bluuebunny/crossref_metadata_2025_split huggingface dataset:
Long-term monitoring of fish in a freshwater reservoir: Different ways of weighting complex spatial samples
Authors: Tesfaye Gashaw C. , Souza Allan T. , Bartoň Daniel , Blabolil Petr , Čech Martin , Draštík Vladislav , Frouzová Jaroslava , Holubová Michaela , Kočvara Luboš , Kolařík Tomáš , Martinez Carlos , Moraes Karlos R. , Muška Milan , Prchalová Marie , Říha Milan , Sajdlová Zuzana , Soukalová Kateřina , Šmejkal Marek , Tušer Michal , Vašek Mojmír , Vejřík Lukáš , Vejříková Ivana , Peterka Jiří , Jůza Tomáš , Kubečka Jan 
Published: December 2022

Anthropogenic activities continue to pose the greatest challenges to freshwater ecosystems. Therefore, long-term monitoring is essential for the management and conservation of these resources. Monitoring programs for freshwater bodies often use a range of indicators, including biological elements such as fish. Existing European standard provides a depth-stratified gillnet sampling approach mainly in benthic habitats and at the deepest part of lakes to account for the uneven distribution of fish. However, the commonly used CEN (European Committee for Standardization) protocol does not weight sufficiently habitat volumes and underrepresent pelagic habitats to calculate whole-lake catch and biomass per unit effort (CPUE and BPUE, respectively). Extended European standard gillnet (4 larger mesh-sizes added in the geometric series) catch data collected over 18 years (2004–2021) in Římov Reservoir (Czech Republic) were used for a method comparison on indices for relative abundance and biomass of fish: CEN protocol without volume-weighting and two volume-weighted approaches. We also evaluated changes in species composition and trends in these fish population over time. Results indicated interannual changes in species composition, relative abundance, and biomass of fish community. The CEN protocol tended to put greater emphasis on benthic habitats which generally have larger CPUE and BPUE. Consequently, the two volume-weighting approaches produced lower estimates of the two parameters, with the exception of the most dominant pelagic bleak Alburnus alburnus (L.). All approaches consistently showed an increasing trend in whole-reservoir fish abundance and a decreasing trend in biomass over the study period. Following our assessment, we put forward the volume-weighting approach that considers the Volume of the depth Stratum (VOST) for weighting as the most realistic approximation of fish populations and therefore recommend its use.
Major histocompatibility complex genomic investigation of endangered Chinese alligator provides insights into the evolution of tetrapod major histocompatibility complex and survival of critically bottlenecked species
Authors: He Ke , Zhu Ying , Yang Shang-Chen , Ye Qing , Fang Sheng-Guo , Wan Qiu-Hong 
Published: December 2022

BackgroundThe major histocompatibility complex (MHC) gene family, a vital immune gene family in vertebrates, helps animals defend against pathogens. The polymorphism of MHC genes is important for a species and is considered to be caused by the numerous alleles of MHC antigen-presenting genes. However, the mechanism of this process is unclear due to the lack of data on the MHC structure. The evolutionary trajectories of the tetrapod MHC are also unclear because of insufficient studies on the reptile MHC architecture. Here, we studied the Chinese alligator (Alligator sinensis), which experienced a population bottleneck, but the population increased rapidly in the past 30 years and is proposed to have a unique MHC system to face pathogenic challenges.ResultsWe successfully constructed a 2 Mb MHC region using bacterial artificial chromosome (BAC) library and genome data of the Chinese alligator and checked the antigen-presenting genes using transcriptome data and the rapid amplification of cDNA ends (RACE) technique. The MHC architecture reported here uncovers adjacent Class I and Class II subregions and a unique CD1 subregion. This newly added information suggested that the Class I-II structure pattern was more ancient in tetrapods and helped reconstruct the evolution of the MHC region architecture. We also found multiple groups of MHC class I (MHC-I) (12 duplicated loci, belonging to three groups, two of which were novel) and MHC class II (MHC-II) (11 duplicated loci, belonging to two groups) inside the 2 Mb MHC region, and there were three more duplicated MHC-I loci outside it. These highly duplicated antigen-presenting loci had differences in expression, amino acid length of antigen-presenting exons, and splice signal of exon and intron, which together promoted the polymorphism of duplicated genes. Although the MHC antigen-presenting genes were identified as monomorphic or oligomorphic in our previous population study, the loci with high copy numbers and many differences can make up for this loss, presenting another mechanism for polymorphism in antigen presentation. These MHC-I and MHC-IIB loci with low polymorphism for each locus, but high numbers in all, may also contribute to MHC antigen-presenting binding variability in a population.ConclusionTo summarize, the fine MHC region architecture of reptiles presented in this study completes the evolutionary trajectories of the MHC structure in tetrapods, and these distinctive MHC gene groups in the Chinese alligator may have helped this species to expand rapidly in the past recent years.
Fatty acid composition and metabolic partitioning of α-linolenic acid are contingent on life stage in human CD3+ T lymphocytes
Authors: West Annette L. , von Gerichten Johanna , Irvine Nicola A. , Miles Elizabeth A. , Lillycrop Karen A. , Calder Philip C. , Fielding Barbara A. , Burdge Graham C. 
Published: December 2022

