bluuebunny/crossref_metadata_2025_split huggingface dataset:
Response of Various Concentrations Of Indole Acetic Acid (IAA) to Morphological Attributes in Different Plum (Prunus domesticaL.) Curltivars
Authors: Ullah Kaleem , Jan Samin , Zamir Roshan , Majeed Abdul , Ahmad Bakhtiyar , Rehman Gouhar 
Published: September 2024

AbstractsThis study was conducted to evaluate the effects of indole-3-acetic acid (IAA) on budwood treated with different concentrations of indole acetic acid i.e. ((300, 600, 900 and 1200 ppm) of three plum varieties (Fazle Manani, Santa Rosa and Red Beauty) in respect of various morphological parameters e.g. days to sprouting, plant height, number of branches, percent sprouting, number of leaves, budling diameter and internode length. Results revealed that different varieties of plum had different responses to the applied concentrations in different plum cultivars. Cultivar Fazle manani showed significant decline in days to sprouting (at 300 ppm dose), plant height (at 600 dose), percent sprouting and budling diameter (at all concentrations) while increase in number of branches (1200 dose), number of leaves (all concentrations except 600 ppm), and internode length (at 300 ppm and 900 ppm concentrations). Days to sprouting in cultivar Santa rosa were non-significantly affected while plant height and internode length were significantly reduced at all concentrations particularly at 300 ppm. Number of branches, number of leaves and percent sprouting increased significantly at 300 ppm and 900 ppm concentrations. Cultivar red beauty exhibited significant decline in days to sprouting at 600 ppm and 900 ppm concentrations while elevated plant height at 900 concentrations. Number of branches, percent sprouting, number of leaves and budling diameter in Red Beauty were inhibited by all concentrations. However, internode length was increased significantly at 300 ppm, 600 ppm and 1200 ppm concentrations but decreased at 900 ppm concentrations. The study revealed that the most effective dose was 300 ppm. These findings demonstrate the differential sensitivity of plum cultivars to IAA and highlight its potential for regulating their growth and morphology.
Quantifying Data Distortion in Bar Graphs in Biological Research
Authors: Lin Teng-Jui , Landry Markita P. 
Published: September 2024

AbstractOver 88% of biological research articles use bar graphs, of which 29% have undocumented data distortion mistakes that over- or under-state findings. We developed a framework to quantify data distortion and analyzed bar graphs published across 3387 articles in 15 journals, finding consistent data distortions across journals and common biological data types. To reduce bar graph-induced data distortion, we propose recommendations to improve data visualization literacy and guidelines for effective data visualization.
Vascular responses of hypercapnia challenge in mice
Authors: Yang Xiuli , Li Yuguo , Wei Zhiliang 
Published: September 2024

AbstractHypercapnia challenge with a few percent of carbon dioxide is popularly used in physiological studies to investigate the dynamic vascular properties. A typical hypercapnia experiment can be divided into four phases: baseline (regular air), transition (CO2enriched), hypercapnia (CO2enriched), and recovery (regular air). Cerebrovascular reactivity (CVR), denoting the percentage of functional changes between baseline and hypercapnia phases, can be measured to assess vascular health. In this study, we focus on the transition and recovery phases to track the built-up of cerebral blood flow (CBF) increase induced by CO2-enriched gas and recovery of CBF after returning to regular air. Dynamic features were compared with those of another potent vasodilatory agent, acetazolamide. Our results reveal that 5 min is sufficiently long to ensure 95% built-up of CBF increase under 5% CO2, but it takes much longer to recover to baseline.
Covariation between metabolic and radioactive dose rates in Chornobyl rodents
Authors: Boratyński Zbyszek , Lavrinienko Anton , Lehmann Philipp , Mousseau Timothy A. , Tukalenko Eugene , Vasylenko Andrii , Watts Phillip C. , Mappes Tapio , Nowick Katja 
Published: September 2024

