bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of orthopaedic surgical intervention on difficult-to-treat rheumatoid arthritis: A propensity score-matched study
Authors: Toyama Shogo , Ishikawa Hajime , Abe Asami , Hao Nariaki , Otani Hiroshi , Takamura Sayuri , Sudo Masanori , Ito Satoshi , Nakazono Kiyoshi , Oda Ryo , Takahashi Kenji , Murasawa Akira 
Published: October 2024

ABSTRACT

Objective:
To elucidate the therapeutic effect of orthopaedic surgical intervention (OSI) in difficult-to-treat rheumatoid arthritis (D2T RA) compared with non-D2T RA.

Methods
A total of 534 recent surgeries were analysed only in patients who had undergone OSI since 2016 and for whom a 12-month postoperative follow-up was available. D2T RA was determined according to the European League against Rheumatism definition, and patients with D2T RA were matched to patients with non-D2T RA using propensity scores calculated by a logistic regression analysis. The Health Assessment Questionnaire-Disability Index (HAQ-DI), Disease Activity Index 28 (DAS28), face scale, and patient’s assessment of general health were measured repeatedly at baseline and 6 and 12 months and were compared using a two-way analysis of variance.

Results
The HAQ-DI, DAS28, face scale, and general health showed significant postoperative improvements, and there were significant differences in the HAQ-DI and face scale scores between D2T RA and non-D2T RA. An additional analysis with DAS28 as a covariate showed no significant interaction for either, suggesting that these improvements in clinical assessment were due to OSI rather than improved disease activity.

Conclusions
In the absence of an effective pharmacological treatment strategy, OSI may be an effective treatment modality for the management of D2T RA.
Symptomatic pachydermodactyly: A case report
Authors: Ito Ayaka , Tsuno Hirotaka , Yano Yusuke , Nogi Shinichi , Tabira Yoshihiko , Ohmatsu Hanako , Honda Shogo , Horita Ayako , Saito Ikuo , Matsui Toshihiro 
Published: October 2024

ABSTRACT
Pachydermodactyly, an uncommon variant of digital fibromatosis, predominantly affects young men and results in fibrous swelling on the sides of the proximal interphalangeal joints. It is generally considered benign and asymptomatic, requiring only regular follow-up. Nevertheless, the absence of established diagnostic criteria has led to misdiagnoses, prompting the administration of unnecessary medications. In this report, we present a 14-year-old Japanese male with symptomatic pachydermodactyly (PDD), necessitating careful differentiation from juvenile idiopathic arthritis (JIA) due to the presence of morning stiffness. Despite exhibiting typical PDD features, the patient’s age and symptoms suggested rheumatoid factor-negative polyarticular JIA. However, the lack of inflammatory findings precluded a JIA diagnosis. Following confirmation of the absence of uveitis and progression of bone destruction, the morning stiffness spontaneously resolved without active treatment. However, the patient underwent surgery for aesthetic reasons to alleviate the persistent swelling. Our case highlights the nuances of symptomatic PDD, with a literature review revealing similarities between symptomatic and asymptomatic cases. This challenges the suitability of asymptomatic status as a definitive diagnostic criterion. Our findings contribute to the ongoing efforts in establishing diagnostic criteria for PDD, aiming to reduce misdiagnoses and unnecessary medications in patients.
scLTdb: a comprehensive single-cell lineage tracing database
Authors: Jiang Junyao , Ye Xing , Kong Yunhui , Guo Chenyu , Zhang Mingyuan , Cao Fang , Zhang Yanxiao , Pei Weike 
Published: October 2024

Abstract
Single-cell lineage tracing (scLT) is a powerful technique that integrates cellular barcoding with single-cell sequencing technologies. This new approach enables the simultaneous measurement of cell fate and molecular profiles at single-cell resolution, uncovering the gene regulatory program of cell fate determination. However, a comprehensive scLT database is not yet available. Here, we present the single-cell lineage tracing database (scLTdb, https://scltdb.com) containing 109 datasets that are manually curated and analyzed through a standard pipeline. The scLTdb provides interactive analysis modules for visualizing and re-analyzing scLT datasets, especially the comprehensive cell fate analysis and lineage relationship analysis. Importantly, scLTdb also allows users to identify fate-related gene signatures. In conclusion, scLTdb provides an interactive interface of scLT data exploration and analysis, and will facilitate the understanding of cell fate decision and lineage commitment in development and diseases.
EGFR-mediated HSP70 phosphorylation facilitates PCNA association with chromatin and DNA replication
Authors: Wang Yingying , Fernandez Anthony , Pei Xinyu , Liu Bing , Shen Lei , Yan Yao , Solanki Hitendra S , Yang Lin , Zhou Mian , Guo Yuming , Wu Jun , Reckamp Karen L , Zheng Li , Shen Binghui 
Published: October 2024

