bluuebunny/crossref_metadata_2025_split huggingface dataset:
Elucidating gastric cancer mechanisms and therapeutic potential of Adociaquinone A targeting EGFR: A genomic analysis and Computer Aided Drug Design (CADD) approach
Authors: Alkhateeb Mariam Abdulaziz , Aljarba Nada H. , Yousafi Qudsia , Anwar Fatima , Biswas Partha 
Published: October 2024

AbstractGastric cancer predominantly adenocarcinoma, accounts for over 85% of gastric cancer diagnoses. Current therapeutic options are limited, necessitating the discovery of novel drug targets and effective treatments. The Affymetrix gene expression microarray dataset (GSE64951) was retrieved from NCBI‐GEO data normalization and DEGs identification was done by using R‐Bioconductor package. Gene Ontology (GO) analysis of DEGs was performed using DAVID. The protein–protein interaction network was constructed by STRING database plugin in Cytoscape. Subclusters/modules of important interacting genes in main network were extracted by using MCODE. The hub genes from in the network were identified by using Cytohubba. The miRNet tool built a hub gene/mRNA‐miRNA network and Kaplan–Meier‐Plotter conducted survival analysis. AutoDock Vina and GROMACS MD simulations were used for docking and stability analysis of marine compounds against the 5CNN protein. Total 734 DEGs (507 up‐regulated and 228 down‐regulated) were identified. Differentially expressed genes (DEGs) were enriched in processes like cell–cell adhesion and ATP binding. Eight hub genes (EGFR, HSPA90AA1, MAPK1, HSPA4, PPP2CA, CDKN2A, CDC20, and ATM) were selected for further analysis. A total of 23 miRNAs associated with hub genes were identified, with 12 of them targeting PPP2CA. EGFR displayed the highest expression and hazard rate in survival analyses. The kinase domain of EGFR (PDBID: 5CNN) was chosen as the drug target. Adociaquinone A from Petrosia alfiani, docked with 5CNN, showed the lowest binding energy with stable interactions across a 50 ns MD simulation, highlighting its potential as a lead molecule against EGFR. This study has identified crucial DEGs and hub genes in gastric cancer, proposing novel therapeutic targets. Specifically, Adociaquinone A demonstrates promising potential as a bioactive drug against EGFR in gastric cancer, warranting further investigation. The predicted miRNA against the hub gene/proteins can also be used as potential therapeutic targets.
Using Keystroke Behavior Patterns to Detect Nonauthentic Texts in Writing Assessments: Evaluating the Fairness of Predictive Models
Authors: Jiang Yang , Zhang Mo , Hao Jiangang , Deane Paul , Li Chen 
Published: October 2024

AbstractThe emergence of sophisticated AI tools such as ChatGPT, coupled with the transition to remote delivery of educational assessments in the COVID‐19 era, has led to increasing concerns about academic integrity and test security. Using AI tools, test takers can produce high‐quality texts effortlessly and use them to game assessments. It is thus critical to detect these nonauthentic texts to ensure test integrity. In this study, we leveraged keystroke logs—recordings of every keypress—to build machine learning (ML) detectors of nonauthentic texts in a large‐scale writing assessment. We focused on investigating the fairness of the detectors across demographic subgroups to ensure that nongenuine writing can be predicted equally well across subgroups. Results indicated that keystroke dynamics were effective in identifying nonauthentic texts. While the ML models were slightly more likely to misclassify the original responses submitted by male test takers as consisting of nonauthentic texts than those submitted by females, the effect sizes were negligible. Furthermore, balancing demographic distributions and class labels did not consistently mitigate detector bias across predictive models. Findings of this study not only provide implications for using behavioral data to address test security issues, but also highlight the importance of evaluating the fairness of predictive models in educational contexts.
Clinical supervision effectiveness in NHS nursing, medical and allied health professionals: Exploring interaction with workplace factors, supervision factors and burnout
Authors: Sellers Emma , Craven‐Staines Sarah , Vaughan Claire 
Published: October 2024

