bluuebunny/crossref_metadata_2025_split huggingface dataset:
Thermostability profiling of MHC-bound peptides: a new dimension in immunopeptidomics and aid for immunotherapy design
Authors: Jappe Emma C. , Garde Christian , Ramarathinam Sri H. , Passantino Ethan , Illing Patricia T. , Mifsud Nicole A. , Trolle Thomas , Kringelum Jens V. , Croft Nathan P. , Purcell Anthony W. 
Published: December 2020

AbstractThe features of peptide antigens that contribute to their immunogenicity are not well understood. Although the stability of peptide-MHC (pMHC) is known to be important, current assays assess this interaction only for peptides in isolation and not in the context of natural antigen processing and presentation. Here, we present a method that provides a comprehensive and unbiased measure of pMHC stability for thousands of individual ligands detected simultaneously by mass spectrometry (MS). The method allows rapid assessment of intra-allelic and inter-allelic differences in pMHC stability and reveals profiles of stability that are broader than previously appreciated. The additional dimensionality of the data facilitated the training of a model which improves the prediction of peptide immunogenicity, specifically of cancer neoepitopes. This assay can be applied to any cells bearing MHC or MHC-like molecules, offering insight into not only the endogenous immunopeptidome, but also that of neoepitopes and pathogen-derived sequences.
Missense variant contribution to USP9X-female syndrome
Authors: Jolly Lachlan A. , Parnell Euan , Gardner Alison E. , Corbett Mark A. , Pérez-Jurado Luis A. , Shaw Marie , Lesca Gaetan , Keegan Catherine , Schneider Michael C. , Griffin Emily , Maier Felicitas , Kiss Courtney , Guerin Andrea , Crosby Kathleen , Rosenbaum Kenneth , Tanpaiboon Pranoot , Whalen Sandra , Keren Boris , McCarrier Julie , Basel Donald , Sadedin Simon , White Susan M. , Delatycki Martin B. , Kleefstra Tjitske , Küry Sébastien , Brusco Alfredo , Sukarova-Angelovska Elena , Trajkova Slavica , Yoon Sehoun , Wood Stephen A. , Piper Michael , Penzes Peter , Gecz Jozef 
Published: December 2020

AbstractUSP9X is an X-chromosome gene that escapes X-inactivation. Loss or compromised function of USP9X leads to neurodevelopmental disorders in males and females. While males are impacted primarily by hemizygous partial loss-of-function missense variants, in females de novo heterozygous complete loss-of-function mutations predominate, and give rise to the clinically recognisable USP9X-female syndrome. Here we provide evidence of the contribution of USP9X missense and small in-frame deletion variants in USP9X-female syndrome also. We scrutinise the pathogenicity of eleven such variants, ten of which were novel. Combined application of variant prediction algorithms, protein structure modelling, and assessment under clinically relevant guidelines universally support their pathogenicity. The core phenotype of this cohort overlapped with previous descriptions of USP9X-female syndrome, but exposed heightened variability. Aggregate phenotypic information of 35 currently known females with predicted pathogenic variation in USP9X reaffirms the clinically recognisable USP9X-female syndrome, and highlights major differences when compared to USP9X-male associated neurodevelopmental disorders.
A metastasis map of human cancer cell lines
Authors: Jin Xin , Demere Zelalem , Nair Karthik , Ali Ahmed , Ferraro Gino B. , Natoli Ted , Deik Amy , Petronio Lia , Tang Andrew A. , Zhu Cong , Wang Li , Rosenberg Danny , Mangena Vamsi , Roth Jennifer , Chung Kwanghun , Jain Rakesh K. , Clish Clary B. , Vander Heiden Matthew G. , Golub Todd R. 
Published: December 2020

AbstractMost deaths from cancer are explained by metastasis, and yet large-scale metastasis research has been impractical owing to the complexity of in vivo models. Here we introduce an in vivo barcoding strategy that is capable of determining the metastatic potential of human cancer cell lines in mouse xenografts at scale. We validated the robustness, scalability and reproducibility of the method and applied it to 500 cell lines1,2 spanning 21 types of solid tumour. We created a first-generation metastasis map (MetMap) that reveals organ-specific patterns of metastasis, enabling these patterns to be associated with clinical and genomic features. We demonstrate the utility of MetMap by investigating the molecular basis of breast cancers capable of metastasizing to the brain—a principal cause of death in patients with this type of cancer. Breast cancers capable of metastasizing to the brain showed evidence of altered lipid metabolism. Perturbation of lipid metabolism in these cells curbed brain metastasis development, suggesting a therapeutic strategy to combat the disease and demonstrating the utility of MetMap as a resource to support metastasis research.
Copy number variations in primary tumor, serum and lymph node metastasis of bladder cancer patients treated with radical cystectomy
Authors: Soave Armin , Kluwe Lan , Yu Hang , Rink Michael , Gild Philipp , Vetterlein Malte W. , Marks Philipp , Sauter Guido , Fisch Margit , Meyer Christian P. , Ludwig Tim , Dahlem Roland , Minner Sarah , Pantel Klaus , Steinbach Bettina , Schwarzenbach Heidi 
Published: December 2020

