bluuebunny/crossref_metadata_2025_split huggingface dataset:
History of Multiple Allergies and Gradual Onset Running-Related Injuries in Distance Runners: SAFER XXXV
Authors: van Vreden Chanel , Schwellnus Martin , Ramagole Dimakatso , Swanevelder Sonja , Jordaan Esme , Sewry Nicola 
Published: July 2024

Objective:
To determine if any gradual onset running-related injury (GORRI) was associated with any allergies, multiple allergies (allergies to animals, plants, medication), and allergy medication use.

Design:
Cross-sectional descriptive study.

Setting:
Two Oceans Marathons (56 km, 21.1 km), South Africa.

Participants:
A total of 76 654 race entrants (2012–2015).

Independent Variables:
The prevalence (%) and prevalence ratios (PR; 95% confidence intervals) for history of (1) any allergies, (2) multiple allergies to broad categories of allergens (animal material, plant material, allergies to medication, and other allergies), and (3) allergy medication use.

Main Outcome Measures:
Using a compulsory online screening questionnaire, the outcome was a history of any GORRIs, and subcategories of GORRIs (muscle, tendon) in the past 12 months and history of GORRIs (and subtypes of GORRIs) were reported.

Results:
In 68 258 records with injury and allergy data, the following were significantly associated with reporting any GORRIs: a history of any allergy (PR = 2.2; P < 0.0001), a history of allergies to broad categories of allergens (animal, plant, medication allergy, other) (P < 0.0001), and the use of allergy medication (P < 0.0001). A history of any allergies (PR = 2.4; P < 0.0001), all broad categories of allergies, and allergy medication use were significantly associated with muscle (P < 0.0001) and tendon injuries (P < 0.0001). The risk of reporting a GORRI increased as the number of reported categories of allergies increased (P < 0.0001).

Conclusions:
A novel finding was the cumulative risk effect with a history of multiple allergies. Further studies should aim to determine the underlying mechanism relating allergies and GORRIs.
Entecavir vs. tenofovir disoproxil fumarate in the treatment of chronic hepatitis B patients with severe acute exacerbation
Authors: Lin Chih-Yang , Sun Wei-Chih , Lu Chia-Ming , Chen Wen-Chi , Tsay Feng-Woei , Tsai Tzun-Jiun , Kuo Feng-Yu , Tsai Wei-Lun 
Published: July 2024

Background
The efficacy of different nucleos(t)ide analogs in the treatment of chronic hepatitis B virus (CHB) with severe acute exacerbation (SAE) remained unclear. Thus, this study aimed to compare the short-term efficacy of tenofovir disoproxil fumarate (TDF) and entecavir (ETV) in patients having CHB with SAE.

Methods
We analyzed consecutive patients with treatment-naive CHB receiving TDF (n = 36) or ETV (n = 65) for SAE. The primary endpoint was overall mortality or receipt of liver transplantation (LT) by 24 weeks. The secondary endpoints are the comparison of ETV vs. TDF influences on renal function and virological and biochemical responses at 4, 12, 24, and 48 weeks.

Results
The baseline characteristics were comparable between the two groups. By 24 weeks, 8 (22%) patients in the TDF group and 10 (15%) patients in the ETV group had either died (n = 15) or received LT (n = 3) (P = 0.367). Cox-regression multivariate analysis revealed age (P = 0.003), baseline international normalized ratio of prothrombin time (P = 0.024), and early presence of hepatic encephalopathy (P = 0.003) as independent factors associated with mortality or LT. The two groups of patients achieved comparable biochemical and virological responses at 48 weeks. No significant difference was found in the estimated glomerular filtration rate (eGFR) between the TDF and the ETV groups. However, a significant reduction in the eGFR at 48 weeks, as compared with the baseline, was found in each group.

Conclusion
TDF and ETV achieved similar short-term clinical outcomes and treatment responses in CHB patients with SAE.
Predictors of residual neoplasia after noncurative (R1) endoscopic submucosal dissection of lesions in the gastrointestinal tract
Authors: Ayoub Fares , Khalaf Mai , Kuang Andrew G. , Keihanian Tara , Jawaid Salmaan , Othman Mohamed O. 
Published: July 2024

Background
Endoscopic submucosal dissection (ESD) is a minimally invasive resection technique that enables the en bloc resection of gastrointestinal lesions. Despite en bloc resection, pathological evaluation of lesions can reveal positive vertical or horizontal margins, which is referred to as R1 resection. Not all R1 lesions referred for surgical resection or endoscopic surveillance show evidence of residual tumor. We aimed to identify the predictors of residual neoplasia in patients with an R1 resection following ESD.