AbstractObjectivesThe study aimed to (1) determine if a variety of workplace and supervision factors predict clinical supervision effectiveness; and (2) establish if clinical supervision effectiveness predicts burnout, amongst a variety of mental health staff (medical, allied health, and nursing staff).DesignThe study adopted a multicentre cross‐sectional online survey design.MethodsParticipants included 204 mental health staff (89 allied health staff, 81 nursing staff, and 34 medical staff). The Manchester Clinical Supervision Scale (MCSS‐26) was used to measure clinical supervision effectiveness, and the Maslach Burnout Inventory (MBI‐HSS) was used to measure burnout. Linear regression analyses and multiple regression analyses were conducted.ResultsThe main findings suggested that supervision frequency, supervision duration, choice of supervisor, workplace setting, and supervisee profession, were all significant predictors of clinical supervision effectiveness. Additionally, clinical supervision effectiveness was a significant negative predictor of burnout.ConclusionsWorkplace and supervision factors should be considered in supervision practice across professional groups. Policies need to promote effective clinical supervision practice.
Fish resilience as an ethical issue
Authors: Meijboom Franck L. B. , Bovenkerk Bernice 
Published: October 2024

AbstractFish resilience can be understood as the capacity of fish to successfully respond to a challenge so that they are able to function and flourish in much the same way as they did prior to the occurrence of the challenge. Resilience is a function not only of individual fish, but also of a whole fish population. Enhancing the resilience of fish requires both adapting the robustness of the animals and adapting the (production) environment to the specific needs of the fish. Rather than a mere biological capacity of fish, resilience also comes with ethical questions. These questions occur at four levels. First, in practice resilience often comes with a “rhetoric” of optimalization. The view that aquaculture that strives for resilient fish is good for both fish welfare and production is inherently normative. It assumes a ‘win–win situation’, but thereby makes certain normative assumptions. Second, especially when the win–win situation is not achievable, resilience means making trade‐offs between preferred responses to challenges from the perspective of individual animals and groups or between individual housing and larger aquaculture systems. Third, the discussions on resilience and fish demonstrate the need to move beyond an animal welfare framework when discussing the treatment of fish in aquaculture. Recently, animal ethics has seen a turn towards centering animals' own agency. This means that we should not only focus on improving animal welfare, but also on asking what the animals themselves want and how they can be given more control over their situation. This may also impact the definition of resilience and how it is made operational. Finally, the use of the concept of resilience may reveal a certain moral outlook with regard to fish. On the one hand, resilience is portrayed as a positive characteristic of animals that enables improvement of the quality of life of fish. At the same time, it raises the question of how far we should stretch the “manufacturability” of fish. When we physically adapt animals so that they can cope with difficult circumstances we may be stretching moral boundaries. For example, this raises the objection that we are instrumentalizing animals. In this article, we reflect on these types of ethical issues and aim to show that the ethical dimensions of resilience need to be taken into account by professionals in aquaculture in order to make resilience operational and to contribute to a responsible interaction with fish in aquaculture.
Differential climatic niche diversification processes in South American rodents (Octodontoidea) across tropical and extratropical regions
Authors: da Silva Darlan , Verzi Diego , Martinez Pablo Ariel 
Published: October 2024

ABSTRACT

Studying niche evolution becomes central to understanding the processes driving species diversification along latitudinal gradients. Octodontoidea rodents serve as a model group for understanding how the colonisation of extratropical regions has shaped the climatic niche evolution of species.

We analyse the time and mode of climatic niche evolution among different Octodontoidea lineages to understand how niche evolutionary processes operate across the spatial gradient of the Neotropical region.

We constructed ecological niche models for living Octodontoidea species to assess the timing and mode of climatic niche evolution across tropical and extratropical lineages. We estimated niche similarity and correlated it with species divergence times, and estimated the rate of climatic niche diversification across lineages.

Our results show a trend of greater niche overlap in more recent lineages and lower niche overlap in older lineages. However, extratropical lineages exhibit lower climatic niche overlaps. From diversification analysis, we detected that the Ctenomyidae group shows higher rates of niche diversification, whereas the tropical Echimyidae group exhibits the lowest rates of climatic niche diversification.