IntroductionImmune function changes across the life course; the fetal immune system is characterised by tolerance while that of seniors is less able to respond effectively to antigens and is more pro-inflammatory than in younger adults. Lipids are involved centrally in immune function but there is limited information about how T cell lipid metabolism changes during the life course.Methods and ResultsWe investigated whether life stage alters fatty acid composition, lipid droplet content and α-linolenic acid (18:3ω-3) metabolism in human fetal CD3+T lymphocytes and in CD3+T lymphocytes from adults (median 41 years) and seniors (median 70 years). Quiescent fetal T cells had higher saturated (SFA), monounsaturated fatty acid (MUFA), and ω-6 polyunsaturated fatty acid (PUFA) contents than adults or seniors. Activation-induced changes in fatty acid composition differed between life stages. The principal metabolic fates of [13C]18:3ω-3 were constitutive hydroxyoctadecatrienoic acid synthesis and β-oxidation and carbon recycling into SFA and MUFA. These processes declined progressively across the life course. Longer chain ω-3 PUFA synthesis was a relatively minor metabolic fate of 18:3ω-3 at all life stages. Fetal and adult T lymphocytes had similar lipid droplet contents, which were lower than in T cells from seniors. Variation in the lipid droplet content of adult T cells accounted for 62% of the variation in mitogen-induced CD69 expression, but there was no significant relationship in fetal cells or lymphocytes from seniors.DiscussionTogether these findings show that fatty acid metabolism in human T lymphocytes changes across the life course in a manner that may facilitate the adaptation of immune function to different life stages.
Characteristics and survival of patients diagnosed with cardiac sarcoidosis: A case series
Authors: Brazile Tiffany L. , Saul Melissa , Nouraie Seyed Mehdi , Gibson Kevin 
Published: December 2022

BackgroundSarcoidosis is a multiorgan system granulomatous disease of unknown etiology. It is hypothesized that a combination of environmental, occupational, and/or infectious factors provoke an immunological response in genetically susceptible individuals, resulting in a diversity of manifestations throughout the body. In the United States, cardiac sarcoidosis (CS) is diagnosed in 5% of patients with systemic sarcoidosis, however, autopsy results suggest that cardiac involvement may be present in &gt; 50% of patients. CS is debilitating and significantly decreases quality of life and survival. Currently, there are no gold-standard clinical diagnostic or monitoring criteria for CS.MethodsWe identified patients with a diagnosis of sarcoidosis who were seen at the Simmons Center from 2007 to 2020 who had a positive finding of CS documented with cardiovascular magnetic resonance (CMR) and/or endomyocardial biopsy as found in the electronic health record. Medical records were independently reviewed for interpretation and diagnostic features of CS including late gadolinium enhancement (LGE) patterns, increased signal on T2-weighted imaging, and non-caseating granulomas, respectively. Extracardiac organ involvement, cardiac manifestations, comorbid conditions, treatment history, and vital status were also abstracted.ResultsWe identified 44 unique patients with evidence of CS out of 246 CMR reports and 9 endomyocardial biopsy pathology reports. The first eligible case was diagnosed in 2007. The majority of patients (73%) had pulmonary manifestations, followed by hepatic manifestations (23%), cutaneous involvement (23%), and urolithiasis (20%). Heart failure was the most common cardiac manifestation affecting 59% of patients. Of these, 39% had a documented left ventricular ejection fraction of &lt; 50% on CMR. Fifty eight percent of patients had a conduction disease and 44% of patients had documented ventricular arrhythmias. Pharmacotherapy was usually initiated for extracardiac manifestations and 93% of patients had been prescribed prednisone. ICD implantation occurred in 43% of patients. Patients were followed up for a median of 5.4 (IQR: 2.4–8.5) years. The 10-year survival was 70%. In addition to age, cutaneous involvement was associated with an increased risk of death (age-adjusted OR 8.47, 95% CI = 1.11–64.73).ConclusionCMR is an important tool in the non-invasive diagnosis of CS. The presence of LGE on CMR in a pattern consistent with CS has been shown to be a predictor of mortality and likely contributed to a high proportion of patients undergoing ICD implantation to decrease risk of sudden cardiac death.Clinical implicationsAdditional studies are necessary to develop robust criteria for the diagnosis of CS with CMR, assess the benefit of serial imaging for disease monitoring, and evaluate the effect of immunosuppression on disease progression.
Hotspots and frontier trends of diabetic associated cognitive decline research based on rat and mouse models from 2012 to 2021: A bibliometric study
Authors: Li Jie , Wang Zhen , Nan Xinyu , Yin Mingjie , Fang Hui 
Published: December 2022

