bluuebunny/crossref_metadata_2025_split huggingface dataset:
A multimodal generative AI copilot for human pathology
Authors: Lu Ming Y. , Chen Bowen , Williamson Drew F. K. , Chen Richard J. , Zhao Melissa , Chow Aaron K. , Ikemura Kenji , Kim Ahrong , Pouli Dimitra , Patel Ankush , Soliman Amr , Chen Chengkuan , Ding Tong , Wang Judy J. , Gerber Georg , Liang Ivy , Le Long Phi , Parwani Anil V. , Weishaupt Luca L. , Mahmood Faisal 
Published: June 2024

AbstractComputational pathology1,2 has witnessed considerable progress in the development of both task-specific predictive models and task-agnostic self-supervised vision encoders3,4. However, despite the explosive growth of generative artificial intelligence (AI), there have been few studies on building general-purpose multimodal AI assistants and copilots5 tailored to pathology. Here we present PathChat, a vision-language generalist AI assistant for human pathology. We built PathChat by adapting a foundational vision encoder for pathology, combining it with a pretrained large language model and fine-tuning the whole system on over 456,000 diverse visual-language instructions consisting of 999,202 question and answer turns. We compare PathChat with several multimodal vision-language AI assistants and GPT-4V, which powers the commercially available multimodal general-purpose AI assistant ChatGPT-4 (ref. 6). PathChat achieved state-of-the-art performance on multiple-choice diagnostic questions from cases with diverse tissue origins and disease models. Furthermore, using open-ended questions and human expert evaluation, we found that overall PathChat produced more accurate and pathologist-preferable responses to diverse queries related to pathology. As an interactive vision-language AI copilot that can flexibly handle both visual and natural language inputs, PathChat may potentially find impactful applications in pathology education, research and human-in-the-loop clinical decision-making.
Chromosome-scale genome assembly of medicinal plant Tinospora sagittata (Oliv.) Gagnep. from the Menispermaceae family
Authors: Alami Mohammad Murtaza , Shu Shaohua , Liu Sanbo , Ouyang Zhen , Zhang Yipeng , Lv Meijia , Sang Yonghui , Gong Dalin , Yang Guozheng , Feng Shengqiu , Mei Zhinan , Xie De-Yu , Wang Xuekui 
Published: June 2024

AbstractTinospora sagittata (Oliv.) Gagnep. is an important medicinal tetraploid plant in the Menispermaceae family. Its tuber, Radix Tinosporae, used in traditional Chinese medicine, is rich in diterpenoids and benzylisoquinoline alkaloids (BIAs). To enhance our understanding of medicinal compounds’ biosynthesis and Menispermaceae’s evolution, we herein report assembling a high-quality chromosome-scale genome with both PacBio HiFi and Illumina sequencing technologies. PacBio Sequel II generated 2.5 million circular consensus sequencing (CCS) reads, and a hybrid assembly strategy with Illumina sequencing resulted in 4483 contigs. The assembled genome size was 2.33 Gb, consisting of 4070 scaffolds (N50 = 42.06 Mb), of which 92.05% were assigned to 26 pseudochromosomes. T. sagittata’s chromosomal-scale genome assembly, the first species in Menispermaceae, aids Menispermaceae evolution and T. sagittata’s secondary metabolites biosynthesis understanding.
Single-nucleus chromatin landscape dataset of mouse brain development and aging
Authors: Ma Yuting , Guo Sicheng , Chen Yixi , Peng Yushan , Su Xi , Jiang Hui , Lin Xiumei , Zhang Jianguo 
Published: June 2024