Our results support the idea that the lineages restricted to tropical regions tend towards niche conservatism. However, some tropical lineages have successfully colonised extratropical regions, and this colonisation has been accompanied by strong selective pressures, leading to higher rates of niche diversification and lower climatic niche overlap among species.
Silent shadows in the rebirth of Czech nation: Unveiling the role of rape and sexual violence in the ethnic cleansing of post‐WWII Czech lands
Authors: Mrňka Jaromír 
Published: October 2024

AbstractThe article explores the harrowing use of sexual violence as a tool in the ethnic cleansing of Germans in post‐World War II Czechoslovakia. By examining the grim realities of internment camps, prisons, and border regions, it reveals a disturbing pattern of abuse aimed primarily at German women by Czech men. This violence was not isolated but integral to the broader project of national cleansing, laying bare the patriarchal foundations of Czechoslovak society. State policies, including the differential treatment of mixed marriages, reinforced a male‐dominated ethos. By stripping Germans of their citizenship and legal protections, Czech authorities fostered a climate of impunity, allowing a wave of sexual violence to persist through the ‘German transfers’. The article sheds light on this dark chapter, exposing how rape was used to reaffirm Czech men's dominance in the nation's postwar rebirth.
A new dimension of leaf economic spectrum: temporal instability of relationships among genotypes
Authors: Pahadi Pratima , Wason Jay , Annis Seanna , McGill Brian , Zhang Yong‐Jiang 
Published: October 2024

Summary
Leaf economic spectrum (LES) relationships have been studied across many different plant lineages and at different organizational scales. However, the temporal stability of the LES relationships is largely unknown. We used the wild blueberry system with high genotypic diversity to test whether trait–trait relationships across genotypes demonstrate the same LES relationships found in the global database (GLOPNET) and whether they are stable across years.
We studied leaf structure, photosynthesis, and leaf nutrients for 16 genotypes of two wild blueberry species semi‐naturally grown in a common farm in Maine, USA, across 4 yr.
We found substantial variation in leaf structure, physiology, and nutrient traits within and among genotypes, as well as across years in wild blueberries. The LES trait–trait relationships (covariance structure) across genotypes were not always found in all years. The trait syndrome of wild blueberries was shifted by changing environmental conditions over the years. Additionally, traits in 1 yr cannot be used to predict those of another year.
Our findings show that LES generally holds among genotypes but is temporally unstable, stressing the significant influence of trait plasticity in response to fluctuating environmental conditions across years, and the importance of temporal dimensions in shaping functional traits and species coexistence.
Light‐induced cryptochrome 2 liquid–liquid phase separation and mRNA methylation
Authors: Jiang Bochen 
Published: October 2024

SummaryLight is essential not only for photosynthesis but also for the regulation of various physiological and developmental processes in plants. While the mechanisms by which light regulates transcription and protein stability are well established, the effects of light on RNA methylation and their subsequent impact on plant growth and development are less understood. Upon exposure to blue light, the photoreceptor cryptochromes form nuclear speckles or nuclear bodies, termed CRY photobodies. The CRY2 photobodies undergo light‐induced homo‐oligomerization and liquid–liquid phase separation (LLPS), which are crucial for their physiological activity. Recent studies have proposed that blue light‐induced CRY2 LLPS increases the local concentration or directly enhances the biochemical activities of RNA N6‐methyladenosine (m6A) methyltransferases, thus, to regulate circadian clock and maintain Chl homeostasis through processes of RNA decay or translation. This review aimed to elucidate the functions of CRY2 and LLPS in RNA methylation, focusing on the light‐controlled reversible phase transitions regulon and the outstanding questions that remain in RNA methylation.
Verification of the Fusarium‐Increasing Properties of the Dominant Dwarfing Gene Ddw1 in triticale (×Triticosecale)
Authors: Miedaner Thomas , Gruner Paul , Maurer Hans Peter 
Published: October 2024

