bluuebunny/crossref_metadata_2025_split huggingface dataset:
Application Value of Whole Exome Sequencing in Screening and Identifying Pathogenic Genes of Hypopharyngeal Carcinoma
Authors: Yao Jingwei , Ding Yubo , Liu Xiong , Huang Jialu , Zhang Minghui , Zhang Yu , Lv Yufan , Xie Zhuoyi , Zuo Jianhong 
Published: July 2021

Abstract
Background: Whole-exome sequencing has been used in many cancer research, but it is rarely used in Hypopharyngeal carcinoma. In our research, we performed whole-exome sequencing of DNA from 10 tumor tissue specimens from patients with hypopharyngeal cancer rather than targeted sequencing of specific genes.Methods: Whole-exome sequencing in 10 patients with hypopharyngeal carcinoma was performed to identify single nucleotide variations (SNVs) and insertions and deletions (INDELs). American College of Medical Genetics and Genomics (ACMG) guidelines were used to evaluate the pathogenicity of the selected variants. Gene Ontology (GO) and pathway enrichment were used to analyze the function and effect of mutated genes. Protein protein interaction (PPI) was analyzed by string online software.Results: 8113 mutation sites in 5326 genes were identified after strict screening. MEGF8, ITPR1, DYSF, DNAH10, CUL7, MYH14, LRP1, ASTN1, TTN, ASH1L, MYH11, KMT2C were mutated in more than 6 patients. We identified 72 pathogenic or potentially pathogenic mutations in 53 genes according to the ACMG guidelines. GO annotation and KEGG enrichment analysis show the possible effect of these pathogenic genes on cancer. Conclusion: We identified novel mutations in patients with hypopharyngeal cancer, and provided a foundation for future research on the pathogenesis of hypopharyngeal carcinoma and targeted treatment of hypopharyngeal carcinoma.
A Novel Multi-Criteria Decision Analysis Technique Considering Various Essential Characteristics
Authors: Bandyopadhyay Susmita 
Published: July 2021

Abstract
This paper has proposed a novel Multi-Criteria Decision Analysis (MCDA) technique that considers relationships among the criteria, relationships among the alternatives, relationships among the criteria and the alternatives, the uncertainty or dilemma that the decision makers face in their decision making, the entropy among the criteria. The dilemma of the decision makers has been captured through the use of Hesitant Fuzzy Elements; the information content among the criteria has been captured by applying the concept of entropy through the application of a technique called IDOCRIW. A kind of sensitivity analysis has been performed to verify the effectiveness of the proposed technique. The proposed method has also been compared with four different types of already existing MCDA techniques, AHP, MAUT, MACBETH and MOORA. Both the sensitivity analysis and the comparison with other methods establish the effectiveness of the proposed technique.
The Human Health Risk Assessment and Countermeasures Study of Groundwater Quality
Authors: Lan Tianshan , Wang Fugang , Bao Shanshan , Miao Jinjie , Bai Yaonan , Jia Sida , Cao Yuqing 
Published: July 2021

Abstract
Background：Groundwater serves as the drinking water source, which chemical components directly affect human health. Different regions own their groundwater hydro-chemical characteristics based on various geological, hydro-geological conditions, human activities. From the perspective of human health, it is necessary to select groundwater quality health risk assessment （GQHR） factors combined with hydro-chemical characteristics of different regions.Methods：In this paper, taking Tongzhou of Beijing,China as the study area, according to the groundwater hydro-chemical characteristics, NO3-, NO2-, NH4+ and F- were extracted as assessment factors to evaluate the GQHR. Based on GQHR results, the formation and concentration characteristics of health risk factors and the prominent controlling role of influencing risk distribution were explored from natural and human factors. Furthermore, the targeted measures to prevent the increase of groundwater health risk were put forward.Results：Assessment factors: NO3-, NO2- and NH4+ are derived by human factors, such as sewage irrigation, fertilization, and F- stems from irrigation of geogenic high fluoride groundwater and fertilizer use. Still, their distribution is affected by natural factors (geology, geomorphology, and climate). The GQHR follows the order: children > adult females > adult males. The low and medium risk regions are located in upper groundwater, which are mainly controlled by natural factors (groundwater depth, aquifer medium, hydraulic conductivity coefficient, etc.) The measures to prevent the increase of groundwater health risk are to control the pollution sources and reduce the change of groundwater hydrodynamic conditions. The high-risk regions are located in eastern part of the study area, which are affected by both natural and human factors. The preventative measures are to reduce pollution caused by human factors and scientific groundwater resource exploitation and management. Conclusions：In this study, corresponding preventative and control measures were proposed for health risks caused by different dominant control effects. Meanwhile, the research results provide a scientific basis for the safety of groundwater supply and environmental exposure in this area. The research ideas and methods can be used as a reference for similar studies.
Pharmacological clearance of senescent cells reverses HFpEF hallmarks by decreasing inflammation, endothelial dysfunction and cardiac fibrosis
Authors: Silva Elsa , Tomé Inês , Vasques-Nóvoa Francisco , Conceição Glória , Silva Andreia , Barros António , Angélico-Gonçalves António , Caetano Carolina , Sousa Daniel , Miranda-Silva Daniela , Gonçalves Nádia , Sampaio-Pinto Vasco , Gonçalves Alexandre , Leite-Moreira Adelino , Falcão-Pires Inês , Pitrez Patrícia , Pinto-do-Ó Perpétua , Santos Susana , Ferreira Lino , Nascimento Diana 
Published: July 2021

