Methods in molecular biology (Clifton, N.J.)Xiaoqian Shi-Kunne, Jan A L van Kan
The availability of a high-quality genome assembly facilitates the analysis of fungal genomes. This chapter outlines the tools and steps involved in genome sequence assembly and annotation of a plant pathogen, Botrytis cinerea. We describe the use of Illumina short-read and Oxford Nanopore long-read sequencing data to assemble the B. cinerea genome. The steps include the pre-processing of sequencing data, genome assembly using Flye, scaffolding with NtLink, and polishing with Racon, Medaka, and NextPolish. The quality of the final assembly is evaluated using BUSCO, which serves as a benchmark for the completeness of a genome. We also provide details on the identification and masking of repetitive elements using the EarlGrey pipeline, as well as the gene prediction and annotation process with Funannotate. The methodologies and insights described can be applied to genome research in other fungal species.
Methods in molecular biology (Clifton, N.J.)Benjamin L Kidder
The rapid growth of biomedical literature has created an urgent need for computational tools that enable researchers to systematically analyze publication trends, identify emerging research themes, and map the evolution of scientific fields. PubMed Atlas is a command-line and web-enabled workflow for topic-driven bibliometrics and trend intelligence using PubMed E-utilities. The pipeline executes PubMed queries, retrieves matching PMIDs, downloads full metadata records in batches, parses structured information (title, abstract, authors/affiliations, MeSH terms, publication types, grants, keywords, DOI), and stores normalized data in a local SQLite database for rapid querying and visualization. A Streamlit dashboard provides interactive exploration of publication trends, journal distributions, MeSH term summaries, geographic distributions, and recent article browsing with direct PubMed links. This protocol describes the installation, configuration, and operation of PubMed Atlas for cancer stem cell and stem cell transcriptional network research, and other fields, enabling investigators to conduct reproducible bibliometric analyses and identify knowledge gaps in rapidly evolving fields.
Scandinavian journal of caring sciencesİlknur Özkan, Seçil Taylan
BACKGROUND: Caring behaviours constitute one of the most visible ways in which "caring" is translated into everyday nursing practice, yet the field has become increasingly heterogeneous across settings, outcomes, and conceptual traditions. A field-level map is therefore needed to clarify how the literature has evolved and where it is currently concentrating. OBJECTIVE: This study aimed to bibliometrically map the literature on caring behaviours in nursing, focusing on global research trends, thematic development, collaboration networks, citation performance, and the field's intellectual structure. METHODS: A bibliometric analysis was conducted on publications indexed in the Web of Science Core Collection between 1987 and 2025, following the SALSA framework. Analyses included performance indicators (publication growth; most productive journals and countries), Author Keyword-based frequency, trend-topic, co-occurrence, and thematic analyses following synonym merging and spelling harmonization, co-authorship network analysis (collaboration patterns), citation analyses, and co-citation mapping to examine the field's intellectual structure. RESULTS: A total of 351 documents from 158 sources (1987-2025) were included. The literature demonstrated steady growth, accelerating after 2016. Core source outlets included BMC Nursing, Journal of Nursing Administration, and Perspectives in Psychiatric Care. The USA, Iran, China, and Turkey were among the most productive countries, while international co-authorship remained limited (14.25%). Thematic signals suggested a shift from earlier emphases on patient satisfaction toward a more recent focus on nursing education, empathy, emotional intelligence, and, most recently, compassion fatigue. The thematic map positioned caring behaviours within the basic-themes quadrant, whereas work environment and related humanistic-care concepts showed greater thematic development. Foundational influences remained anchored in Watson and Swanson, and measurement-oriented works (notably Wu and Wolf) functioned as key intellectual bridges. CONCLUSIONS: Caring behaviours research appears to be a maturing but still expanding field with strong theoretical and measurement "anchors," yet comparatively constrained cross-national collaboration. Future work may benefit from more internationally coordinated programmes and greater attention to cross-cultural validation of measurement tools and to the emotional, organizational, and digitally mediated contexts in which caring behaviours are enacted.
OBJECTIVE: To identify culturally relevant functioning issues experienced by Indian adults with knee osteoarthritis (KOA) using the International Classification of Functioning, Disability and Health (ICF) framework. METHODS: A qualitative descriptive study using semi-structured focus group interviews was conducted with 38 ambulatory adults (35-85 years) diagnosed with knee osteoarthritis (KOA). Participants were recruited from physiotherapy outpatient departments and community settings using maximum variation sampling. Interviews were conducted in Gujarati, audio-recorded, transcribed verbatim, translated into English and analysed using reflexive thematic analysis. Meaningful concepts were systematically linked to ICF categories using established linking rules. Dual independent coding and consensus discussions ensured the analytic rigour. RESULTS: This study included 38 participants with KOA. Fifty-five meaningful second-level categories were identified. The most represented components were activities and participation (41.2%) and body functions (29.4%). Frequently mapped first-level categories included mobility (n = 22), neuromusculoskeletal and movement-related functions (n = 9), d6 domestic life (n = 10), community, social and civic life (n = 7) and products and technology (n = 9). Sixteen additional categories not represented in the existing ICF Core Set for OA emerged, particularly relating to culturally embedded activities such as floor sitting, squatting for toileting and religious participation. Environmental barriers, including inaccessible infrastructure and limited rehabilitation services, influenced disability experience. CONCLUSION: Functioning among Indian adults with KOA is influenced by culturally embedded participation demands and contextual barriers that are insufficiently captured in the existing ICF Core Set for osteoarthritis (OA). These findings provide preliminary empirical support for contextual validation of the ICF Core Set for OA and inform potential culturally responsive adaptation for KOA.
Pakistan journal of pharmaceutical sciencesLi Liqing, Liu Jie
BACKGROUND: The pharmaceutical industry is a strategic emerging sector in China, yet its scientific and technological innovation network remains poorly characterized in terms of structural dynamics and evolutionary pathways. OBJECTIVES: In the field of scientific and technological innovation in China's pharmaceutical industry, this study systematically sorts out the context of research, reveals the structural characteristics and evolutionary laws of the innovation network and provides references for industrial policy formulation and enterprise strategic layout. METHODS: Based on 602 relevant papers collected from the China National Knowledge Infrastructure (CNKI) from 1996 to 2024, VOSviewer and CiteSpace software were comprehensively used to conduct co-occurrence analysis, cluster analysis and burst term detection, so as to construct a multi-dimensional dynamic network model. RESULTS: The number of published papers on scientific and technological innovation in China's pharmaceutical industry increased, with accelerated growth and greater volatility after 2010. A core author group has initially taken shape, but the participation rate of enterprises is only 8.3%, indicating insufficient industry-university-research collaboration. Research hotspots have expanded from traditional biomedicine to emerging technologies such as artificial intelligence-assisted drug design and mRNA vaccines, with industrial clusters and factor collaboration becoming new focuses. CONCLUSION: The innovation of the pharmaceutical industry follows a phased evolutionary path of "technology-driven - cluster development - factor collaboration". At present, it is confronted with structural constraints such as inadequate data sharing, unbalanced resource allocation and a shortage of interdisciplinary talents. It is suggested that enterprises' dominant position in innovation be strengthened, a cross-regional public R and D data platform for the pharmaceutical industry be established, policy incentives shift from project funding to performance-based rewards for innovation alliances and the industry evolve into an adaptive innovation ecosystem.