Patients and methods
All lesions resected via ESD between June 2016 and September 2021 at a tertiary referral center were retrospectively identified. Lesions with an R1 resection and adequate follow-up were eligible for inclusion. Patient, lesion, and procedural characteristics were analyzed to identify predictors of residual neoplasia.

Results
Of 614 lesions, 163 (28%) had R1 resection. Of these, 56 lesions in 51 patients had complete follow-up and were included. Thirteen patients (25.5%) underwent surgical resection and the remainder underwent endoscopic surveillance. Seven (12.5%) patients had residual disease. All patients with residual disease had esophageal carcinoma. Positive deep and lateral margins, severe submucosal fibrosis, and moderate/poorly differentiated tumors were identified as significant predictors of residual neoplasia.

Conclusion
Most R1 lesions (87.5%) resected by ESD did not have residual disease on follow-up. Those without identified risk factors for residual disease, such as esophageal carcinoma, severe submucosal fibrosis, or both histological margin positivity, may benefit from a strategy of close endoscopic surveillance rather than referral for surgical resection.
Causal relationships between psychological disorders and functional gastrointestinal disorders: a bidirectional two-sample Mendelian randomization study
Authors: Liu Tangyi , Wang Zeyu , Kang Xiaoyu , Wang Xiangping , Ren Gui , Lv Yong , Li Jing , Liu Yaling , Liang Shuhui , Nie Yongzhan , Luo Hui , Pan Yanglin 
Published: July 2024

Background and Aims:Observational studies have shown bidirectional associations between psychological disorders (e.g. depression and anxiety) and functional gastrointestinal disorders. However, whether the relationships are causal is uncertain. Here, we used a bidirectional two-sample Mendelian randomization method to investigate the association between psychological disorders and functional gastrointestinal disorders (FGIDs).MethodsWe obtained genome-wide association study summary statistics for two common psychological disorders: depression (170 756 cases) and anxiety (31 977 cases), as well as for three common FGIDs: functional dyspepsia with 6666 cases, constipation with 26 919 cases, and irritable bowel syndrome (IBS) with 7053 cases. These summary statistics were retrieved from several publicly available genome-wide association study databases. The inverse variance weighted method was used as the main Mendelian randomization method.ResultsInverse variance weighted Mendelian randomization analyses showed statistically significant associations between genetically predicted depression and risk of functional dyspepsia [odds ratio (OR): 1.40, 95% confidence interval (CI): 1.08–1.82], constipation (OR: 1.28, 95% CI: 1.13–1.44), and IBS (OR: 1.51, 95% CI: 1.37–1.67). Genetically predicted anxiety was associated with a higher risk of IBS (OR: 1.13, 95% CI: 1.10–1.17) instead of functional dyspepsia and constipation. In addition, genetically predicted IBS instead of functional dyspepsia and constipation was associated with a higher risk of depression (OR: 1.33, 95% CI: 1.12–1.57) and anxiety (OR: 2.05, 95% CI: 1.05–4.03).ConclusionDepression is a causal risk factor for three common FGIDs. A bidirectional causal relationship between IBS and anxiety or depression was also identified.
Gastrointestinal and Gastroesophageal Reflux Scale Reference Values
Authors: Pados Britt Frisk , Hill Rebecca R. 
Published: July 2024

Abstract

Purpose:
The purpose of this study was to determine age-based reference values for the Gastrointestinal and Gastroesophageal Reflux (GIGER) Scale for Infants and Toddlers.

Study Design and Methods:
GIGER data from healthy, full-term born children under 2 years of age were used to determine reference values. For each age group, median, interquartile range, 90th, and 95th percentile scores were calculated for each subscale and the total score. 90th percentile scores were also calculated for each of the 36 items based on the full sample.

Results:
Data from 625 children were used to determine reference values for children 0-2, 2-4, 4-6, 6-8, 8-10, 10-12, and 12-24 months. In healthy, full-term infants, gastrointestinal and gastroesophageal reflux symptoms improved over the first 24 months of life, with the most improvement occurring over the first 2 months.

