bluuebunny/crossref_metadata_2025 huggingface dataset:
CCQM-K170 - electrolytic conductivity at 0.5 S m-1 and 20 S m-1 - final report
Authors: Wang Hai , Wang Meiling , Song Xiaoping , Seitz Steffen , Máriássy Michal , Nagy Daniel , Godínez Jorge Uribe , Aparicio José Luis Ortiz , Vičarová Martina , Quino Jose Luis Gonzales , Quispe Jimena Patricia Torrez , Vásquez Arellán Javier , Rosas Christian Uribe , Quezada Henry Torres , Torres Gina , Suaza Brigette , Gonzaga Fabiano Barbieri , Cunha Kleiton da Cruz , Galli Lic Ariel , Puelles Lic Mabel , Rinaldi Angeles , Sharbanu Maulimgazinova , Fajardo Simone , Gelabert Victoria , Hibino Yuya , Tangpaisarnku Nongluck , Yildirim Emrah , Haraldsson Conny , Hanková Zuzana , Kodadová Zuzana , Uysal Emrah , Liv Lokman , Gençtürk Tosun Serap , Alimova Ing Tatyana E , Prokunin Sergey V , Ovchinnikov RO Yuriy A , Dobrovolskiy Vladimir I , Maria Bednova , Aleksandr Strelnikov
Published: January 2025

Main text

The comparison CCQM-K170 is a subsequent key comparison of CCQM-K36.2016 and CCQM-K92. It aims to demonstrate the capabilities of the participating NMIs/DIs to measure the electrolytic conductivity of aqueous electrolyte solution in the electrolytic conductivity range around 0.5 S m-1 and 20 S m-1. The coordinating institute (NIM) prepared two potassium chloride solutions with the nominal electrolytic conductivity of 0.5 S m-1 and 20 S m-1, and verified their homogeneity and stability. Seventeen and twelve NMIs/DIs, respectively, reported their measurement results of 0.5 S m-1 and 20 S m-1 samples, respectively. The institutes used primary and secondary methods, and commercial instruments. Institutes using non-NMI CRMs as calibrants or CRMs from a participating NMI were excluded from KCRV calculation. The measurement results traceable to CRMs from the same non-participating NMI were combined into one result to be used for KCRV calculation. The results of institutes which have indicated technical problems were also excluded from KCRV calculation. The medians were agreed upon as the KCRVs for 0.5 S m-1 and 20 S m-1 solutions based on CCQM/2013-22 guidance document. Good agreement of the results was observed for the majority of participants. The results of this key comparison are considered representative for electrolytic conductivity measurement of aqueous electrolyte solution in the electrolytic conductivity range 0.15 S m-1 to 1.5 S m-1 and 5 S m-1 to 25 S m-1, respectively. This KC is intended as an updated support for the corresponding calibration and measurement capabilities (CMCs) entries in the key comparison data base of the BIPM.

To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database https://www.bipm.org/kcdb/.

The final report has been peer-reviewed and approved for publication by the CCQM, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).
Causally Enhanced Initial Conditions: a novel soft constraints strategy for Physics Informed neural networks
Authors: Zha Wenshu , Chen Dongsheng , Li Daolun , Shen Luhang , Chen Enyuan
Published: January 2025

Physics Informed Neural Networks (PINNs) is a deep learning 1/22/2025method designed for solving partial differential equations (PDEs). Learning the initial conditions accurately is crucial when employing PINNs for PDEs solve. However, simply adjusting weights and imposing hard constraints may not always lead to better learning of the initial conditions, sometimes it even makes it difficult for neural networks to converge. To enhance the accuracy of PINNs in learning initial conditions, this paper proposes a novel strategy that is named Causally Enhanced Initial Conditions (CEIC). This strategy works by embedding a new loss in the loss function: the loss is constructed by the derivative of the initial condition and the derivative of the neural network at the initial condition. Furthermore, to respect the causality in learning the derivative, a novel causality coefficient be introduced for the training when selecting multiple derivatives. Additionally, because CEIC can provide more accurate pseudo-labels in the first subdomain, it is compatible with the temporal marching strategy. Experiment results demonstrate that CEIC outperforms hard constraints and improves the overall accuracy of PT-PINNs. For the 1d-KdV equation, reaction equation, convection equation, the CEIC method proposed in this paper has reduced the relative error by at least 60% compared to previous methods.
Exploring Lifshitz Transition and Superconductivity in 3R-NbS2 under Pressure
Authors: Chen Kun , Lv Xindeng , Li Simin , Huang Yanping , Cui Tian
Published: January 2025

The interplay among electronic topological phase transitions and superconductivity in the field of condensed matter physics has consistently captivated researchers. Here we have succeeded in modulating the Lifshitz transition by pressure and realized superconductivity. At 25.7 GPa, superconductivity with a transition temperature of 1.9 K has been observed in 3R-NbS2. The Hall coefficient changes from negative to positive at 14 GPa indicating a Lifshitz transition in 3R-NbS2, and the carrier concentration continues to increase with pressure. X-ray diffraction results indicate that the appearance of superconductivity is not attributable to structural transitions. Based on theoretical calculations, the emergence of new band is attributed to a Lifshitz transition and the new band coincide with the Fermi surface at a pressure of 30 GPa. These findings provide new insights into the relationship between the Lifshitz transition and superconductivity.
DAU-Net: a novel U-Net with dual attention for retinal vessel segmentation
Authors: Jian Muwei , Xu Wenjing , Nie ChangQun , Li Shuo , Yang Songwen , Li Xiaoguang
Published: January 2025

