bluuebunny/crossref_metadata_2025_split huggingface dataset:
Women’s visibility at European Society for Clinical Nutrition and Metabolism congresses from 2011 to 2019: Is the floor yours?
Authors: Occhiali Emilie , Demailly Zoe , Clavier Thomas , Achamrah Najate 
Published: November 2022

PurposeParticipating in international conferences is an essential way to promote scholarly work. We aimed to assess the trend of women’s visibility at the European Society for Clinical Nutrition and Metabolism (ESPEN) congress by describing the evolution of the proportion of women speakers between 2011 and 2019.Materials and methodsThis is a retrospective study including public data obtained from the 2011, 2015, and 2019 ESPEN congresses. The primary endpoint was the percentage of women speakers in major oral sessions (oral communications and specific conferences including prestigious lectures). The secondary endpoints were the proportion of women in other high-visibility positions (moderators, industry-led symposia interventions) and countries of origin.ResultsThe proportion of women speakers in oral communications remained stable between 2011 and 2019 [43% (43/100) vs. 41% (46/111), respectively; p = 0.89]. The proportion of women moderators in oral communications sessions significantly increased between 2011 and 2019 [13% (6/45) vs. 41% (19/46), respectively; p = 0.004]. The percentage of women speakers and moderators in industry-led symposia significantly increased between 2011 and 2019 [11% (2/18) vs. 41% (11/27), p = 0.05; 0% (0/6) vs. 60% (6/10), p = 0.03, respectively]. The percentage of women moderators in educational sessions also remained stable during the period with a marked under-representation of women in 2015. During all three congresses, women from the host countries were over-represented as moderators compared to women from other countries.ConclusionThe percentage of women speakers in oral communications remained stable in the last 8 years at ESPEN congresses, although women’s representation in other high-visibility positions has increased. As men remained over-represented, women should be more encouraged to promote their academic work in the field of clinical nutrition, particularly during this international congress.
Treatment beyond progression in non-small cell lung cancer: A systematic review and meta-analysis
Authors: Kuo Wei-Ke , Weng Ching-Fu , Lien Yin-Ju 
Published: November 2022

ObjectivesTreatment beyond progression (TBP) is defined as treatment continuing in spite of disease progression, according to the Response Evaluation Criteria In Solid Tumors. We performed a systematic review and meta-analysis to provide evidence for the effects of TBP on lung cancer survival.Materials and methodsThis study has been conducted following the PRISMA guidelines. A systematic review of PubMed, MEDLINE, Embase, and Cochrane Collaboration Central Register of Controlled Clinical Trials from the inception of each database to December 2021 was conducted. Two authors independently reviewed articles for inclusion and extract data from all the retrieved articles. Random-effects meta-analysis was performed using Comprehensive Meta-Analysis software, version 3 (Biostat, Englewood, NJ, USA). Hazard ratios (HRs) with the corresponding 95% confidence intervals (CI) were used for survival outcomes.ResultsWe identified five (15.6%) prospective randomized trials and twenty-seven (84.4%) retrospective observational studies of a total of 9,631 patients for the meta-analysis. 3,941 patients (40.9%) were in a TBP group and 5,690 patients (59.1%) were in a non-TBP group. There is a statistically significant advantage for patients who received TBP compared with those who did not in post progression progression-free survival (ppPFS), post progression overall survival (ppOS), and overall survival (OS) from initiation of drugs (ppPFS: HR, 0.746; 95% CI, 0.644-0.865; P&lt;0.001; ppOS: HR, 0.689; 95% CI, 0.596-0.797; P&lt;0.001; OS from initiation of drugs: HR, 0.515; 95% CI, 0.387-0.685; P&lt;0.001)ConclusionThis study provides further evidence in support of TBP for NSCLC, however, these results require cautious interpretation. Large, randomized, controlled trials investigating the efficacy of TBP in lung cancer treatment are warranted.Systemic Review Registrationhttps://www.crd.york.ac.uk/PROSPERO/ identifier CRD42021285147
Improved NGS-based detection of microsatellite instability using tumor-only data
Authors: Marques Ana Claudia , Ferraro-Peyret Carole , Michaud Frederic , Song Lin , Smith Ewan , Fabre Guillaume , Willig Adrian , Wong Melissa M. L. , Xing Xiaobin , Chong Chloe , Brayer Marion , Fenouil Tanguy , Hervieu Valérie , Bancel Brigitte , Devouassoux Mojgan , Balme Brigitte , Meyronet David , Menu Philippe , Lopez Jonathan , Xu Zhenyu 
Published: November 2022

