bluuebunny/crossref_metadata_2025_split huggingface dataset:
Yeast EndoG prevents genome instability by degrading cytoplasmic DNA
Authors: Yu Yang , Wang Xin , Fox Jordan , Yu Ruofan , Thakre Pilendra , McCauley Brenna , Nikoloutsos Nicolas , Li Qian , Hastings P. J. , Dang Weiwei , Chen Kaifu , Ira Grzegorz 
Published: December 2023

SummaryIn metazoans release of mitochondrial DNA or retrotransposon cDNA to cytoplasm can cause sterile inflammation and disease. Cytoplasmic nucleases degrade these DNA species to limit inflammation. It remains unknown whether degradation these DNA also prevents nuclear genome instability. To address this question, we decided to identify the nuclease regulating transfer of these cytoplasmic DNA species to the nucleus. We used an amplicon sequencing-based method in yeast enabling analysis of millions of DSB repair products.NuclearmtDNA (NUMTs) and retrotransposon cDNA insertions increase dramatically in nondividing stationary phase cells. Yeast EndoG (Nuc1) nuclease limits insertions of cDNA and transfer of very long mtDNA (>10 kb) that forms unstable circles or rarely insert in the genome, but it promotes formation of short NUMTs (∼45-200 bp). Nuc1 also regulates transfer of cytoplasmic DNA to nucleus in aging or during meiosis. We propose that Nuc1 preserves genome stability by degrading retrotransposon cDNA and long mtDNA, while short NUMTs can originate from incompletely degraded mtDNA. This work suggests that nucleases eliminating cytoplasmic DNA play a role in preserving genome stability.
Phylogenomics resolves key relationships inRumexand uncovers a dynamic history of independently evolving sex chromosomes
Authors: Hibbins Mark S. , Rifkin Joanna L. , Choudhury Baharul I. , Voznesenka Olena , Sacchi Bianca , Yuan Meng , Gong Yunchen , Barrett Spencer C. H. , Wright Stephen I. 
Published: December 2023

AbstractSex chromosomes have evolved independently many times across eukaryotes. Despite a considerable body of literature on the evolution of sex chromosomes, the causes and consequences of variation in the formation, degeneration, and turnover of sex chromosomes remain poorly understood. Comparative approaches in groups with sexual system variation can be valuable for understanding these questions. Plants are well-suited to such comparative studies, with many lineages containing relatively recent origins of dioecy and sex chromosomes as well as hermaphroditic close relatives.Rumexis a diverse genus of flowering plants harboring significant sexual system variation, including hermaphroditic and dioecious clades with XY sex chromosomes. Previous disagreement in the phylogenetic relationships among key species have rendered the history of sex chromosome evolution uncertain. Resolving this history is important to the development ofRumexas a system for the comparative study of sex chromosome evolution. Here, we leverage new transcriptome assemblies from 11 species representing the major clades in the genus, along with a whole-genome assembly generated for a pivotal hermaphroditic species, to further resolve the phylogeny and history of sex chromosome evolution inRumex. Using phylogenomic approaches, we find evidence for two independent origins of sex chromosomes and introgression from unsampled taxa in the genus. Comparative genomics reveals massive chromosomal rearrangements in a dioecious species, with evidence for a complex origin of the sex chromosomes through multiple chromosomal fusions. However, we see no evidence of elevated rates of fusion on the sex chromosome in comparison with autosomes, providing no support for an adaptive hypothesis for the sex chromosome expansion. Overall, our results highlight the dynamic nature of sex chromosome systems inRumexand illustrate the utility of the genus as a model for the comparative study of sex chromosome evolution.
Molecular Species Determination of Cyathostomins from Horses in Ireland
Authors: Byrne Orla , Gangotia Disha , Crowley John , Zintl Annetta , Kiser Liam , Boxall Olivia , McSweeney Daniel , O’Neill Fiona , Dunne Stacey , Lamb Breanna Rose , Walshe Nicola , Mulcahy Grace 
Published: December 2023

