bluuebunny/crossref_metadata_2025_split huggingface dataset:
Primary Versus Revision ACL Reconstruction Using Quadriceps Autograft: A Matched-Control Cohort Study
Authors: Meena Amit , Farinelli Luca , Hoser Christian , Abermann Elisabeth , Hepperger Caroline , Patralekh Mohit Kumar , Herbort Mirco , Fink Christian 
Published: February 2024

Background: The incidence of anterior cruciate ligament (ACL) reconstruction is increasing, and quadriceps tendon (QT) autograft is gaining popularity for both primary and revision ACL reconstruction. Purpose: To evaluate the differences in the patient-reported functional outcomes, concomitant injuries, and graft failure in primary versus revision ACL surgery using QT autograft. Study Design: Cohort study; Level of evidence, 3. Methods: A total of 376 patients with primary ACL reconstruction and 138 patients with revision ACL reconstruction were retrospectively retrieved from a prospectively collected ACL registry. A minimally invasive technique was used for QT autograft harvesting. The surgical procedure and rehabilitation protocol were identical in both groups. To maintain a homogeneous cohort for the study, the groups were matched by age, sex, and preinjury outcome scores (Lysholm knee score, Tegner activity level, and visual analog scale [VAS] for pain). Initial baseline assessments of outcome scores were compared with scores collected at the 2-year postoperative mark. Results: The mean age of the primary group and revision group was 32.9 ± 10.2 years (range, 18-55 years) and 32.3 ± 9.9 years (range, 19-55 years) respectively. Significant preinjury to postoperative improvements were noted in Lysholm (88.2 ± 16.4 vs 83.5 ± 15.0; P = .007) and VAS pain (0.9 ± 1.3 vs 1.5 ± 1.6; P = .001) scores after primary ACL reconstruction compared with revision reconstruction. However, no significant difference was found in Tegner activity level (6.7 ± 1.8 vs 5.9 ± 1.8; P > .430). Primary ACL injury was associated with significantly higher concomitant medial collateral ligament injuries ( P = .019), while the revision group was associated with significantly higher concomitant cartilage ( P = .001) and meniscal ( P = .003) injuries. A significantly higher graft failure rate was noted in the revision group compared with the primary ACL reconstruction group (13.0% vs 5.6%; P = .005). Conclusion: Both primary and revision ACL reconstruction with QT autograft had acceptable functional outcomes. The primary group had better outcomes than the revision group, possibly due to the lower prevalence of meniscal and cartilage injuries in the primary group compared with the revision group. The revision group was associated with higher graft failure than the primary group. QT autograft is a viable graft choice for both primary and revision ACL reconstruction.
The relationship of fat and muscle measurements with emphysema and bronchial wall thickening in smokers
Authors: Bunk Stijn A.O. , Ipema Jetty , Sidorenkov Grigory , Bennink Edwin , Vliegenthart Rozemarijn , de Jong Pim A. , Pompe Esther , Charbonnier Jean-Paul , Luijk Bart H.D. , Aerts Joachim , Groen Harry J.M. , Mohamed Hoesein Firdaus A.A. 
Published: February 2024

IntroductionDifferences in body composition in patients with COPD may have important prognostic value and may provide opportunities for patient-specific management. We investigated the relation of thoracic fat and muscle with computed tomography (CT)-measured emphysema and bronchial wall thickening.MethodsLow-dose baseline chest CT scans from 1031 male lung cancer screening participants from one site were quantified for emphysema, bronchial wall thickening, subcutaneous fat, visceral fat and skeletal muscle. Body composition measurements were performed by segmenting the first slice above the aortic arch using Hounsfield unit thresholds with region growing and manual corrections. COPD presence and severity were evaluated with pre-bronchodilator spirometry testing.ResultsParticipants had a median age of 61.5 years (58.6–65.6, 25th–75th percentile) and median number of 38.0 pack-years (28.0–49.5); 549 (53.2%) were current smokers. Overall, 396 (38.4%) had COPD (256 Global Initiative for Chronic Obstructive Lung Disease (GOLD) 1, 140 GOLD 2–3). Participants with COPD had less subcutaneous fat, visceral fat and skeletal muscle (p<0.001 for all). With increasing GOLD stages, subcutaneous (p=0.005) and visceral fat values (p=0.004) were higher, and skeletal muscle was lower (p=0.004). With increasing severity of CT-derived emphysema, subcutaneous fat, visceral fat and skeletal muscle values were lower (p<0.001 for all). With increasing CT-derived bronchial wall thickness, subcutaneous and visceral fat values were higher (p<0.001 for both), without difference in skeletal muscle. All statistical relationships remained when adjusted for age, pack-years and smoking status.ConclusionCOPD presence and emphysema severity are associated with smaller amounts of thoracic fat and muscle, whereas bronchial wall thickening is associated with fat accumulation.
Upper-limb intervalversusconstant-load exercise in patients with COPD: a physiological crossover study
Authors: Paneroni Mara , Vogiatzis Ioannis , Cavicchia Alessandro , Salvi Beatrice , Bertacchini Laura , Venturelli Massimo , Vitacca Michele 
Published: February 2024