Abstract
Aging and chronic inflammation are associated with the development of heart failure with preserved ejection fraction (HFpEF). However, cellular senescence as a potential mechanistic link between both events and its pathophysiological and therapeutic role were yet unexplored. Here we show that ZSF1-obese rats, a model of cardiometabolic HFpEF, have exacerbated systemic inflammation and endothelial damage compared to ZSF1-lean littermates. In addition, ZSF1-obese rats accumulated immune and endothelial senescent cells in the peripheral blood and myocardium. Accordingly, the frequency of circulating senescent leukocytes associated with markers of disease severity in HFpEF patients. Notably, systemic treatment of ZSF1-obese rats with Navitoclax, a BCL-2 family inhibitor, reduced senescent cell burden, decreased circulating B-type natriuretic peptide levels, and attenuated inflammation, vascular remodeling and cardiac fibrosis. Our findings advance cellular senescence as a key mechanistic pathway leading to HFpEF and provide proof-of-concept evidence that senolytics are a promising treatment for this disease.
From prison induction into the sentence. Analysing prison officer support and assistance in a small island state.
Authors: Scalpello Michela 
Published: July 2021

Abstract
This paper sheds light on male Maltese prisoners and their perception of help and support when incarcerated at Corradino Correctional Facility (CCF), Malta’s only prison. Through thematic analysis, the viewpoints, thoughts, and feelings of 39 males were explored. This was done in relation to programmes aimed to help prisoners in their desistance journey. Thought-provokingly, many prisoners spoke to the lack of support they felt within this prison. Even though there was only one question in the interview schedule which focused on how the prisoners felt in terms of support, this talk of support systems, or lack thereof, featured in many instances, frequently enough to warrant an analysis of its own. Themes emerging from this paper suggest that relationships between prisoners and prison officers are not supportive to any rehabilitative ideal. Prisoners speak of the lack of induction, information, and support, and of being mocked when requesting information or assistance. They state that support is conditional on who they knew, not withholding direct references to corruption, and even though some officers do attempt to provide proper care, they are limited by the institution, and by the colonial mentality of such a small island state.
PSC Scientific Community Resource The PSC Scientific Community Resource: An Asset for Multi-Omics Interrogation of Primary Sclerosing Cholangitis
Authors: Ali Ahmad Hassan , Juran Brian D. , Schlicht Erik M. , Bianchi Jackie K. , McCauley Bryan M. , Atkinson Elizabeth J. , Lazaridis Konstantinos N. 
Published: July 2021