AbstractCyathostomins are globally important equine parasites, responsible for both chronic and acute pathogenic effects. The occurrence of mixed infections with numerous cyathostomin species hinders our understanding of parasite epidemiology, host-parasite dynamics and species pathogenicity. There have been few studies of cyathostomin species occurring in horses in Ireland, where temperate climatic conditions with year-round rainfall provide suitable conditions for infection of grazing animals with bursate nematodes. Here, we amplified and sequenced the ITS-2 region of adult worms harvested at post-mortem from 11 adult horses between August 2018 and June 2020, and recorded species prevalence and abundance of worms recovered from the caecum, right ventral colon and left dorsal colon, using both BLAST and IDTAXA for taxonomic attribution. Phylogenetic relationships and community composition were also recorded and compared with other relevant studies, including a global meta-analysis. Overall, our results agree with previous studies that there does not seem to be a major difference in cyathostomin species occurrence in equids in different geographical regions. We confirmed the results of other workers in relation to the difficulties in discriminating betweenCylicostephanus calicatusandCoronocyclus coronatuson the basis of ITS-2 sequences.
ARHGAP32 as a novel RhoGAP interacting with desmoplakin is required for desmosomal organization and assembly
Authors: Li Hua , Wang Yan , He Yinzhen , Liu Xiayu , Duan Xiufen , Zhou Kaiyao , Wu Gangyun , Ning Wenxiu 
Published: December 2023

AbstractDesmosomes are specialized cell-cell junctions that play a critical role in maintaining tissue barrier integrity, particularly in mechanically stressed tissues. The assembly of desmosomes is regulated by the cytoskeleton and its regulators, and desmosomes also function as a central hub for regulating F-actin. However, the specific mechanisms underlying the crosstalk between desmosomes and F-actin, particularly involving RhoGAP or RhoGEF proteins, remain unclear. In our study, we identified that ARHGAP32, a Rho GTPase-activating protein, is located in desmosomes through its interaction with DSP via its GAB2-interacting domain. Using CRISPR-Cas9 gene knockout system, we confirmed that ARHGAP32 is required for proper desmosomal organization, maturation, and length regulation. Notably, the loss of ARHGAP32 resulted in increased formation of F-actin stress fibers and phosphorylation of MYOSIN at T18/S19, indicating enhanced actomyosin contractility. Furthermore, inhibition of ROCK1 kinase activity using Y27632 effectively restored desmosomal organization. Moreover, we demonstrated that the regulation of desmosomes by ARHGAP32 is crucial for maintaining the integrity of epithelial cell sheets. Collectively, our study unveils ARHGAP32 as a RhoGAP present at desmosomes, potentially facilitating the crosstalk between desmosomes and F-actin. Its presence is indispensable for desmosomal assembly and the preservation of epithelial cell sheet integrity by regulating actomyosin contractility.
New insights on the role ofSlDMR6-1in drought avoidance in tomato
Authors: Alex Maioli , Federica De Marchi , Danila Valentino , Silvia Gianoglio , Davide Patono , Fabio Miloro , Yuling Bai , Cinzia Comino , Sergio Lanteri , Claudio Lovisolo , Alberto Acquadro , Andrea Moglia 
Published: December 2023

ABSTRACTThe DOWNY MILDEW RESISTANCE 6 (DMR6) protein is a 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase, involved in salicylic acid (SA) metabolism, and its inactivation in tomato was found to increase SA levels and to confer disease-resistance against several pathogens. SA is also recognized as an abiotic stress-tolerance enhancer, and we tested the resistance to drought stress inSldmr6-1tomato mutants generated by the CRISPR/Cas9 technique.Wild-type (WT) tomato cultivar ‘San Marzano’ and itsSldmr6-1mutants were subjected to water deprivation for 7 days. At the end of the period, while WT plants exhibited severe wilting, the T2Sldmr6-1mutant plants showed turgid leaves and maintained higher Soil Relative Water Content (SRWC).Sldmr6-1mutants adopted a water saving behaviour reducing transpiration rate (E) by decreasing stomatal conductance (Gs). Assimilation rate (A) decreased in parallel to E under drought stress, resulting in no alteration of the CO2concentration in the sub-stomatal chamber (Ci) and increasing the Water Use Efficiency (WUE, A/E). Defence mechanisms of the photosynthetic machinery triggered inSldmr6-1mutants, that under drought stress showed up-regulation of the genesSlAPXandSlGST(anti-oxidant related) as well as down-regulation ofSlCYP707A2gene, which is involved in ABA catabolism. Our results suggest that the disabling ofSlDMR6-1in tomato plants leads to a drought-avoidance strategy through tight control of stomatal closure controlling water loss. In addition, it was highlighted, for the first time in tomato, thatSldmr6-1mutants showed reduced susceptibility toPhytophthora infestans, the causal agent of Late Blight.
Retractions covered by retraction watch from 2017 to 2022: a perspective from Indian researchers
Authors: R. Shimray Somipam , Tiwari Sakshi , Ramaiah Chennupati Kodand 
Published: December 2023