AbstractThe development and aging of the brain constitute a lifelong dynamic process, marked by structural and functional changes that entail highly coordinated cellular differentiation and epigenetic regulatory mechanisms. Chromatin accessibility serves as the foundational basis for genetic activity. However, the holistic and dynamic chromatin landscape that spans various brain regions throughout development and ageing remains predominantly unexplored. In this study, we employed single-nucleus ATAC-seq to generate comprehensive chromatin accessibility maps, incorporating data from 69,178 cells obtained from four distinct brain regions – namely, the olfactory bulb (OB), cerebellum (CB), prefrontal cortex (PFC), and hippocampus (HP) – across key developmental time points at 7 P, 3 M, 12 M, and 18 M. We delineated the distribution of cell types across different age stages and brain regions, providing insight into chromatin accessible regions and key transcription factors specific to different cell types. Our data contribute to understanding the epigenetic basis of the formation of different brain regions, providing a dynamic landscape and comprehensive resource for revealing gene regulatory programs during brain development and aging.
A dataset on survey designs and quality of social and behavioral science surveys during the COVID-19 pandemic
Authors: Gummer Tobias , Skora Thomas , von Glasenapp Karolina , Naumann Elias 
Published: June 2024

AbstractIn the social and behavioral sciences, surveys are frequently used to collect data. During the COVID-19 pandemic, surveys provided political actors and public health professionals with timely insights on the attitudes and behaviors of the general population. These insights were key in guiding actions to fight the pandemic. However, the data quality of these surveys remains unclear because systematic knowledge about how the survey data were collected during the COVID-19 pandemic is lacking. This is unfortunate, since decades of survey research have shown that survey design impacts data. Our Survey Data Collection and the COVID-19 Pandemic (SDCCP) project deals with this research gap. We collected rich metadata on survey design for 717 social and behavioral science surveys carried out in Germany during the first two years of the COVID-19 pandemic. In this data descriptor, we present a unique resource for a systematic assessment of the survey data collection practices and quality of surveys conducted in Germany during the COVID-19 pandemic.
Differential gene expression in irradiated potato tubers contributed to sprout inhibition and quality retention during a commercial scale storage
Authors: Kumar Sanjeev , Bandyopadhyay Nilantana , Saxena Sudhanshu , Hajare Sachin N. , More Varsha , Tripathi Jyoti , Dahia Yogesh , Gautam Satyendra 
Published: June 2024

AbstractCurrent study is the first ever storage cum market trial of radiation processed (28 tons) of potato conducted in India at a commercial scale. The objective was to affirm the efficacy of very low dose of gamma radiation processing of potato for extended storage with retained quality and to understand the plausible mechanism at the gene modulation level for suppression of potato sprouting. Genes pertaining to abscisic acid (ABA) biosynthesis were upregulated whereas its catabolism was downregulated in irradiated potatoes. Additionally, genes related to auxin buildup were downregulated in irradiated potatoes. The change in the endogenous phytohormone contents in irradiated potato with respect to the control were found to be correlated well with the differential expression level of certain related genes. Irradiated potatoes showed retention of processing attributes including cooking and chip-making qualities, which could be attributed to the elevated expression of invertase inhibitor in these tubers. Further, quality retention in radiation treated potatoes may also be related to inhibition in the physiological changes due to sprout inhibition. Ecological and economical analysis of national and global data showed that successful adoption of radiation processing may gradually replace sprout suppressants like isopropyl N-(3-chlorophenyl) carbamate (CIPC), known to leave residue in the commodity, stabilize the wholesale annual market price, and provide a boost to the industries involved in product manufacturing.
OsTH1 is a key player in thiamin biosynthesis in rice
Authors: Faustino Maria , Lourenço Tiago , Strobbe Simon , Cao Da , Fonseca André , Rocha Isabel , Van Der Straeten Dominique , Oliveira M. Margarida 
Published: June 2024

AbstractThiamin is a vital nutrient that acts as a cofactor for several enzymes primarily localized in the mitochondria. These thiamin-dependent enzymes are involved in energy metabolism, nucleic acid biosynthesis, and antioxidant machinery. The enzyme HMP-P kinase/thiamin monophosphate synthase (TH1) holds a key position in thiamin biosynthesis, being responsible for the phosphorylation of HMP-P into HMP-PP and for the condensation of HMP-PP and HET-P to form TMP. Through mathematical kinetic model, we have identified TH1 as a critical player for thiamin biofortification in rice. We further focused on the functional characterization of OsTH1. Sequence and gene expression analysis, along with phylogenetic studies, provided insights into OsTH1 bifunctional features and evolution. The indispensable role of OsTH1 in thiamin biosynthesis was validated by heterologous expression of OsTH1 and successful complementation of yeast knock-out mutants impaired in thiamin production. We also proved that the sole OsTH1 overexpression in rice callus significantly improves B1 concentration, resulting in 50% increase in thiamin accumulation. Our study underscores the critical role of OsTH1 in thiamin biosynthesis, shedding light on its bifunctional nature and evolutionary significance. The significant enhancement of thiamin accumulation in rice callus upon OsTH1 overexpression constitutes evidence of its potential application in biofortification strategies.
Scintillation of polyester fabric and clothing via proton irradiation and its utilization in surface imaging of proton pencil beams
Authors: Yamamoto Seiichi , Yamashita Tomohiro , Yoshino Masao , Kamada Kei , Yoshikawa Akira , Nishio Teiji , Kataoka Jun 
Published: June 2024