AbstractHigh metabolic rate may provide fitness benefits for individuals. But high metabolic rates incur energetic costs and the need to ingest more food, increasing the risks of ingesting harmful substances from the environment. How organisms respond to elevated levels of ionizing radiation is an important question in the light of increasing pollution from nuclear accidents and waste, as well as ever-increasing reliance on radiation in medical diagnostics and therapies. We investigated how limits to metabolic rate, and aerobic metabolic scope (ceiling of energetic activity above maintenance levels), of wild rodents inhabiting a gradient of radioactive contamination from the Chernobyl accident covary with the biological burden of radionuclides in their bodies. Our results demonstrate that high biological dose rate correlates with high self-maintenance and low aerobic capacity in adults. In contrast, in subadults high dose rate correlates with high aerobic capacity. Consequently, high dose rate correlates with low aerobic scope in adults, but with high aerobic scope in subadults. Despite the uncertainty of the causal mechanisms, whether the dose rate affects the metabolic rate, the reverse or the reciprocal feedback prevail, it can be hypothesized that metabolic down-regulation could contribute to protection against radioactive exposure. Yet, metabolic down-regulation might be constrained by developmental obligations. Understanding the physiological mechanisms affecting responses to radiation exposure is key for risk assessment of environmental contamination, radiotherapies, and space exploration, and may help to rectify discordant opinions concerning the effects of radiation on the ecology of organisms living in Chornobyl.
Exploring midgut expression dynamics: longitudinal transcriptomic analysis of adult femaleAmblyomma americanummidgut and comparative insights with other hard tick species
Authors: Lu Stephen , de Sousa Paula Lucas C. , Ribeiro Jose M.C. , Tirloni Lucas 
Published: September 2024

AbstractBackgroundFemale ticks remain attached to their host for multiple days to complete a blood meal. This prolonged feeding period is accompanied by a significant increase in the tick’s size and body weight, paralleled by noteworthy changes to the tick midgut. While the midgut is recognized for its established role in blood storage and processing, its importance extends to playing a crucial role in the acquisition, survival, and proliferation of pathogens. Despite this, our overall understanding of tick midgut biology is limited.ResultsWe conducted a comprehensive longitudinal transcriptome analysis of the midgut in adult femaleA. americanumticks across various feeding stages, including unfed, slow-feeding, and rapid-feeding phases. Our analysis revealed 15,599 putative DNA coding sequences (CDS) classified within 26 functional groups. Dimensional and differential expression analysis highlighted the dynamic transcriptional changes in the tick midgut as feeding progresses, particularly during the initial period of feeding and the transition from the slow-feeding to the rapid-feeding phase. Additionally, we performed an orthology analysis comparing our dataset with midgut transcriptomes from other hard ticks, such asIxodes scapularisandRhipicephalus microplus. This comparison allowed us to identify transcripts commonly expressed during different feeding phases across these three species.ConclusionOur findings provide a detailed temporal resolution of numerous metabolic pathways inA. americanum, emphasizing the dynamic transcriptional changes occurring in the tick midgut throughout the feeding process. Furthermore, we identified conserved transcripts across three different tick species that exhibit similar expression patterns. This knowledge has significant implications for future research aimed at deciphering the physiological pathways relevant within the tick midgut. It also offers potential avenues for developing control methods that target multiple tick species.
Constructing a Norm for Children’s Scientific Drawing: Distribution Features Based on Semantic Similarity of Large Language Models
Authors: Zhang Yi , Wei Fan , Wang Yan , Yu Yanyan , Chen Jianli , Cai Zipo , Liu Xinyu , Wang Wei , Wang Peng , Li Jingyi , Wang Zhong 
Published: September 2024

AbstractUsing children’s drawings to understand children’s concept learning has been proven to be an effective method, but there are still two major problems in previous research: 1. The drawings heavily relies on the task, so the ecological validity of the conclusions is low; 2. The subjective interpretation of drawings is inevitable. To address these problems, this study uses the Large Language Model (LLM) to identify the drawing contents of 1096 children’s scientific drawings (covering 6 scientific concepts), and uses the word2vec algorithm to calculate their semantic similarity. The study explores whether there are consistent drawing representations among children with the same theme, and attempts to establish a norm for children’s scientific drawings, providing a baseline reference for following children’s drawing research. The results showed that there were significant differences in the consistency of children’s representations of different concepts, and there was a possibility of consistency bias, that is, the appearance of consistency representations misled LLM. At the same time, linear regression tests were used to analyze the relevant factors that affect children’s representation. The results show that sample size and teaching strategies can affect the accuracy of LLM’s image recognition, while the degree of conceptual abstraction may affect the consistency of representation.
MolAR: memory-safe library for analysis of MD simulations written in Rust
Authors: Yesylevskyy Semen 
Published: September 2024