In fundus images, precisely segmenting retinal blood vessels is important for diagnosing eye-related conditions, such as diabetic retinopathy and hypertensive retinopathy or other eye-related disorders. In this work, we propose an enhanced U-shaped network with dual-attention, named DAU-Net, divided into encoder and decoder parts. Wherein, we replace the traditional convolutional layers with ConvNeXt Block and SnakeConv Block to strengthen its recognition ability for different forms of blood vessels while lightweight the model. Additionally, we designed two efficient attention modules, namely Local-Global Attention (LGA) and Cross-Fusion Attention (CFA). Specifically, LGA conducts attention calculations on the features extracted by the encoder to accentuate vessel-related characteristics while suppressing irrelevant background information; CFA addresses potential information loss during feature extraction by globally modeling pixel interactions between encoder and decoder features. Comprehensive experiments in terms of public datasets DRIVE, CHASE_DB1, and STARE demonstrate that DAU-Net obtains excellent segmentation results on all three datasets. The results show an AUC of 0.9818, ACC of 0.8299, and F1 score of 0.9585 on DRIVE; 0.9894, 0.8499, and 0.9700 on CHASE_DB1; and 0.9908, 0.8620, and 0.9712 on STARE, respectively. These results strongly demonstrate the effectiveness of DAU-Net in retinal vessel segmentation, highlighting its potential for practical clinical use.
Marriage and Work
Authors: Ågren Maria , Ling Sofia , Henningsson Linnea
Published: January 2025

This chapter discusses how marital status and gender affected women’s and men’s working lives in the period 1720 to 1880. It shows that because married people tended to have access to more resources than did the unmarried, marital status/household position remained very important for what women and men did to support themselves. Married women were active as producers in primary and secondary sectors and as providers of services and suppliers to markets. When they had the means and opportunities, they delegated childcare to others and their work was consequently, not strongly restricted by such responsibilities. Most marital partnerships can be described with the term two-supporter model. Nevertheless, despite these long-term continuities, there was also change. The chapter goes on to discuss trade activities and shifts in how the word hustru (ever-married woman) was used, and argues that the comparative advantage of being married declined towards the end of the period (1840–80). In tandem with growing social differentiation, there were small but significant shifts that favoured unmarried women and men and disfavoured married women and some married men.
Karyotype variation patterns and phenotypic responses of hybrid progenies of triploid loquat (Eriobotrya japonica) provide new insight into aneuploid germplasm innovation
Authors: Wang Peng , Yang Shangjian , Chen Meiyi , Liu Yingjia , He Qiao , Sun Haiyan , Wu Di , Xiang Suqiong , Jing Danlong , Wang Shuming , Guo Qigao , Dang Jiangbo , Liang Guolu
Published: January 2025

The sexual reproduction of triploids induces chromosomal karyotype variations, which are significant for germplasm resource innovation. Most triploid plants are with low fertility. Therefore, triploid offspring karyotypes’ variation pattern and phenotypic response remain poorly understood. Here, we employed three diploids with diverse genetic distances as male parents to cross-pollinate the female fertile triploid loquat Q24 to construct three experimental populations. The chromosome numbers of 93.82% of hybrid plants were 34~46 in three hybrid populations. All 168 aneuploids with 160 karyotypes and a small percentage of euploids were detected among 178 hybrids by the improved molecular karyotype analysis method. Further analysis revealed that when being transmitted to offspring, chromosome 5 of Q24 as disomy was with the highest frequency (> 50%), while chromosome 12 was with the lowest frequency (≤ 30%). The frequency of Q24’s chromosomes being transmitted to offspring as disomy was influenced by the gene function on the chromosomes and the number of inter-chromosome collinear gene links. Whole genome resequencing showed that the Q24 alleles exhibited segregation distortions in the offspring aneuploid population. Transgenic experiments demonstrated that the EjRUN1 gene, which was on one segregation distortion region of Q24, promoted the seed viability of triploid Arabidopsis. Furthermore, chromosome number, dosage, and male parent genotype affected the aneuploid phenotype. These findings advance the understanding of genome genetic characteristics of triploid loquat, and provide a reference for germplasm innovation of loquat rapidly through triploid sexual reproduction.
A refined method for high-purity isolation of uterine glandular epithelial cells in mouse
Authors: Youssef Asmaa M , Moustafa Ahmed M , Hamada Motoharu , Sugiura-Ogasawara Mayumi , Oishi Hisashi
Published: January 2025

The uterine endometrium consists of luminal epithelium, glandular epithelium, and stromal cells, with uterine glands playing a pivotal role in pregnancy success among mammals. Uterine glands secrete essential factors that regulate embryo development and implantation; however, their cellular biology remains poorly understood. This study presents a refined method for isolating three distinct endometrial cell types with high purity, with a specific emphasis on glandular epithelial cells. The method combines mechanical dissociation, enzymatic digestion, and immunomagnetic separation. The isolated glandular epithelial cells were maintained in culture and exhibited proliferation in response to steroid hormones. Furthermore, estrogen responsiveness was abrogated by Estrogen Receptor 1 (Esr1) knockdown mediated by siRNA. Here, we present an efficient and reproducible method for isolating uterine glandular epithelial cells with high purity, enabling their in vitro maintenance, hormone responsiveness assessment, and functional gene knockdown. These findings establish a robust platform for advancing our understanding of uterine gland biology, facilitating detailed investigations into molecular mechanisms underlying glandular function and their critical roles in establishing pregnancy success. Future research could explore the contribution of these isolated cells to endometrial receptivity and embryo implantation.
Portrayal of Deaf characters in Korean movies
Authors: Chang Andrew , Golos Debbie
Published: January 2025