Clinical Implications:
The GIGER is a 36-item measure of gastrointestinal and gastroesophageal reflux symptoms for children under 2 years old that has evidence of adequate psychometrics for clinical practice and research. The age-based reference values established in this study can be used to guide score interpretation and determine when a child's symptoms warrant further investigation. This may help identify infants and toddlers with significant symptoms earlier so that they can obtain the care they need.
Predictive Factors for Delayed Recovery From Anesthesia in Patients Receiving Free Vascularized Flap Reconstruction for Head and Neck Defects: A Retrospective Cohort Study
Authors: Zeng Meigu , Wu Jiayao , Liu Xiongying , Xiao Xiliang , Cao Minghui , Wang Chengli 
Published: July 2024

Objective:
Free flap reconstruction for head and neck defects is currently a common procedure. This study aimed to create and validate a predictive model for identifying patients at risk of delayed recovery from anesthesia after free flap reconstruction for head and neck defect.

Methods:
Electronic medical records from all patients were retrospectively collected. The primary outcome variable was delayed recovery from anesthesia. The least absolute shrinkage and selection operator regression model was employed to identify the most relevant features, followed by the construction of a nomogram model using multivariable logistic regression analysis. The discriminatory power, calibration, and clinical utility of the nomogram model were assessed using receiver operating characteristic curve analysis, calibration curve analysis, and decision curve analysis, respectively.

Results:
This novel nomogram model incorporated 4 predictors for delayed recovery from anesthesia: preoperative albumin, intraoperative fresh frozen plasma infusion, preoperative platelet-to-lymphocyte ratio, and duration of intraoperative hypotension. The area under the receiver operating characteristic curve (area under the curve) for the nomogram model was determined to be 0.821 (95% CI: 0.803–0.836). After internal validation, the corrected area under the curve was found to be 0.768 (95% CI: 0.639–0.812). In addition, the model exhibited well-fitted calibration curves and demonstrated favorable clinical usability as indicated by the calibration curve and decision curve analysis curve.

Conclusion:
The authors created and validated a novel predictive model utilizing a limited number of 4 predictors, yet exhibiting commendable predictive performance. This innovative tool holds the potential to mitigate delayed recovery from anesthesia and enhance the efficient allocation of medical resources.
Long-Term Outcomes of the Treatment for Gastric Tube Cancer After Esophagectomy for Esophageal Cancer
Authors: Kitadani Junya , Hayata Keiji , Goda Taro , Takeuchi Akihiro , Tominaga Shinta , Fukuda Naoki , Nakai Tomoki , Nagano Shotaro , Ojima Toshiyasu , Kawai Manabu 
Published: July 2024

Background:
The long-term outcomes of gastric tube cancer (GTC) are unclear. This study therefore aimed to clarify clinicopathologic features and the long-term outcomes of patients with GTC.

Methods:
The 25 patients who were diagnosed with GTC between April 2003 and December 2022 at our hospital were eligible for inclusion in this retrospective study, and this included 27 lesions. We retrospectively evaluated clinicopathologic factors based on hospital records.

Results:
In our cohort, 88% of incidences of GTC were located in the middle or lower gastric tube. As the treatment of GTC, we used endoscopic submucosal dissection, gastrectomy, chemoradiotherapy, chemotherapy, and best supportive care for 16 (59%), 6 (22%), 1 (4%), 1 (4%), and 3 (11%) lesions, respectively. Perforation after endoscopic submucosal dissection was observed in 6 of the 16 lesions. Partial gastric tube resection was performed for 3 patients and total gastric tube resection was performed for 3 patients. One patient who underwent total gastric tube resection died due to acute respiratory distress syndrome. In survival analysis, the 3-year overall survival rate was 52% and the 3-year disease-specific survival rate was 74%. Five patients (20%) died of aspiration pneumonia, 2 patients (8%) of another disease, and 1 patient (4%) of another type of cancer. According to multivariate analysis, independent prognostic factors for overall survival were cN status (HR, 18.021; P=0.004) and complication of aspiration pneumonia (HR, 8.373; P=0.004).

Conclusions:
The occurrence of aspiration pneumonia and cN status were prognostic factors after the treatment for GTC. Assessment of dysphagia and surveillance after treatment for GTC are important to improve the prognosis.
Successful Synergistic Use of Gabapentin With Other Antiepileptic Drugs in the Management of Lance-Adams Syndrome Complicated by Alcohol Withdrawal Seizures: A Case Report
Authors: Chowdhury Danial , McCarthy Caitlin 
Published: July 2024