BackgroundThe establishment of rodent models, such as rat and mouse models, plays a critical role in the study of diabetic associated cognitive decline. With the continuous growth of relevant literature information, it is difficult for researchers to accurately and timely capture the topics in this field. Therefore, this study aims to explore the current status and frontier trends of diabetic associated cognitive decline research based on rat and mouse models through a bibliometric analysis.MethodsWe collected 701 original articles on this subject from the Science Citation Index Expanded of the Web of Science Core Collection from 2012 to 2021. Then we utilized CiteSpace and VOSviewer for plotting knowledge maps and evaluating hotpots and trends.ResultsDuring this decade, except for a slight decline in 2020, the number of annual outputs on diabetes associated cognitive decline research using rat and mouse models increased every year. China (country), China Pharmaceutical University (institution), Gao, Hongchang (the author from the School of Pharmacy of Wenzhou Medical University, China), and Metabolic Brain Disease (journal) published the most papers in this research field. The analysis results of co-cited references and co-occurrence keywords indicated that “mechanisms and prevention and treatment methods”, especially “oxidative stress”, “potential association with Alzheimer's disease” and “spatial memory” are research focuses in this subject area. The bursts detection of references and keywords implied that “cognitive impairment of type 1 diabetes” and “autophagy and diabetes associated cognitive decline” will be potential directions for future research in this subject area.ConclusionThis study systematically assessed general information, current status and emerging trends of diabetic associated cognitive decline research using rat and mouse models in the past decade based on a bibliometric analysis. The number of publications was annually increasing although a slight decline was observed in 2020. Contributions from different countries/regions, institutions, authors, co-cited authors, journals and co-cited journals were evaluated, which may also be used to guide future research. Through the analysis of references and keywords, we predicted the future research hotspots and trends in this field.
Comparative safety of multiple doses of erythropoietin for the treatment of traumatic brain injury: A systematic review and network meta-analysis
Authors: Zheng Qingyong , Duan Dan , Xu Jianguo , Wang Xing , Ge Yonggui , Xiong Lu , Yang Jingjing , Wulayin Saimire , Luo Xiaofeng 
Published: December 2022

