bluuebunny/crossref_metadata_2025_split huggingface dataset:
Burden of chronic kidney diseases and underlying causes in Zambia: evidence from the global burden of disease study 2019
Authors: Bosomprah Samuel , Bjonstad Erica C. , Musuku John , Siyumbwa Namasiku , Ngandu Mwila , Chisunka Mukobe , Banda Patrick , Goma Fastone , Mweemba Aggrey 
Published: October 2022

Abstract
Introduction:
Chronic kidney disease (CKD) has been a global public health problem and a major source of suffering and poor quality of life for those afflicted. Using data from the global burden of disease (GBD) study 2019, we estimated the magnitude of the burden of CKD as well as the underlying causes of CKD in the Zambian population.
Method
The data used for this study were extracted from the GBD 2019 study. The GBD 2019 provides estimates of several metrics of disease burden including the commonly used disability-adjusted life year (DALYs) for over 369 diseases and injuries, and 87 risk factors and combinations of these in 204 countries and territories from 1990 to 2019. We estimated the burden of CKD as the number and rates (per 100,000 population) of DALYs, disaggregated by year, sex, and age group. We examined the underlying causes of CKD by estimating the population attributable fraction as the percentage contributions of risk factors to CKD DALY.
Results
The number of DALYs for CKD was estimated as 76.03 million (95% UI: 61.01 to 93.36) in 2019 compared to 39.42 million (95% UI: 33.09 to 45.90) in 1990, representing 93% increase whereas the DALYs rate per 100,000 population was estimated as 416.89 (95% UI: 334.53 to 511.93) in 2019 compared to 496.38 (95% UI: 416.55 to 577.87) in 1990, representing 16% reduction. CKD due to hypertension accounted for 18.7% of CKD DALYs and CKD due to diabetes (types 1 and 2) accounted for 22.7%, while CKD from glomerulonephritis accounted for the most DALYs at 33%. The age group most impacted from CKD were adolescents and young adults.
Conclusion
The burden of CKD remains high in the Zambian population with diabetes, high blood pressure, and glomerulonephritis as important causes. The results highlight the need to develop a comprehensive action plan to prevent and treat kidney disease. Increasing the awareness of CKD among the public as well as adaptation of guidelines for treating patients with end stage kidney disease are important considerations.
Comparative analysis of Acomys cahirinus and Mus musculus responses to genotoxicity, oxidative stress, and inflammation
Authors: Ghebryal Lamees N , Noshy Magda M , El-Ghor Akmal A , Eissa Shaymaa M 
Published: October 2022

AbstractThe Egyptian spiny mouse, Acomys cahirinus, is a recently described model organism for regeneration studies. It has surprising powers of regeneration with relatively fast repairing mechanisms and reduced inflammation form compared to other mammals. Although several studies have documented the exceptional capabilities of Acomys to regenerate different tissues after injury, but its response to different cellular and genetic stresses is not yet investigated. Therefore, the current study aimed to investigate Acomys abilities to resist genotoxicity, oxidative stress and inflammation induced by acute and subacute treatments with lead acetate. Responses of Acomys were compared with those of the lab mouse (Mus musculus), which displays signatures of the “typical” mammalian response to various stressors. Cellular and genetic stresses were induced by using acute and subacute doses of Lead acetate (400 mg/kg and 50 mg/kg for 5 days, respectively). The assessment of genotoxicity was carried out by using comet assay, while oxidative stress was evaluated by measuring the biomarkers; MDA and reduced GSH. Moreover, inflammation was assessed by analyzing the expression of some inflammatory-regeneration-related genes: CXCL1, IL1-β, and Notch 2 in brain tissue, in addition to histopathological examination of brain, liver, and kidneys. The obtained results revealed a unique resistance potency of Acomys to genotoxicity, oxidative stress, and inflammation in certain tissues in comparison to Mus. Altogether, the results revealed an adaptive and protective response to cellular and genetic stresses in Acomys.
Sleep Traits and Risk of End-Stage Renal Disease: A Mendelian Randomization Study
Authors: Li Kaixin , Zhao Jiaxi , Yang Wenjing , Lin Huagang , Ye Zhibin 
Published: October 2022