AbstractIn the realm of radiation therapy, a conspicuous obstacle lies in the dearth of external observation concerning radiation beams aimed at the patient. While real-time monitoring of such beams on the patient's surface during therapy holds promise, the imaging of particle beams has thus far proven to be a formidable task. Here, we show our discovery of polyester fabrics and cloths as auspicious scintillating materials, ideally suited for the visualization of radiation beams upon the patient's surface. The light output of polyester fabrics ranged from 10 to 20% of that observed in plastic scintillators. When exposed to spot scanning proton beams, clear beam spots emerged on the surface of the polyester cloths. The movement of these scanning beams was effectively captured using a CMOS camera in a light-shield-free with lights-off environment. The resulting images provided a means for evaluating spills of the proton beams. The inherent flexibility of polyester fabrics and clothing enhances their appeal for applications in the intricate landscape of radiation therapy, promising a bright future for surface beam imaging endeavors.
Anti-depressant effect of Naringenin-loaded hybridized nanoparticles in diabetic rats via PPARγ/NLRP3 pathway
Authors: El-Marasy Salma A. , AbouSamra Mona M. , Moustafa Passant E. , Mabrok Hoda B. , Ahmed-Farid Omar A. , Galal Asmaa F. , Farouk Hadir 
Published: June 2024

AbstractNaringenin (NAR) has various biological activities but low bioavailability. The current study examines the effect of Naringenin-loaded hybridized nanoparticles (NAR-HNPs) and NAR on depression induced by streptozotocin (STZ) in rats. NAR-HNPs formula with the highest in vitro NAR released profile, lowest polydispersity index value (0.21 ± 0.02), highest entrapment efficiency (98.7 ± 2.01%), as well as an acceptable particle size and zeta potential of 415.2 ± 9.54 nm and 52.8 ± 1.04 mV, respectively, was considered the optimum formulation. It was characterized by differential scanning calorimetry, examined using a transmission electron microscope, and a stability study was conducted at different temperatures to monitor its stability efficiency showing that NAR-HNP formulation maintains stability at 4 °C. The selected formulation was subjected to an acute toxicological test, a pharmacokinetic analysis, and a Diabetes mellitus (DM) experimental model. STZ (50 mg/kg) given as a single i.p. rendered rats diabetic. Diabetic rat groups were allocated into 4 groups: one group received no treatment, while the remaining three received oral doses of unloaded HNPs, NAR (50 mg/kg), NAR-HNPs (50 mg/kg) and NAR (50 mg/kg) + peroxisome proliferator-activated receptor-γ (PPAR-γ) antagonist, GW9662 (1mg/kg, i.p.) for three weeks. Additional four non-diabetic rat groups received: distilled water (normal), free NAR, and NAR-HNPs, respectively for three weeks. NAR and NAR-HNPs reduced immobility time in forced swimming test and serum blood glucose while increasing serum insulin level. They also reduced cortical and hippocampal 5-hydroxyindoeacetic acid, 3,4-Dihydroxy-phenylacetic acid, malondialdehyde, NLR family pyrin domain containing-3 (NLRP3) and interleukin-1beta content while raised serotonin, nor-epinephrine, dopamine and glutathione level. PPAR-γ gene expression was elevated too. So, NAR and NAR-HNPs reduced DM-induced depression by influencing brain neurotransmitters and exhibiting anti-oxidant and anti-inflammatory effects through the activation PPAR-γ/ NLRP3 pathway. NAR-HNPs showed the best pharmacokinetic and therapeutic results.
TPRO-NET: an EEG-based emotion recognition method reflecting subtle changes in emotion
Authors: Zhang Xinyi , Cheng Xiankai , Liu Hui 
Published: June 2024