AbstractThe aim of the present study was to analyze copy number variations (CNV) of multiple oncogenes and tumor suppressor genes in genomic DNA from primary tumor tissue, lymph node metastasis and cell-free DNA (cfDNA) from serum of 72 urothelial carcinoma of bladder (UCB) patients treated with radical cystectomy (RC), using multiplex ligation-dependent probe amplification (MLPA). We hypothesized that primary tumor and lymph node metastasis show similar CNV profiles, and CNV are more present in lymph node metastasis compared to primary tumor tissue. Samples from 43 (59.7%) patients could be analyzed. In total, 35 (83%), 26 (68%) and 8 (42%) patients had CNV in primary tumor, serum and lymph node metastasis, respectively. MYC, CCND1, ERBB2 and CCNE1 displayed the most frequent amplifications. In particular, CNV in ERBB2 was associated with aggressive tumor characteristics. CNV in both ERBB2 and TOP2A were risk factors for disease recurrence. The current findings show that CNV are present in various oncogenes and tumor suppressor genes in genomic DNA from primary tumor, lymph node metastasis and cfDNA from serum. CNV were more present in genomic DNA from primary tumor tissue compared to cfDNA from serum and genomic DNA from lymph node metastasis. Patients with CNV in ERBB2 and TOP2A are at increased risk for disease recurrence following RC. Further studies are necessary to validate, whether these genes may represent promising candidates for targeted-therapy.
The SNP rs7865618 of 9p21.3 locus emerges as the most promising marker of coronary artery disease in the southern Indian population
Authors: Manjula Gorre , Pranavchand Rayabarapu , Kumuda Irgam , Reddy B. Sriteja , Reddy Battini Mohan 
Published: December 2020

AbstractDevelopment of coronary artery disease (CAD) is primarily due to the process of atherosclerosis, however the prognosis of CAD depends on pleiotropic effects of the genes located at 9p21.3 region. Genome wide association studies revealed association of variants in this region with CAD pathology. However, specific marker in predicting CAD development or progression is not yet identified. In the present study, 35 SNPs at 9p21.3 region, located in the cyclin dependent kinase inhibitor (CDKN2A/CDKN2B) genes, were genotyped among 350 CAD cases and 480 controls from the southern Indian population of Hyderabad using fluidigm nanofluidic SNP genotyping system and the data were analyzed using PLINK and R softwares. Of the 35 SNPs analysed, only one SNP, rs7865618, was found to be highly significantly associated with CAD, even after correction for multiple testing (p = 0.008). The AG and GG genotypes of this SNP conferred 3.08 and 1.93 folds increased risk for CAD respectively. In particular, this SNP was significantly associated with severe anatomic (triple vessel disease p = 0.023) and phenotypic (acute coronary syndrome p = 0.007) categories of CAD. Pair wise SNP interaction analysis between the SNPs of 9p21.3 and 11q23.3 regions revealed significantly increased risk of three SNPs of 11q23.3 region that were not associated individually, in conjunction with rs7865618 of 9p21.3.
Field application of an improved protocol for environmental DNA extraction, purification, and measurement using Sterivex filter
Authors: Wong Marty Kwok-Shing , Nakao Mako , Hyodo Susumu 
Published: December 2020

