bluuebunny/crossref_metadata_2025_split huggingface dataset:
New Assessment Method for Upper Limb Function in Patients With Cervical Spondylotic Myelopathy
Authors: Yamada Shohei , Izumi Teiyu , Inokuchi Akihiko , Hamada Takahiro , Imamura Ryuta , Nakamura Kimitaka , Shirasaki Keigo , Yamashita Michinaga , Imasato Yusuke , Tsukahara Kohei , Watanabe Yutaka , Terada Kazumasa , Arizono Takeshi 
Published: October 2024

Study Design.
Retrospective cohort study.

Objective.
Although there are several methods available to assess upper limb function in patients with cervical spondylotic myelopathy, few methods can evaluate the degree of upper limb functional impairment in activities of daily living.

Summary of Background Data.
We devised and evaluated the utility of a new assessment method called the 10 Coins Test, which is based on daily movements.

Materials and Methods.
The study included 39 patients who underwent spinal surgery for cervical spondylotic myelopathy and who were followed up for 1 year postoperatively. The mean age was 65.2±11.5 years, with 31 (79.5%) male and 8 (20.5%) female patients. The 10 Coins Test is a simple examination that measures the time it takes to pick up and move 10 coins forward. Patient satisfaction with surgery was evaluated on a 5-point scale. We compared the 10 Coins Test results, patient satisfaction, and Japanese Orthopaedic Association Cervical Myelopathy Evaluation Questionnaire (JOACMEQ) results before and after surgery.

Results.
The mean time to perform the 10 Coins Test was 27.4 seconds for the dominant hand and 24.5 seconds for the nondominant hand preoperatively. In the control group, the average time was 14.6 seconds for the dominant hand and 15.0 seconds for the nondominant hand. The cut-off value was 16.2 seconds. There was a significant difference in the 10 Coins Test time and satisfaction for both hands at 1 week postoperatively compared with preoperatively. The JOACMEQ upper limb motor function showed a significant improvement 3 months postoperatively compared with preoperatively. The 10 Coins Test result was correlated with satisfaction and the JOACMEQ upper limb motor function.

Conclusion.
The 10 Coins Test allows for the quantitative evaluation of complex movements. It is convenient and highly useful for assessing upper limb function in patients with cervical spondylotic myelopathy.
Evaluating the positive predictive value of code-based identification of cirrhosis and its complications utilizing GPT-4
Authors: Far Aryana T. , Bastani Asal , Lee Albert , Gologorskaya Oksana , Huang Chiung-Yu , Pletcher Mark J. , Lai Jennifer C. , Ge Jin 
Published: October 2024

Background and Aims:
Diagnosis code classification is a common method for cohort identification in cirrhosis research, but it is often inaccurate and augmented by labor-intensive chart review. Natural language processing using large language models (LLMs) is a potentially more accurate method. To assess LLMs’ potential for cirrhosis cohort identification, we compared code-based versus LLM-based classification with chart review as a “gold standard.”

Approach and Results:
We extracted and conducted a limited chart review of 3788 discharge summaries of cirrhosis admissions. We engineered zero-shot prompts using a Generative Pre-trained Transformer 4 to determine whether cirrhosis and its complications were active hospitalization problems. We calculated positive predictive values (PPVs) of LLM-based classification versus limited chart review and PPVs of code-based versus LLM-based classification as a “silver standard” in all 3788 summaries. Compared to gold standard chart review, code-based classification achieved PPVs of 82.2% for identifying cirrhosis, 41.7% for HE, 72.8% for ascites, 59.8% for gastrointestinal bleeding, and 48.8% for spontaneous bacterial peritonitis. Compared to the chart review, Generative Pre-trained Transformer 4 achieved 87.8%–98.8% accuracies for identifying cirrhosis and its complications. Using LLM as a silver standard, code-based classification achieved PPVs of 79.8% for identifying cirrhosis, 53.9% for HE, 55.3% for ascites, 67.6% for gastrointestinal bleeding, and 65.5% for spontaneous bacterial peritonitis.

Conclusions:
LLM-based classification was highly accurate versus manual chart review in identifying cirrhosis and its complications. This allowed us to assess the performance of code-based classification at scale using LLMs as a silver standard. These results suggest LLMs could augment or replace code-based cohort classification and raise questions regarding the necessity of chart review.
Thickness of the Orbital Septum in Comparison to Periorbita and Periosteum
Authors: Kakizaki Hirohiko , Vaidya Aric , Naito Munekazu , Takahashi Yasuhiro 
Published: October 2024

Purpose:
To examine the thickness of the orbital septum in comparison to that of the periorbita and the periosteum of the frontal bone.