Abstract
Background: Primary sclerosing cholangitis (PSC) is a rare, chronic cholestatic liver disease that often progresses to end-stage liver disease and/or the development of hepatobiliary neoplasia. Lack of prognostic tools and treatment options for PSC is driven in part by our poor understanding of its pathogenesis, which is thought to be complex, the interaction of genetic variants, environmental influences and biological response throughout the course of disease. The PSC Scientific Community Resource (PSC-SCR) seeks to overcome previous shortcomings by facilitating novel research in PSC with the ultimate goals of individualizing patient care and improving patient outcomes.Methods: PSC patients who receive their health care at Mayo Clinic or a collaborating site are identified by chart review and invited in person or by mail to participate. Non-Mayo patients are offered enrollment if they provide sufficient access to their medical records to evaluate inclusion/exclusion criteria. Controls without liver disease are identified with assistance of the Mayo Clinic Biobank. Participant consent is obtained at the beginning of the recruitment process by mail-in, electronic or face-to-face protocols. Clinical data is extracted from the medical record by qualified physicians and entered in a custom designed database. Participants fill out a custom-designed, comprehensive questionnaire, which collects scientifically relevant demographic and clinical information. Biospecimens are collected using mail-in kitsthar are returned via overnight carrier service and processed by the biospecimen accessioning and processing facility at Mayo Clinic, which coordinates sample transfers and provides required sample preparation services.The resource is currently being utilized to perform omics-scale projects investigating the exposome, metabolome, methylome, immunome and microbiome in PSC. Datasets and residual biospecimens will be shared with researchers proposing scientifically sound PSC-focused research with approval of the appropriate review boards.Discussion:Patient-based studies leveraging the latest technologies for targeted and wide-scale interrogation of multiple omics layers offer promise to accelerate PSC research through discovery of unappreciated aspects of disease pathogenesis. However, the rarity of PSC severely limits such studies. Here we describe our effort to overcome this limitation, the PSC-SCR, a repository of patient biospecimens coupled with clinical and omics data for use by the broader PSC research community.
Engineering of 2D Materials To Trap And Kill SARS-CoV-2: A New Insight From Multi-Microsecond Atomistic Simulations
Authors: Khedri Mohammad , Maleki Reza , Dahri Mohammad , Sadeghi Mohammad Moein , Rezvantalab Sima , Santos Hélder A. , Shahbazi Mohammad-Ali 
Published: July 2021

Abstract
In late 2019, coronavirus disease 2019 (COVID-19) caused severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Spike protein is one of the surface proteins of SARS-CoV-2 that is essential for its infectious function. Therefore, it received lots of attention for the preparation of antiviral drugs, vaccines, and diagnostic tools. Herein, we use computational methods of chemistry and biology to study the interaction between spike protein and its receptor in the body, angiotensin-I-converting enzyme-2 (ACE2). Additionally, the possible interaction of two-dimensional (2D) structures, including graphene, bismuthene, phosphorene, p-doped graphene, and functionalized p-doped graphene, with spike protein is investigated. The functionalized p-doped graphene nanosheets were found to interfere with spike protein better than the other tested nanomaterials. In addition, the interaction of the proposed nanosheets with the main protease (Mpro) of SARS-CoV-2 was studied. Functionalized p-doped graphene nanosheets showed more capacity to prevent the activity of Mpro. This 2D structure efficiently reduce the transmissibility and infectivity of SARS-CoV-2 by both the deformation of the spike protein and inhibiting the Mpro. The results suggest the potential use of 2D materials in a variety of prophylactic approaches, such as masks or surface coatings, and would deserve further studies in the coming years.
Red Sea tectonics unveil the largest known terrestrial ice stream: New constraints on Late Ordovician ice sheet dynamics
Authors: Elhebiry Mohamed , Sultan Mohamed , Abotalib Abotalib , Kehew Alan , Voice Peter , El-Leil Ibrahim Abu 
Published: July 2021

Abstract
Mega-streamlined landforms on Earth and Mars have been attributed to aeolian, glaciogenic, fluvial, and tectonic processes. Identifying the forces that shaped these landforms is paramount for understanding landscape evolution and constraining paleo-climate models and ice sheet reconstructions. In Arabia, east-northeast, kilometer-scale streamlined landforms were interpreted to have been formed by Quaternary aeolian erosion. We provide field and satellite-based evidence for a Late Ordovician glacial origin for these streamlined landforms, which were exhumed during the Red Sea–related uplift. Then we use Late Ordovician paleo-topographic data to reconstruct the Late Ordovician ice sheet using identified and previously reported glacial deposits and landforms. Our reconstruction suggests these glacial features are part of a major, topographically controlled, marine-terminating ice stream, twice the length of the largest known terrestrial ice streams. Our results support models that advocate for a single, major, and highly dynamic ice sheet and provide new morphological-based constraints for Late Ordovician climate models.
Automated Brain Volumetric Program Measuring Regional Brain Atrophy in Diagnosis of Mild Cognitive Impairment and Alzheimer’s Disease Dementia
Authors: Ryu Dong-Woo , Hong Yun Jeong , Cho Jung Hee , Kwak Kichang , Lee Jong-Min , Shim Yong S , Youn Young Chul , Yang Dong-Won 
Published: July 2021