Abstract
Efficient DNA replication requires highly coordinated programs for the timely recruitment of protein complexes to DNA replication forks. Defects in this process result in replication stress, which in turn activates cell cycle checkpoints, suppresses cell proliferation and induces apoptosis. In response to persistent cell growth signals that speed up DNA replication processes, cells accelerate the recruitment of DNA replication proteins to avoid DNA replication stress. The mechanisms by which cell growth signals induce processes to facilitate the recruitment of DNA replication proteins onto the replication sites remain unclear. Here, we report that the epidermal growth factor receptor (EGFR) phosphorylates heat shock protein 70 (HSP70) for DNA replication. Such a modification promotes nuclear localization and chromatin association of HSP70, which interacts with the DNA replication coordinator, proliferating cell nuclear antigen (PCNA). HSP70 subsequently facilitates the loading of PCNA onto chromatin. Knockdown or chemical inhibition of HSP70 suppresses PCNA association with chromatin and impairs DNA synthesis and Okazaki fragment maturation, leading to replicative DNA double-strand breaks and apoptosis. Furthermore, chemical inhibition of HSP70 potentiates EGFR–tyrosine kinase inhibitor-induced tumor reduction in vivo. This work expands our understanding of oncogenesis-induced DNA replication processes and provides a foundation for improved treatments for EGFR-mutated lung cancer by simultaneously targeting HSP70.
stSNV: a comprehensive resource of SNVs in spatial transcriptome
Authors: Yang Changbo , Liu Yujie , Wang Xiaohua , Jia Qing , Fan Yuqi , Lu Zhenglin , Shi Jingyi , Liu Zhaoxin , Chen Gengdong , Li Jianing , Lu Weijian , Zhou Weiwei , Lv Dezhong , Zou Haozhe , Xu Juan , Li Yongsheng , Jiang Qinghua , Wang Tao , Shao Tingting 
Published: October 2024

Abstract
Single nucleotide variants (SNVs), as important components of genetic variation, affect gene expression, function and phenotype. Mining and summarizing the spatial distribution of SNVs in diseased and normal tissues for a better understanding of their characteristics and potential roles in cell-lineage determination, aging, or disease occurrence is significant. Herein, we have developed a comprehensive spatial mutation resource stSNV (http://bio-bigdata.hrbmu.edu.cn/stSNV/index.jsp), which provides an atlas of spatial SNVs in major diseased and normal tissues of human and mouse. stSNV documents 42 202 spatial mutated genes involving 898 908 SNVs called from 730 067 spots within 450 slices from 19 diseased and 28 normal tissues. Importantly, potential characteristics of SNVs are explored and provided by analyzing the perturbation of the SNVs to gene expression, spatial communication, biological function, region-specific mutated genes, spatial mutant signatures, SNV-cell co-localization and mutation core region. All these spatial mutation data and in-depth analyses have been integrated into a user-friendly interface, visualized through intuitive tables and various image formats. Flexible tools are developed to explore co-localization among clusters, genes, cell types and SNVs in the same slice. In summary, stSNV as a valuable resource helps to dissect intra-tissue genetic heterogeneity and lays the groundwork for understanding the SNVs’ biological regulatory mechanisms.
BacDive in 2025: the core database for prokaryotic strain data
Authors: Schober Isabel , Koblitz Julia , Sardà Carbasse Joaquim , Ebeling Christian , Schmidt Marvin Leon , Podstawka Adam , Gupta Rohit , Ilangovan Vinodh , Chamanara Javad , Overmann Jörg , Reimer Lorenz Christian 
Published: October 2024