Methods:
Histological evaluation of 11 tissues around the upper arcus marginalis, including the orbital septum, periorbita, and periosteum of the frontal bone (5 right, 6 left) from 11 Japanese cadavers (age range: 63–91-year-old, average: 77.1, male: 5 cases and female: 6 cases) was performed. The specimens were fixed in 10% formalin and stained with Masson’s trichrome. The thickness was measured at the 2 mm points from the center of the merging area of these 3 tissues (arcus marginalis). Statistical analyses in 3 groups were performed first with a one-way ANOVA and then with Tukey’s multiple comparison test. Differences in ages or sexes were compared with the Mann–Whitney U test. The significance level was set at 0.05.

Results:
The orbital septum showed similar thickness with the periosteum of the frontal bone (p = 0.784), but was thicker than the periorbita (p = 0.021). The periosteum of the frontal bone was found to be thicker than the periorbita (p = 0.004). Differences between ages (p = 0.315) or sexes (p = 0.126) did not show statistical significance.

Conclusion:
The thickness of the orbital septum was similar to the periosteum of the frontal bone, but was thicker than the periorbita at the 2 mm points from the center of the arcus marginalis. These showed some variation in each case, though. Ages or sexes did not influence the septum thickness after 60 years of age.
Occupational Electronic Health Records
Authors: Fazen Louis E. , Martin Bill E. , Isakari Marcia , Kowalski-McGraw Michele , McLellan Robert K. , Ahsan Raj , Berenji Manijeh 
Published: October 2024

Objective
Occupational and environmental medicine (OEM) clinicians require specialized electronic health records (EHRs) to address the privacy, data governance, interoperability, and medical surveillance concerns that are specific to occupational health.

Methods
The American College of Occupational and Environmental Medicine (ACOEM) Section of Health Informatics evaluated clinical workflow concerns, assessed health information requirements, and developed informatics recommendations through iterative consultation with ACOEM members.

Results
The ACOEM presents 10 recommendations that specialized occupational EHR systems (OEHRs) should meet to serve the information needs and practice requirements of OEM clinicians. Common challenges in OEM practice and potential informatics solutions are used to illustrate each recommendation.

Conclusions
The recommendations serve as a framework for occupational health clinicians to consider in their adoption of OEHRs and provide software engineers a set of requirements to facilitate the development and improvement of OEHRs.
Mapping the scientific landscape and evolution of the International Journal of Surgery: a scientometric analysis (2004–2024)
Authors: Li Chong , Hu Jing , He Anqi , He Chengqi , Zhuang Weihua 
Published: October 2024

Aim:
The purpose of this study was to analyze the publication characteristics and development of the International Journal of Surgery (IJS) over its 20-year history.

Methods:
This study included articles published in IJS during the 20 years from 2004 to 2024. The data were analyzed using the Citespace, VOS viewer, and the ‘Bibliometrix’ package in R software. The authors studied the dynamics and trend patterns of IJS literature production through descriptive bibliometrics and identified the most prolific authors, publications, institutions, and countries. Bibliometric maps were utilized to visualize published articles’ content and identify the most prolific research terms and topics in IJS, as well as their evolution over time.

Results:
A total of 5964 publications in the IJS from 2004 to 2023 and 356 publications in 2024 were included in the analysis. The study revealed a positive trend in literature production, although the number of articles published in IJS has slightly decreased recently. The most productive country was China (n=1211), the most productive institution was Sichuan University (n=151), and the most prolific author was Wang Yang (n=87). The top 15 most cited articles focus primarily on research reporting standard guidelines for surgical studies. Research published in IJS mainly targeted middle-aged and older adults, emphasizing postoperative complications and treatment outcomes. The future research focus in IJS might center on integrating artificial intelligence and deep learning technologies to revolutionize surgical research and practice.