ObjectiveUpper-limb exercise is recommended for patients with COPD, albeit there are limited data concerning the optimal modality to implement. We compared interval (INT-EX) to continuous (CONT-EX) upper-limb exercise in terms of exercise tolerance, ventilatory and metabolic responses when both conditions were sustained at an equivalent work rate.Methods26 stable COPD patients undertook three upper-limb exercise sessions to initially establish peak work rate (PWR)viaan incremental exercise test and subsequently two equivalent work rate tests to the limit tolerance in balanced order: 1) INT-EX consisting of 30-s work at 100% PWR interspersed with 30-s work at 40% of PWR; and 2) CONT-EX at 70% PWR.Results20 patients (76.9%) had longer tolerance during INT-EX, while six out of 26 (23.1%) exhibited longer tolerance during CONT-EX. The average endurance time was 434.1±184.7 and 315.7±128.7 s for INT-EX and CONT-EX, respectively. During INT-EX at isotime (i.e.when work completed was the same between INT-EX and CONT-EX), the majority of patients manifested lower oxygen uptake, minute ventilation, pulmonary hyperinflation, heart rate, symptoms and higher CO2blood concentration. Patients with longer INT-EX had a lower comorbidity score (Cumulative Illness Rating Scale: 1.58±0.30versus1.88±0.29, p=0.0395) and better-preserved lung function (forced vital capacity 84.7±15.31%versus67.67±20.56%, p=0.0367; forced expiratory volume in 1 s 57.15±14.59versus44.67±12.99% predicted, p=0.0725) compared to patients with longer CONT-EX.ConclusionINT-EX is more sustainable than CONT-EX for the majority of COPD patients with moderate obstruction, leading to lower dynamic hyperinflation and symptoms at isotime. Further studies need to define the benefits of its application during pulmonary rehabilitation.
ClusTrast: a short read de novo transcript isoform assembler guided by clustered contigs
Authors: Westrin Karl Johan , Kretzschmar Warren W. , Emanuelsson Olof 
Published: February 2024

Abstract
Background
Transcriptome assembly from RNA-sequencing data in species without a reliable reference genome has to be performed de novo, but studies have shown that de novo methods often have inadequate ability to reconstruct transcript isoforms. We address this issue by constructing an assembly pipeline whose main purpose is to produce a comprehensive set of transcript isoforms.

Results
We present the de novo transcript isoform assembler ClusTrast, which takes short read RNA-seq data as input, assembles a primary assembly, clusters a set of guiding contigs, aligns the short reads to the guiding contigs, assembles each clustered set of short reads individually, and merges the primary and clusterwise assemblies into the final assembly. We tested ClusTrast on real datasets from six eukaryotic species, and showed that ClusTrast reconstructed more expressed known isoforms than any of the other tested de novo assemblers, at a moderate reduction in precision. For recall, ClusTrast was on top in the lower end of expression levels (<15% percentile) for all tested datasets, and over the entire range for almost all datasets. Reference transcripts were often (35–69% for the six datasets) reconstructed to at least 95% of their length by ClusTrast, and more than half of reference transcripts (58–81%) were reconstructed with contigs that exhibited polymorphism, measuring on a subset of reliably predicted contigs. ClusTrast recall increased when using a union of assembled transcripts from more than one assembly tool as primary assembly.

Conclusion
We suggest that ClusTrast can be a useful tool for studying isoforms in species without a reliable reference genome, in particular when the goal is to produce a comprehensive transcriptome set with polymorphic variants.
Multi-label classification with XGBoost for metabolic pathway prediction
Authors: Joe Hyunwhan , Kim Hong-Gee 
Published: February 2024

Abstract

Background

Metabolic pathway prediction is one possible approach to address the problem in system biology of reconstructing an organism’s metabolic network from its genome sequence. Recently there have been developments in machine learning-based pathway prediction methods that conclude that machine learning-based approaches are similar in performance to the most used method, PathoLogic which is a rule-based method. One issue is that previous studies evaluated PathoLogic without taxonomic pruning which decreases its performance.

