bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular phylogenetic relationships among lineages in the genus Carabus (Coleoptera: Carabidae) and radiation of the subgenus Apotomopterus
Authors: Sota Teiji , Liang Hongbin , Pham Hong Thai , Lin Chung-Ping , Hori Michio , Takami Yasuoki , Ikeda Hiroshi 
Published: October 2024

Abstract
The genus Carabus (Coleoptera: Carabidae: Carabinae) is a group of predacious ground beetles found throughout Holarctic temperate zones. The diversification of this group is attributed not only to allopatric speciation but also to diversification in life-history traits and morphological traits that are involved in ecological adaptation and reproductive isolation. Precise phylogenetic reconstruction of Carabus is important to understanding the factors associated with species’ divergence in relation to such character divergence. Here, we analyse the phylogeny of Carabus among higher taxonomic groups and among species of the subgenus Apotomopterus, a hyper-diverse group endemic to East Asia. We used genome-wide sequence data from ultraconserved elements for phylogenetic reconstruction via maximum-likelihood and species-tree reconstruction methods. With regard to the relationships among higher taxonomic groups, the obtained phylogenetic trees resolved two structures with previously unresolved divergence. The subgenus Apotomopterus contained three lineages, i.e. the Vitalisi, Prodigus, and Sauteri groups. It showed diversification of the spinula, a sclerotized male genital structure, and variation in the female elytral notch (preapical emargination). These morphological traits may be involved in copulatory behaviour and potentially affect reproductive isolation, and their character state divergence may have facilitated species divergence of Apotomopterus.
Genetic associations of neuropathic pain and sensory profile in a deeply phenotyped neuropathy cohort
Authors: Åkerlund Mikael , Baskozos Georgios , Li Wenqianglong , Themistocleous Andreas C. , Pascal Mathilde M.V. , Rayner N. William , Attal Nadine , Baron Ralf , Baudic Sophie , Bennedsgaard Kristine , Bouhassira Didier , Comini Maddalena , Crombez Geert , Faber Catharina G. , Finnerup Nanna B. , Gierthmühlen Janne , Granovsky Yelena , Gylfadottir Sandra Sif , Hébert Harry L. , Jensen Troels S. , John Jishi , Kemp Harriet I. , Lauria Giuseppe , Laycock Helen , Meng Weihua , Nilsen Kristian Bernhard , Palmer Colin , Rice Andrew S.C. , Serra Jordi , Smith Blair H. , Tesfaye Solomon , Topaz Leah Shafran , Veluchamy Abirami , Vollert Jan , Yarnitsky David , van Zuydam Natalie , Zwart John Anker , McCarthy Mark I. , Lyssenko Valeriya , Bennett David L. 
Published: October 2024

Abstract
We aimed to investigate the genetic associations of neuropathic pain in a deeply phenotyped cohort. Participants with neuropathic pain were cases and compared with those exposed to injury or disease but without neuropathic pain as control subjects. Diabetic polyneuropathy was the most common aetiology of neuropathic pain. A standardised quantitative sensory testing protocol was used to categorize participants based on sensory profile. We performed genome-wide association study, and in a subset of participants, we undertook whole-exome sequencing targeting analyses of 45 known pain-related genes. In the genome-wide association study of diabetic neuropathy (N = 1541), a top significant association was found at the KCNT2 locus linked with pain intensity (rs114159097, P = 3.55 × 10−8). Gene-based analysis revealed significant associations between LHX8 and TCF7L2 and neuropathic pain. Polygenic risk score for depression was associated with neuropathic pain in all participants. Polygenic risk score for C-reactive protein showed a positive association, while that for fasting insulin showed a negative association with neuropathic pain, in individuals with diabetic polyneuropathy. Gene burden analysis of candidate pain genes supported significant associations between rare variants in SCN9A and OPRM1 and neuropathic pain. Comparison of individuals with the “irritable” nociceptor profile to those with a “nonirritable” nociceptor profile identified a significantly associated variant (rs72669682, P = 4.39 × 10−8) within the ANK2 gene. Our study on a deeply phenotyped cohort with neuropathic pain has confirmed genetic associations with the known pain-related genes KCNT2, OPRM1, and SCN9A and identified novel associations with LHX8 and ANK2, genes not previously linked to pain and sensory profiles, respectively.
Effect of traditional Chinese medicine therapy on labor pain in patients with natural childbirth: A network meta-analysis
Authors: Yi Yangyang , Ju Wenxuan , Fu Danni , Chen Rui , Bai Xue , Zhang Song 
Published: October 2024

Background:
This systematic review compared the efficacy of traditional Chinese medicine (TCM) treatments for outcomes of different stages and labor pain among pregnant women.