Abstract
Background
Epidemiological evidence relating sleep disorders to end-stage renal disease (ESRD) has been obscure. The present study is sought to examine sleep characteristics and ESRD.
Methods
For this analysis, we selected genetic instruments for sleep traits from published genome-wide association studies (GWAS). As instrumental variables, independent genetic variations linked with seven sleep-related features (sleep duration, getting up in the morning, daytime napping, chronotype of morning/evening person, sleeplessness/insomnia, snoring, and daytime dozing) were chosen. A two-sample Mendelian randomization (TSMR) study was conducted to assess the causal relationship between sleep traits and ESRD (N = 16405). The reverse MR analysis subsequently determined the causal relationship between ESRD and sleep traits. The causal effects were estimated using inverse variance weighted, MR-Egger, weighted median. To conduct sensitivity studies, Cochran's Q test, MR-Egger intercept test, MR-PRESSO, leave-one-out analysis, and funnel plot were used. To study the potential mediators, risk factor analyses were undertaken further.
Results
Genetically predicted sleeplessness/ insomnia was associated with an increased risk of ESRD(OR = 6.11, 95%CI 1.00-37.3, P = 0.049). Genetic liability to getting up in the morning easily (OR = 0.23, 95%CI 0.063–0.85; P = 0.0278) and non-snoring (OR 4.76E-02, 95%CI 2.29E-03-0.985, P = 0.0488) reduced the risk for ESRD.
Conclusion
The present TSMR reveals possible causal correlations between genetic susceptibility to several sleep traits and the risk of ESRD.
The Pga59 cell wall protein is an amyloid forming protein involved in adhesion and biofilm establishment in the pathogenic yeast Candida albicans.
Authors: Bachellier-Bassi Sophie , Mourer Thierry , Ghalid Mennat El , Pehaut-Arnaudet Gérard , Kauffmann Brice , Loquet Antoine , Cabral Vitor , d'Enfert Christophe 
Published: October 2022

Abstract
The human commensal fungus Candida albicans can attach to epithelia or indwelling medical devices and form biofilms, that are highly tolerant to antifungal drugs and can evade the immune response. The cell surface protein Pga59 has been shown to influence adhesion and biofilm formation. Here, we present evidence that Pga59 displays amyloid properties. Using electron microscopy, staining with an amyloid fibre-specific dye and X-ray diffraction experiments, we showed that the predicted amyloid-forming region of Pga59 is sufficient to build up an amyloid fibre in vitro and that recombinant Pga59 can also adopt a cross-β amyloid fibre architecture. Further, mutations impairing Pga59 amyloid assembly led to a diminished adhesion to substrates and reduced biofilm production. Immunogold labelling on amyloid structures extracted from C. albicans revealed that Pga59 is used by the fungal cell to build up amyloids within the cell wall in response to adhesion. Altogether, our results suggest that Pga59 amyloid properties are used by the fungal cell to mediate cell-substrate interactions and biofilm formation.
Transformer-based Denoising Adversarial Variational Entity Resolution
Authors: Li Shuaichao , Wu Huaiguang 
Published: October 2022

Abstract
Entity resolution (ER), precisely identifying different representations of the same real-world entities, is critical for data integration. The ER question has been studied for many years, and many methods have been proposed to solve it. Although deep learning has achieved good performance in ER tasks, there are some challenges regarding manual labelling and model transfer. This paper proposes a novel ER model, Transformer-based Denoising Adversarial Variational Entity Resolution (TdavER). For entity embedding, we develop an unsupervised entity embedding model based on denoising autoencoders and pre-trained language models, which takes corrupted input as training data to motivate the encoder to generate rather stable and robust high-quality entity representations. Furthermore, we propose an unsupervised entity feature transformation model based on adversarial variational autoencoders to remove the constraints on entity representations from training data. This transformation model converts low-level entity embeddings to high-level probability distributions, which are not constrained by the source data and contain deep similarity features. To better implement the feature transformation, we adopt adversarial networks to optimize the variational autoencoder's training process and help it learn the correct posterior distribution. Extensive experiments confirm that the performance of our proposed TdavER is comparable with the current state-of-the-art ER methods and that its entity feature transformation model is transferable.
Dietary Oregano aqueous extract improves growth performance and intestinal health of broilers through modulating gut microbial compositions
Authors: Zhang Fan , Yang Jiantao , Zhan Qinyi , Shi Hao , Li Yanhe , Li Yingge , Yang Xiaojun 
Published: October 2022