ObjectiveLance-Adams syndrome is a rare and debilitating disorder characterized by successful cardiopulmonary resuscitation resulting in myoclonus activity. Alcohol withdrawal seizures from alcohol use disorder may further exacerbate Lance-Adams syndrome. We aim to present a case of Lance-Adams syndrome complicated by alcohol withdrawal seizures and successfully treated with a combination of valproate, clonazepam, and gabapentin.Materials and MethodsThe patient's electronic medical record, direct patient care experiences, and a comprehensive literature search were used for this case report. We report a 41-year-old male patient with Lance-Adams syndrome with concurrent alcohol use disorder. Treatment was improved when adding gabapentin for alcohol use disorder treatment, alongside combination antiepileptic therapy. A PubMed search was conducted to examine Lance-Adams syndrome case reports of successful combination antiepileptic therapy, with a secondary evaluation of patients with concurrent alcohol use disorder.ResultsThe literature search yielded 18 articles, which resulted in 21 individual cases in which combination antiepileptic drug therapy was successful in treating myoclonus secondary to Lance-Adams syndrome; however, none of the case reports utilized gabapentin synergistically. One case described Lance-Adams syndrome complicated by alcohol consumption and similar to our patient, the patient used alcohol to abolish myoclonic activity.ConclusionsTo the best of our knowledge, this is the first case report documenting a patient with Lance-Adams syndrome and concurrent alcohol use disorder, with a positive effect of gabapentin use. Gabapentin, when used for alcohol use disorder treatment, may be an appropriate adjunct agent in the management of patients receiving combination antiepileptic therapy for the treatment of Lance-Adams syndrome.
Identification of anaerobic and aerobic bacteria that can be associated with DFI and their therapeutic in Elnaw teaching hospital
Authors: Ahmed Fathi Sharief , Ibrahim Hiba Siddig , Saeed Mohammed Ibrahim 
Published: July 2024

Diabetic foot infection (DFI) is one of the public health concerns especially in the developing countries and it was considered as diabetic foot complications. Adults with diabetes mellitus represent 463 million in 2019 according to the International Diabetes Federation.
The main aim of this study was to identify the anaerobic and aerobic bacteria that related to DFI and their therapeutic regimen for it among diabetic patients in Elnaw teaching hospital - Khartoum state.
This study presented that there wasn’t any an anaerobic organism were isolated while the most often isolated organisms were gram negative rods (70%) which represents (65%) in case of diabetic patients.
For all isolated organism S.aureus represents (30%) followed by E.coli (25%) in control group (non-diabetic), while Klebsiella.spp and S.aureus represents (20%) for each; in the clinic room isolates.
Early diagnosis, optimal management and effective antibiotic therapy are necessary to prevent DFI and amputation.
<xhtml:span xmlns:xhtml="http://www.w3.org/1999/xhtml" xml:lang="en">Bioinformatics analysis of the antigenic epitopes of&#160;L7/L12 protein in the B- and T-Cells active against &#160;Brucella melitensis
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Authors: Zhang Jingjie , Baigued Huricha , Chen Shana , Borigen Haiyan , Tana Tana , Quan Fu , Yang Dezhi 
Published: July 2024

Objective: To analyze the physicochemical properties, spatial structure, and protein–protein interactions (PPIs) of L7/L12 protein using bioinformatics methods and predict their B- and T-cell epitopes to lay a theoretical foundation for developing a novel multiepitope vaccine. Methods: The NCBI database was searched for the amino acid sequences of L7/L12 from Brucella melitensis. In addition, the online softwares, ProtParam and ProtScale, were used to predict the physicochemical properties; NetPhos3.1 and CD-search to predict the phosphorylation sites and conserved domains; SOMPA and SWISS-MODEL to predict the secondary and tertiary structures; the STRING database to analyze the PPIs; and the IEDB, ABCpred, SVMTrip, and SYFPEITHI databases to predict the B- and T-cell epitopes. L7/L12 were docked to TLR4, BCR, MHC Ⅰ-TCR and MHC Ⅱ-TCR complexes, respectively, and the binding ability of L7/L12 to the targeted receptors was tested. Results: L7/L12, consisting of 124 amino acids, was determined to be a stable, intracellular, hydrophilic protein containing 11 phosphorylation sites and ribosomal protein-related conserved domains. α-helices accounted for 70.16%, β-turns for 2.42%, extended strands for 8.87%, and irregular coils for 18.55% of the secondary structure. The PPIs indicated that L7/L12 was involved in the constitution of ribosomes and regulating the accuracy of the translation process. Three B-cell, two CTL and three HTL epitopes were finally screened by comparing multiple databases. L7/L12 binds to TLR4, BCR, MHC Ⅰ-TCR and MHC Ⅱ-TCR complexes and forms stable hydrogen bonds, respectively. Conclusions: L7/L12, which governs the ac translation curate of proteins, possesses several potentially advantageous epitopes, laying a theoretical foundation for designing multiepitope vaccines.
SPArrOW: a flexible, interactive and scalable pipeline for spatial transcriptomics analysis
Authors: Pollaris Lotte , Vanneste Bavo , Rombaut Benjamin , Defauw Arne , Vernaillen Frank , Mortier Julien , Vanhenden Wout , Martens Liesbet , Thoné Tinne , Hastir Jean-Francois , Bujko Anna , Saelens Wouter , Marine Jean-Christophe , Nelissen Hilde , Van Hamme Evelien , Seurinck Ruth , Scott Charlotte L. , Guilliams Martin , Saeys Yvan 
Published: July 2024