Characters in movies have the potential to influence perceptions of how people see themselves. Deaf adolescents who have little opportunity to interact with Deaf peers or family members may be particularly drawn to Deaf people they see in the media. How the media portrays Deaf people may impact Deaf adolescents’ self-perceptions of and language preferences. Yet little is known about the ways Deaf people are portrayed in movies, particularly films developed outside of the United States and not in English. In this study, we utilized content analysis to explore the portrayal of Deaf characters in Korean movies and Deaf involvement in the production of films. Descriptive statistics were used to determine the extent to which characters were portrayed by medical or cultural perspectives of Deaf people. Findings indicate that 68.5% of scenes in the sampled Korean films include medical rather than cultural messages about Deaf people. Additionally, none of the movies had Deaf people directly involved in the production of the films. Implications for future directions regarding identity and portrayal of Deaf people in media are discussed.
Understanding the Psychology of Practical Wisdom
Authors: Nusbaum Howard
Published: January 2025

The longstanding view of doctors as scientists has been an emphasis in the MCAT and medical school training. However, the AAMC recommended recognizing the importance of social and behavioral science for medicine. There is also a growing realization that being a smart problem solver and the physician as scientist model emphasizes a cold cognitive problem-solving paradigm that overlooks other human capacities that may be critical to medical reasoning and decision-making. Considering a smart physician versus a wise physician, intelligence and problem-solving are important, but a wise physician can use other important capacities beyond intelligence and rationality. This could benefit patients by introducing patient and family perspective taking, as well as compassion in doctor-patient interaction. By reconceptualizing professions from the perspective of practical wisdom, this may increase resilience to problems such as burnout. I outline some psychological capacities viewed as important in wise reasoning that are not about traditional views of intelligence. I argue that wise reasoning is not a native talent but a skill that can be developed. I argue that different kinds of experiences can increase aspects of empathy, epistemic humility, perspective taking, and wise reasoning and I examine evidence that wise reasoning may increase resilience.
Atypical femoral fracture in a patient with nutritional osteomalacia: a case report and literature review
Authors: Alshehri Mohammed , Alzahrani Abdulrahman , Aljehani Abdulrahman , Saeed Abdullah , Aljaafri Ziad
Published: January 2025

Atypical femoral fractures (AFF) are rare stress fractures with specific diagnostic criteria, as outlined in a report published by the American Society for Bone and Mineral Research. These criteria are categorized into major and minor features, and AFF can be classified as either complete or incomplete. Bisphosphonates have been shown to increase the risk of AFF, and most cases of AFF are associated with bisphosphonate use. We present a unique case of AFF in a young woman with no history of bisphosphonate use. She was taking oral contraceptive pills and inhaled corticosteroids for asthma. Later, she was diagnosed with nutritional osteomalacia. The patient was managed surgically with bilateral intramedullary nailing, resulting in a favorable outcome.
Laparoscopic and endoscopic co-operative surgery for a non-ampullary duodenal tumor after living-donor liver transplantation: a case report
Authors: Ito Shunichi , Tamazaki Rinka , Maeda Shinsuke , Hosoda Kei
Published: January 2025

Superficial duodenal epithelial tumors were previously considered rare. Laparoscopic and endoscopic cooperative surgery for duodenal tumors (D-LECS) has been developed to achieve successful endoscopic treatment. Patients who have undergone living-donor liver transplantation (LDLT) may have severe abdominal adhesions, and immunosuppressive agents (IAs) may affect the degree of postoperative abdominal adhesions and wound healing, but their effects remain unclear. Herein, we present the first case of D-LECS for duodenal adenoma after LDLT. A 66-year-old man underwent D-LECS for a non-ampullary duodenal high-grade adenoma after LDLT with an IA. The patient’s condition was uneventful 36 months after the surgery. In gastrointestinal surgery, IAs may affect the resected duodenal repair process. For duodenal neoplasms in high-risk patients, D-LECS may be better than endoscopic submucosal dissection alone. D-LECS after LDLT is a feasible and less invasive procedure.
Appetite Self-Regulation in Childhood: A Narrative Review and Conceptual Model of Processes and Mechanisms With Implications for Research and Practice
Authors: Russell Catherine G , Russell Alan
Published: January 2025