Results

In this study, we update the evaluation results from previous studies to demonstrate that PathoLogic with taxonomic pruning outperforms previous machine learning-based approaches and that further improvements in performance need to be made for them to be competitive. Furthermore, we introduce mlXGPR, a XGBoost-based metabolic pathway prediction method based on the multi-label classification pathway prediction framework introduced from mlLGPR. We also improve on this multi-label framework by utilizing correlations between labels using classifier chains. We propose a ranking method that determines the order of the chain so that lower performing classifiers are placed later in the chain to utilize the correlations between labels more. We evaluate mlXGPR with and without classifier chains on single-organism and multi-organism benchmarks. Our results indicate that mlXGPR outperform other previous pathway prediction methods including PathoLogic with taxonomic pruning in terms of hamming loss, precision and F1 score on single organism benchmarks.

Conclusions

The results from our study indicate that the performance of machine learning-based pathway prediction methods can be substantially improved and can even outperform PathoLogic with taxonomic pruning.
Genome-wide identification and transcriptome profiling expression analysis of the U-box E3 ubiquitin ligase gene family related to abiotic stress in maize (Zea mays L.)
Authors: Liu Yongle , Li Changgen , Qin Aokang , Deng Wenli , Chen Rongrong , Yu Hongyang , Wang Yihua , Song Jianbo , Zeng Liming 
Published: February 2024

Abstract
Background
The U-box gene family encodes E3 ubiquitin ligases involved in plant hormone signaling pathways and abiotic stress responses. However, there has yet to be a comprehensive analysis of the U-box gene family in maize (Zea mays L.) and its responses to abiotic stress.

Results
In this study, 85 U-box family proteins were identified in maize and were classified into four subfamilies based on phylogenetic analysis. In addition to the conserved U-box domain, we identified additional functional domains, including Pkinase, ARM, KAP and Tyr domains, by analyzing the conserved motifs and gene structures. Chromosomal localization and collinearity analysis revealed that gene duplications may have contributed to the expansion and evolution of the U-box gene family. GO annotation and KEGG pathway enrichment analysis identified a total of 105 GO terms and 21 KEGG pathways that were notably enriched, including ubiquitin-protein transferase activity, ubiquitin conjugating enzyme activity and ubiquitin-mediated proteolysis pathway. Tissue expression analysis showed that some ZmPUB genes were specifically expressed in certain tissues and that this could be due to their functions. In addition, RNA-seq data for maize seedlings under salt stress revealed 16 stress-inducible plant U-box genes, of which 10 genes were upregulated and 6 genes were downregulated. The qRT-PCR results for genes responding to abiotic stress were consistent with the transcriptome analysis. Among them, ZmPUB13, ZmPUB18, ZmPUB19 and ZmPUB68 were upregulated under all three abiotic stress conditions. Subcellular localization analysis showed that ZmPUB19 and ZmPUB59 were located in the nucleus.

Conclusions
Overall, our study provides a comprehensive analysis of the U-box gene family in maize and its responses to abiotic stress, suggesting that U-box genes play an important role in the stress response and providing insights into the regulatory mechanisms underlying the response to abiotic stress in maize.
Gut microbiota composition and changes in patients with sepsis: potential markers for predicting survival
Authors: Luan Feiyu , Zhou Yang , Ma Xiaohui , Li Yue , Peng Yahui , Jia Xiaonan , Li Nana , Wang Xibo , Luo Yinghao , Man Mingyin , Zhang Qianqian , Wang Chunying , Yu Kaijiang , Zhao Mingyan , Wang Changsong 
Published: February 2024

Abstract
Background
Sepsis can cause immune dysregulation and multiple organ failure in patients and eventually lead to death. The gut microbiota has demonstrated its precise therapeutic potential in the treatment of various diseases. This study aimed to discuss the structural changes of the gut microbiota in patients with sepsis and to analyze the differences in the gut microbiota of patients with different prognoses.

Methods
We conducted a multicenter study in which rectal swab specimens were collected on the first and third days of sepsis diagnosis. A total of 70 specimens were collected, and gut microbiota information was obtained by 16S rRNA analysis.