IntroductionOver the past few decades, advances in traumatic brain injury (TBI) pathology research have dynamically enriched our knowledge. Therefore, we aimed to systematically elucidate the safety and efficacy of erythropoietin (EPO) dosing regimens in patients with TBI.MethodsData search included PubMed, the Cochrane Library, Embase, Web of Science, and ClinicalTrials.gov for related research published before July 2022. The network meta-analysis was conducted using ADDIS 1.16.8, and the CINeMA tool was used to assess the quality level of evidence.ResultsA total of six RCTs involving 981 patients were included in the network meta-analysis. EPO did not significantly reduce mortality in patients with TBI, but its risk of death decreased with increasing dosage (odds ratio (OR) of 12,000u vs. placebo = 0.98, 95% CI: 0.03–40.34; OR of group 30,000u vs. placebo = 0.56, 95% CI: 0.06–5.88; OR of 40,000u vs. placebo = 0.35, 95% CI: 0.01–9.43; OR of 70,000u vs. placebo = 0.29, 95% CI: 0.01–9.26; OR of group 80,000u vs. placebo = 0.22, 95% CI: 0.00–7.45). A total of three studies involving 739 patients showed that EPO did not increase the incidence of deep vein thrombosis in patients with TBI. However, the risk tended to rise as the dosage increased. Another two studies demonstrated that EPO did not increase the incidence of pulmonary embolism. The quality of evidence for all outcomes was low to moderate.ConclusionAlthough the efficacy of EPO was not statistically demonstrated, we found a trend toward an association between EPO dosage and reduced mortality and increased embolic events in patients with TBI. More high-quality original studies should be conducted to obtain strong evidence on the optimal dosage of EPO.Systematic review registrationhttps://www.crd.york.ac.uk/PROSPERO/display_record.php?RecordID=272500. The study protocol was registered with PROSPERO (CRD42021272500).
Multibranch convolutional neural network with contrastive representation learning for decoding same limb motor imagery tasks
Authors: Phunruangsakao Chatrin , Achanccaray David , Izumi Shin-Ichi , Hayashibe Mitsuhiro 
Published: December 2022

IntroductionEmerging deep learning approaches to decode motor imagery (MI) tasks have significantly boosted the performance of brain-computer interfaces. Although recent studies have produced satisfactory results in decoding MI tasks of different body parts, the classification of such tasks within the same limb remains challenging due to the activation of overlapping brain regions. A single deep learning model may be insufficient to effectively learn discriminative features among tasks.MethodsThe present study proposes a framework to enhance the decoding of multiple hand-MI tasks from the same limb using a multi-branch convolutional neural network. The CNN framework utilizes feature extractors from established deep learning models, as well as contrastive representation learning, to derive meaningful feature representations for classification.ResultsThe experimental results suggest that the proposed method outperforms several state-of-the-art methods by obtaining a classification accuracy of 62.98% with six MI classes and 76.15 % with four MI classes on the Tohoku University MI-BCI and BCI Competition IV datasets IIa, respectively.DiscussionDespite requiring heavy data augmentation and multiple optimization steps, resulting in a relatively long training time, this scheme is still suitable for online use. However, the trade-of between the number of base learners, training time, prediction time, and system performance should be carefully considered.
Evaluating breast ultrasound S-detect image analysis for small focal breast lesions
Authors: Xing Boyuan , Chen Xiangyi , Wang Yalin , Li Shuang , Liang Ying-Kui , Wang Dawei 
Published: December 2022

BackgroundS-Detect is a computer-assisted, artificial intelligence-based system of image analysis that has been integrated into the software of ultrasound (US) equipment and has the capacity to independently differentiate between benign and malignant focal breast lesions. Since the revision and upgrade in both the breast imaging-reporting and data system (BI-RADS) US lexicon and the S-Detect software in 2013, evidence that supports improved accuracy and specificity of radiologists’ assessment of breast lesions has accumulated. However, such assessment using S-Detect technology to distinguish malignant from breast lesions with a diameter no greater than 2 cm requires further investigation.MethodsThe US images of focal breast lesions from 295 patients in our hospital from January 2019 to June 2022 were collected. The BI-RADS data were evaluated by the embedded program and as manually modified prior to the determination of a pathological diagnosis. The receiver operator characteristic (ROC) curves were constructed to compare the diagnostic accuracy between the assessments of the conventional US images, the S-Detect classification, and the combination of the two.ResultsThere were 326 lesions identified in 295 patients, of which pathological confirmation demonstrated that 239 were benign and 87 were malignant. The sensitivity, specificity, and accuracy of the conventional imaging group were 75.86%, 93.31%, and 88.65%. The sensitivity, specificity, and accuracy of the S-Detect classification group were 87.36%, 88.28%, and 88.04%, respectively. The assessment of the amended combination of S-Detect with US image analysis (Co-Detect group) was improved with a sensitivity, specificity, and accuracy of 90.80%, 94.56%, and 93.56%, respectively. The diagnostic accuracy of the conventional US group, the S-Detect group, and the Co-Detect group using area under curves was 0.85, 0.88 and 0.93, respectively. The Co-Detect group had a better diagnostic efficiency compared with the conventional US group (Z = 3.882, p = 0.0001) and the S-Detect group (Z = 3.861, p = 0.0001). There was no significant difference in distinguishing benign from malignant small breast lesions when comparing conventional US and S-Detect techniques.ConclusionsThe addition of S-Detect technology to conventional US imaging provided a novel and feasible method to differentiate benign from malignant small breast nodules.
Economic evaluation of first-line sugemalimab plus chemotherapy for metastatic non-small cell lung cancer in China
Authors: Wang Hao , Liao Li , Xu Yuan , Long Yunchun , Wang Ye , Zhou Yujie 
Published: December 2022