Microsatellite instability (MSI) is a molecular signature of mismatch repair deficiency (dMMR), a predictive marker of immune checkpoint inhibitor therapy response. Despite its recognized pan-cancer value, most methods only support detection of this signature in colorectal cancer. In addition to the tissue-specific differences that impact the sensitivity of MSI detection in other tissues, the performance of most methods is also affected by patient ethnicity, tumor content, and other sample-specific properties. These limitations are particularly important when only tumor samples are available and restrict the performance and adoption of MSI testing. Here we introduce MSIdetect, a novel solution for NGS-based MSI detection. MSIdetect models the impact of indel burden and tumor content on read coverage at a set of homopolymer regions that we found are minimally impacted by sample-specific factors. We validated MSIdetect in 139 Formalin-Fixed Paraffin-Embedded (FFPE) clinical samples from colorectal and endometrial cancer as well as other more challenging tumor types, such as glioma or sebaceous adenoma or carcinoma. Based on analysis of these samples, MSIdetect displays 100% specificity and 96.3% sensitivity. Limit of detection analysis supports that MSIdetect is sensitive even in samples with relatively low tumor content and limited microsatellite instability. Finally, the results obtained using MSIdetect in tumor-only data correlate well (R=0.988) with what is obtained using tumor-normal matched pairs, demonstrating that the solution addresses the challenges posed by MSI detection from tumor-only data. The accuracy of MSI detection by MSIdetect in different cancer types coupled with the flexibility afforded by NGS-based testing will support the adoption of MSI testing in the clinical setting and increase the number of patients identified that are likely to benefit from immune checkpoint inhibitor therapy.
Development of a ferroptosis-based model to predict prognosis, tumor microenvironment, and drug response for lung adenocarcinoma with weighted genes co-expression network analysis
Authors: Cheng Tao , Shan Guangyao , Yang Huiqin , Gu Jie , Lu Chunlai , Xu Fengkai , Ge Di 
Published: November 2022

Objective: The goal of this study was to create a risk model based on the ferroptosis gene set that affects lung adenocarcinoma (LUAD) patients’ prognosis and to investigate the potential underlying mechanisms.Material and Methods: A cohort of 482 LUAD patients from the TCGA database was used to develop the prognostic model. We picked the module genes from the ferroptosis gene set using weighted genes co-expression network analysis (WGCNA). The least absolute shrinkage and selection operator (LASSO) and univariate cox regression were used to screen the hub genes. Finally, the multivariate Cox analysis constructed a risk prediction score model. Three other cohorts of LUAD patients from the GEO database were included to validate the prediction ability of our model. Furthermore, the differentially expressed genes (DEG), immune infiltration, and drug sensitivity were analyzed.Results: An eight-gene-based prognostic model, including PIR, PEBP1, PPP1R13L, CA9, GLS2, DECR1, OTUB1, and YWHAE, was built. The patients from the TCGA database were classified into the high-RS and low-RS groups. The high-RS group was characterized by poor overall survival (OS) and less immune infiltration. Based on clinical traits, we separated the patients into various subgroups, and RS had remarkable prediction performance in each subgroup. The RS distribution analysis demonstrated that the RS was significantly associated with the stage of the LUAD patients. According to the study of immune cell infiltration in both groups, patients in the high-RS group had a lower abundance of immune cells, and less infiltration was associated with worse survival. Besides, we discovered that the high-RS group might not respond well to immune checkpoint inhibitors when we analyzed the gene expression of immune checkpoints. However, drug sensitivity analysis suggested that high-RS groups were more sensitive to common LUAD agents such as Afatinib, Erlotinib, Gefitinib, and Osimertinib.Conclusion: We constructed a novel and reliable ferroptosis-related model for LUAD patients, which was associated with prognosis, immune cell infiltration, and drug sensitivity, aiming to shed new light on the cancer biology and precision medicine.
Integrating transcriptomic and metabolomic analysis in roots of wild soybean seedlings in response to low-phosphorus stress
Authors: Li Mingxia , Zhou Ji , Lang Xianyu , Han Defu , Hu Yongjun , Ding Yinan , Wang Guangye , Guo Jixun , Shi Lianxuan 
Published: November 2022