Conclusions:
The International Journal of Surgery significantly contributes to advances in surgical research. IJS prioritized enhancing patient outcomes and advancing surgical techniques, focusing on middle-aged and older adults, postoperative complications, and treatment outcomes. The journal emphasized robust evidence through retrospective, controlled, and cohort surgical studies. Integrating artificial intelligence and deep learning represented a significant frontier poised to revolutionize surgical care, shaping the future landscape of research and practice.
New drugs on the horizon for acute kidney injury
Authors: Mourisse Louis , Pickkers Peter 
Published: October 2024

Purpose of review
Acute kidney injury (AKI) is a frequent and serious complication in critically ill patients. Currently, no effective therapy to prevent or treat AKI is available. This review highlights recently published developments on pharmacological treatments that aim to prevent AKI or to alleviate the severity of AKI in critical ill patients.

Recent findings
Studies on pharmacological interventions aimed to improve hemodynamics, renal perfusion, to mediate inflammation-associated renal damage and to reduce oxidative stress are presented, including several observational studies and randomized trials focused on the potential renal protective effects in relevant patient populations. Different existing and novel compounds are being investigated for the effects on renal endpoints and several show potential to prevent or alleviate the occurrence of AKI. It is now ac
knowledged that different underlying pathophysiological processes are relevant in the development of AKI. Recognition of these sub-endotypes of AKI and knowledge of the therapeutic target of different compounds is of paramount importance to select the right patient for the right treatment at the right time.

Summary
The discovery of reno-protective therapies is hampered by the timely detection and recognition of the overriding mechanism of AKI. Nevertheless, several compounds are under investigation, which hold promise for a future treatment.
Gaps in HIV Pre-exposure Prophylaxis Acceptance: Findings from an Outpatient HIV Testing Service in Italy
Authors: Raccagni Angelo Roberto , Passini Flavia , Diotallevi Sara , Lolatto Riccardo , Bruzzesi Elena , Piromalli Girolamo , Candela Caterina , Castagna Antonella , Nozza Silvia 
Published: October 2024

Background:
The aim of this study is to assess the acceptability of HIV pre-exposure prophylaxis (PrEP) among individuals eligible for prophylaxis.

Setting:
Retrospective study of individuals receiving their first HIV test at the Infectious Diseases Unit of IRCCS San Raffaele Scientific Institute, Milan, Italy.

Methods:
People i) who received their first HIV test (baseline date) between January 2018 (availability of PrEP in Italy) and December 2023 (data lock), ii) with an indication for PrEP based on condomless sex were included; those already on PrEP were excluded. Individuals with a negative HIV test result were offered PrEP counselling and prescription according to guidelines. Characteristics of people who accepted or declined HIV PrEP were compared using Mann-Whitney or Chi-square tests, as appropriate.

Results:
A total of 2627 people were tested for HIV: 175 (6.6%) were diagnosed with HIV. Of the 2452 people with negative HIV test results, 2165 (88.3%) were men; median age was 34.3 years (interquartile range, IQR=28.7-42.4). Sexually transmitted infections (STIs) were detected in 478/2452 (19.5%), most commonly gonorrhoea (206/2452, 8.4%). Overall, 982/2452 (40.0%) people accepted PrEP, including only three women. Non-acceptance was higher among women (p<0.001) and non-Caucasians (p<0.001). Of those who did not accept PrEP, 260 (17.7%) were diagnosed with at least one STI at the time of HIV testing.

Conclusion:
Low PrEP acceptance was observed, particularly among women and people of non-Caucasian origin. Non-acceptance of PrEP was also observed among individuals diagnosed with an STI.
Effect of cardiopulmonary resuscitation on perfusion in a porcine model of severe hemorrhagic shock
Authors: Greiffenstein Patrick , Cavalea Alexander , Smith Alison , Sharp Thomas , Warren Olivia , Dennis Jenna , Gatterer Mary C. , Danos Denise , Byrne Terrence C. , Scarborough Amy , Deville Paige , VanMeter Keith 
Published: October 2024

BACKGROUND
Pulseless electrical activity from hemorrhagic shock has not been shown to benefit from cardiopulmonary resuscitation (CPR). Using a porcine model, our objective was to determine the effects of CPR on brain and skin oxygenation as a measure of perfusion in the setting of severe hemorrhagic shock.

METHODS
Adult swine randomized to non-CPR and CPR were anesthetized. Tissue oxygen sensors were inserted into the parietal cerebral parenchyma and skin. Controlled hemorrhagic shock with mean arterial pressure (MAP) <30 mm Hg was achieved and allowed to persist for 10 minutes. Animals were randomized to either receive automated CPR or no treatment. They were then autotransfused with sufficient blood to achieve MAP >60 mm Hg. Measurements were obtained before, during, and after shock state. Outcomes were modeled using mixed-effects lognormal models.