The purpose of the present narrative review was to propose a unifying generalized conceptual model of mechanisms and processes in appetite self-regulation (ASR) in childhood. Appetite self-regulation, along with other domains of self-regulation, develops across childhood and contributes to energy intake and balance, diet quality, weight, and therefore long-term health outcomes. There have been efforts to conceptualize and measure components of ASR and associated processes/mechanisms, but, at present, there is no unifying conceptualization of ASR in childhood. A search of key databases supplemented by snowballing was undertaken for definitions/conceptions and theoretical models of ASR with a focus on children. An interpretive synthesis approach was used to identify themes from the definitions and models. The themes formed the basis of the proposed unifying generalized model of ASR in childhood, which is the main contribution of the article. At the center of the model is bottom-up reactivity to food, food cues and hunger, satiation and satiety signals, together with top-down regulatory control. An additional contribution is the proposed 5 interacting and overlapping domains (biological, hedonics, cognitive, behavioral, and traits) that function in and influence both bottom-up reactivity and top-down regulation. The domains also contribute to ASR outcomes of enactment and competence. External contextual and intrapersonal factors are conceived as impacting the domains and the bottom-up, top-down processes. The relevance of the model for explanations of ASR phenomena in childhood and children’s food choice and diet quality, as well as its implications for research directions and approaches to preventive intervention, including food parenting practices, are discussed. The model provides a framework for researchers and practitioners to support and interpret children’s problems and competence in self-directing food choices, energy intake, and nutrition.
Association Between Specialty-Specific Physician Salaries and Percentage of Women in the Workforce
Authors: Mujahed Tala , Ofori-Atta Blessing S. , Codden Rachel , Greene Tom , Dudley Nanette , Kadish Howard , Drapkin Zachary
Published: January 2025

Purpose

Several studies have demonstrated that female physicians within specific specialties are compensated less than their male counterparts. Academic institutions seek to address this using Association of American Medical Colleges (AAMC) data for benchmarking and starting salary standardization. However, few studies address whether there is an association between percentage of women across specialties and mean salary for each specialty. The purpose of this study was to examine whether there is an association between mean salary and percentage of women in various specialties.

Method

This cross-sectional study used AAMC Faculty Salary Report data for fiscal year 2022. Surveys were sent to 155 U.S. accredited medical schools, of which 153 schools participated (99% response rate). Univariable and multivariable analyses were performed to assess the association between mean specialty salary, calculated as the weighted mean of male and female salaries for each specialty, and the percentage of women in each specialty using a generalized linear gamma mixed model.

Results

Analysis using data from 124,480 full-time faculty at 153 accredited U.S. medical schools indicated that as the percentage of women in a specialty increases, mean salary decreases. This finding was true for all specialties (r = −0.65), medical specialties (r = −0.83), pediatric specialties (r = −0.80), and surgical specialties (r = −0.73). Multivariable analysis accounting for rank, pediatric vs nonpediatric specialties, procedural vs nonprocedural vs mixed specialties, and years of training showed that every 10% increase in percentage of women in a specialty was associated with a 7% decrease in salary independent of other factors.

Conclusions

An inverse correlation between percentage of women in a specialty and mean salary for that specialty was observed even when controlling for confounding factors. This trend is worth noting because AAMC data are often used as a benchmark to establish physician starting salaries.
Hemostatic Efficacy of TachoSil in Loop Electrosurgical Excisional Procedure: A Prospective Randomized Controlled Study
Authors: Kim Junhwan , Park Jeong-Yeol
Published: January 2025

Objective

The aim of the study was to evaluate the hemostatic efficacy of the fibrin sealant patch (TachoSil) after loop electrosurgical excision (LEEP) and its influence on other complications and quality of life (QoL).

Materials and Methods

This single-blind, prospective, randomized study involved patients undergoing LEEP with or without TachoSil (1:1) between August 2014 and August 2015 in Asan Medical Center, Korea. Primary outcome measures were bleeding duration and the frequency of additional treatment owing to vaginal bleeding within 2 weeks after LEEP. Secondary outcome measures were vaginal bleeding volume using pictorial blood loss assessment chart (PBAC) score, the amount of vaginal discharge, the frequency of external genitalia, vaginal, and cervical infections within 2 weeks after LEEP, and changes in QoL.

Results

Of the 140 patients enrolled, 126 (90.0%) were successfully followed up and analyzed. The median vaginal bleeding duration and frequency of additional treatment owing to vaginal bleeding showed no significant difference in the TachoSil applied and nonapplied groups (p = .96 and p = .61, respectively). In addition, no significant difference was also observed in vaginal bleeding volume between 2 groups (p = .64). In subgroup analysis for patients who underwent large LEEP (the longest dimension of ≥2 cm), significant improvement was observed at physical functioning in QoL at 2–3 (p = .03) and 6 weeks (p = .03) after LEEP of the TachoSil applied group, compared to the nonapplied group.

Conclusions

TachoSil did not demonstrate significant hemostatic efficacy after LEEP. However, TachoSil improved patient recognition on physical function in patients who underwent large LEEP.
Short-term effects of upstream high bolus dose of tirofiban in patients with ST segment elevation myocardial infarction undergoing primary percutaneous coronary intervention
Authors: Abouelnour Amr E.I. , Mohammed Eman Q. , Fouad Doaa A. , Tohamy Aly
Published: January 2025

Background

No-reflow following primary percutaneous coronary intervention (PPCI) is challenging to treat.

Objectives

The objective of this study is to evaluate the efficacy and safety of upstream high-bolus-dose tirofiban administration in ST-segment elevation myocardial infarction (STEMI) cases undergoing PPCI on top of dual antiplatelet therapy, including ticagrelor, in comparison to selective bailout administration.

