bluuebunny/crossref_metadata_2025_split huggingface dataset:
Longitudinal effects of affective distress on disease outcomes in rheumatoid arthritis: a meta-analysis and systematic review
Authors: Sweeney Melissa , Adas Maryam A. , Cope Andrew , Norton Sam 
Published: May 2024

AbstractPatients with rheumatoid arthritis have higher rates of mental health conditions compared to the general population. It is believed that affective distress and rheumatoid arthritis have a bi-directional relationship. This review will examine the associations between affective distress and rheumatoid arthritis outcomes over time. Several disease outcomes are included covering disease activity, function, and disability to provide a broad picture of the various ways patients are impacted. A quality assessment was also conducted. There were 71 studies included in the review. Three measures (disease activity, disability, and mortality) had enough data to complete meta-analyses of odds ratios or hazard ratios. The outcomes included were disease activity, tender joint count, swollen joints, pain, physician global assessment, patient global assessment, physical disability, acute phase reactants, stiffness, fatigue, work disability, and mortality. Numerous measures were included for most of the outcomes due to the variability across studies of measures used. Patients with affective distress had lower rates of remission according to the DAS-28, greater disability, and higher mortality. All of the outcomes covered had studies with mixed results, but swollen joint count, tender joint count, patient global assessment, and physician global assessment had the strongest evidence that they were associated with mental health longitudinally. The relationships between affective distress and disease outcomes are complex and vary depending on the measures. Overall, the effects fade over time. It is important for clinicians to be aware of the differing manifestations of the relationship between affective distress and rheumatoid arthritis outcomes.
Gene identification, expression analysis, and molecular docking of SAT and OASTL in the metabolic pathway of selenium in Cardamine hupingshanensis
Authors: Chen Yushan , Li Yao , Luo Guoqiang , Luo Cihang , Xiao Zhijing , Lu Yanke , Xiang Zhixin , Hou Zhi , Xiao Qiang , Zhou Yifeng , Tang Qiaoyu 
Published: May 2024

Abstract
Key message
Identification of selenium stress-responsive expression and molecular docking of serine acetyltransferase (SAT) and O-acetyl serine (thiol) lyase (OASTL) in Cardamine hupingshanensis.

Abstract
A complex coupled with serine acetyltransferase (SAT) and O-acetyl serine (thiol) lyase (OASTL) is the key enzyme that catalyzes selenocysteine (Sec) synthesis in plants. The functions of SAT and OASTL genes were identified in some plants, but it is still unclear whether SAT and OASTL are involved in the selenium metabolic pathway in Cardamine hupingshanensis. In this study, genome-wide identification and comparative analysis of ChSATs and ChOASTLs were performed. The eight ChSAT genes were divided into three branches, and the thirteen ChOASTL genes were divided into four branches by phylogenetic analysis and sequence alignment, indicating the evolutionary conservation of the gene structure and its association with other plant species. qRT-PCR analysis showed that the ChSAT and ChOASTL genes were differentially expressed in different tissues under various selenium levels, suggesting their important roles in Sec synthesis. The ChSAT1;2 and ChOASTLA1;2 were silenced by the VIGS system to investigate their involvement in selenium metabolites in C. hupingshanensis. The findings contribute to understanding the gene functions of ChSATs and ChOASTLs in the selenium stress and provide a reference for further exploration of the selenium metabolic pathway in plants.
Pre-operative lung ablation prediction using deep learning
Authors: Keshavamurthy Krishna Nand , Eickhoff Carsten , Ziv Etay 
Published: May 2024

Abstract
Objective
Microwave lung ablation (MWA) is a minimally invasive and inexpensive alternative cancer treatment for patients who are not candidates for surgery/radiotherapy. However, a major challenge for MWA is its relatively high tumor recurrence rates, due to incomplete treatment as a result of inaccurate planning. We introduce a patient-specific, deep-learning model to accurately predict post-treatment ablation zones to aid planning and enable effective treatments.

Materials and methods
Our IRB-approved retrospective study consisted of ablations with a single applicator/burn/vendor between 01/2015 and 01/2019. The input data included pre-procedure computerized tomography (CT), ablation power/time, and applicator position. The ground truth ablation zone was segmented from follow-up CT post-treatment. Novel deformable image registration optimized for ablation scans and an applicator-centric co-ordinate system for data analysis were applied. Our prediction model was based on the U-net architecture. The registrations were evaluated using target registration error (TRE) and predictions using Bland-Altman plots, Dice co-efficient, precision, and recall, compared against the applicator vendor’s estimates.