AbstractCurrent spatial transcriptomics technologies are increasingly able to measure large gene panels at subcellular resolution, but a major bottleneck in this rapidly advancing field is the computational analysis and interpretation of the data. To bridge this gap, here we present SPArrOW, a flexible, modular and scalable pipeline for processing spatial transcriptomics data. SPArrOW improves cell segmentation and leads to better overall data quality, resulting in more accurate cell annotations at the single-cell level. Furthermore, it provides the users with numerous visual quality checks that are crucial for the correct interpretation of the data, offering users more control in processing their data. Our workflow is designed to accommodate the various available spatial transcriptomics platforms. Finally, SPArrOW offers interactive visualization and data exploration, enabling sample-specific pipeline optimization by various tuneable parameters and an efficient comparison of different staining and gene allocation strategies.
A probabilistic view of forbidden links: their prevalence and their consequences for the robustness of plant-hummingbird communities
Authors: Duchenne François , Barreto Elisa , Guevara Esteban A. , Beck Holger , Bello Carolina , Bobato Rafaela , Bôlla Daniela , Brenes Emanuel , Büttner Nicole , Caron Ana P. , Chaves-Elizondo Nelson , Gavilanes María J. , Restrepo-González Alejandro , Castro Jose Alejandro , Kaehler Miriam , Machado-de-Souza Tiago , Machnicki-Reis Miguel , Marcayata Andrés Sebastián F. , de Menezes Cauã G. , Nieto Andrea , de Oliveira Rafael , de Oliveira Ricardo A. C. , Richter Friederike , Rojas Bryan G. , Romanowski Luciele L. , L.de Souza Wellinton , Veluza Danila S. , Weinstein Ben , Wüest Rafael , Zanata Thais B. , Zuniga Krystal , Maglianesi María A. , Santander Tatiana , Varassin Isabella G. , Graham Catherine H. 
Published: July 2024

AbstractThe presence in ecological communities of unfeasible species interactions, termed forbidden links, due to physiological or morphological exploitation barriers has been long debated, but little direct evidence has been found. Forbidden links are likely to make ecological communities less robust to species extinctions, stressing the need to assess their prevalence. Here, we used a dataset of plant-hummingbird interactions, coupled with a Bayesian hierarchical model, to assess the importance of exploitation barriers in determining species interactions. We found evidence for exploitation barriers between flowers and hummingbirds across the 32 studied communities, however, the proportion of forbidden links changed drastically among communities, because of changes in trait distributions. The higher the proportion of forbidden links, the more they decreased network robustness, because of constraints on interaction rewiring. Our results suggest that exploitation barriers are not rare in plant-hummingbird communities and have the potential to limit the rescue of species experiencing partner extinction.
TRPML1 gating modulation by allosteric mutations and lipids
Authors: Gan Ninghai , Han Yan , Zeng Weizhong , Jiang Youxing 
Published: July 2024

AbstractTransient Receptor Potential Mucolipin 1 (TRPML1) is a lysosomal cation channel whose loss-of-function mutations directly cause the lysosomal storage disorder mucolipidosis type IV (MLIV). TRPML1 can be allosterically regulated by various ligands including natural lipids and small synthetic molecules and the channel undergoes a global movement propagated from ligand-induced local conformational changes upon activation. In this study, we identified a functionally critical residue, Tyr404, at the C-terminus of the S4 helix, whose mutations to tryptophan and alanine yield gain- and loss-of-function channels, respectively. These allosteric mutations mimic the ligand activation or inhibition of the TRPML1 channel without interfering with ligand binding and both mutant channels are susceptible to agonist or antagonist modulation, making them better targets for screening potent TRPML1 activators and inhibitors. We also determined the high-resolution structure of TRPML1 in complex with the PI(4,5)P2inhibitor, revealing the structural basis underlying this lipid inhibition. In addition, an endogenous phospholipid likely from sphingomyelin is identified in the PI(4,5)P2-bound TRPML1 structure at the same hotspot for agonists and antagonists, providing a plausible structural explanation for the inhibitory effect of sphingomyelin on agonist activation.