Methods

This hospital-based, randomized, single-blinded prospective interventional study was conducted on 150 patients at Assiut University Heart Hospital. Patients with STEMI within 12 h after symptom onset who underwent PPCI were randomized to an upstream group (n = 75) and a selective bailout group (n = 75) based on the timing of the tirofiban bolus administration (25 µg/kg intravenously over 5 min).

Results

The bailout group’s thrombolysis in myocardial infarction (TIMI) frame count was higher than the upstream group’s, despite comparable TIMI flow and myocardial blush grade between the two groups, but only approached statistical significance [14.4 (4–36) vs 12.2 (5–55), P = 0.08]. The enzymatic infarct size tended to be lower in the upstream group. All echocardiographic findings were comparable between the two studied groups, with no significant difference (P > 0.05). There was no significant difference between the two groups regarding clinical outcomes.

Conclusion

Compared to selective bailout administration, upstream high bolus dose of tirofiban in STEMI patients undergoing primary coronary intervention did not significantly affect angiographic outcomes, left ventricular remodeling, or function, despite smaller infarction size.
Adherence to Oral Anticancer Agents Among Adults With Gastrointestinal Tract Cancer
Authors: Chen Yongfeng , Ng Marques Shek Nam , Zhang Mengyue , Chan Carmen Wing Han
Published: January 2025

Background

Patients with gastrointestinal tract cancer reported suboptimal adherence to oral anticancer agents (OAAs), reducing their therapeutic benefit and increasing mortality risk. A scoping review can comprehensively map available evidence on adherence to OAAs and inform appropriate support to improve treatment outcomes.

Objective

The aim of this study was to comprehensively map studies on adherence to OAAs among adults with gastrointestinal tract cancer, including the adherence rate, nonadherence reasons, influential factors, management strategies, and theories that guide these studies.

Methods

The Preferred Reporting Items for Systematic Reviews and Meta-Analyses Extension for Scoping Reviews Checklist and the 5-stage methodological framework of scoping review were followed. According to the 5 research questions, 7 databases were systematically searched for peer-reviewed original studies, and a narrative synthesis was performed.

Results

Fifty-two studies were included. Adherence ranged from 16.7% to 100%, giving a median rate of 68% by self-report. Seven categories of nonadherence reasons were identified, with adverse effects, cancer progression, patient refusal, and forgetfulness being most frequently reported. Furthermore, more than 40 influential factors were identified. They are related to patient, disease condition, therapy, socioeconomic, and healthcare-system dimensions. Education and follow-up care were the main components of management strategies, but the effectiveness was inconsistent. Currently, only 3 of 52 studies adopted theoretical frameworks.

Conclusion

Adherence to OAAs among adults with gastrointestinal tract cancer is suboptimal. Future studies with rigorous designs and theoretical frameworks are needed to develop adherence-enhancing strategies and explain theoretical mechanisms.

Implications for Practice

Routine assessments and preventive actions are suggested to delay modifiable nonadherence.
Prenatal Diagnosis of Berry Syndrome by Fetal Echocardiography
Authors: Ren Jie , Huang Xiang-yang , Zhang Chao-Xue , Yang Dong-Mei
Published: January 2025

Berry syndrome is a rare combination of cardiac malformations, which is characterized by the following malformations, including the aortopulmonary window, aortic right pulmonary origin, interrupted aortic arch or hypoplastic aortic arch or coarctation of the aorta, and an intact ventricular septum. There are few reviews on prenatal diagnosis of Berry syndrome by fetal echocardiography. We used sequential cross-sectional scanning from apex to bottom of the heart to find aortic right pulmonary origin, aortopulmonary window, and hypoplastic aortic arch. This process is like opening a Chinese scroll painting, and the picture gradually extends to reveal the whole picture. As far as we concerned, this is the first report of prenatal diagnosis with Berry syndrome through sequential cross-sectional scanning.
Serious issues with cryo-EM structures of human prothrombinase
Authors: Huntington James A. , Faille Alexandre , Ustok Fatma Isik
Published: January 2025

Thrombin is generated from prothrombin through sequential cleavage at two sites by the enzyme complex prothrombinase, composed of a serine protease, factor (f) Xa and a cofactor, fVa, on phospholipid membranes. In a recent paper published in
Blood
, Ruben
et al
. (Ruben
et al
. 2022
Blood
139
, 3463–3473 (doi:
10.1182/blood.2022015807
)) reported a major breakthrough in the field: the cryogenic electron microscopy structures of human prothrombinase on nanodiscs at 5.5 Å resolution (7TPQ) and of a catalytically inert human prothrombinase with its substrate prothrombin in the absence of any membrane at 4.1 Å resolution (7TPP). As is the norm in structural biology, the original paper was reviewed without access to the coordinates and maps, and it was therefore not possible for referees to assess the validity of the structures or their interpretations. In this article, we provide a post hoc analysis of the quality of the reported coordinates and maps, and look closely at the claimed intermolecular contacts on which the supposed breakthrough depends. We demonstrate that the work is deeply flawed, with not a single claimed intermolecular contact supported by the map, and conclude that the two reported structures do not contain any useful information regarding the assembly or function of the prothrombinase complex.
Stokes flows in a two-dimensional bifurcation
Authors: Xue Yidan , Payne Stephen J. , Waters Sarah L.
Published: January 2025