AbstractEmotion recognition based on Electroencephalogram (EEG) has been applied in various fields, including human–computer interaction and healthcare. However, for the popular Valence-Arousal-Dominance emotion model, researchers often classify the dimensions into high and low categories, which cannot reflect subtle changes in emotion. Furthermore, there are issues with the design of EEG features and the efficiency of transformer. To address these issues, we have designed TPRO-NET, a neural network that takes differential entropy and enhanced differential entropy features as input and outputs emotion categories through convolutional layers and improved transformer encoders. For our experiments, we categorized the emotions in the DEAP dataset into 8 classes and those in the DREAMER dataset into 5 classes. On the DEAP and the DREAMER datasets, TPRO-NET achieved average accuracy rates of 97.63%/97.47%/97.88% and 98.18%/98.37%/98.40%, respectively, on the Valence/Arousal/Dominance dimension for the subject-dependent experiments. Compared to other advanced methods, TPRO-NET demonstrates superior performance.
A systematic review and bayesian meta-analysis of medical devices used in chronic pain management
Authors: Shetty Ashish , Delanerolle Gayathri , Deng Chunli , Thillainathan Anish , Cavalini Heitor , Yang Xiaojie , Bouchareb Yassine , Boyd Amy , Phiri Peter , Shi Jian Qing , Deer Timothy 
Published: June 2024

AbstractWhilst. pharmacological therapies remain the cornerstone of pain management in chronic pain, factors including the current opioid epidemic have led to non-pharmacological techniques becoming a more attractive proposition. We explored the prevalence of medical device use and their treatment efficacy in non-cancer pain management. A systematic methodology was developed, peer reviewed and published in PROSPERO (CRD42021235384). Key words of medical device, pain management devices, chronic pain, lower back pain, back pain, leg pain and chronic pelvic pain using Science direct, PubMed, Web of Science, PROSPERO, MEDLINE, EMBASE, PorQuest and ClinicalTrials.gov. All clinical trials, epidemiology and mixed methods studies that reported the use of medical devices for non-cancer chronic pain management published between the 1st of January 1990 and the 30th of April 2022 were included. 13 studies were included in systematic review, of these 6 were used in the meta-analysis. Our meta-analysis for pain reduction showed that transcutaneous electrical nerve stimulation combined with instrument-assisted soft tissue mobilization treatment and pulsed electromagnetic therapy produced significant treatment on chronic lower back pain patients. Pooled evidence revealed the use of medical device related interventions resulted in 0.7 degree of pain reduction under a 0–10 scale. Significant improvement in disability scores, with a 7.44 degree reduction in disability level compared to a placebo using a 50 score range was also seen. Our analysis has shown that the optimal use of medical devices in a sustainable manner requires further research, needing larger cohort studies, greater gender parity, in a more diverse range of geographical locations.
Single-cell transcriptome analysis reveals secretin as a hallmark of human enteroendocrine cell maturation
Authors: Hysenaj Franc , Lauber Michael , Bast-Habersbrunner Andrea , List Markus , Klingenspor Martin 
Published: June 2024

