sμG (0.16 G) using a random positioning machine. Relative to control, hWJSCs cultured under sμG exhibited marked reductions in growth but not viability. Cell population expression of characteristic stemness markers (CD 73, 90, 105) was significantly reduced under sμG conditions. hWJSCs had 308 significantly upregulated and 328 significantly downregulated genes when compared to 1.0 G culture conditions. Key markers of cell replication, including MKI67, were inhibited. Significant upregulation of osteocyte–chondrocyte lineage markers, including SERPINI1, MSX2, TFPI2, BMP6, COMP, TMEM119, LUM, HGF, CHI3L1 and SPP1, and downregulation of cell fate regulators, including DNMT1 and EZH2, were detected in sμG-exposed hWJSCs. When returned to 1.0 G for 3 days, sμG-exposed hWJSCs had accelerated growth, and expression of stemness markers increased, approaching normal (i.e. 95%) levels. Our data support earlier findings that acute sμG significantly reduces the cell division potential of hWJSCs and suggest that acute sμG-exposure induces reversible changes in cell growth accompanied by osteocyte–chondrocyte changes in lineage differentiation.
PacBio Hi-Fi genome assembly of Sipha maydis, a model for the study of multipartite mutualism in insects
Authors: Renoz François , Parisot Nicolas , Baa-Puyoulet Patrice , Gerlin Léo , Fakhour Samir , Charles Hubert , Hance Thierry , Calevro Federica 
Published: May 2024

AbstractDependence on multiple nutritional endosymbionts has evolved repeatedly in insects feeding on unbalanced diets. However, reference genomes for species hosting multi-symbiotic nutritional systems are lacking, even though they are essential for deciphering the processes governing cooperative life between insects and anatomically integrated symbionts. The cereal aphid Sipha maydis is a promising model for addressing these issues, as it has evolved a nutritional dependence on two bacterial endosymbionts that complement each other. In this study, we used PacBio High fidelity (HiFi) long-read sequencing to generate a highly contiguous genome assembly of S. maydis with a length of 410 Mb, 3,570 contigs with a contig N50 length of 187 kb, and BUSCO completeness of 95.5%. We identified 117 Mb of repetitive sequences, accounting for 29% of the genome assembly, and predicted 24,453 protein-coding genes, of which 2,541 were predicted enzymes included in an integrated metabolic network with the two aphid-associated endosymbionts. These resources provide valuable genetic and metabolic information for understanding the evolution and functioning of multi-symbiotic systems in insects.
The phased Solanum okadae genome and Petota pangenome analysis of 23 other potato wild relatives and hybrids
Authors: Achakkagari S. R. , Bozan I. , Camargo-Tavares J. C. , McCoy H. J. , Portal L. , Soto J. , Bizimungu B. , Anglin N. L. , Manrique-Carpintero N. , Lindqvist-Kreuze H. , Tai H. H. , Strömvik M. V. 
Published: May 2024

AbstractPotato is an important crop in the genus Solanum section Petota. Potatoes are susceptible to multiple abiotic and biotic stresses and have undergone constant improvement through breeding programs worldwide. Introgression of wild relatives from section Petota with potato is used as a strategy to enhance the diversity of potato germplasm. The current dataset contributes a phased genome assembly for diploid S. okadae, and short read sequences and de novo assemblies for the genomes of 16 additional wild diploid species in section Petota that were noted for stress resistance and were of interest to potato breeders. Genome sequence data for three additional genomes representing polyploid hybrids with cultivated potato, and an additional genome from non-tuberizing S. etuberosum, which is outside of section Petota, were also included. High quality short reads assemblies were achieved with genome sizes ranging from 575 to 795 Mbp and annotations were performed utilizing transcriptome sequence data. Genomes were compared for presence/absence of genes and phylogenetic analyses were carried out using plastome and nuclear sequences.
A Dataset for Evaluating Contextualized Representation of Biomedical Concepts in Language Models
Authors: Rouhizadeh Hossein , Nikishina Irina , Yazdani Anthony , Bornet Alban , Zhang Boya , Ehrsam Julien , Gaudet-Blavignac Christophe , Naderi Nona , Teodoro Douglas 
Published: May 2024