ABSTRACTDwarfing genes that are considerably reducing plant height are used in many cereals. In triticale, the rye‐derived dominant dwarfing gene Ddw1 was introgressed in commercial varieties. It has already been shown that this gene increases Fusarium head blight (FHB) susceptibility in one segregating population. We aimed for verifying this effect in the genetically unrelated doubled haploid (DH) population Cando (Ddw1) × Tritikon (ddw1), with 182 progenies in an experiment with artificial inoculation across six location–year combinations (environments). Linkage mapping was performed with DArTseq markers. The progenies significantly (p < 0.001) varied for FHB severity, plant height and heading stage with high entry‐mean heritabilities (0.85–0.98). The population showed a bimodal distribution for plant height. A significant QTL on chromosome 5RL was found for all three traits explaining 38%, 62% and 43% of the genotypic variation for FHB severity, plant height and heading stage, respectively, and most likely representing Ddw1. This gene increased FHB severity by 5.6 percentage points, delayed heading by 2.7 EC stages and reduced plant height by 29.6 cm on average. To use this gene in practical triticale breeding, the genetic background must be enriched with FHB resistance QTL to counterbalance the negative effect of Ddw1 either by introgression of major FHB QTL from exotic sources or by genomic selection within the adapted gene pool.
Enhancement of the angiogenic differentiation in the periodontal ligament stem cells using fibroblast growth factor 2 and photobiomodulation: An in vitro investigation
Authors: Atarbashi‐Moghadam Fazele , Mahmoudian Amirhosein , Taghipour Niloofar , Hakimiha Neda , Azadi Ali , Nokhbatolfoghahaei Hanieh 
Published: October 2024

AbstractThis study aims to evaluate and compare the effect of fibroblastic growth factor 2 (FGF‐2) and photobiomodulation, solely or in combination, in angiogenic differentiation of human periodontal ligament stem cells (hPDLSCs). The study comprises the following groups: control group (hPDLSCs only), FGF‐2 (50 ng/mL) group, two photobiomodulation groups with a 4 J/cm2 energy density of 808 nm diode laser (1‐Session or 2‐Session), and two groups with the combination of each 1‐Session or 2‐Session photobiomodulation with FGF‐2 (50 ng/mL). The 4′,6‐diamidino‐2‐phenylindole (DAPI) staining, and Methyl Thiazolyl Tetrazolium (MTT) assay were undertaken on days 2, 4, and 6. Quantitative Real‐time Polymerase Chain Reaction (RT‐qPCR) analysis on days 2, 4, 6, 8, and 11 was conducted to investigate VEGF‐A and ANG‐I genes. Coherently, the results of the DAPI and MTT showed the Laser (2‐Session) group had higher cell viability than others on day 6. All groups demonstrated a growth pattern in the expression of VEGF‐A and ANG‐I from day 2 to 8 and, afterward, a significant downgrowth to day 11 (p < 0.05). The most amounts of expression of VEGF‐A and ANG‐I on day 8 were seen in the Laser (2‐Session) group. Two‐time application of photobiomodulation using a diode laser with 808 nm wavelength after 2 and 4 days of cell seeding can be associated with higher cell viability and angiogenic differentiation of hPDLSCs compared to the one‐time application of photobiomodulation and administration of FGF‐2.
Fast Competitive Swimmers Demonstrate a Diminished Diving Reflex
Authors: Fujii Naoto , Ishii Yuji , Moriyama Shodai , Matsutake Ryoko , Sengoku Yasuo , Nishiyasu Takeshi 
Published: October 2024

ABSTRACTCompetitive swimmers complete 50‐m front crawl swimming without breathing or with a limited number of breaths. Breath holding during exercise can trigger diving reflex including bradycardia and diminished active muscle blood flow, whereas oxygen supply to vital organ such as brain is maintained. We hypothesized that swimmers achieving faster time in 50‐m front crawl with limited number of breaths demonstrate a blunted diving reflex of cardiac and active muscle blood flow responses with elevated cerebral perfusion to counteract peripheral and central fatigues. Twenty‐eight competitive swimmers (12 females) underwent a 50‐m front crawl swimming time trial with minimum respiratory interruptions, following which they were categorized into two groups: Fast (n = 13) and Slow (n = 15). Additionally, they performed knee extension exercises with maximal voluntary breath‐ holding, wherein leg blood flow (Doppler ultrasound), cardiac output (Modelflow), heart rate (electrocardiogram), and middle cerebral artery mean blood velocity (transcranial Doppler ultrasound) were evaluated. The pattern of leg blood flow response differed between the two groups (p = 0.031) with the Fast group experiencing a delayed onset of reductions in leg blood flow (p = 0.035). The onset of bradycardia was also delayed in the Fast group (p = 0.014), with this group demonstrating a higher value of the lowest heart rate (between‐trial difference in average: 15.9 [3.73, 28.2] beats/min) and cardiac output (between‐trial difference in median: 2.84 L/min) (both, p ≤ 0.013). Middle cerebral artery mean blood velocity was similar between the groups (all p ≥ 0.112). We show that swimmers with superior performance in 50‐m front crawl swim with limited breaths display a diminished diving reflex.
Do young American children essentialize ethnicity? Examining inductive inferences about Hispanic/Latinx individuals in an ethnically diverse sample
Authors: Pronovost Megan A. , Scott Rose M. 
Published: October 2024