Abstract
Background
Intestinal health plays a pivotal role in broiler chicken growth. Oregano aqueous extract (OAE) effectively exerts anti-inflammatory and antibacterial effects. However, the protective effects of OAE on intestinal health in broilers and the underlying mechanism remain unclear. This study aimed to investigate the potential effects of OAE on growth performance, the gut microbiota and intestinal health. A total of 840 1-day-old male and female broilers (Arbor Acres) were randomly allocated into 6 groups as follows: basal diet (Con), Con + antibiotics (Anti, Mycolistin sulfate 7 g/kg, Locke sand arsine 35 g/kg), Con + 400, 500, 600 and 700 mg/kg OAE (OAE400, OAE500, OAE600 and OAE700). Subsequently, fermentation in vitro together with oral administration trials were carried out to further assess the function of OAE on intestinal health of broilers.
Results
Dietary 700 mg/kg OAE supplementation resulted in an increase (P < 0.05) in body weight and a decrease (P < 0.05) in feed conversion ratio when compared with the control during D22 ~ D42 of the trial. OAE addition resulted in lower (P < 0.05) jejunal crypt depth and mRNA expression of IL-4 and IL-10 at D42. In addition, dietary OAE addition increased the abundance of Firmicutes (P = 0.087) and Lactobacillus (P < 0.05) in the cecum, and increased (P < 0.05) the content of acetic acid and butyric acid. In the in vitro fermentation test, OAE significantly increased (P < 0.05) the abundance of Lactobacillus, decreased (P < 0.05) the abundance of Unspecified_Enterobacteriaceae, and increased the content of acetic acid (P < 0.05). In the oral administration trial, higher (P < 0.05) IL-4 expression was found in broilers when oral inoculation with oregano fermentation microorganisms at D42. And SIgA content in the ileum was significantly increased (P = 0.073) when giving OAE fermentation supernatant.
Conclusions
Dietary OAE addition could maintain intestinal health and improve growth performance through enhancing intestinal mucosal immunity and barrier function mediated by gut microbiota changes.
Effects of exogenous abscisic acid on kernel water content of Different Maize Varieties during grain filling
Authors: He Jiawen , Li Chuan , Zhang Meiwei , Zhang Panpan , Niu Jun , Shao Ruixin , Guo Hanxiao , Mu Weilin , Qiao Jiangfang 
Published: October 2022

Abstract

The kernel water content during harvest is the key factor affecting mechanized grain harvest application in China. The kernel water content during corn harvest is affected by the grain filling rate, the water content at physiological maturity, and the dehydration rate after physiological maturity. In this study, two maize varieties with differing dehydration rates: DK517 (fast dehydration) and ZD1002 (slow dehydration), were treated with exogenous ABA after heading and powdering. The effect on grain filling, water content at harvest, yield, and key differential protein expression and metabolic pathways were then determined. Yield was significantly lower in DK517 than ZD1002 after application of exogenous ABA. ABA also had a greater effect on the grain filling rate in DK517, while the timing of maximum grain filling occurred 5.72 days later than that of the control and the active grain filling period was 15.49 days longer. At 60 d after pollination, the grain water content was 23.55% in DK517 and 30.42% in ZD1002, 8.88% higher and 0.26% lower than that of the control, respectively. In DK517, a total of 861 differentially expressed proteins were screened after exogenous ABA application, and of these, 246 were up-regulated and 615 were down-regulated. In ZD1002, 118 proteins were identified, of which 56 were up-regulated and 62 were down-regulated. The findings suggest that application of exogenous ABA has differing effects on the grain filling characteristics of different maize varieties, with a greater overall effect on varieties such as DK517 with a faster dehydration rate.
Assessment between follicular fluid multiple element concentrations and hormonal profiles of women with polycystic ovary syndrome
Authors: Zou Xiaojie , Chen Yiqin , Ouyang Yang , Hu Shanwen , He Ye , Wu Yan , Wang Wenxiang 
Published: October 2022