Results
The data included 113 unique ablations from 72 patients (median age 57, interquartile range (IQR) (49–67); 41 women). We obtained a TRE ≤ 2 mm on 52 ablations. Our prediction had no bias from ground truth ablation volumes (p = 0.169) unlike the vendor’s estimate (p < 0.001) and had smaller limits of agreement (p < 0.001). An 11% improvement was achieved in the Dice score. The ability to account for patient-specific in-vivo anatomical effects due to vessels, chest wall, heart, lung boundaries, and fissures was shown.

Conclusions
We demonstrated a patient-specific deep-learning model to predict the ablation treatment effect prior to the procedure, with the potential for improved planning, achieving complete treatments, and reduce tumor recurrence.

Clinical relevance statement
Our method addresses the current lack of reliable tools to estimate ablation extents, required for ensuring successful ablation treatments. The potential clinical implications include improved treatment planning, ensuring complete treatments, and reducing tumor recurrence.
Dual-Energy CT muscle fat fraction as a new imaging biomarker of body composition and survival predictor in critically ill patients
Authors: Erley Jennifer , Roedl Kevin , Ozga Ann-Kathrin , de Heer Geraldine , Schubert Niklas , Breckow Julia , Burdelski Christoph , Tahir Enver , Kluge Stefan , Huber Tobias B. , Yamamura Jin , Adam Gerhard , Molwitz Isabel 
Published: May 2024

Abstract
Objective
To analyze changes in the muscular fat fraction (FF) during immobilization at the intensive care unit (ICU) using dual-energy CT (DECT) and evaluate the predictive value of the DECT FF as a new imaging biomarker for morbidity and survival.

Methods
Immobilized ICU patients (n = 81, 43.2% female, 60.3 ± 12.7 years) were included, who received two dual-source DECT scans (CT1, CT2) within a minimum interval of 10 days between 11/2019 and 09/2022. The DECT FF was quantified for the posterior paraspinal muscle by two radiologists using material decomposition. The skeletal muscle index (SMI), muscle radiodensity attenuation (MRA), subcutaneous-/ visceral adipose tissue area (SAT, VAT), and waist circumference (WC) were assessed. Reasons for ICU admission, clinical scoring systems, therapeutic regimes, and in-hospital mortality were noted. Linear mixed models, Cox regression, and intraclass correlation coefficients were employed.

Results
Between CT1 and CT2 (median 21 days), the DECT FF increased (from 20.9% ± 12.0 to 27.0% ± 12.0, p = 0.001). The SMI decreased (35.7 cm2/m2 ± 8.8 to 31.1 cm2/m2 ± 7.6, p < 0.001) as did the MRA (29 HU ±  10 to 26 HU ± 11, p = 0.009). WC, SAT, and VAT did not change. In-hospital mortality was 61.5%. In multivariable analyses, only the change in DECT FF was associated with in-hospital mortality (hazard ratio (HR) 9.20 [1.78–47.71], p = 0.008), renal replacement therapy (HR 48.67 [9.18–258.09], p < 0.001), and tracheotomy at ICU (HR 37.22 [5.66–245.02], p < 0.001). Inter-observer reproducibility of DECT FF measurements was excellent (CT1: 0.98 [0.97; 0.99], CT2: 0.99 [0.96–0.99]).

Conclusion
The DECT FF appears to be suitable for detecting increasing myosteatosis. It seems to have predictive value as a new imaging biomarker for ICU patients.

Clinical relevance statement
The dual-energy CT muscular fat fraction appears to be a robust imaging biomarker to detect and monitor myosteatosis. It has potential for prognosticating, risk stratifying, and thereby guiding therapeutic nutritional regimes and physiotherapy in critically ill patients.

Key Points

The dual-energy CT muscular fat fraction detects increasing myosteatosis caused by immobilization.

Change in dual-energy CT muscular fat fraction was a predictor of in-hospital morbidity and mortality.

Dual-energy CT muscular fat fraction had a predictive value superior to established CT body composition parameters.
Standalone deep learning versus experts for diagnosis lung cancer on chest computed tomography: a systematic review
Authors: Wang Ting-Wei , Hong Jia-Sheng , Chiu Hwa-Yen , Chao Heng-Sheng , Chen Yuh-Min , Wu Yu-Te 
Published: May 2024

Abstract
Purpose
To compare the diagnostic performance of standalone deep learning (DL) algorithms and human experts in lung cancer detection on chest computed tomography (CT) scans.