IntroductionPlants undergo divergent adaptations to form different ecotypes when exposed to different habitats. Ecotypes with ecological adaptation advantages are excellent germplasm resources for crop improvementMethodshis study comprehensively compared the differences in morphology and physiological mechanisms in the roots of two different ecotypes of wild soybean (Glycine soja) seedlings under artificially simulated low-phosphorus (LP) stress.ResultThe seedlings of barren-tolerant wild soybean (GS2) suffered less damage than common wild soybean (GS1). GS2 absorbed more phosphorus (P) by increasing root length. In-depth integrated analyses of transcriptomics and metabolomics revealed the formation process of the ecological adaptability of the two different ecotypes wild soybean from the perspective of gene expression and metabolic changes. This study revealed the adaptation process of GS2 from the perspective of the adaptation of structural and molecular metabolism, mainly including: (1) Enhancing the metabolism of phenolic compounds, lignin, and organic acid metabolism could activate unavailable soil P; (2) Up-regulating genes encoding pectinesterase and phospholipase C (PLC) specifically could promote the reuse of structural P; (3) Some factors could reduce the oxidative damage to the membranes caused by LP stress, such as accumulating the metabolites putrescine and ascorbate significantly, up-regulating the genes encoding SQD2 (the key enzyme of sulfolipid substitution of phospholipids) substantially and enhancing the synthesis of secondary antioxidant metabolite anthocyanins and the AsA-GSH cycle; (4) enhancing the uptake of soil P by upregulating inorganic phosphate transporter, acid phosphatase ACP1, and purple acid phosphatase genes; (5) HSFA6b and MYB61 are the key TFs to resist LP stress.DiscussionIn general, GS2 could resist LP stress by activating unavailable soil P, reusing plant structural P, rebuilding membrane lipids, and enhancing the antioxidant membrane protection system. Our study provides a new perspective for the study of divergent adaptation of plants.
In silico evidence for the utility of parsimonious root phenotypes for improved vegetative growth and carbon sequestration under drought
Authors: Schäfer Ernst D. , Ajmera Ishan , Farcot Etienne , Owen Markus R. , Band Leah R. , Lynch Jonathan P. 
Published: November 2022

Drought is a primary constraint to crop yields and climate change is expected to increase the frequency and severity of drought stress in the future. It has been hypothesized that crops can be made more resistant to drought and better able to sequester atmospheric carbon in the soil by selecting appropriate root phenotypes. We introduce OpenSimRoot_v2, an upgraded version of the functional-structural plant/soil model OpenSimRoot, and use it to test the utility of a maize root phenotype with fewer and steeper axial roots, reduced lateral root branching density, and more aerenchyma formation (i.e. the ‘Steep, Cheap, and Deep’ (SCD) ideotype) and different combinations of underlying SCD root phene states under rainfed and drought conditions in three distinct maize growing pedoclimatic environments in the USA, Nigeria, and Mexico. In all environments where plants are subjected to drought stress the SCD ideotype as well as several intermediate phenotypes lead to greater shoot biomass after 42 days. As an additional advantage, the amount of carbon deposited below 50 cm in the soil is twice as great for the SCD phenotype as for the reference phenotype in 5 out of 6 simulated environments. We conclude that crop growth and deep soil carbon deposition can be improved by breeding maize plants with fewer axial roots, reduced lateral root branching density, and more aerenchyma formation.
The long-term impact of the COVID-19 pandemic on primary and specialized care provision and disease recognition in Germany
Authors: Platen Moritz , Bohlken Jens , Hoffmann Wolfgang , Kostev Karel , Michalowsky Bernhard 
Published: November 2022