International journal of psychology : Journal international de psychologieIgor de Almeida, Yukiko Uchida, Kongmeng Liew, Lean Franzl Lim Yao, Eiji Aramaki
Culture significantly influences human psychology, making it essential for psychological research, particularly in social psychology, to acknowledge its importance. However, the majority of psychological research ignores or marginalises culture and context. This is problematic because, despite representing a small portion of humanity (specifically Western, Educated, Industrialized, Rich and Democratic (WEIRD) populations) mainstream psychology is published as if it represented the whole humanity. Among the subfields of psychology, social psychology is arguably the one in which this issue should be least prevalent. To investigate this, we conducted a study on titles and abstracts of articles from 69 social psychology journals published between 1990 and 2020, examining how cultural diversity and awareness of its importance changed over time. The results indicate that cultural awareness is more prominent in journals focused on culture, international or local issues; while remaining almost entirely absent in journals focused on theory, reviews and business. Furthermore, cultural awareness displays an imbalance regarding culture: while WEIRD mentions remain most common, mentions of other regions appear to be disproportionately represented or 'inflated' in specific contexts. The generalizability of psychological theories will remain impossible if culture is not integrated as a central factor in research.
Rapid communications in mass spectrometry : RCMNanna Sofie Eskesen, Yann Leblanc, Justine Lempereur, Martin Ørgaard, Elizabeta Madzharova, Trine M Sloth, Simon Krabbe, Alexandra K Rebak, Magali André, Perni…
RATIONALE: Non-reduced trypsin digestion of therapeutic antibodies can generate large disulfide-linked peptide complexes that exhibit poor chromatographic and mass spectrometric performance. This limits the confident characterization of posttranslational modifications (PTMs) in specific antibody regions, such as the heavy-chain constant region 1 (CH1) domain, where conventional digestion produces 8-kDa complexes with poor fragmentation. METHODS: We developed automated multistep and multienzyme digestion workflows using immobilized trypsin, chymotrypsin, and proteinase K on magnetic beads. These workflows were implemented on a robotic platform and evaluated for their ability to characterize engineered cysteine residues in the CH1 domain of antibody-drug conjugate (ADC) intermediates. Analysis was performed using liquid chromatography-tandem mass spectrometry (LC-MS/MS). RESULTS: The multienzyme workflows generated highly orthogonal peptide pools; for instance, selected workflows using trypsin only, trypsin combined with chymotrypsin, and trypsin combined with proteinase K yielded 13%, 14%, and 34% unique peptide identifications, respectively. In the challenging CH1 region, the multienzyme approach identified six distinct cysteine adducts at engineered Cys152. These included cysteinylation, homocysteinylation, and an unexpected, putative process-related impurity, thioglycolic acid capping, which was validated with unambiguous MS and MS/MS evidence using selected multienzyme workflows. Relative extracted-ion current-based levels of these cappings were observed and found to be similar across selected workflows; for instance, relative levels of thioglycolic acid capping from 12% to 15% were observed across selected workflows. CONCLUSIONS: The presented automated multienzyme workflows serve as complementary tools in an analytical toolbox, which can be strategically deployed for targeting challenging regions of biopharmaceutical products. We demonstrate significantly improved precursor signal quality and MS/MS sequence coverage compared to trypsin-only protocols. The presented workflows are fast (36-92 min total runtime) and utilize commercially available reagents and instrumentation, making them suitable for direct implementation in biopharmaceutical analytical development and quality control laboratories.
Personality and mental healthGunnar Valdemar Grunert, Erik Simonsen, Mickey T Kongerslev, Bo Bach
The new ICD-11 Personality Disorder (PD) classification introduces a global severity classification (i.e., mild, moderate, and severe) of personality dysfunction, which may be further accompanied by up to five trait domain specifiers delineating individual manifestations of personality disturbance (i.e., Negative affectivity, Detachment, Dissociality, Disinhibition, and Anankastia). Although these trait domains are conceptualized as dimensions, the ICD-11 only allows clinicians to code them as being categorically present versus absent. It is therefore appropriate to examine the ability of clinicians' judgements in capturing variance in trait domains using dichotomous trait ratings. A total sample of 238 patients was characterized by their clinicians using both dimensional and dichotomous single-item ratings for each trait domain. Subsequently, clinicians filled out the Informant Personality Inventory for ICD-11 (IPiC) as a standardized criterion-measure for trait domains. The dichotomous ratings were all moderately associated with their corresponding IPiC score, except for Negative Affectivity, which only showed a small but statistically significant association. The dimensional ratings were all moderately to strongly associated with their corresponding IPiC scores. However, only the dimensional single-item ratings of Disinhibition and Dissociality were significantly superior to the dichotomous single-item ratings in capturing the IPiC trait domain scores. Findings overall support the use of categorical assignment of trait domain specifiers in the ICD-11 although dimensional formats improve the accuracy of clinicians' judgements.
Endocrinology, diabetes & metabolismYanbing Wang, Zhanru Liu, Shifeng Wang, Cuiyan Lv, Hesham R El-Seedi, Shaden A M Khalifa, Haiyan Wang
AIM: To characterize the global development, collaboration structure, publication landscape, citation influence and thematic evolution of research on selective GLP-1 receptor agonists and GLP-1-based multi-receptor agonists in T2DM. METHODS: A bibliometric analysis was conducted on 3736 original articles published between 2004 and 2025 and retrieved from the Web of Science Core Collection. Publication trends, research contributions, collaboration networks, citation impact and thematic evolution were evaluated using complementary bibliometric indicators and network analysis. RESULTS: Annual publication output increased substantially. Selective-only studies remained the cumulative core of the evidence base, while mixed/comparative and multi-receptor-only studies expanded rapidly in recent years. The United States led in research output and international connectivity, and Novo Nordisk and Eli Lilly were the most prominent institutional contributors based on author affiliation analysis. Diabetes, Obesity and Metabolism was the leading source journal. Research output was highly concentrated across countries but more widely distributed across institutions and authors. Thematic emphasis shifted from incretin biology and glycemic efficacy toward cardiovascular and kidney outcomes, obesity, integrated treatment strategies and real-world evidence. Major trials, particularly LEADER and REWIND, and ADA/EASD consensus statements exerted strong citation influence. Sensitivity analysis supported the overall robustness of the principal findings. CONCLUSIONS: Research on GLP-1-based agonists in T2DM has expanded rapidly and shifted toward an integrated cardiovascular-kidney-metabolic framework. Studies of selective GLP-1RAs remain central to the literature, while studies of newer GLP-1-based multi-receptor agonists are contributing to its diversification. Evidence remains comparatively less developed for longer-term outcomes of emerging agents, treatment sustainability in routine care, patient experience and diverse populations and settings.
BACKGROUND: Sleep deprivation and poor sleep quality are critical problems among intensive care unit (ICU) patients, with significant implications for recovery, delirium onset and clinical outcomes. Despite growing scientific interest, no bibliometric study has systematically mapped the intellectual structure and thematic evolution of this field. AIM: To analyse the bibliometric characteristics and thematic structure of publications on sleep deprivation, sleep promotion and sleep quality in ICU patients indexed in the Web of Science (WoS) database between 1983 and 2026. STUDY DESIGN: A descriptive and evaluative bibliometric analysis was conducted. Data were retrieved on April 26, 2026, from the WoS Core Collection using a comprehensive search strategy. Publications were filtered by document type, WoS categories (nursing, critical care medicine, anaesthesiology) and index (SCI-EXPANDED, SSCI, ESCI). Data were analysed using R software with the Biblioshiny interface, and annual publication trends were evaluated using Microsoft Excel. RESULTS: Of 11 418 publications retrieved, 379 met the inclusion criteria, spanning 37 years (1983-2026). Linear regression revealed a statistically significant positive trend in publication output (β = 0.643, R2 = 0.704, r = 0.839, p < 0.001), with mean annual publications of 10.24 ± 8.83 and notable acceleration from the 2000s onwards. Thematic mapping identified 'sleep', 'sleep deprivation' and 'delirium' as motor themes both highly central and well developed. Emerging concepts included circadian rhythm, actigraphy, fatigue, pain and anxiety. CONCLUSIONS: ICU sleep research has grown substantially over four decades, with sleep deprivation and delirium emerging as co-dominant research priorities. Thematic gaps and emerging clusters identified in this analysis highlight important directions for future nursing research and evidence-based practice development in critical care. RELEVANCE TO CLINICAL PRACTICE: This bibliometric analysis identified sleep deprivation and delirium as the co-dominant motor themes of ICU sleep research, and intervention-related concepts such as earplugs, eye masks and melatonin as emerging clusters. These evidence-based trends can guide ICU nurses in prioritizing targeted sleep promotion protocols and support policymakers in directing resources toward the most scientifically mature intervention areas in critical care.