Materials and methods
This study searched for studies on PubMed, Embase, and Web of Science from their inception until November 2023. We focused on adult lung cancer patients and compared the efficacy of DL algorithms and expert radiologists in disease diagnosis on CT scans. Quality assessment was performed using QUADAS-2, QUADAS-C, and CLAIM. Bivariate random-effects and subgroup analyses were performed for tasks (malignancy classification vs invasiveness classification), imaging modalities (CT vs low-dose CT [LDCT] vs high-resolution CT), study region, software used, and publication year.

Results
We included 20 studies on various aspects of lung cancer diagnosis on CT scans. Quantitatively, DL algorithms exhibited superior sensitivity (82%) and specificity (75%) compared to human experts (sensitivity 81%, specificity 69%). However, the difference in specificity was statistically significant, whereas the difference in sensitivity was not statistically significant. The DL algorithms’ performance varied across different imaging modalities and tasks, demonstrating the need for tailored optimization of DL algorithms. Notably, DL algorithms matched experts in sensitivity on standard CT, surpassing them in specificity, but showed higher sensitivity with lower specificity on LDCT scans.

Conclusion
DL algorithms demonstrated improved accuracy over human readers in malignancy and invasiveness classification on CT scans. However, their performance varies by imaging modality, underlining the importance of continued research to fully assess DL algorithms’ diagnostic effectiveness in lung cancer.

Clinical relevance statement
DL algorithms have the potential to refine lung cancer diagnosis on CT, matching human sensitivity and surpassing in specificity. These findings call for further DL optimization across imaging modalities, aiming to advance clinical diagnostics and patient outcomes.

Key Points

Lung cancer diagnosis by CT is challenging and can be improved with AI integration.

DL shows higher accuracy in lung cancer detection on CT than human experts.

Enhanced DL accuracy could lead to improved lung cancer diagnosis and outcomes.
Contribution of motile rubble-dwelling cryptofauna to the diet of invertivorous coral reef fishes
Authors: Kamen Zebilon F. , Mumby Peter J. , Wolfe Kennedy 
Published: May 2024

AbstractOne of the least understood trophic pathways on coral reefs is the linkage between highly productive cryptic motile invertebrates (herein: cryptofauna) and the predatory vertebrates that underpin reef fisheries. As cryptofauna are difficult to observe and quantify, particularly in coral rubble where they proliferate, the diets of invertivores that forage in rubble have largely been determined through relative gut content analyses. Without congruent quantification of prey diversity, biomass, and rates of predation specific to rubble, it remains challenging to develop models of productivity and energy transfer. We calculated bite rates of six wrasses (Labridae) and a goatfish (Mullidae) commonly found foraging in rubble, using in situ videography on a coral reef in Palau, Western Micronesia. Consumption rates (i.e. individuals consumed) and prey preferences were determined using tank-based feeding experiments, where individual fish were presented with a diverse rubble community characterised before and after 2 h feeding trials. The motile cryptofauna community and invertivore diet consisted predominantly of Arthropoda (83% and > 58%, respectively), with calanoid copepods and mysids positively selected and harpacticoids, decapods and ostracods negatively selected. The interspecific mean (± standard error) rate of consumption was 3.5 ± 0.2 ind. min−1 from rubble, estimated to equal 9.5 ± 0.9 mg min−1 of invertebrate biomass consumed per fish, with biased uptake of small fauna. Bite and consumption rates varied among species with the greatest efficiency in biomass uptake evident in Halichoeres melanurus. This study provides a first attempt at characterising diverse cryptofauna communities pre- and post-trial to identify feeding rates and preferences of coral reef invertivores from the rubble benthos, and highlights the importance of addressing the bioavailability of lower trophic entities in energy pathways.
Staged urethroplasty with groin full-thickness skin graft for managing complex anterior urethral strictures: surgical outcomes and predictive factors
Authors: Cho Min Chul , Lee Jooho , Kim Soo Woong 
Published: May 2024

Abstract
Purpose
To describe outcomes of staged-urethroplasty in complex anterior urethral strictures using full-thickness-skin-graft (FTSG) harvested from the hairless groin area, and to identify factors influencing successful outcomes.