The flow network model is an established approach to approximate pressure–flow relationships in a bifurcating network, and has been widely used in many contexts. Existing models typically assume unidirectional flow and exploit Poiseuille’s law, and thus neglect the impact of bifurcation geometry and finite-sized objects on the flow. We determine the impact of bifurcation geometry and objects by computing Stokes flows in a two-dimensional (2D) bifurcation using the Lightning-AAA Rational Stokes algorithm, a novel mesh-free algorithm for solving 2D Stokes flow problems utilizing an applied complex analysis approach based on rational approximation of the Goursat functions. We compute the flow conductances of bifurcations with different channel widths, bifurcation angles, curved boundary geometries and fixed circular objects. We quantify the difference between the computed conductances and their Poiseuille law approximations to demonstrate the importance of incorporating detailed bifurcation geometry into existing flow network models. We parametrize the flow conductances of 2D bifurcation as functions of the dimensionless parameters of bifurcation geometry and a fixed object using a machine learning approach, which is simple to use and provides more accurate approximations than Poiseuille’s law. Finally, the details of the 2D Stokes flows in bifurcations are presented.
Complete genome and comparative analysis of Xanthomonas oryzae pv. oryzae isolated from northern Thailand
Authors: Boondech Atirada , Ainmani Phatthira , Khieokhajonkhet Anurak , Boonsrangsom Thanita , Pongcharoen Pongsanat , Rungrat Tepsuda , Sujipuli Kawee , Ratanasut Kumrop , AEKSIRI NIRAN
Published: January 2025

Rice (Oryza sativa L.) is a vital global crop with a predominant presence in Asia, including Thailand. However, it faces a significant threat from bacterial blight disease (BB), primarily caused by Xanthomonas oryzae pv. oryzae (Xoo). This research aims to provide an insights into the genetic virulence and variation of Xoo strains isolated in Thailand. Our phylogenetic analysis unveils that the 20 Thai strains align with the Asian strains, setting them apart from African and USA strains. Remarkably, the Average Nucleotide Identity (ANI) values, in comparison to the Xanthomonas oryzae type strain 35933 (XO35933), consistently exceed 99%. These strains can be classified into three assigned ribosomal sequence types (rST). Our investigation into the pangenome and the phylogenetic relationships of these 20 Xoo genomes reveals a diverse genetic landscape, with the pangenome comprising 11,872 orthologous gene clusters, of which roughly 30% form the core genome. Notably, all of these genomes exhibit the presence of a CRISPR-Cas I-C array, indicative of their adaptive immune mechanisms. All strains belonged to BXO1 type LPS cassette with high identity. Furthermore, our analysis identifies two distinct types of plasmids, namely, Xanthomonas oryzae pv. oryzicola strain GX01 plasmid pXOCgx01 (A46, A57, A83, A112, D, and E) and the Xanthomonas oryzae strain AH28 plasmid pAH28 (A97). This genomic resource will be valuable for advancing research on surveillance, prevention, management, and comparative studies of this critical pathogen in the future.
Hybrid strains of enterotoxigenic/Shiga toxin-producing Escherichia coli, United Kingdom, 2014–2023
Authors: Rodwell Ella V. , Greig David R. , Gokool Suzanne , Olonade Israel , Swift Craig , Chan Yung-Wai , Jenkins Claire
Published: January 2025

Introduction. Diarrhoeagenic Escherichia coli (DEC) pathotypes are defined by genes located on mobile genetic elements, and more than one definitive pathogenicity gene may be present in the same strain. In August 2022, UK Health Security Agency (UKHSA) surveillance systems detected an outbreak of hybrid Shiga toxin-producing E. coli/enterotoxigenic E. coli (STEC–ETEC) serotype O101:H33 harbouring both Shiga toxin (stx) and heat-stable toxin (st).

Gap statement. These hybrid strains of DEC are a public health concern, as they are often associated with enhanced pathogenicity. However, little is known about their epidemiology, clinical significance and associated public health burden.

Aim. The aim of this study was to describe the microbiology, epidemiology and genomic analysis of this novel hybrid serotype in the context of the STEC–ETEC strains in the UKHSA archive.

Methodology. From 2014 to 2023, STEC isolated from faecal specimens testing positive for STEC by PCR were sequenced on the NextSeq 1000 short read platform and a subset were selected for long read nanopore sequencing. Genomes were analysed to determine serotype, stx subtype, DEC pathogenicity genes and antimicrobial resistance determinants.

Results. There were 162 STEC–ETEC strains isolated between 2014 and 2023, of which 117/162 were human clinical isolates and 45 were of food or animal origin. An average of 16 STEC–ETEC strains were identified each year, exhibiting a range of different stx subtypes, the most common profiles being stx2g,st (n=65, 40%) and stx2a,st (n=48, 30%). The most common sequence types were ST329 and ST200 (n=24 each), and the most frequently detected serotype was O187:H28 (n=25). Nine cases of genetically linked STEC–ETEC O101:H33, stx1a,st were detected between 8 August and 21 September 2022. Although the temporal and geographical distribution of the cases was characteristic of a foodborne outbreak, the contaminated vehicle was not identified.