Personality and mental healthAgnė Grigaitė, Elena Gaudiešiūtė, Joost Hutsebaut, Rasa Barkauskienė
As personality functioning has become central to contemporary conceptualizations of personality pathology, understanding its structure and optimal assessment has emerged as an important research priority, particularly in adolescence. This study examined the latent structure of the Semi-Structured Interview for Personality Functioning DSM-5 (STiP-5.1) and its incremental validity in predicting functional impairment beyond self-reported personality functioning. Participants were 178 adolescents aged 11-18 years, including a clinical sample (n = 104) and a community sample (n = 74). Confirmatory factor analyses (CFA) and bifactor modeling were used to evaluate the latent structure of the STiP-5.1. Hierarchical regression analyses examined whether clinician-rated personality functioning explained additional variance in functional impairment (WHODAS 2.0) beyond self-reported personality functioning assessed with the LoPF-Q 12-18 Short. The bifactor model demonstrated the best overall fit and supported the predominance of a strong general factor. Most reliable variance was attributable to this factor, whereas self- and interpersonal-specific factors contributed little unique variance. A four-factor CFA model also demonstrated excellent fit, supporting differentiation among identity, self-direction, empathy, and intimacy. Clinician-rated personality functioning explained additional variance in functional impairment beyond self-report measures. Self-functioning, particularly the element of self-direction, emerged as a unique predictor of functional impairment. Findings support a predominantly unidimensional conceptualization of personality functioning in adolescence while retaining clinically meaningful differentiation across LPFS domains and elements. The STiP-5.1 provides unique information beyond self-report assessment, supporting multimethod approaches to the assessment of personality functioning in adolescents.
Nursing in critical careSeher Ünver, Seda Cansu Yeniğün Akbulut
BACKGROUND: Delirium is a common and serious postoperative complication in intensive care units, associated with increased morbidity, mortality and long-term cognitive impairment, and despite the pivotal role of nurses in its assessment and management, variations in prevalence and gaps in intervention-focused nursing research persist, underscoring the need for a bibliometric evaluation of the literature. AIM: The aim of the study was to quantitatively analyse and visually map trends, citations, key terms and country contributions in nursing research on postoperative delirium in intensive care as well as to characterize the overall structure of the literature. STUDY DESIGN: This study was conducted as a retrospective and descriptive research using the bibliometric analysis method on December 1, 2025. No time restrictions were imposed on the literature. Data analysis was performed using R Studio software. RESULTS: The earliest study on postoperative delirium in intensive care units within the field of nursing was published in 2001, and the analysed publications covered the period from 2001 to December 2025. In addition, 55.96% of all publications have been released in the past 7 years. The journal with the highest number of publications is Nursing in Critical Care, while the United States stands out as the country with the highest research output. It can be suggested that topics such as 'cardiac surgery', 'nursing care', 'postoperative delirium', 'postoperative care' and the 'Confusion Assessment Method for the Intensive Care Unit' represent areas that warrant further investigation and development in future research. CONCLUSIONS: The analysis showed a marked increase in publications on postoperative delirium in intensive care nursing in recent years. The United States and the Journal Nursing in Critical Care were identified as the leading contributors to the literature. Thematic mapping indicated that the literature primarily focused on delirium assessment and intensive care nursing, with several interconnected research areas. RELEVANCE TO CLINICAL PRACTICE: The findings emphasize the critical role of nurses in delirium screening and management in intensive care units. While assessment tools are well represented in the literature, further research is needed to develop and evaluate nurse-led interventions aimed at delirium prevention and care. Enhancing nursing education and institutional support may contribute to improved patient outcomes and quality of postoperative intensive care.
Protein science : a publication of the Protein SocietyAdeyemi Ogunbowale, Elaheh Hadadianpour, Olamide Ishola, Md Majharul Islam, Natalie Ramos, Arvin Saffarian Delkhosh, Elka R Georgieva
HIV-1 Vpu supports viral adaptation through host-protein interactions. Although mainly membrane-associated, we recently identified a soluble Vpu form that forms a stable complex with Ca2+-bound calmodulin (Ca2+-CaM), potentially influencing Vpu trafficking. Here, to determine the binding affinity and identify regions of soluble Vpu involved in CaM binding, we used ensemble Förster resonance energy transfer (eFRET). We tested Cy3-labeled full-length (FL) Vpu, a C-terminal fragment (helices 2 and 3), and a Cy3-labeled FL Vpu V22A/W23Y/I33N mutant with substitutions of key residues in Vpu's helix 1 and helices 1-to-2 loop having a role in the interaction with Ca2+-CaM. All Vpu variants were labeled at residue L42C. Ca2+-CaM was tagged with Cy5 at residue S39C. eFRET analysis of 100 nM Cy3-Vpu variants mixed with Cy5-Ca2+-CaM (in the range 100 nM-2.5 μM) revealed heterocomplexes formation with characteristic dissociation constants (Kd) and binding free energies (∆G). FL Vpu-Ca2+-CaM showed highest stability (Kd ~74 nM, ∆G ~-9.7 kcal/mol), while the truncated C-terminal region and V22A/W23Y/I33N mutant formed weaker complexes with Ca2+-CaM (Kd~182 nM and 800 nM, ∆G ~-9.2 kcal/mol and ~-8.3 kcal/mol). The reduced Vpu-Ca2+-CaM stability after disruption of binding sites in and near Vpu helix 1 may explain how this interaction is regulated, including through lipid competition that promotes Vpu membrane insertion. We propose that, at the membrane, hydrophobic helix 1 dissociates from Ca2+-CaM and inserts into the lipid bilayer, weakening the complex and releasing CaM. These findings clarify HIV-1 Vpu interactions with cellular components and may inform antiviral development.
Protein science : a publication of the Protein SocietyAlina K Bakunova, Ilya O Matyuta, Mikhail E Minyaev, Konstantin M Boyko, Vladimir O Popov, Ekaterina Yu Bezsudnova
Pyridoxal-5'-phosphate (PLP)-dependent enzymes of fold type IV exhibit remarkable catalytic diversity, catalyzing either S- and R-selective transamination or β-elimination within a highly conserved structural scaffold. Here, we report the identification, biochemical characterization, and structural analysis of PLP fold type IV 4-amino-4-deoxychorismate lyase (ADCL) from Micromonospora aurantiaca (Micau5708). Sequence-structural analysis revealed a hybrid architecture of the active site of Micau5708. It combines a D-amino acid transaminase (DATA) conserved phenylalanine (F30) and arginine (R87) residues with an ADCL-specific threonine residue (T32) and a (R)-selective amine transaminase-specific histidine residue (H25). While Micau5708 shows only ADCL activity, substitution H25R introduces transamination activity, preserving ADCL activity. The 1.85 Å resolution crystal structure of Micau5708 in complex with substrate analog chorismate provides the first direct visualization of substrate binding in an ADCL active site. Site-directed mutagenesis, together with comparative analysis of DATAs of group II demonstrates that ADCL/DATA catalytic promiscuity is enabled by a specific amino acid combination in the active site: phenylalanine, threonine, and arginine residues (F30, T32, and R87), and arginine at position 25 with a flexible side chain. Furthermore, the Micau5708-chorismite complex structure has helped revise the catalytic mechanism of ADCLs, demonstrating the T32 assistance in protonation of the oxygen atom rather than the β-methylene carbon of the leaving enol-pyruvate. Together, these findings provide new insights into the structural basis of reaction specificity, catalytic promiscuity, and evolutionary plasticity within the PLP fold type IV enzyme superfamily. They also highlight the limitations of sequence-based functional prediction.