BackgroundThe COVID-19 pandemic and the imposed lockdowns severely affected routine care in general and specialized physician practices.ObjectiveTo describe the long-term impact of the COVID-19 pandemic on the physician services provision and disease recognition in German physician practices and perceived causes for the observed changes.DesignObservational study based on medical record data and survey data of general practitioners and specialists' practices.Participants996 general practitioners (GPs) and 798 specialist practices, who documented 6.1 million treatment cases for medical record data analyses and 645 physicians for survey data analyses.Main measuresWithin the medical record data, consultations, specialist referrals, hospital admissions, and documented diagnoses were extracted for the pandemic (March 2020–September 2021) and compared to corresponding pre-pandemic months in 2019. The additional online survey was used to assess changes in practice management during the COVID-19 pandemic and physicians' perceived main causes of affected primary and specialized care provision.Main resultsHospital admissions (GPs: −22% vs. specialists: −16%), specialist referrals (−6 vs. −3%) and recognized diseases (−9 vs. −8%) significantly decreased over the pandemic. GPs consultations initially decreased (2020: −7%) but compensated at the end of 2021 (+3%), while specialists' consultation did not (−2%). Physicians saw changes in patient behavior, like appointment cancellation, as the main cause of the decrease. Contrary to this, they also mentioned substantial modifications of practice management, like reduced (nursing) home visits (41%) and opening hours (40%), suspended checkups (43%), and delayed consultations for high-risk patients (71%).ConclusionThe pandemic left its mark on primary and specialized healthcare provision and its utilization. Both patient behavior and organizational changes in practice management may have caused decreased and non-compensation of services. Evaluating the long-term effect on patient outcomes and identifying potential improvements are vital to better prepare for future pandemic waves.
Association between sedentary time and metabolic syndrome: A cross-sectional study among Chinese Garze Tibetans
Authors: Guo Lei , Liu Yixuan , Xue Tingting , Liang Liang , Nima Yongcuo , Yang Yang , Li Qun , Zhang Qiushi 
Published: November 2022

BackgroundChinese Tibetans have long hours of sitting without much physical activity given their religious behavior, raising potential harmful health hazards. However, the relationship between sedentary time and metabolic syndrome (MetS) has not been investigated in Chinese Tibetans.MethodsFrom Jan 2021 to Jun 2022, residents in Garze Tibetan Autonomous Prefecture in Southwest China's Sichuan province were recruited using a multi-stage, stratified, random-cluster sampling strategy. MetS were ascertained using definition proposed by the International Diabetes Federation. Associations between sedentary time and the prevalence of MetS in the total sample and by age and sex were estimated using logistic regression models.ResultsAmong 971 Chinese Tibetan participants (mean age 41.1 years and 73.8% female), 319 (32.9%) were diagnosed as having MetS. We found positive associations of sedentary time over 11 h per day with the prevalence of MetS in crude (OR: 1.23; 95% CI: 1.12–1.36, p &lt; 0.001), age and sex adjusted (OR: 1.18; 95% CI: 1.08–1.29, p &lt; 0.001), and fully adjusted (OR: 1.17; 95% CI: 1.08–1.29, p &lt; 0.001) models, compared to those who had &lt;8 h of sedentary time per day. Sensitivity analyses suggest consistent positive association between sedentary time and each metric of MetS.ConclusionsSedentary time longer than 11 h per day is significantly associated with increased risk of MetS, suggesting that polices to advocate health education may alleviate the health burden of MetS among Tibetans in China.
COVID-19 outbreaks analysis in the Valencian Region of Spain in the prelude of the third wave
Authors: Fuente David , Hervás David , Rebollo Miguel , Conejero J. Alberto , Oliver Nuria 
Published: November 2022

