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https://www.readbyqxmd.com/read/28551763/mesenchymal-stromal-cell-and-osteoblast-responses-to-oxidized-titanium-surfaces-pre-treated-with-%C3%AE-%C3%A2-%C3%A2-808%C3%A2-nm-gaalas-diode-laser-or-chlorhexidine-in-vitro-study
#1
Flaminia Chellini, Marco Giannelli, Alessia Tani, Lara Ballerini, Larissa Vallone, Daniele Nosi, Sandra Zecchi-Orlandini, Chiara Sassoli
Preservation of implant biocompatibility following peri-implantitis treatments is a crucial issue in odontostomatological practice, being closely linked to implant re-osseointegration. Our aim was to assess the responses of osteoblast-like Saos2 cells and adult human bone marrow-mesenchymal stromal cells (MSCs) to oxidized titanium surfaces (TiUnite(®), TiU) pre-treated with a 808 ± 10 nm GaAlAs diode laser operating in non-contact mode, in continuous (2 W, 400 J/cm(2); CW) or pulsed (20 kHz, 7 μs, 0...
May 27, 2017: Lasers in Medical Science
https://www.readbyqxmd.com/read/28549078/herod-a-human-ethnic-and-regional-specific-omics-database
#2
Xian Zeng, Lin Tao, Zhang Peng, Chu Qin, Shangying Chen, Weidong He, Ying Tan, Hong Xia Liu, Sheng Yong Yang, Zhe Chen, Yu Yang Jiang, Yu Zong Chen
Motivation: Genetic and gene expression variations within and between populations and across geographical regions have substantial effects on the biological phenotypes, diseases, and therapeutic response. The development of precision medicines can be facilitated by the OMICS studies of the patients of specific ethnicity and geographic region. However, there is an inadequate facility for broadly and conveniently accessing the ethnic and regional specific OMICS data. Results: Here, we introduced a new free database, HEROD, a human ethnic and regional specific OMICS database...
May 26, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28549074/cwdprnp-a-tool-for-cervid-prion-sequence-analysis-in-program-r
#3
William L Miller, W David Walter
Summary: Chronic wasting disease is a fatal neurological, disease caused by an infectious prion protein, which affects economically and ecologically important members of the family Cervidae. Single nucleotide polymorphisms within the prion protein gene have been linked to differential susceptibility to the disease in many species. Wildlife managers are seeking to determine the frequencies of disease-associated alleles and genotypes and delineate spatial genetic patterns. The CWDPRNP package, implemented in program R, provides a unified framework for analyzing prion protein gene variability and spatial structure...
May 26, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28545285/-effects-of-apigenin-on-lipopolysaccharide-induced-proliferation-of-rat-aortic-vascular-smooth-muscle-cells
#4
H M Yao, Y P Jia, Z Xue, M Guo, J Y Lyu
Objective: To investigate the effect of natural active compounds apigenin (API) on the proliferation of rat aortic vascular smooth muscle cells (VSMCs) induced by lipopolysaccharide (LPS) and related mechanisms. Methods: VSMCs of primary cultured SD rats were obtained and the cytotoxic effects of API (0, 10, 20, 40 and 80 μmol/L) was explored by CCK-8 method. Impact of LPS (0, 0.1, 1, 10 and 100 μg/ml) on VSMCs proliferation and the impact of API (0, 10, 20, 40 μmol/L) on LPS (10 μmol)-induced VSMCs proliferation by CCK-8 methods...
April 24, 2017: Zhonghua Xin Xue Guan Bing za Zhi
https://www.readbyqxmd.com/read/28541603/comparison-of-first-line-chemotherapy-including-escalated-beacopp-versus-chemotherapy-including-abvd-for-people-with-early-unfavourable-or-advanced-stage-hodgkin-lymphoma
#5
REVIEW
Nicole Skoetz, Andrea Will, Ina Monsef, Corinne Brillant, Andreas Engert, Bastian von Tresckow
BACKGROUND: There are two different international standards for the treatment of early unfavourable and advanced stage Hodgkin lymphoma (HL): chemotherapy with escalated BEACOPP (bleomycin/etoposide/doxorubicin/cyclophosphamide/vincristine/procarbazine/prednisone) regimen and chemotherapy with ABVD (doxorubicin/bleomycin/vinblastine/dacarbazine) regimen. OBJECTIVES: To determine the advantages and disadvantages of chemotherapy including escalated BEACOPP compared to chemotherapy including ABVD in the treatment of early unfavourable or advanced stage HL as first-line treatment...
May 25, 2017: Cochrane Database of Systematic Reviews
https://www.readbyqxmd.com/read/28541490/glanet-genomic-loci-annotation-and-enrichment-tool
#6
Burçak Otlu, Can Firtina, Sündüz Keles, Oznur Tastan
Motivation: Genomic studies identify genomic loci representing genetic variations, transcription factor (TF) occupancy, or histone modification through next generation sequencing (NGS) technologies. Interpreting these loci requires evaluating them with known genomic and epigenomic annotations. Results: We present GLANET as a comprehensive annotation and enrichment analysis tool which implements a sampling-based enrichment test that accounts for GC content and/or mappability biases, jointly or separately...