AbstractThe traditional nomenclature of enteroendocrine cells (EECs), established in 1977, applied the “one cell - one hormone” dogma, which distinguishes subpopulations based on the secretion of a specific hormone. These hormone-specific subpopulations included S cells for secretin (SCT), K cells for glucose-dependent insulinotropic polypeptide (GIP), N cells producing neurotensin (NTS), I cells producing cholecystokinin (CCK), D cells producing somatostatin (SST), and others. In the past 15 years, reinvestigations into murine and human organoid-derived EECs, however, strongly questioned this dogma and established that certain EECs coexpress multiple hormones. Using the Gut Cell Atlas, the largest available single-cell transcriptome dataset of human intestinal cells, this study consolidates that the original dogma is outdated not only for murine and human organoid-derived EECs, but also for primary human EECs, showing that the expression of certain hormones is not restricted to their designated cell type. Moreover, specific analyses into SCT-expressing cells reject the presence of any cell population that exhibits significantly elevated secretin expression compared to other cell populations, previously referred to as S cells. Instead, this investigation indicates that secretin production is realized jointly by other enteroendocrine subpopulations, validating corresponding observations in murine EECs also for human EECs. Furthermore, our findings corroborate that SCT expression peaks in mature EECs, in contrast, progenitor EECs exhibit markedly lower expression levels, supporting the hypothesis that SCT expression is a hallmark of EEC maturation.
Enhancing the yield of Xenocoumacin 1 in Xenorhabdus nematophila YL001 by optimizing the fermentation process
Authors: Han Yunfei , Zhang Shujing , Wang Yang , Gao Jiangtao , Han Jinhua , Yan Zhiqiang , Ta Yongquan , Wang Yonghong 
Published: June 2024

AbstractXenocoumacin 1 (Xcn 1), antibiotic discovered from secondary metabolites of Xenorhabdus nematophila, had the potential to develop into a new pesticide due to its excellent activity against bacteria, oomycetes and fungi. However, the current low yield of Xcn1 limits its development and utilization. To improve the yield of Xcn1, response surface methodology was used to determine the optimal composition of fermentation medium and one factor at a time approach was utilized to optimize the fermentation process. The optimal medium composed of in g/L: proteose peptone 20.8; maltose 12.74; K2HPO4 3.77. The optimal fermentation conditions were that 25 °C, initial pH 7.0, inoculum size 10%, culture medium 75 mL in a 250 mL shake flask with an agitation rate of 150 rpm for 48 h. Xenorhabdus nematophila YL001 was produced the highest Xcn1 yield (173.99 mg/L) when arginine was added to the broth with 3 mmol/L at the 12th h. Compared with Tryptic Soy Broth medium, the optimized fermentation process resulted in a 243.38% increase in Xcn1 production. The obtained results confirmed that optimizing fermentation technology led to an increase in Xcn1 yield. This work would be helpful for efficient Xcn1 production and lay a foundation for its industrial production.
Design of intelligent controller for obstacle avoidance and navigation of electric patrol mobile robot based on PLC
Authors: Liu Zhenfang , Li Mengyuan , Fu Dongshuai , Zhang Shuai 
Published: June 2024

AbstractCurrently, the obstacle avoidance control of patrol robots based on intelligent vision lacks professional controller module assistance. Therefore, this paper proposes a design method of intelligent controller for obstacle avoidance and navigation of electrical inspection mobile robot based on PLC control. The controller designs a laser range finder to determine the required position of electrical patrol inspection. Use PLC as the core controller, and combine sensors, actuators, communication module and PLC selection module in the process of hardware design to achieve autonomous navigation and obstacle avoidance functions of the robot. Then design the software including the PLC compiler system and the virtual machine module. Based on the above steps, design the control module of obstacle avoidance navigation, which realizes the key link of robot autonomous navigation. The test results show that the controller can successfully avoid obstacles, improve the efficiency and quality of inspection, and achieve accurate and fast obstacle avoidance navigation for the electrical inspection mobile robot.
An enhanced nonparametric quality control chart with application related to industrial process
Authors: Abid Muhammad , Sun Mei , Shabbir Aroosa , Bakr M. E. , Abbas Tahir 
Published: June 2024

AbstractIn various practical situations, the information about the process distribution is sometimes partially or completely unavailable. In these instances, practitioners prefer to use nonparametric charts as they don’t restrict the assumption of normality or specific distribution. In this current article, a nonparametric double homogeneously weighted moving average control chart based on the Wilcoxon signed-rank statistic is developed for monitoring the location parameter of the process. The run-length profiles of the newly developed chart are obtained by using Monte Carlo simulations. Comparisons are made based on various performance metrics of run-length distribution among proposed and existing nonparametric counterparts charts. The extra quadratic loss is used to evaluate the overall performance of the proposed and existing charts. The newly developed scheme showed comparatively better results than its existing counterparts. For practical implementation of the suggested scheme, the real-world dataset related to the inside diameter of the automobile piston rings is also used.