AbstractDue to the complexity of the biomedical domain, the ability to capture semantically meaningful representations of terms in context is a long-standing challenge. Despite important progress in the past years, no evaluation benchmark has been developed to evaluate how well language models represent biomedical concepts according to their corresponding context. Inspired by the Word-in-Context (WiC) benchmark, in which word sense disambiguation is reformulated as a binary classification task, we propose a novel dataset, BioWiC, to evaluate the ability of language models to encode biomedical terms in context. BioWiC comprises 20’156 instances, covering over 7’400 unique biomedical terms, making it the largest WiC dataset in the biomedical domain. We evaluate BioWiC both intrinsically and extrinsically and show that it could be used as a reliable benchmark for evaluating context-dependent embeddings in biomedical corpora. In addition, we conduct several experiments using a variety of discriminative and generative large language models to establish robust baselines that can serve as a foundation for future research.
Centrality dependency of proton, deuteron, and triton’s temperatures in Au+Au collisions at 200 GeV
Authors: Khan Imran , Qudus Abdul , Salouci Moustafa , Ismail Abd Haj 
Published: May 2024

AbstractThe transverse momentum (pT) spectra of protons (p), deuterons (d), and tritons (t) in 200 GeV gold–gold (Au + Au) collisions at RHIC are examined across a range of centrality bins using the Levy Tsallis (TS) statistical model. The model's predictions closely match the experimental results from PHENIX (p) and STAR (d and t) Collaborations. Kinetic freeze-out temperatures of hadrons are obtained from particle spectra. The results showed that the kinetic freeze-out temperature decreases as collisions move from center to the periphery. This work found mass-dependent kinetic freeze-out temperatures, heavier particles arrive to the freeze-out phase before lighter ones. Comparison with same data fitted by blast wave function with Tsallis statistics (BWTS) showed that T0 values are increasing from central to peripheral collisions, while in case of TS function (current analysis) it decreases. This behavior puts a question mark on the reliability of using such functions for temperature extraction.
Biosynthesized BiFe2O4@Ag nanoparticles mediated Scenedesmus obliquus induce apoptosis in AGS gastric cancer cell line
Authors: Shamsi Hossein , Yari Reza , Salehzadeh Ali 
Published: May 2024

AbstractThe use of magnetic metal nanoparticles has been considered in cancer treatment studies. In this study, BiFe2O4@Ag nanoparticles were synthesized biologically by Scenedesmus obliquus for the first time and their anticancer mechanism in a gastric cancer cell line was characterized. The physicochemical properties of the nanoparticles were evaluated by fourier transform infrared spectroscopy (FT-IR), X-ray diffraction (XRD), energy-dispersive X-ray spectroscopy (EDS), scanning electron microscopy (SEM), transmission electron microscopy (TEM), dynamic Light Scattering (DLS), and zeta potential analyses. Cell viability and nuclear damage were investigated by the MTT and Hoechst staining assays, respectively. Flow cytometry analysis was performed to determine the frequency of the necrotic and apoptotic cells as well as cell cycle analysis of the nanoparticles-treated cells. Physicochemical characterization showed that the synthesized particles were spherical, without impurities, in a size range of 38–83 nm, with DLS size and zeta potential of 295.7 nm and -27.7 mV, respectively. BiFe2O4@Ag nanoparticles were considerably more toxic for the gastric cancer cells (AGS cell line) than HEK293 normal cells with IC50 of 67 and 117 µg/ml, respectively. Treatment of AGS cells with the nanoparticles led to a remarkable increase in the percentage of late apoptosis (38.5 folds) and cell necrosis (13.4 folds) and caused cell cycle arrest, mainly at the S phase. Also, nuclear fragmentation and apoptotic bodies were observed in the gastric cancer cells treated with the nanoparticles. This study represents BiFe2O4@Ag as a novel anticancer candidate against gastric cancer that can induce cell apoptosis through DNA damage and inhibition of cell cycle progression.
Effective food waste management model for the sustainable agricultural food supply chain
Authors: Handayati Yuanita , Widyanata Chryshella 
Published: May 2024

AbstractThe extensive research examines the current state of agricultural food supply chains, with focus on waste management in Bandung Regency, Indonesia. The study reveals that a significant proportion of food within the agricultural supply chain goes to waste and discusses the various challenges and complexities involved in managing food waste. The research presents a conceptual model based on the ADKAR change management paradigm to promote waste utilization, increase awareness and change people's behaviors. The model emphasizes the importance of creating awareness, fostering desire, providing knowledge, implementing changes, and reinforcing and monitoring the transformation process. It also addresses the challenges, barriers, and drivers that influence waste utilization in the agricultural supply chain, highlighting the need for economic incentives and a shift in public awareness to drive meaningful change. Ultimately, this study serves as a comprehensive exploration of food waste management in Bandung Regency, shedding light on the complexities of the issue and offering a systematic approach to transition towards more sustainable waste utilization practices.
Estimating neutrosophic finite median employing robust measures of the auxiliary variable
Authors: Masood Saadia , Ibrar Bareera , Shabbir Javid , Shokri Ali , Movaheedi Zabihullah 
Published: May 2024