RESULTS
A total of 12 swine were used, and the results were analyzed (non-CPR, n = 5; CPR, n = 7). One animal in the CPR group died during shock. One cerebral probe sensor malfunctioned, and these data were excluded. Baseline characteristics were similar between groups. MAP during shock was similar between groups; however, the CPR group had significantly higher systolic blood pressure (62.8 vs. 48.8 mm Hg, p = 0.010) and lower diastolic blood pressure (12.8 vs. 27.8 mm Hg, p < 0.001). Both cerebral (pBO2) and skin oxygenation (TcO2) dropped significantly as a result of shock. The CPR group had lower overall measures of tissue perfusion during shock, but only TcO2 at the shoulder was significantly lower during shock (11.5 vs. 21.1 mm Hg, p = 0.027) and recovery (33.3 vs. 62 mm Hg, p = 0.033).

CONCLUSION
Our model showed that adding CPR during hemorrhagic shock did not improve end-organ oxygenation/perfusion, but did significantly diminish skin perfusion. This experiment corroborates existing literature on the potential detrimental effects of CPR during hemorrhagic pulseless electrical activity, but further work is needed to confirm this observation.
Association of NTRK2 gene with suicidality: a meta-analysis
Authors: Ye Wenzhu , Zhang Ruo Su , Hosang Georgina M. , Fabbri Chiara , King Nicole , Strauss John , Jones Ian , Jones Lisa , Breen Gerome , Kennedy James L. , Vincent John B. , Zai Clement C. 
Published: October 2024

Background
Previous studies have shown that genes in brain development pathways may have important roles in affecting risk of suicidal behaviors, with our previous meta-analysis supporting a role of the brain-derived neurotrophic factor (BDNF) gene. NTRK2 is a gene that encodes the neurotrophic receptor tyrosine kinase 2, which is a receptor for BDNF. In the current study, we aim to examine the potential association between NTRK2 single nucleotide polymorphism (SNPs) and suicidal ideation/behaviors.

Methods
We first conducted a literature search using keywords like ‘NTRK2’, ‘TRKB’, and ‘suicid*’ to identify papers on NTRK2 SNPs and suicidal ideation/behaviors. In addition, we have individual-level genotype data for all the identified SNPs in literature search. We used the R meta package to perform meta-analyses on both the genotype count and the allele count data. Moreover, we performed meta-analyses on specific haplotypes within each haplotype block.

Main results
Following our literature search and meta-analyses on 20 NTRK2 SNPs across up to 8467 samples, we found three SNPs, rs10868235 [N = 5,318, odds ratio (OR) = 1.34, P = 0.02], rs1867283 (N = 5,134, OR = 0.73, P = 0.04), and rs1147198 (N = 5,132, OR = 1.36, P = 0.03) to be nominally associated with suicidal attempts. Those three findings, however, did not survive multiple-testing corrections. Also, none of the haplotype blocks showed significant involvement in suicidality.

Conclusion
Our results suggest that the NTRK2 gene may not have a major role in suicidality. Future efforts, however, should explore gene–gene interaction and pathway analyses.
Nurseries and garden centres as hubs of alien plant invasions
Authors: Sonkoly Judit , Molnár V Attila , Török Péter , Süveges Kristóf , Takács Attila 
Published: October 2024

AbstractThe growing global horticultural trade is having a steadily increasing impact on the rate at which alien species are introduced into new areas, partly because horticultural trade also entails the unintentional dispersal of many contaminant species. Although there are reports about noteworthy occurrences of alien plant species in garden centres, this phenomenon has hardly been studied systematically. To bridge this knowledge gap, we conducted systematic field surveys in 12 garden centres in Hungary to assess their alien flora. We hypothesised that (i) the number of alien species inhabiting a garden centre is positively correlated with its size, (ii) relative to their size, garden centres host a disproportionately large proportion of the local alien flora, and (iii) alien species inhabiting garden centres differ from the regional alien flora in their traits. We recorded altogether 93,788 individuals of 67 introduced species, seven of which have not yet been reported from the country. There was considerable variability in the number of species and individuals found in each garden centre, but there was no correlation between the size of the garden centres and the number of species they host. Despite their relatively small size, the studied garden centres hosted a considerable proportion of the local alien flora, indicating that they strongly accumulate alien species and that they can act as invasion hubs for several alien species. Alien species inhabiting garden centres differed from the regional alien flora in some of their trait values, indicating that the species that are most successful at establishing populations inside garden centres are both good dispersers and possess an effective resource-acquisitive strategy. We conclude that established alien plant populations in garden centres may induce local invasions, and in the meantime, individuals and seeds inside the containers of ornamental plants are regularly transported to distant areas by the customers. Therefore, plant species dispersed as contaminants of horticultural stock need to be better considered in invasion biology to reduce the threat they may present.
Transcriptional reprogramming and microbiome dynamics in garden pea exposed to high pH stress during vegetative stage
Authors: Thapa Asha , Hasan Md Rokibul , Kabir Ahmad H. 
Published: October 2024