AbstractEnvironmental DNA (eDNA) is increasingly popular as a useful non-invasive method to monitor and study biodiversity and community structure in freshwater and marine environments. To effectively extract eDNA from the filter surface is a fundamental factor determining the representativeness of the samples. We improved the eDNA extraction efficiency of an established Sterivex method by 12- to 16-fold using a larger volume of lysis buffer mix coupled with backflushing the cartridges. The DNeasy extraction column could be overloaded when the environmental sample input is high, possibly due to a higher nonspecific binding present in environmental samples, thus resulting in a relatively lower quantity measured. Therefore, we included an internal control DNA in the extraction to monitor the extraction and purification efficiencies in field samples, which is crucial for quantification of original eDNA concentration. The use of Takara Probe qPCR Mix supplemented with protein-based additives improved the robustness of the real time PCR assay on inhibitor-rich environmental samples, but prior purification by Qiagen PowerClean Pro Cleanup kit could be essential for inhibitor-rich water samples, even though the recovery rate was unexpectedly low (average 33.0%). The improved extraction and quantification complement the qualitative analyses including metabarcoding and metagenomics in field application.
Radiographic and clinical assessment of unidirectional porous hydroxyapatite to treat benign bone tumors
Authors: Kunisada Toshiyuki , Hasei Joe , Fujiwara Tomohiro , Nakata Eiji , Yokoo Suguru , Demiya Koji , Ozaki Toshifumi 
Published: December 2020

AbstractUnidirectional porous hydroxyapatite (UDPHAp) was developed as an excellent scaffold with unidirectional pores oriented in the horizontal direction with interpore connections. The purpose of this study was to assess radiographic changes and clinical outcomes and complications following UDPHAp implantation to treat benign bone tumors. We retrospectively analyzed 44 patients treated with intralesional resection and UDPHAp implantation for benign bone tumors between 2010 and 2015. Clinical and radiographic findings were evaluated postoperatively at regular follow-up visits. The mean follow-up was 49 months. Radiographic changes were classified into five stages based on bone formation in the implanted UDPHAp according to Tamai’s classification. All patients showed excellent bone formation inside and around implanted UDPHAp. Absorption of UDPHAp and bone marrow cavity remodeling was identified in 20 patients at a mean of 17 months postoperatively, and was significantly more common in young patients. Preoperative cortical thinning was completely regenerated in 26 of 31 patients on average 10 months after surgery. There were no cases of delayed wound healing, postoperative infection, or allergic reaction related to implanted UDPHAp. UDPHAp is a useful bone-filling substitute for treating benign bone tumor, and the use of this material has a low complication rate.
Carotid imaging changes and serum IL-1β, sICAM-1, and sVAP-1 levels in benign paroxysmal positional vertigo
Authors: Chen Xiaoxu , Feng Huimin , Liu Hongjin , Xu Xianrong , Wang Jianchang , Jin Zhanguo 
Published: December 2020

AbstractBenign paroxysmal positional vertigo (BPPV) is the most common cause of vertigo. This study was performed to evaluate serum levels of inflammatory factors and changes in B-mode carotid ultrasound findings in patients with BPPV. The study population consisted of 90 BPPV patients and 90 age- and sex-matched controls. ELISA was used to compare the levels of inflammatory factors, such as interleukin-1β (IL-1β), tumor necrosis factor-alpha (TNF-α), soluble intercellular adhesion molecule-1 (sICAM-1), prostaglandin-E2 (PG-E2), and soluble vascular adhesion protein-1 (sVAP-1), between BPPV patients and controls. In addition, the results of ultrasonographic imaging to determine carotid intima-media thickness (C-IMT), carotid atheromatous plaque, and vertebral artery stenosis were also compared between the BPPV and control groups. Serum levels of IL-1β, sICAM-1, and sVAP-1 were significantly higher in BPPV patients than controls (P < 0.001,P < 0.05, andP < 0.001, respectively). C-IMT and vertebral artery stenosis were significantly different in BPPV patients compared to controls (bothP < 0.05). There were no significant relations between other parameters and BPPV. IL-1β, sICAM-1, and sVAP-1 are potentially associated with the pathogenesis of BPPV, and C-ITM and carotid vertebral stenosis may be useful reference imaging findings for the diagnosis of BPPV.
The role of 18F-fluorodeoxyglucose-positron emission tomography/computed tomography in the differential diagnosis of pericardial disease
Authors: Hyeon Cheol Won , Yi Hyun Kyung , Kim Eun Kyoung , Park Sung-Ji , Lee Sang-Chol , Park Seung Woo , Oh Jae K. , Choi Joon Young , Chang Sung-A 
Published: December 2020