AbstractTransition to the memory safe natively compiled programming languages is a major software development trend in recent years, which eliminates memory-related security exploits, enables a fearless concurrency and parallelization, and drastically improves ergonomics and speed of software development. Modern memory-safe programing languages, such as Rust, are currently not used for developing molecular modeling and simulation software despite such obvious benefits as faster development cycle, better performance and smaller amount of bugs. In this work we present MolAR -the first memory-safe library for analysis of MD simulations written in Rust. MolAR is intended to explore the advantages and challenges of implementing molecular analysis software in the memory-safe natively compiled language and to develop specific memory-safe abstractions for this kind of software. MolAR demonstrates an excellent performance in benchmarks outperforming popular molecular analysis libraries, which makes it attractive for implementing computationally intensive analysis tasks.MolAR is freely available under Artistic License 2.0 athttps://github.com/yesint/molar.
Evolutionary fingerprint in rodent PD1 confers weakened activity and enhanced tumor immunity compared to human PD1
Authors: Masubuchi Takeya , Chen Lin , Marcel Nimi , Wen George A. , Caron Christine , Zhang Jibin , Zhao Yunlong , Morris Gerald P. , Chen Xu , Hedrick Stephen M. , Lu Li-Fan , Wu Chuan , Zou Zhengting , Bui Jack D. , Hui Enfu 
Published: September 2024

SUMMARYMechanistic understanding of the immune checkpoint receptor PD1 is largely based on mouse models, but human and mouse PD1 orthologs exhibit only 59.6% identity in amino acid sequences. Here we show that human PD1 is more inhibitory than mouse PD1 due to stronger interactions with the ligands PDL1 and PDL2 and with the effector phosphatase Shp2. A novel motif highly conserved among PD1 orthologs in vertebrates except in rodents is primarily responsible for the differential Shp2 recruitment. Evolutionary analysis suggested that rodent PD1 orthologs uniquely underwent functional relaxation, particularly during the K-Pg boundary. Humanization of the PD1 intracellular domain disrupted the anti-tumor activity of mouse T cells while increasing the magnitude of anti-PD1 response. Together, our study uncovers species-specific features of the PD1 pathway, with implications to PD1 evolution and differential anti-PD(L)1 responses in mouse models and human patients.
Observation of general and specific adverse effects of organic solvents onCaenorhabditis elegansby toxicity testing using behavioral analysis
Authors: Tomioka Masahiro 
Published: September 2024

SummaryNovel chemical compounds are continuously being developed and are used in various industries as well as in our daily lives. Workers in industries estimate and avoid chemical hazardous risks based on published information on chemical toxicities. However, it is challenging to avoid hazards caused by chemicals with unknown toxicity. Therefore, it is necessary to understand the toxicities of chemicals in high-throughput and multifaceted ways. In this study, I develop a high-throughput method to assess chemical toxicities through the quantitative measurement of behavior inCaenorhabditis elegans. I determine the acute toxicity of 30 organic solvents that are widely used in industries with motility as an endpoint. The adverse effects of organic solvents on motility were proportional to the lipid solubility of chemicals, which is similar to the positive relationship between the anesthetic effects of volatile organic chemicals and their lipid solubility in organisms, including humans. In addition to the general toxicity on motility, organic solvents caused adverse effects on posture during locomotion in different ways depending on the chemical’s functional group. Alcohols and cellosolves, both of which have a hydroxyl group, reduced the amplitude of body bending, whereas ketones and acetate esters, both of which have a ketone group, increased it during undulatory locomotion. Furthermore, organic solvents caused defects in behavioral plasticity based on the association of starvation and chemical signals at concentrations lower than those that affect locomotion, which suggests that sensory processing is more susceptible to organic solvents than motor function. This study provides a high-throughput method for acute chemical toxicity testing and new insights into the behavioral toxicity of organic solvents based on comprehensive behavioral analysis.
Supplemental Dietary Nano Zinc Can Impart Higher Antioxidant Status by Modulating Cu-Zn SOD Expression
Authors: Tah Amrita , Pal Aruna , De Debasis , Chatterjee P.N. 
Published: September 2024