Abstract
A quantitative analysis of brain volume can assist in diagnosis of Alzheimer’s disease (AD) ususally accompannied by brain atrophy. With an automated analysis program Quick Brain Volumetry (QBraVo) developed for volumetric measurements, we measured regional volumes and ratios to evaluate their performance in discriminating AD dementia (ADD) and mild cognitive impairment (MCI) patients from normal controls (NC). Validation of QBraVo was based on intra-rater and inter-rater reliability with a manual measurement. The regional volumes and ratios to total intracranial volume (TIV) and to total brain volume (TBV) or total cerebrospinal fluid volume (TCV) were compared among subjects. The regional volume to total cerebellar volume ratio named Standardized Atrophy Volume Ratio (SAVR) was calculated to compare brain atrophy. Diagnostic performances to distinguish among NC, MCI, and ADD were compared between MMSE, SAVR, and the predictive model. In total, 56 NCs, 44 MCI, and 45 ADD patients were enrolled. The average run time of QBraVo was 5 minutes 36 seconds. Intra-rater reliability was 0.999. Inter-rater reliability were high for TBV, TCV, and TIV (R = 0.97, 0.89 and 0.93, respectively). The medial temporal SAVR showed the highest performance for discriminating ADD from NC (AUC = 0.808, diagnostic accuracy = 80.2%). The predictive model using both MMSE and medial temporal SAVR improved the diagnostic performance for MCI in NC (AUC = 0.844, diagnostic accuracy = 79%). Our results demonstrated QBraVo as a fast and accurate method to measure brain volume. The regional volume calculated as SAVR could help to diagnose ADD and MCI and increase diagnostic accuracy for MCI.
Exploring the Spatial Distribution and Regional Differences of Obstetric Complications Across India: Evidence-Based on NFHS- 4: 2015-16.
Authors: Bajaj Shriya , Jha Rahul 
Published: July 2021

Abstract
Background: In recent years, obstetric complications have increased among pregnant women, which leads to disease burden among them in the later stages of life and sometimes resulting in deaths after birth. The spatial research helps to know the pattern and trait at a regional level, and accordingly, the interventions can take place in terms of health care services.Method: The study is based on National Family Health Survey-4 (NFHS-4) conducted in India in the year 2015-16. This study focused on ever-married women aged 15-49 years who have delivered at least once during the five years preceding the survey. GeoDa was used to generate local indicators of spatial association (LISA) significance and cluster maps and Moran Index. It measured the correlation among neighbouring observations in a pattern and the levels of spatial clustering among neighbouring.Results: The regions identified under different pregnancy complications were different. The pregnancy complications during pregnancy and after pregnancy were high in India's Northern and Eastern provinces. While complication during delivery was high in Northern and Southern India. The local spatial autocorrelation showed that the high-high regions of the pregnancy complication were located in the low prevalence regions (high-low).Conclusion: Despite several programmes and policies for pregnant women the obstetric complications still exist in several pockets of India. The spatial analysis gives us insights to provide special attention to specific regions; the pregnancy complication is one of the main reasons for higher maternal mortality.
Path Planning For Robotic Polishing of Sheet Metal Parts
Authors: Liu Yuezhi (Sean) , Xi Fengfeng (Jeff) , Faieghi Reza 
Published: July 2021

Abstract
Unlike solid parts, the deformation caused by a contact force during robotic polishing of sheet metal parts has become an issue. In this paper, a path planning method is purposed to resolve this issue. This method includes three steps. The first step is to apply the Hertz theory to compute the contact areas between the tool head and the free-form surface of a sheet metal part. The second step is to apply the finite element method to compute the deformation under a contact force. The third step is to reconstruct the deformed free-form surface and modify the contact areas accordingly. The underlying problem is dynamic because the deformed surface shape changes as the tool head moves along a tool path. Based on the proposed method, an optimal path can be determined to achieve full coverage of the entire surface without over or under polishing.
Evaluation of Optimal Sites for the Insertion of Orthodontic Mini-implants at Mandibular Symphysis Region Through Cone-beam Computed Tomography
Authors: Zhang Shizhen , Wei Xiaoyu , Wang Lufei , Wu Zhouqiang , Liu Lu , Yan Xinyu , Pu Lingling , Lai Wenli , Long Hu 
Published: July 2021