AbstractOur study explores neutrosophic statistics, an extension of classical and fuzzy statistics, to address the challenges of data uncertainty. By leveraging accurate measurements of an auxiliary variable, we can derive precise estimates for the unknown population median. The estimators introduced in this research are particularly useful for analysing unclear, vague data or within the neutrosophic realm. Unlike traditional methods that yield single-valued outcomes, our estimators produce ranges, suggesting where the population parameter is likely to be. We present the suggested generalised estimator's bias and mean square error within a first-order approximation framework. The practicality and efficiency of these proposed neutrosophic estimators are demonstrated through real-world data applications and the simulated data set.
Evaluation of the relationship between body composition and dietary habits of physically active people with disabilities
Authors: Pelc Agnieszka , Walicka-Cupryś Katarzyna , Puszkarz Gabriela , Styś Kamila , Chmiel Elżbieta , Wilk Sebastian , Ludwikowski Grzegorz , Placek Katarzyna 
Published: May 2024

AbstractPhysical activity offers numerous physical and mental health benefits for individuals with disabilities, while nutrition plays a crucial role in maintaining bodily homeostasis. This study aimed to assess the relationship between body composition and dietary habits among physically active people with disabilities. Fifty-five participants aged 16 to 61, including 28 with disabilities and 27 without, were included in the study. The FFQ-6 questionnaire, Tanita body composition analyzer, and Stadiometer were utilized. No significant differences in BMI were observed between the two groups. However, individuals with disabilities showed higher body fat, metabolic age, or pulse values, whereas the control group exhibited higher muscle mass, muscle quality, body type, or bone mass. Participants with disabilities were more likely to consume vegetables (p = 0.004) and animal fats (p = 0.027), while those without disabilities were more inclined to consume fast food, instant products (p = 0.006), sweetened beverages (p < 0.001), and alcohol (p < 0.001). People with disabilities often have a higher percentage of body fat, cautioning against the consumption of processed fruits, dried fruits, fast food, and red meat. Conversely, in non-disabled individuals, frequent consumption of eggs, animal fats, sugar, and sweets is not recommended due to the potential for increased body fat, visceral fat, and higher BMI.
Development of a simple polymer-based sensor for detection of the Pirimicarb pesticide
Authors: Saadatidizaji Zahra , Sohrabi Negin , Mohammadi Reza 
Published: May 2024

AbstractIn this study, a sensitive and selective fluorescent chemosensor was developed for the determination of pirimicarb pesticide by adopting the surface molecular imprinting approach. The magnetic molecularly imprinted polymer (MIP) nanocomposite was prepared using pirimicarb as the template molecule, CuFe2O4 nanoparticles, and graphene quantum dots as a fluorophore (MIP-CuFe2O4/GQDs). It was then characterized using X-ray diffraction (XRD) technique, Fourier transforms infrared (FT-IR) spectroscopy, scanning electron microscope (SEM), and transmission electron microscopy (TEM). The response surface methodology (RSM) was also employed to optimize and estimate the effective parameters of pirimicarb adsorption by this polymer. According to the experimental results, the average particle size and imprinting factor (IF) of this polymer are 53.61 nm and 2.48, respectively. Moreover, this polymer has an excellent ability to adsorb pirimicarb with a removal percentage of 99.92 at pH = 7.54, initial pirimicarb concentration = 10.17 mg/L, polymer dosage = 840 mg/L, and contact time = 6.15 min. The detection of pirimicarb was performed by fluorescence spectroscopy at a concentration range of 0–50 mg/L, and a sensitivity of 15.808 a.u/mg and a limit of detection of 1.79 mg/L were obtained. Real samples with RSD less than 2 were measured using this chemosensor. Besides, the proposed chemosensor demonstrated remarkable selectivity by checking some other insecticides with similar and different molecular structures to pirimicarb, such as diazinon, deltamethrin, and chlorpyrifos.
Molecular and SEM studies on Thaparocleidus vistulensis (Siwak, 1932) (Monopisthocotyla, Ancylodiscoididae)
Authors: Wan Sajiri Wan Muhammad Hazim , Székely Csaba , Molnár Kálmán , Kjeldgaard-Nintemann Sebastian , Kania Per Walter , Buchmann Kurt , Sellyei Boglárka 
Published: May 2024