Methods:
Eight databases were electronically searched for TCM on labor pain between January 2012 and January 2022. The studies were recorded and screened according to inclusion criteria and subsequently entered in Note Express. The quality of the included studies was evaluated using the Cochrane risk of bias tool, and network meta-analysis was conducted with Stata 16.0. Forest plots and league tables were used to compare different treatment modalities’ effect sizes. Additionally, the probabilities of various treatment modalities for each outcome under the cumulative ranking curve were determined. The protocol was registered in PROSPERO (CRD42022336091). This study adhered to the Preferred Reporting Items for Systematic Reviews and Meta-analyses guidelines.

Results:
Thirty articles encompassing 3277 participants were included in the network meta-analysis with 9 different treatment modalities. In terms of pain of labor at 30 minutes, acupuncture + autonomic nerve block was the most effective treatment modality. With regard to the 60-minute pain and the first stage of labor, acupressure + acupuncture therapy was most effective.

Conclusion:
In general, a combined treatment with acupressure and acupuncture is the most effective approach for relieving labor pain and shortening the duration of labor. Based on these data, we intend to explore further clinical TCM therapy for relieving maternal pain.
Robot-assisted congenital diaphragmatic hernia repair in adults: A case series
Authors: Huang Yu-Jen , Fang Yue-Lin 
Published: October 2024

Rationale:
Congenital diaphragmatic hernia (CDH) is a rare condition predominantly affecting neonates, with only a few cases remaining undetected until adulthood. Surgical repair is the primary treatment approach for adults with confirmed CDH. Traditionally, these procedures include laparotomy, thoracotomy, and minimally invasive techniques such as thoracoscopy and laparoscopy. However, only a few cases of robotic diaphragmatic hernia repair have been reported in recent decades.

Patient concerns:
The patients, aged 31 and 71 years, presented with atypical symptoms of chest tightness and fever. Imaging studies revealed a left-sided Bochdalek CDH in 1 patient and a right-sided Morgagni CDH in the other.

Diagnoses:
The patients were diagnosed as CDH in adult with different symptoms.

Interventions:
Both patients received robot-assisted diaphragmatic hernia repair at our institution.

Outcomes:
The patients received robotic-assisted diaphragmatic hernia repair with acceptable surgery outcome and safety. There was no complication or recurrence.

Lessons:
This case series indicates that the robotic transabdominal approach for CDH repair in adults can be an optimal minimally invasive approach for selected patients, demonstrating adequate surgical safety and favorable outcomes.
Adult-onset neuronal ceroid lipofuscinosis misdiagnosed as autoimmune encephalitis and normal-pressure hydrocephalus: A 10-year case report and case-based review
Authors: Huang Huasheng , Liao Yuqi , Yu Yanni , Qin HuiHui , Wei Yi Zhi , Cao Liming 
Published: October 2024

Rationale:
Neuronal ceroid lipofuscinoses (NCLs) are rare, fatal, inherited neurodegenerative disorders characterized by myoclonic epilepsy, cognitive decline, brain atrophy, and retinopathy. The pathogenesis and clinical manifestations of NCL are not well understood and frequently result in misdiagnosis and overtreatment. The aim of this case report and review is to improve our understanding of the clinical features and management of NCL.

Patient concerns:
A 36-year-old woman initially presented with refractory epilepsy.

Diagnoses:
Initially diagnosed with autoimmune encephalitis, the patient was later diagnosed with normal-pressure hydrocephalus. A definitive diagnosis of adult-onset neuronal ceroid lipofuscinosis (ANCL) was established after 10 years of observation, utilizing biopsy and genetic testing.

Interventions:
High-dose intravenous immunoglobulin and methylprednisolone were administered, along with the insertion of a ventriculoperitoneal shunt.

Outcomes:
Despite various treatments, the patient’s condition did not improve.

Lessons:
ANCL typically presents with the clinical triad of refractory seizures, progressive cognitive decline, and movement disorders. Neuroimaging often reveals progressive brain atrophy on magnetic resonance imaging, while electroencephalograms frequently show epileptiform discharges. The prognosis is generally poor. Improved understanding of ANCL from both clinical and radiological perspectives, coupled with early consideration of differential diagnoses, could minimize unnecessary interventions and optimize patient care.
The relationship between health literacy and healthy lifestyle behaviors: A meta-analysis
Authors: Elkin Nurten 
Published: October 2024

Background:
Health literacy and healthy lifestyle behaviors are both pivotal elements for public health improvement. This meta-analysis aims to scrutinize studies investigating the nexus between health literacy and healthy lifestyle behaviors and to examine the correlation between health literacy and such behaviors.