AbstractThis study aimed to assess the role of 18F-fluorodeoxyglucose-positron emission tomography/computed tomography (18FDG-PET/CT) in the differential diagnosis of pericardial disease. The diagnosis is often troublesome because pericardial fluid analysis or biopsy does not always provide answers. 18FDG-PET/CT can visualize both inflammation and malignancy and offers a whole-body assessment. Patients who visited the Pericardial Disease Clinic of Samsung Medical Center with an 18FDG-PET/CT order code were extracted. Exclusion criteria were as follows: (1) the purpose of the differential diagnosis was not pericardial disease; (2) the patient had a known advanced-stage malignancy; (3) the patient already have confirmative diagnosis using a serology, pericardial effusion analysis or biopsy. The analysis included 107 patients. The most common final diagnosis was idiopathic (n = 46, 43.0%), followed by tuberculosis (n = 30, 28.0%) and neoplastic (n = 11, 10.3%). A maximum standardized uptake value (SUVmax) ≥ 5 typically indicates tuberculosis or neoplastic pericarditis except in just one case of autoimmune pericarditis); especially all of the SUVmax scores ≥ 10 had tuberculosis. The diagnostic yield of pericardial biopsy was very low (10.2%). Interestingly, all of the pericardium with an SUVmax < 4.4 had nondiagnostic results. In contrast, targeted biopsies based on 18FDG uptake demonstrated a higher diagnostic yield (38.7%) than pericardium. The sensitivity of 18FDG-PET/CT was 63.6%. The specificity was 71.9%. The positive predictive value was 20.6%. The negative predictive value 94.5%, and the accuracy was 71.0% for excluding malignancy based upon the FDG uptake patterns. It is possible to explore the differential diagnosis in some patients with difficult pericardiocentesis or pericardial biopsy in a noninvasive manner using on the SUVmax or uptake patterns. In addition, the biopsy strategy depending on 18FDG uptake is helpful to achieve biopsy more safely and with a higher yield. 18FDG-PET may enhance the diagnostic efficacy in patients with pericardial disease.
2D nanosheets and composites for EMI shielding analysis
Authors: Khan Ramsha , Khan Zeeshan Mehmood , Aqeel Hamza Bin , Javed Sofia , Shafqat Ahmed , Qazi Ibrahim , Basit Muhammad Abdul , Jan Rahim 
Published: December 2020

AbstractLiquid exfoliated, 2-dimensional (2D), few layered graphene and molybdenum disulfide nanosheets (GNS and MNS) are size selected for EMI shielding application. Scanning electron microscopy (SEM) has confirmed the lateral dimensions increase (1–2 µm for GNS and MNS) with lowering centrifugation speed (1000 to 500 rpm). The micron size (~ 15 µm) restacked structures of GNS and MNS (L ~ 2 µm) over a nylon membrane have shown ~ 16 dB and ~ 6 dB EMI shielding effectiveness (1–8 GHz frequency), respectively. The enhanced EMI shielding effectiveness for GNS-500 may be credited to its high carrier mobility as well as high aspect ratio of nanosheets. The GNS-500 are further dispersed (0.3 wt.%) in thermoplastic polyurethane for their applicability as flexible EMI shielding material. The dielectric characteristics predicted an enhancement for the attenuation (200 MHz–1 GHz). The experimental results (1–8 GHz) suggested the maximum attenuation ~ 18 dB showing the composite applicability as a broadband EMI shielding material.
Effect of rhegmatogenous retinal detachment on preoperative and postoperative retinal sensitivities
Authors: Noda Hiroshi , Kimura Shuhei , Hosokawa Mio Morizane , Shiode Yusuke , Doi Shinichiro , Takahashi Kosuke , Matoba Ryo , Kanzaki Yuki , Fujiwara Atsushi , Morizane Yuki 
Published: December 2020

AbstractThis retrospective study investigated foveal and perifoveal retinal sensitivities using microperimetry before and after surgery for rhegmatogenous retinal detachment (RRD). Consecutive patients with RRD who underwent vitrectomy or scleral buckling were included. Comprehensive ophthalmological examinations, including microperimetry and swept-source optical coherence tomography, were performed before and 6 months after surgery. Pre- and postoperative retinal sensitivities at the fovea and 4 perifoveal measurement points farthest from the fixation point, both vertically and horizontally (superior, inferior, nasal, and temporal) were examined. A total of 34 foveal and 136 perifoveal measurement points in 34 eyes of 34 patients were evaluated. The postoperative retinal sensitivity was significantly higher than the preoperative value at foveal and perifoveal points with (P < 0.001 for both) and without (fovea: P = 0.005, perifovea: P < 0.001) RRD. The postoperative retinal sensitivity was significantly lower at foveal (P < 0.01) and perifoveal (P < 0.001) points with preoperative RRD than at points without preoperative RRD; furthermore, it was significantly better at points with ellipsoid zone (Ez) continuity than at points with Ez discontinuity (fovea: P < 0.01, perifovea: P < 0.001). RRD deteriorates retinal sensitivity, regardless of its presence or absence at the measurement point before surgery. Postoperative Ez continuity is important for good postoperative retinal sensitivity.
High energy density hybrid supercapacitors derived from novel Ni3Se2 nanowires in situ constructed on porous nickel foam
Authors: Li Wei , Chen Tianqi , Li Ao , Shi Peng , Wu Ming , Li Tingting , Yue Hongwei , Chen Yifeng , Huang Baojun , Lou Xiaojie 
Published: December 2020