AbstractHispanic and Latinx individuals represent one of the largest and fastest growing ethnic groups in the United States. Yet research has not investigated whether young children hold essentialist beliefs about this prevalent social category. The present study addressed this issue by examining whether children used this ethnic category to make inductive inferences about novel individuals, one dimension of essentialism. A total of 108 children, 5 to 7 years of age (54 female; 56 Hispanic, 46 non‐Hispanic), completed a forced‐choice inference task. Children did not expect members of the same ethnic group to share properties, and this did not vary with their own ethnic group membership. This suggests that in the US, the belief that ethnicity is causally informative undergoes a protracted developmental trajectory, as has been observed for essentialist beliefs about race.
Identification of the Novel HLA‐A*33:03:68 Allele in a Chinese Platelet Donor
Authors: Yang Fan , Gao Su‐Qing , Xia Wen‐Xia , Xu Yun‐Ping 
Published: October 2024

ABSTRACTThe novel HLA‐A*33:03:68 allele differs from HLA‐A*33:03:01:01 by 1 variation in exon 3.
Identification of the Novel HLA‐DQB1*03:01:01:69 Allele in a Candidate Bone Marrow Donor by Next Generation Sequencing
Authors: Kouniaki Diamanto , Tsirogianni Alexandra 
Published: October 2024

ABSTRACTThe HLA‐DQB1*03:01:01:69 allele differs from HLA‐DQB1*03:01:01:03 by a single nucleotide substitution in intron 2.
Sequence diversity in the monooxygenases involved in oxime production in plant defense and signaling: a conservative revision in the nomenclature of the highly complex CYP79 family
Authors: Koleva Donka Teneva , Bengochea Anthony W. , Mellor Silas B. , Ochoa‐Fernandez Rocio , Nelson David R. , Møller Birger Lindberg , Gillam Elizabeth M. J. , Sørensen Mette 
Published: October 2024

SUMMARYCytochrome P450 monooxygenases of the CYP79 family catalyze conversion of specific amino acids into oximes feeding into a variety of metabolic plant pathways. Here we present an extensive phylogenetic tree of the CYP79 family built on carefully curated sequences collected across the entire plant kingdom. Based on a monophyletic origin of the P450s, a set of evolutionarily distinct branches was identified. Founded on the functionally characterized CYP79 sequences, sequence features of the individual substrate recognition sites (SRSs) were analyzed. Co‐evolving amino acid residues were identified using co‐evolutionary sequence analysis. SRS4 possesses a specific sequence pattern when tyrosine is a substrate. Except for the CYP79Cs and CYP79Fs, substrate preferences toward specific amino acids could not be assigned to specific subfamilies. The highly diversified CYP79 tree, reflecting recurrent independent evolution of CYP79s, may relate to the different roles of oximes in different plant species. The sequence differences across individual CYP79 subfamilies may facilitate the in vivo orchestration of channeled metabolic pathways based on altered surface charge domains of the CYP79 protein. Alternatively, they may serve to optimize dynamic interactions with oxime metabolizing enzymes to enable optimal ecological interactions. The outlined detailed curation of the CYP79 sequences used for building the phylogenetic tree made it appropriate to make a conservative phylogenetic tree‐based revision of the naming of the sequences within this highly complex cytochrome P450 family. The same approach may be used in other complex P450 subfamilies. The detailed phylogeny of the CYP79 family will enable further exploration of the evolution of function in these enzymes.