Abstract
Background: This study evaluates the overall bone thickness (OBT) and cortical bone thickness (CBT) of mandibular symphysis and to determine the optimal sites for the insertion of orthodontic mini-implants.Methods: Cone-beam computed tomography (CBCT) images of 32 patients (18 males, 14 females), including 16 adults and 16 adolescents were included in this study. The sample was further categorized into three facial types: low angle, average angle, and high angle. OBT and CBT were measured at the mandibular symphysis region. All measurements were performed at six different heights (2 mm, 4 mm, 6 mm, 8 mm, 10 mm, and 12 mm from cementoenamel junction [CEJ]) and at seven different angles (0, 10, 20, 30, 40, 50, 60 degrees to the occlusal plane). Results: Neither OBT nor CBT was influenced by age or sex, except for that CBT was significantly thicker in adults than in adolescents. OBT and CBT were significantly thicker in low-angle cases than in average- and high-angle cases. Both OBT and CBT were significantly influenced by insertion locations, insertion heights, insertion angles, and their interactions. CBT and OBT gained the greatest value at the location between two lower central incisors, and became greater with the increase of insertion height and insertion angle. Both recommended and optimal insertion sites were mapped. Conclusions: Mandibular symphysis region was suitable for the placement of orthodontic mini-implants. The optimal insertion site was 6-10 mm apical to CEJ between two lower central incisors with an insertion angle being 0-60 degrees to the occlusal plane.
Brush Swab As A Noninvasive Surrogate for Tissue Biopsies in Oral Cancer Patients To Develop Clinically Translatable Epigenetic Biomarkers
Authors: Viet Chi Tonglien , Zhang Xinyu , Xu Ke , Yu Gary , Asam Kesava , Thomas Carissa M. , Callahan Nicholas F. , Doan Coleen , Walker Paul C. , Nguyen Khanh , Kidd Stephanie C. , Lee Steve C. , Grandhi Anupama , Allen Clint T. , Young Simon , Melville James C. , Shum Jonathan W. , Viet Dan T. , Herford Alan S. , Roden Dylan F. , Aouizerat Bradley E. 
Published: July 2021

Abstract
Background

Oral squamous cell carcinoma (OSCC) has poor survival rates. There is a pressing need to develop more precise risk assessment methods to tailor clinical treatment. Epigenome-wide association studies in OSCC have not produced a viable biomarker. These studies have relied on methylation array platforms, which are limited in their ability to profile the methylome. In this study, we use MethylCap-Seq (MC-Seq), a comprehensive methylation quantification technique, and brush swab samples, to develop a noninvasive, readily translatable approach to profile the methylome in OSCC patients.
Methods

Three OSCC patients underwent collection of cancer and contralateral normal tissue and brush swab biopsies, totaling 4 samples for each patient. Epigenome-wide DNA methylation quantification was performed using the SureSelectXT Methyl-Seq platform. DNA quality and methylation site resolution were compared between brush swab and tissue samples. Correlation and methylation value difference were determined for brush swabs vs. tissues for each respective patient and site (i.e., cancer or normal). Correlations were calculated between cancer and normal tissues and brush swab samples for each patient to determine the robustness of DNA methylation marks using brush swabs in clinical biomarker studies.
Results

There were no significant differences in DNA yield between tissue and brush swab samples. Mapping efficiency exceeded 90% across all samples, with no differences between tissue and brush swabs. The average number of CpG sites with at least 10x depth of coverage was 2,716,674 for brush swabs and 2,903,261 for tissues. Matched tissue and brush swabs had excellent correlation (r = 0.913 for cancer samples and r = 0.951 for normal samples). The methylation profile of the top 1,000 CpGs was significantly different between cancer and normal samples (mean p-value = 0.00021) but not different between tissues and brush swabs (mean p-value = 0.11).
Conclusions

Our results demonstrate that MC-Seq is an efficient platform for epigenome profiling in cancer biomarker studies, with broader methylome coverage than array-based platforms. Brush swab biopsy provides adequate DNA yield for MC-Seq, and taken together, our findings set the stage for development of a non-invasive methylome quantification technique for oral cancer with high translational potential.