Purpose
The purpose of this study is to examine characteristics of retracted publications from Indian authors and inspect a relationship between journal impact factor (JIF) and the number of authors (NoA).

Design/methodology/approach
The authors examined the general characteristics of retracted publications and investigated the correlation between JIF and NoA from Indian authors from January 1, 2017, to December 31, 2022. Data were mined from retraction watch http://retractiondatabase.org/ (n = 1,459) and determined the year of publication, year of retraction, authors, journals, publishers and causes of the retractions. A journal citation report was extracted to gather the JIFs.

Findings
About one-third of retracted papers were published in 2020; 2022 has the highest retraction rate (723); studies with two authors represent about one-third (476) of the published articles; Journal of Ambient Intelligence and Humanized Computing (354) has the highest number of retractions; Springer published the most retracted papers (674); and the majority of the journal (1,133) is indexed in journal citation reports, with impact factor extending from 0.504 to 43.474. Retraction due to legal reasons/legal threats was the most predominant reason for retraction.

Originality/value
This study reflects growth in author collaborations with a surge in the JIF. This study recommends that quick retraction is essential to reduce the adverse effects of faulty research.
The differential effect of three types of conflicting online reviews on perceived informativeness
Authors: Xian Chunyi , Vali Hessam , Tian Ruwen , Xu Jingjun David , Yildirim Mehmet Bayram 
Published: December 2023

PurposeThe authors investigate the varying impact of three categories of conflicting consumer reviews (i.e. conflicting opinions on attributes of a product item, conflicting ratings of an item and the intensity of conflicting reviews of an item) on the potential customers' perceived informativeness, which is expected to affect the perceived correct purchase.Design/methodology/approachTo test their proposed hypotheses, the authors conducted an experiment using a 2 × 2 × 2 factorial design for each conflict type comprising two levels (low vs high).FindingsThe results of this study found that conflicting opinions on product attributes can enhance potential customers' perceptions of informativeness and subsequent correct purchase decisions while conflicting ratings and the intensity of conflicting reviews can diminish potential customers' perceptions of informativeness. In addition, conflicting ratings negatively moderate the effect of conflicting attributes on perceived informativeness such that the positive effect of conflicting attributes on perceived informativeness will be less prominent when conflicting ratings are present (vs absent).Originality/valueWhile potential customers are browsing product descriptions, reviews and comments from other purchasers are also playing a role in influencing a potential customer's purchase decision. However, given the different experiences and temperaments of individuals, the subjective remarks and ratings of individuals are sometimes inconsistent or even conflicting, which can lead to confusion among potential customers. The authors categorize the positive or negative effects of the three conflicting reviews based on the two dimensions of ease of capture and product diagnosticity. The findings can help platforms optimize the display of product reviews to help potential customers make more accurate purchase decisions.
Molecular simulation for food protein–ligand interactions: A comprehensive review on principles, current applications, and emerging trends
Authors: Jin Zihan , Wei Zihao 
Published: December 2023