Results
The relative abundance of Enterococcus decreased in rectal swab specimens during the first three days of diagnosis in patients with sepsis, while the relative abundance of inflammation-associated Bacillus species such as Escherichia coli, Enterobacteriaceae, and Bacteroidetes increased. By comparing the differences in the flora of the survival group and the death group, we found that the abundance of Veillonella and Ruminococcus in the death group showed an increasing trend (p < 0.05), while the abundance of Prevotella_6 and Prevotella_sp_S4_BM14 was increased in surviving patients (p < 0.05).

Conclusions
The Firmicutes/Bacteroidetes ratio, reflecting overall gut microbial composition, was significantly lower on day three of sepsis diagnosis. Changes in the abundance of specific gut microbiota may serve as prognostic markers in patients with sepsis.
Disseminated Nocardia nova in a child with relapsed acute lymphoblastic leukemia: a case report
Authors: Arahirwa Victor , Thahir Sahal , Hernandez Lauren , Willis Zachary Inskeep 
Published: February 2024

Abstract
Background
Nocardiosis is a rare infection that typically results from inhalation of or inoculation with Nocardia organisms. It may cause invasive disease in immunocompromised patients. This case describes nocardiosis with bacteremia and pulmonary involvement in a child with a hematologic malignancy.

Case presentation
A boy with testicular relapsed acute lymphoblastic leukemia with marrow involvement presented with sudden onset of fever, body aches, headaches, chills, and moderate respiratory distress during continuation 2 chemotherapy. Radiographic imaging demonstrated consolidation and ground glass opacities in bilateral lower lungs. Central line blood cultures grew Nocardia nova complex, prompting removal of the central line and initiation of triple therapy with imipenem-cilastatin, linezolid, and trimethoprim-sulfamethoxazole with rapid improvement of symptoms. Antibiotic susceptibilities showed a multidrug-susceptible isolate. The patient is anticipated to remain on trimethoprim-sulfamethoxazole for at least 12 months.

Conclusions
In an immunocompromised child, blood cultures, chest imaging, and head imaging can aid in the diagnosis of disseminated nocardiosis. Long-term antibiotic therapy is necessary, guided by the organism and simplified with the results of antimicrobial susceptibility testing.
A multicentric, single arm, open-label, phase I/II study evaluating PSMA targeted radionuclide therapy in adult patients with metastatic clear cell renal cancer (PRadR)
Authors: Kryza David , Vinceneux Armelle , Bidaux Anne-Sophie , Garin Gwenaelle , Tatu Delphine , Cropet Claire , Badel Jean-Noël , Perol David , Giraudet Anne-Laure 
Published: February 2024

Abstract
Background
Despite advancements in managing metastatic clear cell renal carcinoma (mccRCC) through antiangiogenic tyrosine kinase inhibitors and immunotherapy, there remains a demand for novel treatments for patients experiencing progression despite the use of these medications. There is currently no established standard treatment for patients receiving third therapy line. Prostate Specific Membrane Antigen (PSMA) whose high expression has been demonstrated in metastatic aggressive prostate adenocarcinoma is also highly expressed in neovessels of various solid tumors including renal cell carcinoma (RCC): 86% of clear cell RCC, 61% of chromophobe RCC, and 28% of papillary RCC. Therefore, PSMA may be a target expressed in metastatic ccRCC for radionuclide therapy using PSMA ligands radiolabeled with Lutetium-177 (PRLT). 177Lu-PSMA delivers ß-particle radiation to PSMA-expressing cells and the surrounding microenvironment with demonstrated efficacy in metastatic prostate cancer.

Methods
This is a multicenter phase I/II study designed to assess the tolerability and effectiveness of 177Lu-PSMA-1 in individuals with PSMA-positive metastatic clear cell renal cell carcinoma (ccRCC), identified through 68Ga-PSMA PET, conducted in France (PRadR). 48 patients will be treated with 4 cycles of 7.4 GBq of 177Lu-PSMA-1 every 6 weeks. The primary objective is to evaluate the safety of 177Lu-PSMA-1 (phase I) and the efficacy of 177Lu-PSMA-1 in mccRCC patients (phase II). Primary endpoints are incidence of Severe Toxicities (ST) occurring during the first cycle (i.e. 6 first weeks) and disease Control Rate after 24 weeks of treatment (DCR24w) as per RECIST V1.1. Secondary objective is to further document the clinical activity of 177Lu-PSMA-1 in mccRCC patients (duration of response (DoR), best overall response rate (BORR), progression fee survival (PFS) and overall survival (OS).

Discussion
Our prospective study may lead to new potential indications for the use of 177Lu-PSMA-1 in mccRCC patients and should confirm the efficacy and safety of this radionuclide therapy with limited adverse events. The use of 177Lu-PSMA-1may lead to increase disease control, objective response rate and the quality of life in mccRCC patients.