AbstractHigh soil pH severely impacts plant growth and productivity, yet the transcriptomic changes and microbial dynamics underlying stress adaptation in garden pea (Pisum sativumssp.hortense) remain unclear. This study demonstrates that high soil pH leads to stunted growth, reduced biomass, impaired photosynthesis, and nutrient status in garden pea. Further, disruption in key nitrogen-fixing bacteria (Rhizobium indicum, R. leguminosarum,andR. redzepovicii), along with the downregulation ofNifAandNifDgenes and upregulation ofNifHin nodules highlight the critical role of micronutrient balance in legume-microbe symbiosis and a compensatory response to maintain nitrogen status. RNA-seq analysis revealed extensive transcriptional reprogramming in roots, characterized by the upregulation of oxidative stress response genes (e.g., oxidoreductase and glutathione transferase activities, metal ion transporters) and the downregulation of genes related to ammonia-lyase activity and ion binding, reflecting broader disruptions in nutrient homeostasis. KEGG pathway analysis identified enrichment of MAPK signaling pathway, likely interacting with other pathways associated with stress tolerance, metabolic adjustment, and structural reorganization as part of adaptive responses to high pH. Root microbiome analysis showed significant enrichment ofVariovorax, Shinella,andChaetomium, suggesting host-driven recruitment under high pH stress. Stable genera such asPseudomonas, Novosphingobium, Mycobacterium, Herbaspirillum,andPaecilomycesdisplayed resilience to stress conditions, potentially forming core microbiome components for adaptation to high pH. In a targeted study, inoculation of plants with an enriched microbiome, particularlyC. globosum, under high pH conditions improved growth parameters and increased the abundance ofStenotrophomonasandPseudomonasin the roots. It suggests that these bacterial genera may act as helper microbes toC. globosum, collectively promoting stress resilience in pea suffering from high pH. These findings provide a foundation for microbiome-aided breeding programs and the development of microbial consortia to enhance the adaptation of pea plants to high pH conditions.
JunB-HBZ nuclear translocation by TGF-β is a key driver in HTLV-1–mediated leukemogenesis
Authors: Zhang Wenyi , Shichijo Takafumi , Chen Xueda , Matsuoka Masao , Yasunaga Jun-ichirou 
Published: October 2024

AbstractTheHTLV-1 bZIP factor(HBZ) gene, which is the only viral gene conserved and consistently expressed in all adult T-cell leukemia-lymphoma (ATL) cases, is critical for ATL oncogenesis. Although HBZ protein is found in both the nucleus and the cytoplasm, the dynamics of HBZ protein localization and its contribution to oncogenesis have not been fully elucidated. In this study, we analyzed the subcellular expression pattern of HBZ in primary HTLV-1–infected T cells from asymptomatic carriers and leukemic cells of ATL patients using the Proximity Ligation Assay. Nuclear localization of HBZ protein was significantly higher in fresh ATL cells than in HTLV-1–infected cells from carriers. Importantly, translocation of HBZ protein from the cytoplasm to the nucleus after TGF-β activation was observed in ATL patients, but not in HTLV-1 carriers. In ATL cells, the cellular transcription factors JunB and pSmad3 interact with HBZ and facilitate its nuclear translocation upon TGF-β stimulation.JUNBknockdown inhibits cell proliferationin vitroandin vivoand promotes apoptosis in ATL cells but not in HTLV-1–infected non-leukemic cells, indicating that JunB has important roles in maintaining ATL cells. In conclusion, TGF-β-induced nuclear translocation of HBZ-JunB complexes is associated with ATL oncogenesis.