AbstractIn recent years, investigations on molecular interaction mechanisms between food proteins and ligands have attracted much interest. The interaction mechanisms can supply much useful information for many fields in the food industry, including nutrient delivery, food processing, auxiliary detection, and others. Molecular simulation has offered extraordinary insights into the interaction mechanisms. It can reflect binding conformation, interaction forces, binding affinity, key residues, and other information that physicochemical experiments cannot reveal in a fast and detailed manner. The simulation results have proven to be consistent with the results of physicochemical experiments. Molecular simulation holds great potential for future applications in the field of food protein–ligand interactions. This review elaborates on the principles of molecular docking and molecular dynamics simulation. Besides, their applications in food protein–ligand interactions are summarized. Furthermore, challenges, perspectives, and trends in molecular simulation of food protein–ligand interactions are proposed. Based on the results of molecular simulation, the mechanisms of interfacial behavior, enzyme‐substrate binding, and structural changes during food processing can be reflected, and strategies for hazardous substance detection and food flavor adjustment can be generated. Moreover, molecular simulation can accelerate food development and reduce animal experiments. However, there are still several challenges to applying molecular simulation to food protein–ligand interaction research. The future trends will be a combination of international cooperation and data sharing, quantum mechanics/molecular mechanics, advanced computational techniques, and machine learning, which contribute to promoting food protein–ligand interaction simulation. Overall, the use of molecular simulation to study food protein–ligand interactions has a promising prospect.
Analysis of friction ridge evidence for trace amounts of paracetamol in various pharmaceutical industries by Raman spectroscopy
Authors: Czarnomska Martyna , Lewkowicz Aneta , Pierpaoli Mattia , Gruszczyńska Emilia , Kasprzak Magdalena , Gryczyński Zygmunt , Bojarski Piotr , Steinborn Sławomir , Woźniewski Krzysztof 
Published: December 2023

AbstractThe detection of potentially harmful substances presents a multifaceted challenge. On one hand, it can directly save lives, on the other, it can significantly aid and enhance police work, thereby increasing the effectiveness of investigations. The research conducted in this study primarily aims to identify paracetamol in fingerprints, considering situations involving direct contact of a person with paracetamol either chronically or in a single dose. The identification procedure presented, utilizing Raman spectroscopy, aims to rapidly detect the xenobiotic following ingestion by an individual, which involves touching the tablet with their fingers—this can be termed as touch evidence in forensic science investigations. Additionally, the authors focus on assessing the impact of additives present in drugs containing paracetamol as the main active ingredient. The screening results obtained will enable us to analyze the composition of drugs in terms of potentially toxic substances, and their influence on the physicochemical activity of the active substance. We successfully identified the paracetamol molecule using a noninvasive forensic trace detection method. Samples in the form of common drugs containing 500 mg of paracetamol were studied. Throughout the study, comprehensive validation of the method was ensured through the utilization of a statistical model, which excluded sensitivity to the presence of other substances, whether additives or from the external environment. The proposed approach to trace the content of substances in fingerprint using Raman scattering analysis provides a useful starting point to enhance current analytical methods not only in forensic science but also in toxicology.
Clinical and genetic characteristics of maturity‐onset diabetes of the young type 13: A systematic review of the literature
Authors: Chen Yaning , Hu Xiaodong , Zhao Mingwei 
Published: December 2023

AbstractObjectiveMaturity‐onset diabetes of the young type 13 (MODY13), a rare type of monogenic diabetes, is often misdiagnosed as type 1 or type 2 diabetes. To improve early diagnosis and precise treatment, we performed a systematic review and analysis of the literature about MODY13.MethodsPubMed, Cochrane, Embase, China National Knowledge Infrastructure (CNKI), Chinese BioMedical (CBM) Literature Database, and Wanfang Database were searched using the following search terms: “MODY13,” “KCNJ11 maturity‐onset diabetes of the young,” “KCNJ11‐MODY,” “maturity‐onset diabetes of the young type 13,” and “neonatal diabetes mellitus KCNJ11.” The demography, clinical characteristics, and gene mutations of patients were expressed with descriptive statistical methods.ResultsA total of 33 reports were included in this study, including 75 patients and 28 types of mutations. Thirty‐six patients were male. The mean onset age was 25.20 ± 15.26 years. The averages of recorded body mass index, glycated hemoglobin (HbA1c), and fasting C‐peptide were 23.45 ± 4.56kg/m2, 10.07 ± 1.96%, and 0.31 ± 0.23nmol/L, respectively. Most of the mutation sites were located in the cytosolic region of N‐ and C‐terminal domains of Kir6.2. Seven patients were reported to have diabetic chronic complications.ConclusionMODY13 was diagnosed later than other types of MODY and was associated with low fasting C‐peptide. Mutation sites of MODY13 were mostly concentrated in N‐ and C‐terminal intracellular domains. The majority of KCNJ11 gene mutations causing MODY 13 were from G to A. The incidence rates of chronic complications were lower than type 1 and type 2 diabetes.image
Current applications of algorithmic artificial intelligence in interventional radiology: A review of the literature
Authors: O'Brien Andrew J , Vrazas John I , Clements Warren 
Published: December 2023