Methods:
Studies conducted from 2013 to 2023 exploring the association between health literacy and healthy lifestyle behaviors, as well as the impact of gender and chronic disease status on health literacy, were included. The selection criteria for the meta-analysis involved a literature search utilizing databases such as PubMed, Google Academic, Web of Science, and the National Thesis Center. The keywords “health literacy” and “healthy lifestyle behaviors” were employed, identifying 206 studies. Subsequently, 53 studies meeting predetermined criteria were deemed suitable for inclusion in the meta-analysis.

Results:
The analysis of the relationship between health literacy and healthy lifestyle behaviors revealed no publication bias. Despite heterogeneity among the studies, the correlation effect size was determined to be 0.278 using the random effect model. In the meta-analysis examining the effect of gender on health literacy, no publication bias was detected. Since there was heterogeneity among the studies, the average effect size was calculated as 0.078 according to the random effect model. Regarding the meta-analysis on the effect of chronic disease status on health literacy, no publication bias was observed, and due to homogeneity between the studies, the average effect size was determined to be −0.098 using the fixed effect model.

Conclusion:
A positive yet weak relationship was identified between health literacy and healthy lifestyle behaviors. Notably, gender was a significant sociodemographic factor affecting health literacy, with higher levels observed in women. Moreover, individuals without chronic diseases exhibited higher mean health literacy scores than those with chronic diseases.
H2-driven xylitol production inCupriavidus necatorH16
Authors: Jämsä Tytti , Claassens Nico J. , Salusjärvi Laura , Nyyssölä Antti 
Published: October 2024

AbstractBackgroundBiocatalysis offers a potentially greener alternative to chemical processes. For biocatalytic systems requiring cofactor recycling, hydrogen emerges as an attractive reducing agent. Hydrogen is attractive because all the electrons can be fully transferred to the product, and it can be efficiently produced from water using renewable electricity. In this article, resting cells ofCupriavidus necatorH16 harboring a NAD-dependent hydrogenase were employed for cofactor recycling to reduce D-xylose to xylitol, a commonly used sweetener. To enable this bioconversion, D-xylose reductase fromScheffersomyces stipitiswas heterologously expressed inC. necator.ResultsD-xylose reductase was successfully expressed inC. necator, enabling almost complete bioconversion of 30 g/L of D-xylose into xylitol. It was found that over 90% of the energy and protons derived from hydrogen were spent for the bioconversion, demonstrating the efficiency of the system. The highest xylitol productivity reached was 0.7 g L-1h-1. Additionally, the same chassis efficiently produced L-arabitol and D-ribitol from L-arabinose and D-ribose, respectively.ConclusionsThis study highlights the efficient utilization of renewable hydrogen as a reducing agent to power cofactor recycling. Hydrogen-oxidizing bacteria, such asC. necator, can be promising hosts for performing hydrogen-driven biocatalysis.
Three-spined sticklebacks recognise familiar individuals by facial recognition
Authors: Sogawa Shumpei , Inoue Izumi , Awata Satoshi , Ikeya Koki , Kawasaka Kento , Kohda Masanori 
Published: October 2024

AbstractSocial vertebrates often recognise familiar individuals by facial recognition, a basal cognitive ability by which animals establish stable sociality, including territoriality. The three-spined stickleback (Gasterosteus aculeatus), a model species for behavioural studies, is territorial; its ability to visually recognise familiar individuals remains unclear. Here, we report that this species has individual-specific facial colour morph features and can recognise familiar individuals by facial recognition. Territorial neighbours of the same sex established a “dear enemy relationship” with each other. These focal fish were exposed to composite photographic models of four combinations of faces and bodies of familiar neighbours and unknown strangers of the same sex. Focal fish of both sexes frequently attacked photographs of strangers (stranger-face/stranger-body) more frequently than familiar neighbours (neighbour-face/neighbour-body). Furthermore, they attacked composite photographs of stranger-face/neighbour-body more frequently (similar to the stranger model) but less frequently attacked photographs of neighbour-face/stranger-body (similar to the neighbour model). These results suggest that the three-spined stickleback distinguishes familiar neighbours from unknown fish exclusively via facial recognition. The aggressiveness of males was independent of the presence of red nuptial colour on photograph-models. Our findings suggest that this fish controls its aggressiveness against opponent conspecifics in the context of social relationships independent of the sign-stimulus.
Sequence-dependent scale for translocon-mediated insertion of interfacial helices in membranes
Authors: Grau Brayan , Kormos Rian , Bañó-Polo Manuel , Chen Kehan , García-Murria María J. , Hajredini Fatlum , Sánchez del Pino Manuel M. , Jo Hyunil , Martínez-Gil Luis , von Heijne Gunnar , DeGrado William F. , Mingarro Ismael 
Published: October 2024