A novel Ni3Se2 nanowires are synthesized in situ on the surface of nickel foam through a one-step hydrothermal reaction under the reaction time of 24 h, and it demonstrates excellent energy storage performance for hybrid supercapacitors.
Effects of physical activity on the progression of diabetic nephropathy: a meta-analysis
Authors: Cai Zixin , Yang Yan , Zhang Jingjing 
Published: December 2020

Abstract
Background: Diabetic nephropathy (DN) is an important microvascular complication of diabetes. Physical activity (PA) is part of a healthy lifestyle for diabetic patients; however, the role of PA in DN has not been clarified. Our aim was to conduct a meta-analysis to explore the association between PA and DN risk.
Methods: PubMed, Embase, Cochrane Library and Web of Science were systematically searched for articles examining PA in diabetic patients and its effect on renal function. Standardized mean differences (SMDs) and odds ratios (ORs) with 95% confidence intervals (CIs) were calculated. The study protocol is registered with PROSPERO (CRD42020191379).
Results: A total of 38991 participants were identified from 18 studies. The results indicated that PA was associated with increases in the glomerular filtration rate (SMD = 0.01, 95% CI = [0.02–0.17]) and decreases in the urinary albumin creatinine ratio (SMD = −0.53, 95% CI: −0.72 to −0.34), rate of microalbuminuria (OR = 0.61, 95% CI = [0.46–0.81]), rate of acute kidney injury (OR = 0.02, 95% CI = [0.01–0.04]), rate of renal failure (OR = 0.71, 95% CI = [0.52–0.97]) and risk of DN in patients with Type 1 diabetes (OR = 0.67, 95% CI = [0.51–0.89]).
Conclusions: This meta-analysis indicated that PA is effective for improving DN and slowing its progression; however, more high-quality randomized controlled trials are required on this topic.
An epithelial–mesenchymal transition-related long noncoding RNA signature correlates with the prognosis and progression in patients with bladder cancer
Authors: Tong Hang , Li Tinghao , Gao Shun , Yin Hubin , Cao Honghao , He Weiyang 
Published: December 2020

Abstract
Bladder cancer is a common malignant tumour worldwide. Epithelial–mesenchymal transition (EMT)-related biomarkers can be used for early diagnosis and prognosis of cancer patients. To explore, accurate prediction models are essential to the diagnosis and treatment for bladder cancer. In the present study, an EMT-related long noncoding RNA (lncRNA) model was developed to predict the prognosis of patients with bladder cancer. Firstly, the EMT-related lncRNAs were identified by Pearson correlation analysis, and a prognostic EMT-related lncRNA signature was constructed through univariate and multivariate Cox regression analyses. Then, the diagnostic efficacy and the clinically predictive capacity of the signature were assessed. Finally, Gene set enrichment analysis (GSEA) and functional enrichment analysis were carried out with bioinformatics. An EMT-related lncRNA signature consisting of TTC28-AS1, LINC02446, AL662844.4, AC105942.1, AL049840.3, SNHG26, USP30-AS1, PSMB8-AS1, AL031775.1, AC073534.1, U62317.2, C5orf56, AJ271736.1, and AL139385.1 was constructed. The diagnostic efficacy of the signature was evaluated by the time-dependent receiver-operating characteristic (ROC) curves, in which all the values of the area under the ROC (AUC) were more than 0.73. A nomogram established by integrating clinical variables and the risk score confirmed that the signature had a good clinically predict capacity. GSEA analysis revealed that some cancer-related and EMT-related pathways were enriched in high-risk groups, while immune-related pathways were enriched in low-risk groups. Functional enrichment analysis showed that EMT was associated with abundant GO terms or signaling pathways. In short, our research showed that the 14 EMT-related lncRNA signature may predict the prognosis and progression of patients with bladder cancer.