Abstract
In 2025, the bacterial diversity database BacDive is the leading database for strain-level bacterial and archaeal information. It has been selected as an ELIXIR Core Data Resource as well as a Global Core Biodata Resource. Since its initial release more than ten years ago, BacDive (https://bacdive.dsmz.de) has grown tremendously in content and functionalities, and is a comprehensive resource covering the phenotypic diversity of prokaryotes with data on taxonomy, morphology, physiology, cultivation, and more. The current release (2023.2) contains 2.6 million data points on 97 334 strains, reflecting an increase by 52% since the previous publication in 2021. This remarkable growth can largely be attributed to the integration of the world-wide largest collection of Analytical Profile Index (API) test results, which are now fully integrated into the database and searchable. A novel BacDive knowledge graph provides powerful search options through a SPARQL endpoint, including the possibility for federated searches across multiple data sources. The high-quality data provided by BacDive is increasingly being used for the training of artificial intelligence models and resulting genome-based predictions with high confidence are now used to fill content gaps in the database.
MOBIDB in 2025: integrating ensemble properties and function annotations for intrinsically disordered proteins
Authors: Piovesan Damiano , Del Conte Alessio , Mehdiabadi Mahta , Aspromonte Maria Cristina , Blum Matthias , Tesei Giulio , von Bülow Sören , Lindorff-Larsen Kresten , Tosatto Silvio C E 
Published: October 2024

Abstract
The MobiDB database (URL: https://mobidb.org/) aims to provide structural and functional information about intrinsic protein disorder, aggregating annotations from the literature, experimental data, and predictions for all known protein sequences. Here, we describe the improvements made to our resource to capture more information, simplify access to the aggregated data, and increase documentation of all MobiDB features. Compared to the previous release, all underlying pipeline modules were updated. The prediction module is ten times faster and can detect if a predicted disordered region is structurally extended or compact. The PDB component is now able to process large cryo-EM structures extending the number of processed entries. The entry page has been restyled to highlight functional aspects of disorder and all graphical modules have been completely reimplemented for better flexibility and faster rendering. The server has been improved to optimise bulk downloads. Annotation provenance has been standardised by adopting ECO terms. Finally, we propagated disorder function (IDPO and GO terms) from the DisProt database exploiting sequence similarity and protein embeddings. These improvements, along with the addition of comprehensive training material, offer a more intuitive interface and novel functional knowledge about intrinsic disorder.
Tobacco Smoking Functional Networks: A Whole-Brain Connectome Analysis in 24 539 Individuals
Authors: Pan Yezhi , Bi Chuan , Ye Zhenyao , Lee Hwiyoung , Yu Jiaao , Yammine Luba , Ma Tianzhou , Kochunov Peter , Hong L Elliot , Chen Shuo 
Published: October 2024

Abstract

Introduction
Nicotine addiction, a multifaceted neuropsychiatric disorder, profoundly impacts brain functions through interactions with neural pathways. Despite its significance, the impact of tobacco smoking on the whole-brain functional connectome remains largely unexplored.

Aims and Methods
We conducted a whole-brain analysis on 24 539 adults aged 40 and above from the United Kingdom Biobank cohort. Subjects were categorized into individuals who use nicotine and those who do not use nicotine based on current and chronic tobacco smoking information. Functional connectivity was assessed using resting-state functional magnetic resonance imaging. We employed a network analysis method to assess the systematic effects of tobacco smoking on brain connectome by identifying subnetworks that show nicotine-use-related differences.

Results
Our analyses revealed two nicotine-use-related subnetworks with distinct network structure (permutation p &lt; .001). In the first network, there is a significant decrease in resting-state functional connectivity (rsFC) between the basal ganglia regions (eg, nucleus accumbens) and 73% of the remaining brain regions, emphasizing the central hub role of basal ganglia in addictive smoking behaviors. Additionally, a data-driven subnetwork, mainly involving regions from frontal and occipital lobes, showed reduced rsFC among individuals who use nicotine.

Conclusions
The results suggest significant alterations in the communication and coordination among the basal ganglia and the broader network of brain regions. The observed changes in rsFC indicate a widespread disruption in the connectivity patterns associated with nicotine use.