Journal of peptide science : an official publication of the European Peptide SocietyUyen N P Nguyen, Yen N D Pham, Hoang Vu Dinh, Dang Ngoc Quang, Tran Dinh Thang, Tran Dai Lam, Tien T Dang
Plant-derived peptides represent a rich source of structurally diverse and biologically potent scaffolds, characterized by high stability and a wide range of mechanisms of action. This review examines the structure-activity relationships (SAR) of these peptides, focusing on how key structural features-including disulfide connectivity, loop architecture, charge distribution, and backbone cyclization-govern their biological activity, selectivity, and toxicity. Representative peptide families such as cyclotides, defensins, thionins, and snakins are discussed to highlight conserved structural motifs alongside variable regions that contribute to functional diversity. We further explore rational design and engineering strategies, including loop grafting, cyclization, charge modulation, and backbone stabilization, supported by selected case studies demonstrating improved pharmacological profiles, membrane interactions, and target specificity. Building on these insights, we propose a design-oriented framework that integrates SAR-guided peptide engineering with experimental toxicology and pharmacological evaluation to facilitate the development of plant-derived peptides as therapeutic leads and molecular tools. This peptide-centric perspective aims to complement existing studies on plant bioactive peptides and to advance the rational design of next-generation peptide-based therapeutics.
Zhonghua yi xue yi chuan xue za zhi = Zhonghua yixue yichuanxue zazhi = Chinese journal of medical geneticsLi Xiao, Xiaowei Zhu, Rongrong Dou, Aihua Huang, Yonglin Yang
OBJECTIVE: To report on a case of Dubin-Johnson syndrome (DJS) with a rare ABCC2 nonsense variant. METHODS: Clinical, histopathological, MRP2 immunohistochemical, and whole-exome sequencing findings were retrospectively analyzed. This study was approved by the Medical Ethics Committee of Taizhou People's Hospital (Ethics No.: 20250522). RESULTS: A 58-year-old woman with mild conjugated hyperbilirubinemia with normal aminotransferases and cholestatic enzymes, and black liver was incidentally discovered during laparoscopy. Histology showed melanin-like pigment deposition, and MRP2 immunohistochemistry was negative. Two heterozygous ABCC2 variants, namely c.2063T>C and c.4120C>T, were identified. The previously unreported nonsense variant c.4120C>T was predicted to truncate the MRP2 protein within the second nucleotide-binding domain (NBD2). Retrospective analysis of SLCO1B1 and SLCO1B3 had not identified any pathogenic/likely pathogenic variants for Rotor syndrome. As family samples were unavailable, the allelic phase of the two ABCC2 variants could not be determined. CONCLUSION: The clinical, histopathological, and immunohistochemical findings in the woman had supported the diagnosis of DJS. The two unphased heterozygous ABCC2 variants provided supportive molecular evidence, but confirmation of biallelic involvement requires further segregation or phase analysis.
Zhonghua yi xue yi chuan xue za zhi = Zhonghua yixue yichuanxue zazhi = Chinese journal of medical geneticsLei Zheng, Yanhong Wang, Yajun Lian, Shiyue Mei, Xuechao Zhao
OBJECTIVE: To explore the pathogenicity and characteristics of a heterozygous splicing variant of SCN1A gene in a Chinese pedigree affected with Genetic epilepsy with febrile seizures plus (GEFS+). METHODS: A retrospective analysis was carried out on the clinical data and results of genetic testing of a GEFS+ pedigree consisting of 5 members who had visited the First Affiliated Hospital of Zhengzhou University on July 1, 2024. Pathogenicity of the splicing variant of the SCN1A gene was validated with a minigene splicing assay. This study was approved by the Medical Ethics Committee of the the First Affiliated Hospital of Zhengzhou University (Ethics No.: KS-2018-KY-36). RESULTS: The proband, a 24-year-old female, presented with FS in conjunct with focal seizures, and both of her younger brothers had Dravet syndrome. All of the three patients had carried a c.4476+5G>T variant of the SCN1A gene, which was unreported previously. Minigene experiment verified that the variant could cause loss of the first 7 bps of exon 24 and 138 bps from exon 23 of the SCN1A gene, resulting in alteration p.V1447_1495delfs*6 and affecting splicing. Based on the guidelines from American College of Medical Genetics and Genomics (ACMG), the variant was predicted as likely pathogenic (PVS1+PM2_Supporting). CONCLUSION: The c.4476+5G>T variant at an intronic site of the SCN1A gene probably underlay the pathogenesis of GEFS+ in this pedigree.
Zhonghua yi xue yi chuan xue za zhi = Zhonghua yixue yichuanxue zazhi = Chinese journal of medical geneticsChao Geng, Shaofang Shangguan, Xiaoli Chen, Lin Wang, Hua Xie
OBJECTIVE: To explore the genetic characteristics and clinical phenotypes of three children with novel DEAF1 gene variants. METHODS: Three children who were referred to Capital Children's Medical Center Affiliated to Capital Medical University between January 2018 and December 2025 were selected as study subjects and underwent whole exome sequencing (WES). Candidate variants were verified by Sanger sequencing, and their pathogenicity was evaluated based on the guidelines from American College of Medical Genetics and Genomics (ACMG). A systematic search of databases including PubMed and CNKI was conducted to compile previously reported cases of DEAF1 variants for clinical phenotype comparison. For the non-canonical splice site variant c.870+5G>C located in the intronic region, wild-type and mutant minigene reporter vectors were constructed and transfected into HeLa and 293T cells, respectively, and the splicing patterns were analyzed by RT-PCR and Sanger sequencing. This study was approved by the Medical Ethics Committee of Capital Institute of Pediatrics (Ethics No.: SHERLL 2020001). RESULTS: All three children were found to have carried de novo heterozygous variants of the DEAF1 gene, including two missense variants (c.764G>A, c.641T>C) in the important SAND domain and a splice site variant (c.870+5G>C) in a non-canonical splicing region. The c.764G>A and c.870+5G>C variants were unreported previously. All children had presented with intellectual developmental delay, and two were accompanied by autism spectrum disorder, and two had epilepsy and sleep disorders. In vitro minigene splicing assay showed that the c.870+5G>C variant can lead to abnormal splicing. CONCLUSIONS: This study reported three children with novel DEAF1 variants, two of which have not been previously described, thereby enriched the mutational spectrum of the DEAF1 gene. In vitro functional assay combined with the clinical manifestations of the patients confirmed the pathogenicity of the non-canonical splice site variant in the intronic region.
World journal of microbiology & biotechnologyJinqi Kou, Hongbo Yan, Ju Zhang, Weidong Sun, Yintong Zhang, Haiyue Nan
To characterize the genomic features of the extracellular polysaccharide-overproducing strain Schizophyllum commune SC-N, genome assembly and functional annotation were performed using a hybrid sequencing strategy combining Nanopore long reads and Illumina short reads, followed by comparative genomic analyses with S. commune H4-8 and representative basidiomycetes. The SC-N genome was 45.62 Mb in size, with a GC content of 55.45% and a contig N50 of 3.71 Mb. A total of 13,832 protein-coding genes were predicted, and the BUSCO completeness score reached 95.12%. In independent fermentation experiments, SC-N produced 3.91 g/L of extracellular polysaccharide (EPS), and Fourier transform infrared spectroscopy (FTIR) revealed spectral features consistent with a β-glucan-rich EPS. Comparative genomic analyses showed that, within the selected comparative panel, SC-N contained 131 strain-specific orthologous groups comprising 531 predicted protein-coding genes. The composition of carbohydrate-active enzyme families, particularly glycosyltransferases (GTs), glycoside hydrolases (GHs), and carbohydrate esterases (CEs), differed markedly between SC-N and the closely related reference strain S. commune H4-8. In addition, local tandem duplication patterns were observed in genes associated with ORP/Osh proteins, glucose-6-phosphate dehydrogenase (G6PD), GTP cyclohydrolase II, and the E1 component of 2-oxoglutarate dehydrogenase. The copy number of the GT48 family was generally conserved among the compared strains, whereas differences between SC-N and S. commune H4-8 were observed in the predicted transcription factor-binding motif composition of the upstream regions of FKS1 and FKS2 and in local predicted protein structural features. Collectively, these findings reveal distinctive genomic features of SC-N related to carbohydrate metabolism, membrane homeostasis, and β-glucan-associated functional modules, providing a genomic foundation for further elucidation of its enhanced EPS-producing phenotype and for functional validation of key candidate genes.