Methods
Through retrospective chart review, we identified a total of 67 men who underwent the first-stage operation (grafting) using groin-FTSG for staged-urethroplasty to treat complex anterior urethral strictures unsuitable for one-stage urethroplasty. Among these, 59 underwent the second-stage operation (tubularization) at a median duration of 5.1-months after grafting. Patients were assessed for outcomes as scheduled after tubularization outcomes were analyzed only for 48 patients for whom ≥ 1-year follow-up data after tubularization were available. Their mean follow-up duration was 27.1 months. Success was defined as achieving physiologic voiding without requiring further procedures.

Results
Median stricture-length was 5.5 cm in all 67 patients. After grafting, neourethral-opening-narrowing occurred in 18. Partial graft-loss occurred in 8, of whom only 3 underwent re-grafting. The percentage of patients who achieved successful outcomes was 81.3%. Improvements in maximum-urine-flow-rate and post-void-residual-urine-volume were maintained until the last follow-up visit. A urethrocutaneous-fistula occurred in one patient, while meatal-stenosis occurred in two. On multivariate-regression-analysis, the presence of neourethral-opening-narrowing was the only predictor of non-success after tubularization. Furthermore, the presence of hypertension, longer stricture-length, and a history of prior direct-vision-internal-urethrotomy were predictors of the occurrence of neourethral-opening-narrowing.

Conclusion
Staged-urethroplasty using groin-FTSG is well worth considering as a useful therapeutic option for complex anterior urethral strictures, with an acceptable success rate and low morbidity. The absence of neourethral-opening-narrowing after the first-stage operation leads to success.
Ophthalmologische Forschung in Deutschland: Evaluation durch ein internationales Expertengremium
Authors: Ader Marius , Cursiefen Claus , Fauser Sascha , Gliem Martin , Helbig Horst , Lagrèze Wolf , Marshall John , Roesky Christian , Sahel José-Alain , Schlötzer-Schrehard Ursula , Sieving Paul , Ueffing Marius 
Published: May 2024

Zusammenfassung
Ziel
Die Forschungsleistung in der Augenheilkunde in Deutschland auf der Grundlage der Ergebnisse der aktuellen DOG-Analyse (Forschungslandkarte der Deutschen Ophthalmologischen Gesellschaft [DOG]) zu bewerten und der DOG sowie der Politik Strategien für zukünftige Verbesserungen auf nationaler Ebene vorzuschlagen. Der Fokus liegt dabei auf der präklinischen und translationalen, klinischen Forschung.

Methoden
Internationale Expertenpanelauswertung und Diskussion, organisiert von dem Arbeitskreis Forschung der Deutschen Ophthalmologischen Gesellschaft (DOG).

Ergebnisse
Die deutsche Forschungslandschaft in der Ophthalmologie ist international gut anerkannt. Das Preis-Leistungs-Verhältnis wurde als sehr gut bewertet. Da Deutschland mit einer alternden Gesellschaft konfrontiert ist und Sehbehinderungen eine immer größere sozioökonomische Belastung darstellen werden, schlugen die Gutachter mehrere Ziele für zukünftige Aktivitäten vor: eine verstärkte Aktivität zur Sicherung des geistigen Eigentums, mehr Lobbyarbeit mit Patientenvertretern, eine intensivere nationale Zusammenarbeit und der Aufbau einer kritischen Masse zwischen den „Leuchttürmen“ der ophthalmologischen Forschung in Deutschland sowie die Einrichtung eines „Deutschen National Eye Institutes“.

Schlussfolgerung
Die ophthalmologische Forschungsleistung in Deutschland wurde von einem internationalen Expertengremium als sehr gut bewertet. Dennoch wurden deutliche Verbesserungen in den Bereichen Translation (klinische Studien, IP), Synergie zwischen spezialisierten Einrichtungen und die staatliche Förderung eines deutschen Zentrums für Gesundheitsforschung zum Thema Augenheilkunde gefordert.
Atypical atrial flutter ablation: follow-up and predictors of arrhythmia recurrence
Authors: Michał Peller , Bartosz Krzowski , Kacper Rutkowski , Michał Marchel , Cezary Maciejewski , Karolina Mitrzak , Grzegorz Opolski , Marcin Grabowski , Paweł Balsam , Piotr Lodziński 
Published: May 2024