Abstract
Polycystic ovary syndrome (PCOS) is the most common endocrine disorder among reproductive-aged women. Follicular fluid quality affects early embryonic development and multiple stages of pregnancy. This study measured 12 elements in follicular fluid and 5 blood hormones, aiming to identify the associations between multielement concentrations, as well as blood hormone levels, and PCOS to investigate the interference of multielement coexposure on PCOS and examine the potential roles of hormones. Eight elements (As, Cu, Se, Sr, V, Zn, Cr, Ca), but not Mg, showed a positive dose–effect relationship with PCOS. The OPLS models of follicle-stimulating hormone (FSH) and anti-Müllerian hormone (AMH) with relevant elements showed that Mg, Zn, Fe, Se and V had a more significant effect on FSH and that As, Se, V, Cu and Zn were positively correlated with AMH (VIP > 1). Further analysis indicated a synergistic effect for FSH and Mg, both of which were protective factors against PCOS; the associations between the five elements and PCOS incidence were mediated by AMH. Changes in hormone levels between multielement coexposure and PCOS development suggest that FSH and Mg are protective against PCOS; female exposure to As, Se, V, Cu, and Zn may affect PCOS progression by perturbing AMH levels.
Subject-independent EEG classification of motor imagery based on a dual-branch feature fusion
Authors: Dong Yanqing , Han Dan , Wen Xin , Gao Chengxin , Cao Ruochen , Guo Yuxiang , Xiang Jie , Cao Rui 
Published: October 2022

Abstract
Background: Brain-computer interface (BCI) system helps people with motor dysfunction interact with external environment. With the advancement of technology, the BCI system has been applied in practice, but its practicability and usability are still greatly challenged. A large amount of calibration time is often required before BCI systems are used, which can consume the patient’s energy and patience and can easily lead to anxiety. We propose a subject-independentzero calibration approach to solve this problem.
Methods: A dual-branch multiscale autoencoder network(MSAENet) is proposed realize the subject-independent classification in motor imagery, aiming to realize the plug-and-play of BCI. Firstly, the network consists of a multiscale branch and an autoencoder (AE) for feature learning from different perspectives. Secondly, the covariance between the EEG signal and the common spatial pattern in the 8-30 Hz band was used as spatio-spectral features, and the feature pre-extracted information is used as the input of MSAENet. Finally, The network introduces a central loss function to improve the classification ability. Testing network generalizability on three publicly available datasets BCIIV2a, SMR-BCI, and OpenBMI.
Results: The results show that our proposed network shows good results on all three datasets. In the case of subject-independence, MSAENet outperformed the other four comparison methods on the BCIIV2a and SMR-BCI datasets,while achieving F1 score values as high as 69. 34% on the OpenBMI dataset.Subject-dependent results with the best classification performance were significantly better than the other four advanced comparison methods. Our method can maintain a better classification accuracy while ensuring a small amount of parameters and a short prediction time.
Conclusions: MSAENet verifies the following three points: (1)Spatial frequency domain features can extract effective information from raw EEG signals. (2)Two-branch multiscale feature fusion can extract features more comprehensively. (3)The integration of the central loss function compensates for the fact that Softmax classifiers only consider class spacing and ignore intra-class distance. Our proposed method achieves zero calibration, and the problem that requires a lot of calibration time in BCI applications is effectively solved.Keywords: BCI; Motor imagery; Subject-independent; Feature fusion; Zero Calibration
COL22A1 and DNAH8 mutations are associated with tumor mutation burden and prognosis of lung adenocarcinoma patients
Authors: Zhang Chenchen , SONG Xin , Wang Changming 
Published: October 2022

Abstract
Lung cancer is one of the leading causes of death in patients with tumor around the world. Lung adenocarcinoma (LUAD) is most frequent histological subtype in lung cancer. Immune therapy has now become an effective method of treating LUAD. Tumor mutation burden (TMB) shows predictive biomarker potential for identification of cancer patients responding to immune checkpoint inhibitors. The mutation rate of lung adenocarcinoma was the third in various cancers. However, it is not clear whether heterogeneous genetic mutations are associated with TMB and immunity in the patients with LUAD. In our study, First, somatic mutation data of LUAD were downloaded from International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA) datasets, and found that 88 same common mutated genes were involved in two cohorts including TNN, TP53, MUC16, CSMD3, RYR2, ZFHX4, LRP1B, USH2A, KRAS, XIRP2, FLG, SPTA1, and so on. Among them, Collagen XXII (COL22A1) and Dynein Axoneme Heavy Chain 8 (DNAH8) mutations were correlated with higher TMB and showed a poorer clinical outcome. Then, In the basis of CIBERSORT algorithm as well as Gene set enrichment analysis (GSEA), we found that COL22A1 or DNAH8 mutation participated in the activation or raising process of immune-related signaling pathways and enhanced antitumor immune reaction. To sum up, COL22A1 or DNAH8 are most common mutated in LUAD, and their mutations are related with higher TMB and poorer prognosis as well as promotes antitumor immunity, which may regard as a biomarker to predict immune reaction.
Differential group delay behavior in homogeneous weakly coupled multicore fiber under bending and twisting condition
Authors: Farooque Umar , Kumar Amit , Singh Sandhir Kumar , Singh Dharmendra Kumar , Ranjan Rakesh 
Published: October 2022