AbstractPresenting new molecular and scanning electron microscope (SEM) features, this study gives additional data to the better knowledge of Thaparocleidus vistulensis (Siwak, 1932) (Monopisthocotyla, Ancylodiscoididae), a parasite of the European catfish Silurus glanis Linnaeus, 1758 (Siluriformes, Siluridae) cultured in a commercial fish farm in Hungary. In addition, notes on the early development of sclerotized anchors are also provided. The main morphological difference of T. vistulensis compared to other congeneric species is associated with the male copulatory organ, which exhibits 5–7 loops in the middle of the penis length and a long open V-shaped sclerotized accessory piece, dividing terminally into two parts, securing the terminal part of the penis tube. The present study provides for the first time molecular characterization data based on the 2694 bp long nucleotide sequence of rDNA (ITS1, 5.8S, ITS2, and flanked with partial 18S and partial 28S) submitted in GenBank with the accession number OR916383. A phylogenetic tree based on ITS1 sequences supports a well-defined clade including T. vistulensis, forming a sister group with T. siluri, a species-specific monopisthocotylan parasite to S. glanis. The morphological characterization of T. vistulensis, especially for the male copulatory organ, together with the molecular data in the present study, extends knowledge about this monopisthocotylan species and provides new information for future phylogeny studies.
Deciphering mycobiota and its functional dynamics in root hairs of Rhododendron campanulatum D. Don through Next-gen sequencing
Authors: Khan Nafeesa Farooq , Ahmed Sheikh Sajad , Abdulraheem Mukhtar Iderawumi , Reshi Zafar Ahmad , Wahab Abdul , Abdi Gholamreza 
Published: May 2024

AbstractThe Himalayas provide unique opportunities for the extension of shrubs beyond the upper limit of the tree. However, little is known about the limitation of the biotic factors belowground of shrub growth at these cruising altitudes. To fill this gap, the present study deals with the documentation of root-associated microbiota with their predicted functional profiles and interactions in the host Rhododendron campanulatum, a krummholz species. While processing 12 root samples of R. campanulatum from the sites using Omics we could identify 134 root-associated fungal species belonging to 104 genera, 74 families, 39 orders, 17 classes, and 5 phyla. The root-associated microbiota members of Ascomycota were unambiguously dominant followed by Basidiomycota. Using FUNGuild, we reported that symbiotroph and pathotroph as abundant trophic modes. Furthermore, FUNGuild revealed the dominant prevalence of the saptroptroph guild followed by plant pathogens and wood saprotrophs. Alpha diversity was significantly different at the sites. The heatmap dendrogram showed the correlation between various soil nutrients and some fungal species. The study paves the way for a more in-depth exploration of unidentified root fungal symbionts, their interactions and their probable functional roles, which may serve as an important factor for the growth and conservation of these high-altitude ericaceous plants.
Characterization of PANoptosis-related genes and the immune landscape in moyamoya disease
Authors: Zhou Zhenyu , Wang Yanru , Zhang Junze , Liu Ziqi , Hao Xiaokuan , Wang Xilong , He Shihao , Wang Rong 
Published: May 2024

AbstractMoyamoya disease (MMD) is a cerebrovascular narrowing and occlusive condition characterized by progressive stenosis of the terminal portion of the internal carotid artery and the formation of an abnormal network of dilated, fragile perforators at the base of the brain. However, the role of PANoptosis, an apoptotic mechanism associated with vascular disease, has not been elucidated in MMD. In our study, a total of 40 patients’ genetic data were included, and a total of 815 MMD-related differential genes were screened, including 215 upregulated genes and 600 downregulated genes. Among them, DNAJA3, ESR1, H19, KRT18 and STK3 were five key genes. These five key genes were associated with a variety of immune cells and immune factors. Moreover, GSEA (gene set enrichment analysis) and GSVA (gene set variation analysis) showed that the different expression levels of the five key genes affected multiple signaling pathways associated with MMD. In addition, they were associated with the expression of MMD-related genes. Then, based on the five key genes, a transcription factor regulatory network was constructed. In addition, targeted therapeutic drugs against MMD-related genes were obtained by the Cmap drug prediction method: MST-312, bisacodyl, indirubin, and tropanyl-3,5-dimethylbenzoate. These results suggest that the PANoptosis-related genes may contribute to the pathogenesis of MMD through multiple mechanisms.