AbstractBackground: Ablation techniques have evolved greatly with advances in high-density 3D mapping systems over the last few years. Some patients develop atypical atrial flutter (AAFL) after pulmonary vein isolation (PVI). The data regarding follow-up after AAFL ablation as well as predictors of arrhythmia recurrence are lacking. This analysis aims to report procedure success rates and establish predictors of long-term success. Methods and Results: This retrospective cohort study included 45 patients (median age: 69 years; 40% female) who qualified for their first AAFL after PVI. The procedures were performed with the use of conventional ablation-index-guided ThermoCool Smarttouch SF and QDOT MICRO catheters. Freedom from arrhythmia recurrence was used as a primary end point. After 52 weeks of follow-up, 60% of patients suffered from arrhythmia recurrence, but over 70% of the studied cohort reported symptom improvement. In multivariate analysis, class I antiarrhythmics prescription (HR = 0.24 [95% CI 0.06–0.94], p = 0.04) was associated with the lack of arrhythmia recurrence during the follow-up, while cardioversion during procedure was associated with increased risk of arrhythmia recurrence (HR = 7.05 [95% CI 2.09–23.72], p = 0.002). Conclusions: Long-term success of AAFL ablation procedures is not satisfactory despite improvement in symptoms. Class I antiarrhythmics prescription at the discharge contributes to higher chances of sinus rhythm maintenance, whereas cardioversion during the procedure is related to increased risk of arrhythmia recurrence.
Evaluation of foreign national cases applied to Tokat Gaziosmanpasa University Hospital Forensic Medicine Department, 2014–2022
Authors: Çetin Selçuk , Gedikbaş Mete , Gedikbaş Şule Sinem 
Published: May 2024

Abstract
Introduction/aim
Turkey has experienced a heavy migration burden in recent years due to its location and benevolent policies. This study aimed to retrospectively examine and discuss the reports prepared for foreign nationals who requested assistance at the Forensic Medicine Department of Tokat Gaziosmanpaşa University Hospital in Tokat, which is located in the Middle Black Sea Region of Turkey, between 2014 and 2022.

Materials and methods
This study retrospectively evaluated reports prepared between 2014 and 2022 in the outpatient clinics of Forensic Medicine at Tokat Gaziosmanpaşa University Hospital.

Results
Based on the files reviewed, 219 cases were included in the study, of which 70.8% (n = 155) were male and 29.2% (n = 64) were female. Among the 75 cases referred by judicial authorities, 34.6% (n = 26) involved assault, 28% (n = 21) involved determination of the ability to understand the legal significance and consequences of the act, 16% (n = 12) involved traffic accidents, 8% (n = 6) involved poisoning, 9.3% (n = 7) involved abuse, and 4% (n = 3) involved age determinations.

Discussion
Problems with immigrants, which have always been a reality due to Turkey’s location on migration routes, have increased significantly in recent years. For this reason, we believe that studies with multicenter and larger series should be conducted to determine the current situation that foreigners create for themselves and Turkey to facilitate necessary arrangements, determine proposed solutions, increase the quality of services offered, and develop plans for the future.
A novel subtype based on driver methylation–transcription in lung adenocarcinoma
Authors: Wang Xin , Xu Zhenyi , Zhao Shuang , Song Jiali , Yu Yipei , Yang Han , Hou Yan 
Published: May 2024

Abstract
Aims
To identify driver methylation genes and a novel subtype of lung adenocarcinoma (LUAD) by multi-omics and elucidate its molecular features and clinical significance.

Methods
We collected LUAD patients from public databases, and identified driver methylation genes (DMGs) by MethSig and MethylMix algrothms. And novel driver methylation multi-omics subtypes were identified by similarity network fusion (SNF). Furthermore, the prognosis, tumor microenvironment (TME), molecular features and therapy efficiency among subtypes were comprehensively evaluated.

Results
147 overlapped driver methylation were identified and validated. By integrating the mRNA expression and methylation of DMGs using SNF, four distinct patterns, termed as S1-S4, were characterized by differences in prognosis, biological features, and TME. The S2 subtype showed unfavorable prognosis. By comparing the characteristics of the DMGs subtypes with the traditional subtypes, S3 was concentrated in proximal-inflammatory (PI) subtype, and S4 was consisted of terminal respiratory unit (TRU) subtype and PI subtype. By analyzing TME and epithelial mesenchymal transition (EMT) features, increased immune infiltration and higher expression of immune checkpoint genes were found in S3 and S4. While S4 showed higher EMT score and expression of EMT associated genes, indicating S4 may not be as immunosensitive as the S3. Additionally, S3 had lower TIDE and higher IPS score, indicating its increased sensitivity to immunotherapy.

Conclusion
The driver methylation-related subtypes of LUAD demonstrate prognostic predictive ability that could help inform treatment response and provide complementary information to the existing subtypes.