May 24, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28541456/crisprcloud-a-secure-cloud-based-pipeline-for-crispr-pooled-screen-deconvolution
#7
Hyun-Hwan Jeong, Seon Young Kim, Maxime Wc Rousseaux, Huda Y Zoghbi, Zhandong Liu
Summary: We present a user-friendly, cloud-based, data analysis pipeline for the deconvolution of pooled screening data. This tool, CRISPRcloud, serves a dual purpose of extracting, clustering and analyzing raw next generation sequencing files derived from pooled screening experiments while at the same time presenting them in a user-friendly way on a secure web-based platform. Moreover, CRISPRcloud serves as a useful web-based analysis pipeline for reanalysis of pooled CRISPR screening datasets...
May 24, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28541376/dna-sequence-shape-kernel-enables-alignment-free-modeling-of-transcription-factor-binding
#8
Wenxiu Ma, Lin Yang, Remo Rohs, William Stafford Noble
Motivation: Transcription factors (TFs) bind to specific DNA sequence motifs. Several lines of evidence suggest that TF-DNA binding is mediated in part by properties of the local DNA shape: the width of the minor groove, the relative orientations of adjacent base pairs, etc. Several methods have been developed to jointly account for DNA sequence and shape properties in predicting TF binding affinity. However, a limitation of these methods is that they typically require a training set of aligned TF binding sites...
May 24, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28538708/accuracy-in-wrist-worn-sensor-based-measurements-of-heart-rate-and-energy-expenditure-in-a-diverse-cohort
#9
Anna Shcherbina, C Mikael Mattsson, Daryl Waggott, Heidi Salisbury, Jeffrey W Christle, Trevor Hastie, Matthew T Wheeler, Euan A Ashley
The ability to measure physical activity through wrist-worn devices provides an opportunity for cardiovascular medicine. However, the accuracy of commercial devices is largely unknown. The aim of this work is to assess the accuracy of seven commercially available wrist-worn devices in estimating heart rate (HR) and energy expenditure (EE) and to propose a wearable sensor evaluation framework. We evaluated the Apple Watch, Basis Peak, Fitbit Surge, Microsoft Band, Mio Alpha 2, PulseOn, and Samsung Gear S2. Participants wore devices while being simultaneously assessed with continuous telemetry and indirect calorimetry while sitting, walking, running, and cycling...
May 24, 2017: Journal of Personalized Medicine
https://www.readbyqxmd.com/read/28535831/csolnp-numerical-optimization-engine-for-solving-non-linearly-constrained-problems
#10
Mahsa Zahery, Hermine H Maes, Michael C Neale
We introduce the optimizer CSOLNP, which is a C++ implementation of the R package RSOLNP (Ghalanos & Theussl, 2012, Rsolnp: General non-linear optimization using augmented Lagrange multiplier method. R package version, 1) alongside some improvements. CSOLNP solves non-linearly constrained optimization problems using a Sequential Quadratic Programming (SQP) algorithm. CSOLNP, NPSOL (a very popular implementation of SQP method in FORTRAN (Gill et al., 1986, User's guide for NPSOL (version 4.0): A Fortran package for nonlinear programming (No...
May 24, 2017: Twin Research and Human Genetics: the Official Journal of the International Society for Twin Studies
https://www.readbyqxmd.com/read/28535296/metasra-normalized-human-sample-specific-metadata-for-the-sequence-read-archive
#11
Matthew N Bernstein, AnHai Doan, Colin N Dewey
Motivation: The NCBI's Sequence Read Archive (SRA) promises great biological insight if one could analyze the data in the aggregate; however, the data remain largely underutilized, in part, due to the poor structure of the metadata associated with each sample. The rules governing submissions to the SRA do not dictate a standardized set of terms that should be used to describe the biological samples from which the sequencing data are derived. As a result, the metadata include many synonyms, spelling variants, and references to outside sources of information...
May 23, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28533810/tc003132-is-essential-for-the-follicle-stem-cell-lineage-in-telotrophic-tribolium-oogenesis
#12
Matthias Teuscher, Nadi Ströhlein, Markus Birkenbach, Dorothea Schultheis, Michael Schoppmeier
BACKGROUND: Stem cells are undifferentiated cells with a potential for self-renewal, which are essential to support normal development and homeostasis. To gain insight into the molecular mechanisms underlying adult stem cell biology and organ evolution, we use the telotrophic ovary of the beetle Tribolium. To this end, we participated in a large-scale RNAi screen in the red flour beetle Tribolium, which identified functions in embryonic and postembryonic development for more than half of the Tribolium genes...
2017: Frontiers in Zoology
https://www.readbyqxmd.com/read/28532394/circularlogo-a-lightweight-web-application-to-visualize-intra-motif-dependencies
#13
Zhenqing Ye, Tao Ma, Michael T Kalmbach, Surendra Dasari, Jean-Pierre A Kocher, Liguo Wang
BACKGROUND: The sequence logo has been widely used to represent DNA or RNA motifs for more than three decades. Despite its intelligibility and intuitiveness, the traditional sequence logo is unable to display the intra-motif dependencies and therefore is insufficient to fully characterize nucleotide motifs. Many methods have been developed to quantify the intra-motif dependencies, but fewer tools are available for visualization. RESULT: We developed CircularLogo, a web-based interactive application, which is able to not only visualize the position-specific nucleotide consensus and diversity but also display the intra-motif dependencies...