Conclusions. Phylogenetic analysis and long-read sequencing of the outbreak strain provided insight into the stepwise acquisition of st and stx and the evolutionary history of STEC–ETEC pathotypes. The integration of epidemiological data and whole-genome sequencing for routine surveillance of gastrointestinal pathogens is key to understanding the emergence of zoonotic hybrid DEC pathotypes and monitoring foodborne threats to public health.
The capability of plant-bacteria consortia to reduce the genotoxicity of unsymmetrical dimethylhydrazine in the environment
Authors: Novoyatlova Uliana S. , Kessenikh Andrew G. , Kononenko Neonila V. , Baranova Ekaterina N. , Chalkin Stanislav Ph. , Bazhenov Sergey V. , Manukhov Ilya V.
Published: January 2025

Unsymmetrical dimethylhydrazine (UDMH) despite its proven high toxicity continues to be used in rocket technology and some other areas of human activity. In this work, the ability of plant-bacteria consortia to reduce the genotoxicity of UDMH incomplete oxidation products was investigated. Genotoxicity was assessed using a specific lux-biosensorEscherichia coliMG1655 pAlkA-lux sensitive to DNA alkylation in cell. For microbiological biodegradation, theBacillus subtilisKK1112 strain was obtained by the isolation from soil with a subsequent selection for resistance to high UDMH concentrations (more than 5000 MAC). Its ability to biodegrade UDMH was shown by observing the reduction of DNA alkylation of the KK1112-treated UDMH. The ability of KK1112 cells to act in a bacterial-plant consortium with following fodder halo-phytes was studied:Bromus inermisLeyss,Medicago variaMart. andPhleum pratenseL. A synergistic reduction in the alkylating properties of UDMH oxidation products was observed under the combined use of bacteria and plant seedlings. The greatest effect was obtained when bacteria was used in combination withB. inermis. It was shown that KK1112 cells accelerate the seedlings development and mitigate the growth inhibition that occurs during incubation with UDMH. The obtained results indicate that it is optimal to introduce the bacterium KK1112 in combination withB. inermisplants for soils in arid climate zones during reclamation after UDMH exposure.
The show must go on: What are the available tools to assess readiness to return to dance post injury in elite dancers? A scoping review protocol
Authors: Cahalan Roisin , Purcell Ciaran , Schmieg Rose , Quin Edel
Published: January 2025

Injury in elite dance is commonplace and pernicious. The decision to return to dance practice after injury requires careful consideration to ensure that the dancer is ready to safely resume practice. There are a limited number of pertinent assessment tools in dance, which largely consider predominantly physical domains and refer to specific dance genres only. Therefore, this scoping review aims to explore biopsychosocial domains identified in dance and sport literature to inform the safe return to practice post-injury in elite dance. The scoping review will conform to Joanna Briggs Institute (JBI) Evidence Synthesis guidelines. Ten databases will be searched for relevant articles. Two independent reviewers will conduct title and abstract screening followed by full-text screening. Data charting will be completing using a modified standardised form. Descriptive results will be reported using tabular and graphical media. The published scoping review will be disseminated to relevant stakeholders including those in the world of elite dance in both performance and educational settings, as well as to clinicians working with these artists. The resulting outputs will be in the form of both peer-reviewed and non-peer reviewed publications (e.g. blog posts, academic publications and conference presentations to reach key stakeholders such as dancers and their support teams). An infographic of key findings will be developed and shared on social media platforms as appropriate. The findings of this scoping review will inform a subsequent e-Delphi project involving dancers, teachers and clinicians to develop a dance-specific tool to inform safe return to dance post injury. Ethical approval was not required for this study.
Antisense Oligonucleotide Quantification via Splint-Ligation PCR Assay in Non-Human Primate Central Nervous System Tissues and Biofluids
Authors: Jepp Thomas , Christian Sarah , Dindot Scott V.
Published: January 2025

Antisense oligonucleotides (ASOs) are chemically modified single-stranded oligonucleotides used to modulate the expression or processing of a target RNA transcript. The development of ASOs to treat human disease requires extensive preclinical studies in animal models. A critical component of these studies is determining the concentration of the ASO in tissues and biofluids, which are used to estimate the distribution, half-life, and dose-response relationship. The methods used to quantify ASOs are often constrained by low sensitivities, poor dynamic ranges, and the use of highly specialized equipment. Here, we describe the development of a Splint-Ligation-based quantitative PCR assay to measure the concentration of ASOs in nonhuman primate tissues and biofluids. Our results show that the Splint-Ligation Assay is highly sensitive and has a broad dynamic range in nonhuman primate central nervous system tissues and biofluids, ranging from picomolar to micromolar concentrations. Overall, our results show that the Splint-Ligation PCR Assay is a reliable, sensitive, and feasible method of ASO quantification.
Unlocking Precision Diagnostics: A Multimodal Framework Integrating Metabolomics with Advanced Machine Learning Techniques
Authors: Shahnazari PARISA , Kavousi Kaveh , Khorram Khorshid Hamid Reza , Goliaei Bahram , Salek Reza
Published: January 2025