Trial registration
ClinicalTrials.gov: NCT06059014.
Short-term exposure to extreme temperature and outpatient visits for respiratory diseases among children in the northern city of China: a time-series study
Authors: Wu Ya , Liu Xiaobo , Gao Lijie , Sun Xiaohong , Hong Qianqi , Wang Qian , Kang Zhen , Yang Chao , Zhu Sui 
Published: February 2024

Abstract
Background
Although studies have indicated that extreme temperature is strongly associated with respiratory diseases, there is a dearth of studies focused on children, especially in China. We aimed to explore the association between extreme temperature and children’s outpatient visits for respiratory diseases and seasonal modification effects in Harbin, China.

Methods
A distributed lag nonlinear model (DLNM) was used to explore the effect of extreme temperature on daily outpatient visits for respiratory diseases among children, as well as lag effects and seasonal modification effects.

Results
Extremely low temperatures were defined as the 1st percentile and 2.5th percentile of temperature. Extremely high temperatures were defined as the 97.5th percentile and 99th percentile of temperature. At extremely high temperatures, both 26 °C (97.5th) and 27 °C (99th) showed adverse effects at lag 0–6 days, with relative risks (RRs) of 1.34 [95% confidence interval (CI): 1.21–1.48] and 1.38 (95% CI: 1.24–1.53), respectively. However, at extremely low temperatures, both − 26 °C (1st) and − 23 °C (2.5th) showed protective effects on children’s outpatient visits for respiratory diseases at lag 0–10 days, with RRs of 0.86 (95% CI: 0.76–0.97) and 0.85 (95% CI: 0.75–0.95), respectively. We also found seasonal modification effects, with the association being stronger in the warm season than in the cold season at extremely high temperatures.

Conclusions
Our study indicated that extremely hot temperatures increase the risk of children’s outpatient visits for respiratory diseases. Efforts to reduce the exposure of children to extremely high temperatures could potentially alleviate the burden of pediatric respiratory diseases, especially during the warm season.
Associations of triglyceride-glucose index with hyperuricemia among Royal Thai Army personnel
Authors: Lertsakulbunlue Sethapong , Sangkool Tanatip , Bhuriveth Varathpavee , Mungthin Mathirut , Rangsin Ram , Kantiwong Anupong , Sakboonyarat Boonsub 
Published: February 2024

Abstract
Background
Hyperuricemia has placed an immense burden on the global healthcare system. Studies have discovered a close correlation between serum uric acid (SUA) and insulin resistance (IR). The objective of this investigation is to examine the association between the triglyceride-glucose (TyG) index, a simple surrogate for IR, and the presence of hyperuricemia.

Methods
Between 2017 and 2021, an epidemiologic study was conducted on Royal Thai Army (RTA) personnel aged 35–60 years, involving a total of 231,286 participants. In the study, hyperuricemia was defined as a SUA level of 7 mg/dL and 6 mg/dL among male and female participants, respectively. Using linear regression analysis and logistic regression analysis, the association between the TyG index and SUA was determined.

Results
A positive relationship was demonstrated between the TyG index and the SUA. Overall, SUA increased by 0.32 per unit of TyG index growth (95% CI: 0.31–0.32). In comparison with the first quartile, employees in the fourth TyG quartile had a greater likelihood of having hyperuricemia [adjusted odds ratio (AOR): 2.45, 95% CI: 2.38–2.52]. Effect modification by obesity on the association between the TyG index and SUA was observed (P-interaction < 0.001). Among individuals with obesity, compared with the first TyG index quartile, the AOR for hyperuricemia was 2.15 (95% CI: 2.06–2.25) and 2.14 (95% CI: 1.81–2.53) for the fourth quartile of the TyG index for males and females, respectively. However, for nonobese personnel, in comparison to the top quartile of the TyG index, the AOR for hyperuricemia was 2.73 (95% CI:2.61–2.84) and 5.03 (95% CI: 4.03–6.29) for the fourth quartile of the TyG index for males and females, respectively. Personnel in the fourth TyG index quartile revealed that the prevalence of hyperuricemia reached 44.2%.

Conclusion
A robust positive association between the TyG index and SUA was illustrated among active-duty RTA personnel. Obesity was identified as a modifier influencing this relationship. Furthermore, individuals in the fourth quarter of the TyG index, regardless of their obesity status, could be considered appropriate candidates for screening SUA levels.