Implications
This study identifies rsFC subnetworks related to chronic nicotine use through whole-brain connectome analysis. The findings confirm that widespread alterations in rsFC are centered around hub nodes within the basal ganglia, including bilateral nucleus accumbens, putamen, caudate, and globus pallidus. In addition, our analysis found a clique-forming subnetwork vulnerable to tobacco smoking consisting of regions from the visual, dorsal/ventral attention, and frontoparietal networks.
(Mis)Governing World Football? Agency and (Non)Accountability in FIFA
Authors: Brett EA , Tomlinson Alan 
Published: October 2024

Abstract
—We identify the variables that have enabled the Fédération Internationale de Football Association (FIFA) to evade internal and external legal and juridical rules and processes, allowing it to prioritise the interests of its leaders and staff rather than its stakeholders. An interdisciplinary theoretical framework highlights the weaknesses of the legal systems, democratic processes, market mechanisms and regulatory regimes governing FIFA’s activities since its foundation. The historical processes transforming FIFA into a wealthy enterprise whose leaders could abuse their power with impunity are reviewed. An evaluation of the structural reforms introduced in 2016 following the exposure of FIFA corruption by US authorities in 2015 then shows how they have strengthened the internal and external rules and procedures enabling stakeholders to hold FIFA to account, whilst arguing that the reforms have not eliminated the leadership’s ability to ‘capture’ its democratic processes, exploit its monopolistic controls over lucrative contracts and evade regulatory controls.
Buyer’s market-oriented culture, strategic procurement capability, and customer performance in the public procurement of innovations
Authors: Tammi Timo , Saastamoinen Jani , Reijonen Helen 
Published: October 2024

Abstract
The public procurement of innovations is a demand-side policy instrument that harnesses supplier innovations to improve products and services delivered to the customers. This study analyses a nation-wide survey of Finnish public sector contracting authorities. A sequential mediation model suggests that the public sector buyer’s market-oriented culture is positively associated with the procurer’s strategic procurement capability, which in turn predicts the use of public procurement of innovations to create customer value for customers. These results are robust to a potentially biased perception of customer performance.
Maternal depressive symptoms in and beyond the perinatal period: associations with infant and preschooler sleep.
Authors: Carter Mikaela L , Paine Sarah-Jane , Sweeney Bronwyn M , Taylor Joanne E , Signal T Leigh 
Published: October 2024

Abstract

Study Objectives
(1) To describe sleep in infancy and early childhood among children born to mothers with and without clinically significant depressive symptoms, and (2) to explore the relationships between maternal depressive symptoms and sleep patterns and problems during infancy and early childhood.

Methods
Secondary analysis of longitudinal data from the Moe Kura: Mother and Child, Sleep and Wellbeing in Aotearoa/New Zealand study. Data were collected in pregnancy (T1), 12 weeks postpartum (T2), and 3 years post-birth (T3). Participants were 262 Māori and 594 non-Māori mother–child dyads. Chi-square and independent t-tests measured bivariate associations between maternal mood (T1, T2, and T3) and child sleep characteristics (T2 and T3). Binary logistic regression models examined longitudinal and concurrent associations between maternal depressive symptoms and infant and preschooler sleep. Adjusted models accounted for key socio-demographic variables, as well as infant sleep variables in preschooler models.

Results
Bivariate associations were found between prior and concurrent depressive symptomology and many of the infant and preschooler sleep outcomes. In adjusted models, prenatal depressive symptoms remained independently associated with shorter-than-recommended sleep durations in preschoolers. In these models, concurrent depression was also associated with night waking, night LSRSP, and perceived sleep problems at 12 weeks postpartum, and CSHQ-determined and perceived sleep problems at 3 years post-birth.

Conclusions
Longitudinal and cross-sectional associations were found between maternal depressive symptoms and child sleep. Sleep appears to be one pathway by which maternal depression confers risk for suboptimal child health outcomes. Findings support the need for earlier and better maternal mental health services.
Safety and feasibility of umbilical cord blood transplantation in children with neuronal ceroid lipofuscinosis: a retrospective study
Authors: Bauchat Andrea , Polishchuk Veronika , Fabrizio Vanessa A , Brondon Jennifer E , Page Kristin M , Driscoll Timothy A , Martin Paul L , Mahadeo Kris M , Kurtzberg Joanne , Prasad Vinod K 
Published: October 2024