Integrating multiple omics modalities is a crucial strategy in cancer research, particularly in metabolomics, enabling early detection and detailed exploration of cancer biomarker signatures. This study evaluates five strategies for integrating metabolomics data from liquid chromatography-mass spectrometry, gas chromatography-mass spectrometry, and nuclear magnetic resonance. Deep Transfer Learning and Multiple Kernel Learning demonstrated superior performance, significantly improving classification accuracy, sensitivity, and robustness compared to single-modality analyses. Deep Transfer Learning employed a custom autoencoder for feature extraction followed by artificial neural network classification, while Multiple Kernel Learning optimized kernel matrices across different modalities. Feature extraction in the Deep Transfer Learning approach, combined with the selection of important features and subsequent analysis, revealed elevated levels of monounsaturated phospholipids such as phosphatidylcholine 30:1, phosphatidylethanolamine 32:1, and sphingomyelin 32:1 in HER2-positive cases. Additionally, β-alanine, gluconic acid, and N-acetylaspartic acid were increased, whereas 5'-deoxy-5'-methylthioadenosine and nicotinamide were decreased. These methods advance cancer detection, biomarker discovery, and the development of precise diagnostic and therapeutic tools while offering robust and adaptable strategies for multi-omics data integration across diverse biological datasets.
Virtual Brain Inference (VBI): A flexible and integrative toolkit for efficient probabilistic inference on virtual brain models
Authors: Ziaeemehr Abolfazl , Woodman Marmaduke , Domide Lia , Petkoski Spase , Jirsa Viktor , Hashemi Meysam
Published: January 2025

Network neuroscience has proven essential for understanding the principles and mechanisms underlying complex brain (dys)function and cognition. In this context, whole-brain network modeling—also known as virtual brain modeling—combines computational models of brain dynamics (placed at each network node) with individual brain imaging data (to coordinate and connect the nodes), advancing our understanding of the complex dynamics of the brain and its neurobiological underpinnings. However, there remains a critical need for automated model inversion tools to estimate control (bifurcation) parameters at large scales and across neuroimaging modalities, given their varying spatio-temporal resolutions. This study aims to address this gap by introducing a flexible and integrative toolkit for efficient Bayesian inference on virtual brain models, called Virtual Brain Inference (VBI). This open-source toolkit provides fast simulations, taxonomy of feature extraction, efficient data storage and loading, and probabilistic machine learning algorithms, enabling biophysically interpretable inference from non-invasive and invasive recordings. Through in-silico testing, we demonstrate the accuracy and reliability of inference for commonly used whole-brain network models and their associated neuroimaging data. VBI shows potential to improve hypothesis evaluation in network neuroscience through uncertainty quantification, and contribute to advances in precision medicine by enhancing the predictive power of virtual brain models.
NLO SMEFT electroweak corrections to Higgs boson decays to four leptons in the narrow width approximation
Authors: Dawson Sally , Forslund Matthew , Giardino Pier Paolo
Published: January 2025

Some of the most precise measurements of Higgs boson couplings are from the Higgs decays to 4 leptons, where deviations from the Standard Model predictions can be quantified in the framework of the Standard Model effective field theory (SMEFT). In this work, we present a complete next-to-leading order (NLO) SMEFT electroweak calculation of the rate for H→ℓ+ℓ−Z which we combine with the NLO SMEFT result for Z→ℓ+ℓ− to obtain the NLO rate for the H→4 lepton process in the narrow width approximation. The NLO calculation provides sensitivity to a wide range of SMEFT operators that do not contribute to the rate at lowest order and demonstrates the importance of including correlations between the effects of different operators when extracting limits on SMEFT parameters. We show that the extraction of the Higgs trilinear coupling from the decay H→ℓ+ℓ−Z,Z→ℓ+ℓ− in the narrow width approximation strongly depends on the contributions of other operators that first occur at NLO.

Published by the American Physical Society
2025
Constraints on the
U(1)B−L
model from global QCD analysis
Authors: Wang X. G. , Hunt-Smith N. T. , Melnitchouk W. , Sato N. , Thomas A. W. ,   [JAM collaboration (BSM Analysis Group) ]
Published: January 2025

We perform the first global QCD analysis of electron-nucleon deep-inelastic scattering and related high-energy data including the beyond the Standard Model U(1)B−L gauge boson, Z′. Contrary to the dark photon case, we find no improvement in the χ2 relative to the baseline result. The finding allows us to place exclusion limits on the coupling constant of the Z′ with mass in the range MZ′=2 to 160 GeV.

Published by the American Physical Society
2025
Topological
SU(3)f
approach for two-body
Ωc
weak decays
Authors: Wang Y. L. , Zhao H. J. , Hsiao Y. K.
Published: January 2025

We explore the two-body nonleptonic weak decays of Ωc0 into final states B(*)M and B(*)V, where B(*) denotes an octet (a decuplet) baryon and M(V) represents a pseudoscalar (vector) meson. We employ the topological SU(3)f approach to depict and parametrize the W-emission and W-exchange processes. We find that the topological parameters can be associated and combined, making them extractable for calculation. Consequently, we explain the partially measured branching fractions relative to B(Ωc0→Ω−π+), recombined or kept as the following ratios: B(Ωc0→Ξ*0K¯*0)/B(Ωc0→Ω−ρ+)=0.28±0.11, B(Ωc0→Ξ−π+)/B(Ωc0→Ξ0K¯0)=0.10±0.02, and B(Ωc0→Ω−K+)/B(Ωc0→Ω−π+)=0.06±0.01. In particular, we present B(Ωc0→Ξ0π0)=(2.3±0.2)×10−4 as half the value of B(Ωc0→Ξ−π+) in the approximate isospin relation, and highlight potential candidates for testing SU(3)f symmetry breaking.

Published by the American Physical Society
2025