AbstractBiological membranes consist of a lipid bilayer studded with integral and peripheral membrane proteins. Most α-helical membrane proteins require protein-conducting insertases known as translocons to assist in their membrane insertion and folding. While the sequence-dependent propensities for a helix to either translocate through the translocon or insert into the membrane have been codified into numerical hydrophobicity scales, the corresponding propensity to partition into the membrane interface remains unraveled. By engineering diagnostic glycosylation sites around test peptide sequences inserted into a host protein, we devised a system that can differentiate between water-soluble, surface-bound, and transmembrane (TM) states of the sequence based on its glycosylation pattern. Using this system, we determined the sequence-dependent propensities for transfer from the translocon to a TM, interfacial or extramembrane space. UMAP analysis of a large collection of TM and water-soluble helices provide useful embeddings for analysis of these propensities and aid in understanding the physical properties and functions of antimicrobial, lytic, and fusogenic peptides.
A Genomic Language Model for Chimera Artifact Detection in Nanopore Direct RNA Sequencing
Authors: Li Yangyang , Wang Ting-You , Guo Qingxiang , Ren Yanan , Lu Xiaotong , Cao Qi , Yang Rendong 
Published: October 2024

AbstractChimera artifacts in nanopore direct RNA sequencing (dRNA-seq) can significantly distort transcriptome analyses, yet their detection and removal remain challenging due to limitations in existing basecalling models. We present Deep-Chopper, a genomic language model that precisely identifies and removes adapter sequences from base-called dRNA-seq long reads at single-base resolution, operating independently of raw signal or alignment information to effectively eliminate chimeric read artifacts. By removing these artifacts, DeepChopper substantially improves the accuracy of critical downstream analyses, such as transcript annotation and gene fusion detection, thereby enhancing the reliability and utility of nanopore dRNA-seq for transcriptomics research.
CHK1-mediated regulation of TOP1 catalytic activity suppresses replication and transcription-associated genomic instability
Authors: Majumdar Ananda Guha , Chauhan Nitish , Gupta Pooja , Subramanian Mahesh , Patro Birija Sankar 
Published: October 2024

AbstractThe Topoisomerase 1 (TOP1) catalytic cycle involves a TOP1-DNA-covalent-complex (TOP1cc), which, if stabilized, can induce rapid accumulation of potentially lethal DNA double strand breaks (DSBs). Although TOP1cc are critically associated with genome instability, it is not yet precisely known how cells regulate TOP1cc level, under unperturbed physiological-condition, to prevent its accumulation and lethal consequences. We discovered a key role of CHK1 in phosphorylating TOP1 at Serine-320 and stimulating TOP1-catalytic cycle to minimise genome wide accumulation of TOP1cc in cancers. Pharmacological or genetic ablation of CHK1-mediated TOP1-phosphorylation leads to stalled replication forks and generates copious amounts of replication/transcription-associated DSBs, R-loops and transcription-replication collisions, eventually leading to chromosomal instability. Further, TOP1ccs stabilized due to CHK1 inhibition are not efficiently targeted by cellular TOP1cc-removal machineries. Since multiple patient clinical trials are ongoing with TOP1- and CHK1-targeting drugs, current finding of CHK1-mediated regulation of TOP1cc may help in better understanding the therapeutic outcomes.
Abl kinases regulate FGF signaling independent of Crk phosphorylation to prevent Peters anomaly
Authors: Wu Hao , Mao Yingyu , Wang Qian , Yu Honglian , Bouaziz Michael , Makrides Neoklis , Koleske Anthony J. , Radice Glenn L. , Zhang Xin 
Published: October 2024