Journal of helminthologyW B B Sousa, W T Hasuike, P O F Yamada, M F B G Diniz, B Scorsim, M Tavares-Dias, A V Oliveira, R M Takemoto, F H Yamada
Using an integrative taxonomic approach, we describe two new species of Monopisthocotyla, Mymarothecioides leporini n. sp. and Mymarothecioides paranaensis n. sp., parasitising the gills of anostomid fishes from the Jaguaribe River and Paraná River basins, Brazil. These descriptions represent the first record of species of Mymarothecioides in hosts of the family Anostomidae. Mymarothecioides leporini n. sp. is distinguished by a male copulatory organ (MCO) with a spoon-shaped distal portion and a ventral bar with an ornamented anteromedial process. Mymarothecioides paranaensis n. sp. differs from its congeners by possessing a sclerotised, arcuate MCO with a rounded tip and a rectangular-shaped basal flap. Molecular analyses of Large Subunit ribosomal DNA (LSU rDNA) and Mitochondrial Region of Cytochrome C Oxidase subunit 1 (COI mtDNA) markers support the validity of both taxa, placing them as distinct molecular operational taxonomic units (MOTUs). High genetic distances (17.8%-18.7% for COI) confirmed the separation between the two new species. Additionally, this study provides the first molecular characterisation for the genus. These findings expand the known geographical distribution and host range of Mymarothecioides, contributing to the knowledge of dactylogyrid diversity in Neotropical freshwater systems.
Archives of orthopaedic and trauma surgerySaidan Shetty, Sandeep Vijayan, K G Mohandas Rao, Sharath K Rao, Yogendra Nayak, Bincy M George
BACKGROUND: Total Knee Arthroplasty (TKA) is one of the fastest-growing orthopaedic procedures in India, driven by demographic transitions, increased life expectancy, and the rising burden of knee osteoarthritis. With expanding procedural volumes, periodic evaluation of scientific output is essential to identify evolving research priorities, institutional leadership, and collaborative patterns. This study aimed to perform a bibliometric analysis of Indian TKA research published over the past five years. METHODS: Publications were retrieved from the Scopus database using a structured search strategy for TKA-related terms. The search was restricted to studies published between 1 January 2021 and 30 December 2025 and conducted in an Indian setting. Bibliometric indicators assessed publication trends, document types, journals, authorship, institutional productivity, and state-wise contributions. Network-based bibliometric visualizations were generated using VOSviewer. RESULTS: A total of 860 publications were identified, showing a steady increase in research output with peak productivity in 2025 (n = 221). Maharashtra and Delhi were the leading contributors, and the All-India Institute of Medical Sciences was the most productive institution. Original research articles accounted for 69.5% of publications. Emerging themes included robotic-assisted surgery, AI-based modeling, and advanced rehabilitation. International collaboration was observed in 24.18% of studies, mainly with the UK and USA. CONCLUSION: Indian TKA research has demonstrated substantial growth and increasing thematic maturity over the past five years, with a shift toward technology-driven and collaborative research. Strengthening national registries, encouraging multicentric collaboration, and expanding research beyond metropolitan centers are essential to sustain future impact. TRIAL REGISTRATION: Not applicable.
MicroRNAs (miRNAs) play essential roles in posttranscriptional regulation of gene expression. During miRNA biosynthesis, miRNA precursors are cleaved by Dicer at their loop structure to generate mature miRNAs. However, the functional consequences of sequence alterations in the loop region remain poorly understood. The silkworm Bombyx mori is a lepidopteran insect with many genetic strains. In a B. mori strain exhibiting translucent larval skin, we unexpectedly identified a mutant form of miR-3260 in which part of the predicted loop structure was deleted. Here, we aimed to analyze the function of wild-type miR-3260 and the impact of this loop structure mutation in B. mori. First, we predicted potential binding partners for wild-type miR-3260 using the RNAhybrid tool and identified eight candidates, including two juvenile hormone (JH)-related genes. Expression analysis revealed high miR-3260 expression in the corpora allata. Furthermore, treatment of BmN cells with JH led to upregulated miR-3260 expression, suggesting a relationship between miR-3260 and JH signaling. Although miR-3260 mimics and inhibitors altered the expression of two JH-related candidate genes, the observed changes were not consistent with the predicted regulatory effects of miR-3260, and no observable larval phenotype was detected. Additionally, analysis of Dicer processing showed that neither the wild-type nor mutant miR-3260 precursor underwent Dicer-mediated cleavage. Although miR-3260 responds to JH, its function as a conventional miRNA was not supported. These findings suggest that miR-3260 may act as a JH-responsive non-coding RNA or represent a novel atypical RNA distinct from canonical miRNAs.
Nuclear medicine communicationsHao Long, Xu-Hua Qiao, Xu Li, Xiang-Jun Kong, Qin-Wen Liu
OBJECTIVE: To characterize publication growth, modality trends, and thematic evolution in prostate-specific membrane antigen (PSMA) radioligand therapy (RLT) for prostate cancer from 2015 to 2025, emphasizing beta-emitting RLT, targeted alpha therapy, and dosimetry-related terminology. METHODS: The Web of Science Core Collection was searched using a prespecified topic strategy. A fixed bibliographic snapshot was exported on 1 January 2026, covering records through 31 December 2025. English-language articles and reviews were included. After screening and postexport cleaning, 908 publications underwent bibliometric analysis using bibliometrix, keyword mapping, and reference co-citation analysis. Therapeutic modality was assigned by deterministic text mining of titles, abstracts, and keywords with a prespecified alpha-priority rule; dual-label analyses assessed alpha/beta co-mentioning. Dosimetry-related terminology was identified using prespecified dictionaries. Two reviewers independently assessed modality in a random sample of 200 records. RESULTS: Annual output increased from four publications in 2015 to 199 in 2025, although 2025 counts should be interpreted cautiously because of possible indexing delay. Under the primary classification, beta-emitting RLT predominated (698/908, 76.9%), whereas alpha-therapy-related publications accounted for 193/908 (21.3%). Under dual labeling, 149/908 publications (16.4%) co-mentioned alpha- and beta-based approaches. Dosimetry-related terminology increased over time and stabilized at approximately one-third of annual output after 2020. Inter-reviewer agreement was nearly perfect (kappa, 0.947-0.949). CONCLUSION: The PSMA RLT literature expanded rapidly and remained dominated by beta-emitting therapy, with increasing alpha-therapy activity and broader incorporation of dosimetry-related terminology. These bibliometric findings characterize publication-level trajectories in PSMA RLT research and suggest priorities for standardized reporting, scalable dosimetry, and prospective treatment-optimization studies.