Abstract
Ceroid lipofuscinosis neuronal (CLN) encompasses rare inherited neurodegenerative disorders that present in childhood with clinical features including epilepsy, psychomotor delay, progressive vision loss, and premature death. Published experience utilizing umbilical cord blood transplant (UCBT) for these disorders is limited. This retrospective analysis includes patients with CLN (2, 3, and 5) who underwent UCBT from 2012 to 2020. All subjects (n = 8) received standard-of-care myeloablative conditioning. Four also enrolled in clinical trial NCT02254863 and received intrathecal DUOC-01 cells posttransplant. Median age at UCBT was 5.9 years. All subjects achieved neutrophil engraftment with &gt;95% donor chimerism at a median of 28.5 days. Sinusoidal obstructive syndrome was not observed. Severe acute graft-versus-host disease occurred in 12.5%. Other complications included autoimmune hemolytic anemia (25%) and viral reactivation/infection (62.5%). No transplant-related mortality was observed. Two CLN2 patients died, 1 from progressive disease and 1 from unknown cause at days +362 and +937, respectively. With median follow-up of 8 years, overall survival at 100 days and 24 months was 100% and 88%, respectively. Three of 4 CLN3 subjects stabilized Hamburg motor and language scores. While UCBT appears safe and feasible in these patients, given the variable expression and natural history, extended follow-up and further studies are needed to elucidate the potential impact of UCBT on clinical outcomes.
Duct of Luschka leak
Authors: Van Wieren Alizabeth , Haseeb Abdul 
Published: October 2024

ABSTRACT
Bile leakage is a serious early postoperative complication of cholecystectomy. A leak in the duct of Luschka, though rare, can cause significant patient morbidity after a cholecystectomy. Early recognition of this uncommon complication allows for early therapeutic intervention.
Improving Academic Promotion Success via Implementation of Targeted Preparation Strategies and Coaching Processes
Authors: Hill Jacqueline , Haddad Enam , Braet Sarah , Rush Eric , Bratcher Denise 
Published: October 2024

Abstract

Problem
Academic promotion is important for faculty career development and retention in academic medicine. However, the promotion process is time consuming, with little guidance offered to ensure successful outcomes. The authors describe their institution’s standardized approach to providing clear and reliable academic promotion support and share associated outcomes.

Approach
An academic promotion support process, comprising 4 targeted preparation strategies and 3 coaching processes, was implemented in 2020 at Children’s Mercy Kansas City to prepare faculty to submit promotion applications. Targeted preparation strategies include communication plans, an intent to apply process, how-to guides and templates, and institutional promotion committee review. Coaching processes include structured conversations with an immediate faculty leader, an Office of Faculty Development director, and, after committee review of applications, an institutional promotion committee reviewer. Descriptive statistics and promotion outcomes were compared preimplementation (2012–2019) and postimplementation (2020–2023).

Outcomes
In 2012–2019 (8 promotion cycles), prior to implementation of the academic promotion support process, 247 faculty applied for academic promotion. After implementation, in 2020–2023 (4 cycles), 196 faculty applied. From pre- to postimplementation, the mean volume of applications per cycle significantly increased from 31 to 49 (P = .03), and the proportion of approved promotion applications significantly increased from 89.5% (221/247) to 99.0% (194/196) (P < .001). No significant differences were observed in the proportions of applicants who were female (P = .77) or non-White (P = .51).

Next Steps
Creation of an institutional academic promotion support process can be effective in increasing the volume of applications and the likelihood of successful outcomes. Future research should focus on increasing the proportions of non-White faculty and female faculty who apply for promotion and analyzing longer-term outcomes for faculty who are promoted, such as progression to leadership roles.
The evolving role of medical thoracoscopy on therapeutic management of pleural disease
Authors: Fong Clare , Lee Y.C. Gary , Maskell Nick , Lee Pyng 
Published: October 2024

Purpose of review
The use of medical thoracoscopy (MT) has gained widespread acceptance for the diagnosis and management of pleural disease. It is less invasive compared to video-assisted thoracoscopic surgery (VATS), can be performed in the endoscopy suite and in patients who are unfit to undergo general anaesthesia. It is safe, with high diagnostic yield, and enables pulmonologists to intervene therapeutically.

Recent findings
There have been several developments in this field, particularly for malignant pleural effusions (MPE). Specifically, we discuss further techniques that can be employed during MT to distinguish between benign and malignant pleural disease. There is also potential for combined thoracoscopic talc poudrage (TTP) and indwelling pleural catheter (IPC) insertion to shorten hospital stay.

Summary
Beyond MPE, we discuss the role of MT in patients with pneumothorax and pleural infection. We discuss the advantages and disadvantages of MT over traditional practices in a variety of conditions – diagnosis of exudative pleural effusions, prevention of recurrent MPE and pneumothoraces as well as treatment of pleural infections, so as to better aid physicians in selecting the optimum procedure for patients.