AbstractPeters anomaly, the most common cause of congenital corneal opacity, stems from corneal-lenticular adhesion. Despite numerous identified mutations, a cohesive molecular framework of the disease’s etiology remains elusive. Here, we identified Abl kinases as pivotal regulators of FGF signaling, as genetic ablation of Abl kinases restores lens induction even in the absence of FGF signaling. Intriguingly, bothAblkinase deficiency and increased FGF-Ras activity result in Peters anomaly independent of ERK signaling, which can be rescued by allelic deletion of Abl substrate, Crk. However, contrary to the prevailing belief that Abl kinases regulate Crk proteins by direct phosphorylation, mutations at Abl kinase phosphorylation sites on Crk and CrkL did not yield any observable effects. Instead, our findings reveal that Abl kinases phosphorylate Ptpn12, which in turn inhibits p130Cas phosphorylation and Crk recruitment, crucial for Rho GTPases activation and cytoskeletal dynamics. Consequently, Abl kinase deficiency reduces actomyosin contractility within the lens vesicle and genetically interacts with RhoA inhibition. Conversely,Rac1deletion mitigates Peters anomaly in models with aberrant FGF, Abl kinase and RhoA signaling. Our results demonstrate that Abl kinases regulate FGF signaling to balance RhoA and Rac1 activity via the Ptpn12-p130Cas pathway, suggesting that targeting tension-mediated lens vesicle separation could be a therapeutic strategy for Peters anomaly.
Inhibition ofCandida albicansvirulence factor by cyclic dipeptides derived fromAeromonas veroniiV03
Authors: Sekar Jinendiran , Parasuraman Gokul , Dharumadurai Dhanasekaran , Dileep Kumar B.S. , Natesan Sivakumar 
Published: October 2024

AbstractCandida albicansis the most common human fungal pathogen with high mortality rates and limited antifungal treatments. Inhibition ofC. albicanspathogenesis by targeting virulence factors provides a promising strategy for the development of novel antifungal drugs and overcoming drug resistance. In this study, four structurally different cyclic dipeptides (or diketopiperazine(DKP) were isolated and identified as cyclo(L-Pro-L-Leu), cyclo(L-Pro-L-Val), cyclo(D-Pro-L-Phe), and cyclo(L-Pro-D-Tyr) fromAeromonas veroniiV03 and their antimicrobial potentials were evaluated. Results revealed that identified DKPs exhibited antibacterial activity against bacterial pathogens, such asStaphylococcus aureus, Proteus mirabilis,Pseudomonas aeruginosa,andAeromonas hydrophila. Importantly, cyclo(D-Pro-L-Phe) lacking hydroxyl groups showed potent inhibitory effects againstC. albicansand non-albicans species with low concentrations. Moreover, identified DKPs inhibited the virulence traits ofC. albicans,including yeast-to-hyphae transition, secreted hydrolases (aspartic proteases and phospholipase) and biofilm formation in a dose-dependent manner. Collectively, our findings suggest that cyclic dipeptides from DKPs derived fromA. veroniiV03 could potentially be developed as antivirulence agents againstC. albicansinfection.
Sphingolipid imbalance aggravates fibrillar Tau-induced endomembrane rigidification and rupture
Authors: Tittelmeier Jessica , Sandhof Carl Alexander , Martin Nicole , El-Kabarity Deike , Ngonza-Nito Soki-Bradel , Melki Ronald , Nussbaum-Krammer Carmen 
Published: October 2024

AbstractNumerous studies have implicated endolysosomal dysfunction in Alzheimer’s disease (AD) and related tauopathies. However, the mechanisms driving these disturbances remain poorly understood. UsingC. elegans, we recently identified genes involved in sphingolipid metabolism as crucial for the maintenance of endolysosomal integrity. Abnormal sphingolipid metabolism is increasingly reported in AD, but its impact on Tau pathology remains unclear. Here, we investigated the role of sphingolipid metabolism in endolysosomal membrane homeostasis and its effect on Tau aggregation and toxicity inC. elegansand human cell culture models. Fluorescence recovery after photobleaching (FRAP) analysis and C-Laurdan dye imaging revealed that silencing of sphingolipid metabolism genes reduced the fluidity of endolysosomal vesicle membranes, and increased their susceptibility to rupture. The accumulation of aggregated Tau in endolysosomal vesicles further exacerbated endomembrane rigidification and damage. Moreover, enhanced membrane rigidity facilitated seeded Tau aggregation in a biosensor cell line. Restoring membrane fluidity by supplementation with the polyunsaturated omega-3 fatty acid alpha-linoleic acid suppressed endomembrane rupture and seeded Tau aggregation in cell models and neurotoxicity inC. elegans. This study provides mechanistic insights into how impaired sphingolipid homeostasis leads to endolysosomal membrane damage and how this might contribute to the progression of tau pathology.