IntroductionThe COVID-19 pandemic has led to unprecedented social and mobility restrictions on a global scale. Since its start in the spring of 2020, numerous scientific papers have been published on the characteristics of the virus, and the healthcare, economic and social consequences of the pandemic. However, in-depth analyses of the evolution of single coronavirus outbreaks have been rarely reported.MethodsIn this paper, we analyze the main properties of all the tracked COVID-19 outbreaks in the Valencian Region between September and December of 2020. Our analysis includes the evaluation of the origin, dynamic evolution, duration, and spatial distribution of the outbreaks.ResultsWe find that the duration of the outbreaks follows a power-law distribution: most outbreaks are controlled within 2 weeks of their onset, and only a few last more than 2 months. We do not identify any significant differences in the outbreak properties with respect to the geographical location across the entire region. Finally, we also determine the cluster size distribution of each infection origin through a Bayesian statistical model.DiscussionWe hope that our work will assist in optimizing and planning the resource assignment for future pandemic tracking efforts.
Bone metastasis risk and prognosis assessment models for kidney cancer based on machine learning
Authors: Ji Lichen , Zhang Wei , Huang Jiaqing , Tian Jinlong , Zhong Xugang , Luo Junchao , Zhu Senbo , He Zeju , Tong Yu , Meng Xiang , Kang Yao , Bi Qing 
Published: November 2022

BackgroundBone metastasis is a common adverse event in kidney cancer, often resulting in poor survival. However, tools for predicting KCBM and assessing survival after KCBM have not performed well.MethodsThe study uses machine learning to build models for assessing kidney cancer bone metastasis risk, prognosis, and performance evaluation. We selected 71,414 kidney cancer patients from SEER database between 2010 and 2016. Additionally, 963 patients with kidney cancer from an independent medical center were chosen to validate the performance. In the next step, eight different machine learning methods were applied to develop KCBM diagnosis and prognosis models while the risk factors were identified from univariate and multivariate logistic regression and the prognosis factors were analyzed through Kaplan-Meier survival curve and Cox proportional hazards regression. The performance of the models was compared with current models, including the logistic regression model and the AJCC TNM staging model, applying receiver operating characteristics, decision curve analysis, and the calculation of accuracy and sensitivity in both internal and independent external cohorts.ResultsOur prognosis model achieved an AUC of 0.8269 (95%CI: 0.8083–0.8425) in the internal validation cohort and 0.9123 (95%CI: 0.8979–0.9261) in the external validation cohort. In addition, we tested the performance of the extreme gradient boosting model through decision curve analysis curve, Precision-Recall curve, and Brier score and two models exhibited excellent performance.ConclusionOur developed models can accurately predict the risk and prognosis of KCBM and contribute to helping improve decision-making.
Association between physical activity and major adverse cardiovascular events in northwest China: A cross-sectional analysis from the Regional Ethnic Cohort Study
Authors: Wang Yutong , Liu Huimeng , He Dandan , Zhang Binyan , Liu Yezhou , Xu Kun , Cao Suixia , Huo Yating , Liu Jingchun , Zeng Lingxia , Yan Hong , Dang Shaonong , Mi Baibing 
Published: November 2022

BackgroundTo examine the association between daily physical activity (PA) and major adverse cardiovascular events (MACEs) in northwest China.MethodsThe data in this analysis were part of the baseline survey of the Regional Ethnic Cohort Study in Northwest China from June 2018 to May 2019 in Shaanxi Province. This study used standardized self-reported total physical activity (continuous and categorical variables) and self-reported outcomes of MACEs. All analyses were conducted using the logistic regression model and stratified by age, sex, body mass index (BMI), and region. The dose-response relationships were assessed with a restricted cubic spline.ResultsThe average level of total PA was 17.60 MET hours per day (MET-h/d). Every increase of four MET-h/d of total PA was associated with a lower risk of MACEs [adjusted OR = 0.95 (95% CI, 0.93~0.98)]. Compared with participants in the bottom quartile of total PA, a lower risk of MACEs was observed in the top quartile group [≥23.3 MET-h/d, 0.68 (0.55~0.83)]. Stratified analyses showed similar results in males, females, participants over 45 years old, participants in the rural region, and normal weight range participants (BMI &lt; 24 kg/m2). Total participants also observed a dose-response relationship after adjusting for socioeconomic and lifestyle factors.ConclusionsA higher level of PA was associated with a lower MACE risk. Future research should examine the longitudinal association of prospectively measured PA and the risk of MACEs.