BMJ openLorenzo Billiet, Stijn De Baets, Dominique Van de Velde, Ruth M A van Nispen, Hilde P A van der Aa
OBJECTIVES: To systematically examine the methodologies used in the development of International Classification of Functioning, Disability and Health (ICF) Core Sets (CSs) across all developmental phases, and to identify methodological variation in stakeholder involvement, geographical representation, consensus procedures and validation approaches to inform the future development of ICF CSs. DESIGN: Scoping review conducted in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses Extension for Scoping Reviews (PRISMA-ScR) and Joanna Briggs Institute methodological guidance. SETTING: Literature published between January 2001 and July 2024. Publications were identified through PubMed, supplemented by reference list screening and author contact where necessary. PARTICIPANTS: We identified 170 relevant publications related to the development, validation and implementation, covering 34 CS across diverse health conditions. Eligible publications comprised preparatory studies (eg, systematic reviews, patient perspective studies, expert surveys), protocol/discussion papers, consensus conference reports, validation and implementation studies. RESULTS: Most publications originated from Europe. The comprehensive CS averaged 97 ICF categories (SD 29) and the brief CS 26 (SD 12). In 38% of the studies, the focus was only on validity research. Variations were observed in patient and expert involvement during development. Considerable variation was observed in stakeholder involvement, geographical representation, consensus procedures and validation approaches across developmental phases. CONCLUSION: This review demonstrates substantial methodological diversity in ICF CS development across the different phases. While the developmental framework proposed by Selb et al was generally reflected across studies, considerable variation existed in how developmental phases were operationalised. Future ICF CS developments may benefit from stakeholder involvement, more balanced geographical representation, and continued attention to validation and implementation activities.
Laboratory medicineYusuf Yesil, Alpay Medetalibeyoglu, Evin Ademoglu
INTRODUCTION: Routine laboratory panels are nearly universal, but the panels' joint information is underused. We evaluated contemporaneous classification of International Statistical Classification of Diseases, Tenth Revision (ICD-10) code groups from same-encounter laboratory results. METHODS: We developed 17 eXtreme Gradient Boosting (XGBoost) classifiers in 242 648 adult internal medicine encounters using age, sex, and results from 34 assays, with ICD-10 codes used only as outcomes. Stratified 10-fold cross-validation assessed discrimination, calibration, and decision curve performance. Leakage-free recalibration and fold-specific thresholds targeted 95% specificity. Using an 80-patient temporal holdout cohort, we compared the model with 3 large language models accessed through an application programming interface and findings from 1 specialist physician. RESULTS: The mean cross-validated area under the curve (AUC) was 0.893. With identical preprocessing, the mean AUC was 0.892 for XGBoost and 0.809 for logistic regression. Recalibration changed the mean intercept and slope to -0.002 and 0.999, respectively, and the Brier score from 0.099 to 0.044. The holdout micro-averaged AUC was 0.880 vs 0.729 to 0.739 for language models; paired differences were 0.141 to 0.151 (all P < .005). Matched-specificity sensitivity differences favored the model but were imprecise. DISCUSSION: Routine panels contain substantial information about contemporaneous ICD-10 coding, supporting prospective multicenter evaluation rather than a diagnostic claim.
Fish physiology and biochemistryJiajun Li, Fengxiao Ji, Yuru Li, Limiao Zhao, Gang Xu, Bin Wang, Jun Chen
The tachykinin family comprises highly conserved neuropeptides that regulate diverse physiological processes in vertebrates. However, the molecular characteristics and reproductive functions of this system remain poorly understood in seahorses, which exhibit the unique reproductive trait of male pregnancy. In the present study, we cloned the major tachykinin ligand genes of the big-belly seahorse (Hippocampus abdominalis) and investigated their temporal expression patterns across the first reproductive cycle, gestation, and brood pouch development via real-time quantitative PCR (RT-qPCR). Open reading frames of tac1 and tac3, as well as two transcript variants of tac4, namely tac4-S and tac4-L, were identified. Sequence alignment and phylogenetic analyses showed that these precursors were conserved among teleosts. Tissue distribution analysis showed that tac1 and tac3 were mainly enriched in the brain-pituitary complex, while tac4 transcripts exhibited marked male-biased expression and tac4-L had a wider peripheral distribution including the testis and brood pouch. Developmental profiling of these genes during the first reproductive cycle revealed distinct age-dependent and sex-dependent patterns, suggesting that tac1 may act mainly during early gonadal development, tac3 may function in the middle developmental stage of ovaries or testes, tac4 may primarily act in the late developmental stage of female ovaries or the middle and late developmental stage of male testes. During pregnancy, tac4-L expression was significantly decreased in the brain-pituitary complex but significantly increased in the testis and brood pouch of pregnant males, suggesting a close association between tac4-L and male pregnancy. Remarkable changes of tac3 and tac4 transcripts during the brood pouch growth revealed that tac3 and tac4-L may participate in regulating early and middle pouch development, while tac4-S may exert its effects during the late brood pouch growth. Taken together, these results reveal functional divergence among tachykinin ligands of the big-belly seahorse, which also provide a foundation for exploring roles of tachykinin system in regulating gonadal growth, male pregnancy, and brood pouch remodeling of seahorses.
Proceedings of the National Academy of Sciences of the United States of AmericaDivyanshu Shukla, Jonathan Martin, Faruck Morcos, Davit A Potoyan
Proteins can be studied through their sequence statistics or structural properties. These represent complementary views that are useful but lack a quantitative framework to tell, family by family, which is most informative and how to combine them. We introduce a framework that builds both views in parallel: amino acid (AA) alignments are translated into parallel alignments over a 3D interaction (3Di) structure-informed alphabet. Variational autoencoders compress each into a two-dimensional map, and direct coupling analysis places a shared coevolutionary energy on both maps, turning them into latent generative landscapes. On these landscapes, we define information-theoretic distance metrics that quantify how sequence changes drive structural and functional variation in protein families. We demonstrate the framework on five families: in malate dehydrogenases, the 3Di landscape identifies the structurally conserved scaffold that this family uses to encode thermal adaptation via sequence variability revealed in the AA landscape. In globins and transient receptor potential melastatin (TRPM), the 3Di landscape recovers known functional subfamilies. In the Flaviviridae E1 and E2 glycoproteins, structure reveals evolutionary relationships invisible at the sequence level. Because many sequences encode the same fold, our framework lets us disentangle family-sequence variability from structural and functional variation. These generative landscapes allow sampling near functional regions, and we show they can help us gain mechanistic insight into the evolutionary forces shaping sequence-structure-function variation and guide the design of new proteins.
JMIR human factorsLouise Nørgaard Olsen, Philipp Harbig, Anna Bay Laurberg, Jacob Laurberg, Morten Haaning Charles
BACKGROUND: Administrative workload in general practice limits time for direct patient care. AI-assisted documentation has been proposed as a way to reduce the documentation burden, but evidence from routine primary care settings remains limited. OBJECTIVE: This study aimed to evaluate general practitioners' (GPs) acceptance of AI-assisted documentation and its association with documentation time and clinical note quality in routine Danish general practice. METHODS: We conducted a quantitative pragmatic pre-post quality improvement evaluation in Danish general practice. A total of 20 GPs documented 239 consultations before and 236 consultations after implementation of an AI-assisted documentation system. Documentation quality, structure, clinical clarity, and documentation time categories were self-assessed using standardized audit forms completed immediately after each consultation. Technology acceptance and usability were assessed using the technology acceptance model (TAM) and the System Usability Scale (SUS). RESULTS: Self-assessed documentation structure increased from 3.99 to 4.45, while self-reported documentation time categories decreased from 2.85 to 2.29. Technology acceptance and usability were high (TAM domain means 3.76-4.19; SUS mean 77.5). GP-level paired analyses showed moderate improvements in structure and clarity and a reduction in documentation time. Combined blinded external assessments showed higher postimplementation scores for quality, structure, and clinical clarity, although reviewer-specific ratings diverged, and interrater reliability was low. The association between documentation time and perceived quality was negligible. TAM and SUS indicated high clinician acceptance. CONCLUSIONS: AI-assisted documentation was associated with lower self-reported documentation time categories while maintaining or modestly improving perceived clinical note quality. These findings support the feasibility of AI-assisted documentation in primary care, while highlighting the need for controlled studies with objective time measurement and longer follow-up.