SummaryArtificial intelligence is a rapidly evolving area of technology whose integration into healthcare delivery infrastructure is predicted to have profound implications for medicine delivery in the 21st century. Artificial intelligence as it relates to healthcare is a term used to cover a wide scope of computer‐based algorithms whose application varies from patient selection to enhancements in imaging and postoperative prognostication. This article reviews the literature to contextualise how AI is currently being implemented in interventional radiology. This review considers the literature from a preoperative, intraoperative and postoperative perspective.
Deep learning‐based facial analysis for predicting difficult videolaryngoscopy: a feasibility study
Authors: Xia M. , Jin C. , Zheng Y. , Wang J. , Zhao M. , Cao S. , Xu T. , Pei B. , Irwin M. G. , Lin Z. , Jiang H. 
Published: December 2023

SummaryWhile videolaryngoscopy has resulted in better overall success rates of tracheal intubation, airway assessment is still an important prerequisite for safe airway management. This study aimed to create an artificial intelligence model to identify difficult videolaryngoscopy using a neural network. Baseline characteristics, medical history, bedside examination and seven facial images were included as predictor variables. ResNet‐18 was introduced to recognise images and extract features. Different machine learning algorithms were utilised to develop predictive models. A videolaryngoscopy view of Cormack‐Lehane grade of 1 or 2 was classified as ‘non‐difficult’, while grade 3 or 4 was classified as ‘difficult’. A total of 5849 patients were included, of whom 5335 had non‐difficult and 514 had difficult videolaryngoscopy. The facial model (only including facial images) using the Light Gradient Boosting Machine algorithm showed the highest area under the curve (95%CI) of 0.779 (0.733–0.825) with a sensitivity (95%CI) of 0.757 (0.650–0.845) and specificity (95%CI) of 0.721 (0.626–0.794) in the test set. Compared with bedside examination and multivariate scores (El‐Ganzouri and Wilson), the facial model had significantly higher predictive performance (p < 0.001). Artificial intelligence‐based facial analysis is a feasible technique for predicting difficulty during videolaryngoscopy, and the model developed using neural networks has higher predictive performance than traditional methods.
Integrating novel immunotherapeutic approaches in organ‐preserving therapies for bladder cancer
Authors: Michaud Éva , Mansure José Joao , Kassouf Wassim 
Published: December 2023

AbstractBladder cancer (BC) is a prevalent malignancy with significant morbidity and mortality. Over the years, the landscape of bladder cancer treatment has witnessed notable advancements, particularly in the realm of immunotherapy. Immunotherapy has emerged as a promising adjunct to organ‐preserving approaches, harnessing the immune system's potential to target and eliminate cancer cells. Organ preservation strategies offer viable alternatives to radical cystectomy to avoid the morbidities associated with radical surgery, as well as to respond to the needs of patients unfit for or who have refused surgery. However, the challenge lies in achieving durable disease control while minimizing treatment‐related toxicities. This review highlights the significance of immune checkpoint inhibitors, such as anti‐programmed cell death 1 (PD‐1)/programmed cell death 1 ligand 1 (PD‐L1) antibodies, in the treatment of localized bladder cancer. The clinical efficacy of immune checkpoint inhibitors, as both neoadjuvant and adjuvant therapies in combination with radiation or chemotherapy, is discussed. Moreover, the potential of immunotherapies beyond immune checkpoint inhibition, including combinations with bacillus Calmette–Guérin (BCG) instillations and/or investigational gene therapies, is explored. Furthermore, the predictive value of the tumour immune microenvironment for the success of these strategies is examined. Understanding the complex interplay between tumour immunity and therapeutic interventions can aid in identifying predictive biomarkers and tailoring personalized treatment strategies. Further research and clinical trials are warranted to optimize the use of immunotherapy in conjunction with organ‐preserving therapies, potentially leading to enhanced patient outcomes and quality of life.