ObjectiveTo evaluate the economics of sugemalimab plus chemotherapy in the first-line treatment of metastatic non-small cell lung cancer, and to provide a reference for the formulation of relevant medical insurance policies and rational drug use.MethodsFrom the perspective of the Chinese health system, a three-state partitioned survival model was constructed based on data from a phase III randomized clinical trial (GEMSTONE 302) to evaluate the cost-utility of sugemalimab plus chemotherapy compared with chemotherapy in first-line treatment of metastatic non-small cell lung cancer. Model results were expressed as total cost, life years, quality-adjusted life years, and incremental cost-effectiveness ratio. The robustness of the underlying analysis results was verified using one-way sensitivity analysis and probabilistic sensitivity analysis.ResultsThe results of the base-case analysis showed that sugemalimab plus chemotherapy yielded 1.63 QALYs at a total cost of 130,667.70 USD, chemotherapy yielded 1.04 QALYs at a total cost of 64,001.02 USD, and the ICER was 113,155.52 USD/QALY, which was well above the current willingness-to-pay threshold in China (3 times 2021 per capita GDP) (36,203.88 USD).ConclusionThis study suggests that sugemalimab in combination with a chemotherapy regimen is more effective but not economical for patients with metastatic non-small cell lung cancer receiving first-line therapy in China and that a reasonable reduction in drug prices could improve the probability of it being economical.
Fecal HBD-2 and Claudin-3 may be potential biomarkers to predict the deterioration of necrotizing enterocolitis: A prospective study
Authors: Liu Xiao-Chen , Li Lu-Quan , Ling Ke-Ran , Guo Lu , Hu Xiao-Yu , Li Chun 
Published: December 2022

Background and purposeNecrotizing enterocolitis (NEC) is a critical gastrointestinal disease. We aim to explore the value of fecal human β-defensin 2 (HBD-2), Claudin-3, high-mobility group box-1 protein (HMGB-1), and resistin-like molecule β (Relmβ) as well as some laboratory metrics to predict the deterioration of NEC.MethodsInfants diagnosed with NEC at Stage II were enrolled in our study. Those who progressed to Stage III were included in the Stage III group and the rest were included in the Stage II group. Clinical data and laboratory metrics of the infants were collected. Fecal samples of HBD2, HMGB-1, Claudin-3, and Relmβ collected during their enrollment were determined by using enzyme-linked immunosorbent assay (ELISA) kits. Student's t-test, the Mann–Whitney U test, the chi-square test, receiver operating characteristic (ROC), and logistic regression analysis were performed.ResultsSixty infants diagnosed with NEC at Stage II were enrolled in our study, with 27 in the Stage III group (n = 27) and 33 in the Stage II group (n = 33). Although many of these NEC cases were late preterm and term infants, the infants in the Stage III group had a lower gestational age (P &lt; 0.05). The incidence of gestational diabetes mellitus, peritonitis, intestinal adhesion, and sepsis was higher and more infants in the Stage III group underwent surgeries (P &lt; 0.05). The levels of HBD-2 and Claudin-3 were higher and neutrophil count was lower in the Stage III group than in the Stage II Group, and the area under the curve (AUC) was 0.754, 0,755, and 0.666, respectively (P &lt; 0.05). HBD-2 ≥ 1649.02 ng/g and Claudin-3 ≥ 2488.71 pg/g were included in the multivariate stepwise logistic regression analysis (P &lt; 0.05), and the AUC of the model was 0.805 (95% CI: 0.688–0.922).ConclusionFecal HBD-2 and Claudin-3 may be potential biomarkers to predict the deterioration of NEC from Stage II to Stage III.