BACKGROUND: Bone diseases, including osteoporosis, arthritis, and spinal disorders, pose significant global health challenges, especially with an aging population. Traditional treatment methods often fall short in addressing the complexity and variability of these conditions. Three-dimensional (3D) printing technology has emerged as a transformative tool in orthopedics, enabling the creation of patient-specific implants, surgical guides, and anatomical models that enhance precision and personalization in treatment. Despite its potential, challenges such as regulatory barriers, high costs, and limited scalability hinder widespread clinical adoption. OBJECTIVE: This study aims to conduct a bibliometric analysis of the research landscape surrounding the application of 3D printing in bone diseases, identifying emerging trends, influential contributors, and knowledge gaps to inform future research and clinical translation. METHODS: This study analyzed publications on 3D printing in bone diseases from 2005 to 2024 using data from the Web of Science Core Collection. We performed co-occurrence mapping, keyword clustering, and citation analysis using CiteSpace, R Bibliometrix, and GraphPad Prism. We examined trends in research output, collaboration among countries and institutions, and thematic developments. RESULTS: Between 2005 and 2024, 544 relevant publications were identified, with a rapid growth phase observed post-2016. China and the USA emerged as leading contributors, collectively accounting for over 50% of global research output. Key application areas included scaffolds for bone regeneration, tissue engineering integrating stem cell technology, and drug delivery systems. Keyword analysis highlighted "scaffolds," "tissue engineering," and "additive manufacturing" as central themes. Despite progress, challenges in standardization, material biocompatibility, and cost-effective manufacturing persist. CONCLUSION: 3D printing is reshaping research and clinical applications in bone diseases by offering innovative solutions for bone regeneration, surgical precision, and personalized treatment. Overcoming challenges such as regulatory complexities, scalability, and interdisciplinary collaboration is critical for full clinical integration. Future research should focus on advancing bioprinting techniques, optimizing hybrid manufacturing, and leveraging artificial intelligence -driven design for enhanced patient-specific outcomes.
MedicineAmr Chaabeni, Wissem Dhahbi, Amine Kalai, Ismail Dergaa, Halil İbrahim Ceylan, Raul Ioan Muntean, Karim Chamari, Anis Jellad
BACKGROUND: This study aimed to systematically map the intellectual structure, evolution, and research landscape of artificial intelligence (AI) applications in sports biomechanics through comprehensive bibliometric analysis. METHODS: A mixed-methods bibliometric analysis was conducted using Web of Science Core Collection as the primary data source. A three-component Boolean search query targeting the intersection of AI methods, biomechanical assessments, and sports applications was implemented to identify relevant publications from January 2015 to December 2024. Performance analysis and science mapping techniques were employed using VOSviewer and Bibliometrix R-package, including co-occurrence analysis, bibliographic coupling, author collaboration networks, and thematic mapping using Callon's centrality-density model. RESULTS: The analysis encompassed 8789 publications demonstrating exceptional growth with an annual growth rate of 12.05%, peaking at 1496 articles in 2024. The research involved 30,012 authors across 1798 journals, with high collaboration patterns (5.46 coauthors per document) and substantial international cooperation (27.57%). China led production with 2382 articles (27.1%), followed by the United States with 1303 articles (14.8%). Sensors emerged as the dominant journal (664 articles), while Chen X was identified as the most impactful author (H-index 22). Science mapping revealed machine learning as the central integrative hub connecting biomechanics, electromyography, and rehabilitation. Five distinct thematic clusters were identified, with electromyography, sensors, and kinematics emerging as motor themes representing well-developed research areas. CONCLUSION: AI applications in sports biomechanics represent a rapidly maturing field characterized by robust international collaboration and clear thematic organization around sensor technologies and movement analysis, indicating successful integration of computational methods with traditional biomechanical approaches for performance enhancement and injury prevention.
MedicineMuhammad Hamza Shah, Aditya Gaur, Pearl Ohenewaa Tenkorang, Fionnuala McKeown, Subham Roy, Sakshi Roy, Umar Akram, Khabab Abbasher Hussien Mohamed Ahmed
BACKGROUND: Optic pathway gliomas (OPGs), including optic nerve gliomas, are uncommon tumors of the anterior visual pathway that arise mainly in young children, often with neurofibromatosis type 1 (NF1). The literature is now substantial, but its structure is undescribed. We mapped the most-cited OPG publications to characterize citation patterns, contributors, collaboration, and thematic development. METHODS: Scopus was searched on April 30, 2025 using a title-abstract-keyword strategy combining 4 OPG-specific phrases, with no year or document-type restriction. Records were ranked by total citations, and the 100 most-cited were retained. Two reviewers screened independently with a 3rd adjudicating; each was then classified by how directly it addressed OPG. Metadata were analyzed in Bibliometrix and VOSviewer. Distributions were assessed with the Shapiro-Wilk test and summarized as medians with interquartile ranges (IQRs); associations used Spearman correlation. Reporting follows the preliminary guideline for reporting bibliometric reviews of the biomedical literature. RESULTS: The 100 records, published between 2000 and 2021, were cited 9305 times, with a median of 75 citations per article (IQR 59-108; range 41-289) and a median annual rate of 5.7 (IQR 4.2-7.8). Output peaked in 2010 (n = 9) and again in 2012, 2015, and 2016 (n = 8 each). First authors spanned 17 countries, 53 from the United States. Washington University School of Medicine appeared most often, and David H. Gutmann and Robert A. Avery were the most central authors. Neuro-Oncology (n = 9), Cancer Research (n = 5), and the International Journal of Radiation Oncology Biology Physics (n = 5) led; about four-fifths appeared in 1st-quartile journals. Keyword co-occurrence formed 3 clusters: clinical/chemotherapy, NF1 molecular biology, and imaging/diagnostics. Recent articles were cited faster than older ones (rho = 0.475, publication year vs. annual rate; P < .001). Excluding the 9 peripherally related records left every statistic essentially unchanged (median 76; IQR 59-109). CONCLUSION: Among the most-cited OPG publications, emphasis has shifted over 2 decades from descriptive clinical series toward NF1 tumor biology, mitogen-activated protein kinase kinase-directed therapy, and quantitative imaging, with output concentrated in a few North American centers. These findings describe how attention has been distributed, not clinical importance or study quality, and are subject to the known limits of citation analysis.
Journal of medical systemsHyeonhoon Lee, Seonhye Choi, Duyeon Kim, Kyunglan Hong, Hyeonsik Kim, Chang Wook Jeong, Hyung-Chul Lee
Systematized Nomenclature of Medicine-Clinical Terminology (SNOMED CT) is the principal international standard for semantic interoperability of clinical information, but mapping free-text clinical narratives to SNOMED CT concepts remains labor-intensive. We developed a large language model agent system for mapping bilingual clinical text to SNOMED CT concepts and evaluated its effect on mapping accuracy and efficiency within a human-AI collaborative workflow. We designed a three-module agent system comprising translation, abbreviation expansion, and vector-based retrieval components, integrated with a pre-embedded SNOMED CT vector database. Three health information managers independently mapped bilingual clinical text segments using three approaches: human-only, Agent-only, and Agent-assisted human mapping. Performance was evaluated by using hit rate, precision, recall, and F1 score at k = 1 and 5, and R-precision. Mapping time was compared between human-only and human-AI collaborative approaches. A total of 2,261 de-identified clinical text segments across nine clinical categories were collected at a tertiary academic hospital in South Korea. The human-AI collaborative workflow, which expanded the set of valid SNOMED CT candidates presented at each mapping decision, raised pooled hit rate@1 from 0.837 to 0.868 (difference 0.031, 95% confidence interval [CI] 0.021 to 0.042; p < 0.001), raised R-precision from 0.632 to 0.674 (difference 0.042, 95% CI 0.034 to 0.051; p < 0.001), and reduced total mapping time by 53.9% (from 1.57 to 0.72 min per segment, including agent processing). By expanding the space of valid SNOMED CT candidates available to expert mappers, the human-AI collaborative approach improved SNOMED CT mapping accuracy while reducing time by about half. Its modular architecture, supporting periodic vector database updates without retraining, offers a sustainable and efficient solution for bilingual clinical terminology standardization.