Abstract
The impacts of core count/layout on the mode effective refractive index, bend and twist induced differential group delay (DGD) of different cores, worst-case DGD, and intercore DGD, in weakly coupled homogeneous multicore fibers (WC-HMCFs) have been analyzed to select the proper core layout with low DGD value for a particular core count. Further, in order to calculate the intercore DGD values, the generalized expressions of core pitch for the different core layouts have been derived. Moreover, the impacts of core radius, relative refractive index difference, and core pitch on the mode effective refractive index and DGD levels for the 3-core WC-HMCFs, with linear and triangular core layouts, have been analyzed numerically by using the finite element method based FemSIM simulation platform, and MATLAB. It is observed that for a certain core count value, the core layout and core pitch have significant impacts on the DGD levels; while, the variations in the values of core radius and relative refractive index difference have no significant impact on the DGD levels. Further, increase in core count normally increases the DGD levels in all core layouts. On the other hand, for the fixed values of core count, cladding diameter, and outer cladding thickness, the core layout which has the lowest core pitch leads to the lowest value of intercore DGD, as compared to the other core layouts. The investigations carried out in this work may provide the guidelines in different MCF applications, such as MCF based multi-parameter sensing, signal processing in microwave photonics, etc.
Community types of the human gut virome are associated with endoscopic outcome in ulcerative colitis
Authors: Jansen Daan , Falony Gwen , Vieira-Silva Sara , Simsek Ceren , Marcelis Tine , Caenepeel Clara , Machiels Kathleen , Raes Jeroen , Vermeire Severine , Matthijnssens Jelle 
Published: October 2022

Abstract

Background
Inflammatory Bowel Diseases (IBD) are a group of chronic inflammatory diseases of the gut. IBD patients have an altered gut microbiota; however, the relationship to disease is unknown. The gut microbiota is a complex ecosystem and bacterial community-typing is an established approach to condense the microbial complexity into enterotypes. A viral counterpart of enterotypes might allow stratification of individuals based on their gut virome. We aim to investigate the existence of such viral community types and assess the impact of therapeutic outcome (and other covariates) on the gut virome in IBD patients.
Methods
Viral particle enrichment followed by deep sequencing (1.52TB) was performed on 432 faecal samples from 181 IBD patients (CD = 126;UC = 55) starting biological therapy. Redundancy analysis and Dirichlet Multinomial Mixtures were applied to determine covariates of the virome composition and to condense the gut virota into viral community types, respectively.
Results
IBD patients were stratified based on unsupervised machine learning into two viral community types. Community type CA showed a low α-diversity and a high relative abundance of Caudoviricetes [non-CrAss] phages and was associated to the dysbiotic Bact2-enterotype. Community type CrM showed a high α-diversity and a high relative abundance of Caudoviricetes [CrAss] and Malgrandaviricetes phages. The gut virome variation was explained by several factors: patient individuality (75.8%), disease location (1.4%), age (0.5%) and faecal moisture (0.3%), whereas diagnosis did not show a non-redundant effect. Despite our expectations the choice of biological therapy did not show an association with the virome variation. During post-interventional analysis, endoscopic outcome (0.5%) was associated to gut virome variation. Remitting UC, but not CD, patients revealed a high percentage of community type CrM, a high Shannon diversity and a low lysogenic potential. Conversely, non-remitting UC, but not CD, patients revealed a high percentage of community type CA, a low Shannon diversity and a high lysogenic potential. During pre-interventional analysis, we discovered five novel phages associated with treatment success.
Conclusion
The gut virota shows the existence of distinct virome configurations that are associated with endoscopic outcome. Therefore, community typing could be a valuable tool to improve our understanding about IBD subtypes, pathology, and activity.