AbstractZinc seems to be the most critical micronutrients dietary adequacy of which ensures optimum health and body defence. Considering its immunomodulation potency, zinc is often used for dietary fortification more particularly in face of challenges. However indiscriminate use of zinc as therapeutic agent often leads to secondary deficiencies of other critical nutrients due to the unwanted antagonism with other interacting nutrients available in gut. In the present study we targeted to devise a nano-structured zinc which will remain inert to other dietary micronutrients present in gut to ensure its high bioavailability. An environment benign colloidal chemistry route was employed for the synthesis of nano-dimensional zinc oxide. The microanalytical characterizations revealed that the apparent particle size of our nano-Zinc oxide ranged between 30-40 nm. The as-synthesized ZnO-NP was used for dietary fortification and the MTT assay confirmed the safe limit for its dietary inclusion. The antioxidant potential of the synthesized nano-zinc was evaluated in milk fish (Chanos chanos) considering it as a model organism. We have employed Cu-Zn SOD gene as molecular marker for antioxidant assessment with integral zinc binding sites. We have characterized Cu-Zn SOD gene inChanos chanosfor the first time and identified certain important zinc binding sites present in the Cu-Zn SOD. A significantly better expression profile of Cu-Zn SOD was observed among the fish fed dietary ZnO-NP and the best effect was observed when the fish feed was fortified with 20 ppm ZnO-NP. The outcome of this study ensures the higher bioavailability of the synthesized ZnO-NP to be assimilated into Cu-Zn SOD, which in turn imparts higher body antioxidant. Nano zinc being inert, may directly bind through the zinc binding sites of Cu-Zn SOD molecules thereby leads to its better expression and more antioxidant status through molecular interaction with other molecules throughlongevity regulating pathwayas explored by the String and KEGG pathway analysis carried out in the present investigation.
From Biobanking to Personalized Medicine: the journey of the Estonian Biobank
Authors: Milani Lili , Alver Maris , Laur Sven , Reisberg Sulev , Haller Toomas , Aasmets Oliver , Abner Erik , Alavere Helene , Allik Annely , Annilo Tarmo , Fischer Krista , Hudjashov Georgi , Jõeloo Maarja , Kals Mart , Karo-Astover Liis , Kasela Silva , Kolde Anastassia , Krebs Kristi , Krigul Kertu Liis , Kronberg Jaanika , Kruusmaa Karoliina , Kukuškina Viktorija , Kõiv Kadri , Lehto Kelli , Leitsalu Liis , Lind Sirje , Luitva Laura Birgit , Läll Kristi , Lüll Kreete , Metsalu Kristjan , Metspalu Mait , Mõttus René , Nelis Mari , Nikopensius Tiit , Nurm Miriam , Nõukas Margit , Oja Marek , Org Elin , Palover Marili , Palta Priit , Pankratov Vasili , Pantiukh Kateryna , Pervjakova Natalia , Pujol-Gualdo Natàlia , Reigo Anu , Reimann Ene , Smit Steven , Sokurova Diana , Taba Nele , Talvik Harry-Anton , Teder-Laving Maris , Tõnisson Neeme , Vaht Mariliis , Vainik Uku , Võsa Urmo , Esko Tõnu , Kolde Raivo , Mägi Reedik , Vilo Jaak , Laisk Triin , Metspalu Andres 
Published: September 2024