BACKGROUND: The pathogenesis and pathological progression of ankylosing spondylitis (AS) remain unclear. Owing to the absence of a gold standard for diagnosing AS, diagnostic delays are frequently encountered in clinical practice, exacerbating the disease burden. In the past 16 years, several diagnostic studies on AS have been published. This study aimed to summarize the developmental trends and frontier hotspots in AS diagnosis through a bibliometric review. METHODS: Data were extracted from English publications on AS diagnosis from the Web of Science Core Collection (January 1, 2008-October 21, 2024). CiteSpace, VOSviewer, and the Biblioshiny R package were used to analyze the overview of the publication output, countries/regions, institutions, authors, sources, references, and keywords. RESULTS: A total of 1205 articles from 396 journals across 65 countries were included. The highest annual output occurred in 2021 (n = 111, 9.21%), whereas 2015 had the highest average number of citations (n = 5.1). Clinical Rheumatology (n = 76, 6.31%) was the most influential journal. China (n = 244, 20.25%), Berlin Institute of Health (n = 116, 9.63%), and Sieper J (n = 28, 2.32%) ranked first in terms of country, institution, and author productivity, respectively. The top 3 reference clusters were "diagnostic criteria," "therapeutics," and "recommendations." Burst detection identified 4 emerging post-2021 keywords: "children," "cells," "spondyloarthritis," and "expression." CONCLUSION: AS diagnosis research has evolved through a growth phase (2008-2021), followed by a transitional or reorientation phase (2022-2024). Magnetic resonance imaging, Mendelian randomization, and biomarkers are current hotspots; Mendelian randomization serves as an etiological adjunct with the potential to inform biomarker discovery, though its findings do not yet constitute diagnostic tools. The apparent slowdown in recent years largely reflects evolving terminology (AS vs radiographic axial spondyloarthritis) and bibliometric time-lag bias rather than true intellectual stagnation, alongside fragmented pathophysiological insights and a lack of specific clinical features.
Journal of helminthologyS Achouri, I Hamdi, S Bahri
Cestode larvae of Anthobothrium sp. were collected from the caecum and stomach of the common squid Loligo vulgaris Lamarck, 1798 (Cephalopoda: Loliginidae) in Tunisian waters (Bay of Bizerte and Gulf of Tunis), with the highest prevalence recorded in the Gulf of Tunis (52.94%). These specimens were morphologically characterised and compared to previously described Anthobothrium larvae from other hosts. Molecular analysis using 28S ribosomal DNA (rDNA), combined with phylogenetic reconstruction (maximum likelihood and pairwise distances), revealed that the sequences cluster with adult specimens from several elasmobranch species. These definitive hosts include Carcharhinus obscurus and Carcharhinus limbatus, which are common in Tunisian waters, thereby providing new insights into the potential life cycle of this parasite. Loligo vulgaris represents a new host record for Anthobothrium sp. larvae and appears to be its preferred cephalopod host in the Mediterranean. Finally, a comprehensive checklist of metacestodes recorded in L. vulgaris is provided.
Journal of helminthologyC Mata-Marcano, L Andrade-Gómez, B Pérez-Órtega, G Pérez-Ponce de León
The limestone soil of the Yucatán Peninsula is highly permeable, allowing fluvial waters to filter into the aquifer, resulting in the absence of rivers on the surface and the formation of underground reservoirs that, on some occasions, open to the surface, forming the so-called cenotes (or sinkholes). Information about the freshwater fish parasite diversity of cenotes in the Yucatán Peninsula is scarce. Only 50 cenotes of the approximately 9,000 occurring in the peninsula have been sampled to assess the fish parasite fauna. Available information predates the molecular era and is based on morphological assessments solely. Here, specimens of 7 fish species were sampled in 15 localities distributed along an area known as the 'Ring of Cenotes', a depression associated with the Chicxulub crater formed by the impact of a meteorite. Trematode metacercariae were collected, sorted by morphotype, and sequenced for the partial 28S rRNA and/or COI mtDNA genes. Twelve trematode metacercariae were identified, seven to species level and five to genus or family level, since they did not match any known sequenced species available in the BLAST search. Metacercariae corresponded to three families; Diplostomidae was the most diverse with eight taxa. The cichlid Mayaheros urophthalmus harboured the greatest number of taxa, with nine. Three species of Clinostomum were identified molecularly in what previous findings considered a single species on morphological grounds. The importance of continually expanding the genetic library of larval trematodes and establishing links between adults and larval forms to fully assess and understand trematode diversity is discussed.
Protein science : a publication of the Protein SocietyMariandrea Aranda-Barba, Laura Marina Franco-Herrera, Paul Montaño-Silva, Eréndira Patricia Pérez-Muñoz, Jorge H Ramirez-Prado, Jorge Verdín
Hyaluronic acid (HA) is a biologically versatile polysaccharide synthesized by vertebrates and several microbial pathogens. To date, Cryptococcus neoformans CPS1p is the only reported bona fide hyaluronic acid synthase (HAS) in fungi, which is functionally related to bacterial HASs. Considering the phylogenetic and biochemical connection between HASs and chitin synthases (CHSs), essential for fungal cell wall synthesis, it is reasonable to hypothesize the former might be more common in fungi than expected. In this work, a comprehensive in silico survey of putative HASs in the Fungal Tree of Life was carried out. 68 putative HASs, mainly in Basidiomycota, were found, although other artificial intelligence-inferred putative HASs were found among Ascomycota. Global fold and arrangement of essential amino acids were shared by all kingdoms' HASs; however, C. neoformas CPS1p and additional putative fungal HASs (fungal HASs) showed exclusive conserved sequence signatures. Moreover, fungal HASs bore an only 3-helices transmembrane pore and their gating loop, which regulates the entrance of substrates to the catalytic site, was directly connected to an also exclusive intrinsically disordered C-terminus. Phylogenetically, fungal HASs were found in a clade different to that of bacterial, animal and viral HASs, and might share a common ancestor with Class I, III or VI CHSs. The atypical features of fungal HASs could influence the size and biological role of the HA they potentially synthesize and also highlight regulatory differences among HASs at the level of the gating loop configuration.
Protein science : a publication of the Protein SocietyMarcus D Hartmann, Birte Hernandez Alvarez, Mikel Martinez-Goikoetxea, Andrei N Lupas
Coiled coils are formed by α-helices winding around each other into superhelical bundles. They are characterized by a specific geometry of interaction, called knobs-into-holes, in which residues in the core of the structure mesh regularly along a seam that runs the length of the helices. While these residues are predominantly hydrophobic, hydrophilic residues occur occasionally. In dimeric coiled coils, their sidechains are often sufficiently long to allow the head-groups to extend out of the core and be solvated by water, but in trimeric and tetrameric coiled coils, they often cannot gain access to solvent and instead point inward, coordinating water molecules and ions along the central axis of the coiled coil. Building on this insight, we have used sequence motifs derived from trimeric autotransporter adhesins to design coiled-coil sequences that lack hydrophobic sidechains for three or more consecutive heptads. Their crystal structures illustrate the strategies for accommodating extended stretches of hydrophilic residues within the coiled-coil fold, which are confidently predicted as intrinsically disordered, raising questions about the actual structure of such proteins in their native environment.