AbstractLarge biobanks have set a new standard for research and innovation in human genomics and implementation of personalised medicine. The Estonian Biobank was founded a quarter of a century ago, and its biological specimens, clinical, health, omics, and lifestyle data have been included in over 800 publications to date. What makes the biobank unique internationally is its translational focus, with active efforts to conduct clinical studies based on genetic findings, and to explore the effects of return of results on participants. In this review we provide an overview of the Estonian Biobank, highlight its strengths for studying the effects of genetic variation and quantitative phenotypes on health-related traits, development of methods and frameworks for bringing genomics into the clinic, and its role as a driving force for implementing personalized medicine on a national level and beyond.
Large-scale multi-omic analysis identifies noncoding somatic driver mutations and nominatesZFP36L2as a driver gene for pancreatic ductal adenocarcinoma
Authors: Zhong Jun , O’Brien Aidan , Patel Minal , Eiser Daina , Mobaraki Michael , Collins Irene , Wang Li , Guo Konnie , TruongVo ThucNhi , Jermusyk Ashley , O’Neill Maura , Dill Courtney D. , Wells Andrew D. , Leonard Michelle E. , Pippin James A. , Grant Struan F.A. , Zhang Tongwu , Andresson Thorkell , Connelly Katelyn E. , Shi Jianxin , Arda H. Efsun , Hoskins Jason W. , Amundadottir Laufey T. 
Published: September 2024

AbstractIdentification of somatic driver mutations in the noncoding genome remains challenging. To comprehensively characterize noncoding driver mutations for pancreatic ductal adenocarcinoma (PDAC), we first created genome-scale maps of accessible chromatin regions (ACRs) and histone modification marks (HMMs) in pancreatic cell lines and purified pancreatic acinar and duct cells. Integration with whole-genome mutation calls from 506 PDACs revealed 314 ACRs/HMMs significantly enriched with 3,614 noncoding somatic mutations (NCSMs). Functional assessment using massively parallel reporter assays (MPRA) identified 178 NCSMs impacting reporter activity (19.45% of those tested). Focused luciferase validation confirmed negative effects on gene regulatory activity for NCSMs nearCDKN2AandZFP36L2. For the latter, CRISPR interference (CRISPRi) further identifiedZFP36L2as a target gene (16.0 – 24.0% reduced expression,P= 0.023-0.0047) with disrupted KLF9 binding likely mediating the effect. Our integrative approach provides a catalog of potentially functional noncoding driver mutations and nominatesZFP36L2as a PDAC driver gene.
Multi-organ transcriptomic atlas reveals hallmarks of labor
Authors: Ni Duan , Nanan Ralph 
Published: September 2024

Pregnancy and labor are dynamic processes involving various rapid biological changes. Previous studies found that during pregnancy there are gradual alterations in immune and metabolic pathways. In contrast, changes linked to labor are less well-known, generally limited to reports on specific differentially expressed genes, lacking a more comprehensive overview of changes of the overall signalling landscapes. Moreover, most previous works were standalone, based on individual organs. Here, we aimed to present a more systematic and holistic overview of the impacts of labor on both the maternal and fetal aspects. For this purpose, we collated a multi-organ transcriptomic atlas to decipher the influences of labor on multiple maternal and fetal compartments, covering the maternal adipose tissues (subcutaneous and visceral fat), peripheral blood, myometrium and placenta and fetal cord blood mononuclear cells (CBMCs), and spanning both physiological and pathological conditions. During labor, activation of pro-inflammatory TNF signaling was found in all maternal compartments except adipose tissues, which, along with myometrium, showed upregulation in glycolysis. Myc signaling, as a critical nexus within the intracellular signaling network, was generally enhanced in labor. Contrarily, fetal CBMCs in labor upregulated the anti-inflammatory TGFβ pathway. Importantly, changes in the maternal TNF signaling were conserved across the spectrum of healthy pregnancy of different parities, and pathological conditions like preterm pregnancy and smoking-affected pregnancy. Mechanistically, it might be explained by the reduction in progestin hormonal signals during labor but not by the mechanical stress.Collectively, we present a comprehensive multi-organ transcriptomic atlas elucidating the maternal and fetal immune and metabolic landscapes associated with labor, shedding light on the complex physiology.