May 22, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28531269/change-in-the-rate-of-biological-aging-in-response-to-caloric-restriction-calerie-biobank-analysis
#14
Daniel W Belsky, Kim M Huffman, Carl F Pieper, Idan Shalev, William E Kraus
Biological aging measures have been proposed as proxies for extension of healthy lifespan in trials of geroprotective therapies that aim to slow aging. Several methods to measure biological aging show promise; but it is not known if these methods are sensitive to changes caused by geroprotective therapy. We conducted analysis of two proposed methods to quantify biological aging using data from a recently concluded trial of an established geroprotector, caloric restriction. We obtained data from the National Institute on Aging CALERIE randomized trial through its public-access biobank (https://calerie...
May 22, 2017: Journals of Gerontology. Series A, Biological Sciences and Medical Sciences
https://www.readbyqxmd.com/read/28530006/kindergarten-elementary-school-teachers-and-web-based-oral-health-related-resources-an-exploration
#15
Marita Rohr Inglehart, Gabrielle A Zuzo, Joshua J Wilson
PURPOSE: The percentage of U.S. children with poor oral health continues to be high. Kindergarten/elementary school educators could play an important role in teaching students about oral health promotion. The objectives were to assess which oral health-related web-based resources teachers consider most helpful and how teachers' attitudes, knowledge, and behavioural intentions concerning oral health-related teaching change between before and after having access to a resource website. MATERIALS AND METHODS: Web-based survey data were collected from 95 kindergarten/elementary school educators before and after they accessed a website with oral health-related information for teachers (web-link: http://media...
May 19, 2017: Oral Health & Preventive Dentistry
https://www.readbyqxmd.com/read/28529706/expresso-a-database-and-web-server-for-exploring-the-interaction-of-transcription-factors-and-their-target-genes-in-arabidopsis-thaliana-using-chip-seq-peak-data
#16
Delasa Aghamirzaie, Karthik Raja Velmurugan, Shuchi Wu, Doaa Altarawy, Lenwood S Heath, Ruth Grene
Motivation: The increasing availability of chromatin immunoprecipitation sequencing (ChIP-Seq) data enables us to learn more about the action of transcription factors in the regulation of gene expression. Even though in vivo transcriptional regulation often involves the concerted action of more than one transcription factor, the format of each individual ChIP-Seq dataset usually represents the action of a single transcription factor. Therefore, a relational database in which available ChIP-Seq datasets are curated is essential...
2017: F1000Research
https://www.readbyqxmd.com/read/28529078/hcsgd-an-integrated-database-of-human-cellular-senescence-genes
#17
Qiongye Dong, Hongqing Han, Xuehui Liu, Lei Wei, Wei Zhang, Zhen Zhao, Michael Q Zhang, Xiaowo Wang
Cellular senescence is an irreversible cell cycle arrest program in response to various exogenous and endogenous stimuli like telomere dysfunction and DNA damage. It has been widely accepted as an anti-tumor program and is also found closely related to embryo development, tissue repair, organismal aging and age-related degenerative diseases. In the past decades, numerous efforts have been made to uncover the gene regulatory mechanisms of cellular senescence. There is a strong demand to integrate these data from various resources into one open platform...
April 29, 2017: Journal of Genetics and Genomics, Yi Chuan Xue Bao
https://www.readbyqxmd.com/read/28528753/healthcare-access-and-quality-index-based-on-mortality-from-causes-amenable-to-personal-health-care-in-195-countries-and-territories-1990-2015-a-novel-analysis-from-the-global-burden-of-disease-study-2015
#18
(no author information available yet)
BACKGROUND: National levels of personal health-care access and quality can be approximated by measuring mortality rates from causes that should not be fatal in the presence of effective medical care (ie, amenable mortality). Previous analyses of mortality amenable to health care only focused on high-income countries and faced several methodological challenges. In the present analysis, we use the highly standardised cause of death and risk factor estimates generated through the Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) to improve and expand the quantification of personal health-care access and quality for 195 countries and territories from 1990 to 2015...
May 18, 2017: Lancet
https://www.readbyqxmd.com/read/28525573/noreva-normalization-and-evaluation-of-ms-based-metabolomics-data
#19
Bo Li, Jing Tang, Qingxia Yang, Shuang Li, Xuejiao Cui, Yinghong Li, Yuzong Chen, Weiwei Xue, Xiaofeng Li, Feng Zhu
Diverse forms of unwanted signal variations in mass spectrometry-based metabolomics data adversely affect the accuracies of metabolic profiling. A variety of normalization methods have been developed for addressing this problem. However, their performances vary greatly and depend heavily on the nature of the studied data. Moreover, given the complexity of the actual data, it is not feasible to assess the performance of methods by single criterion. We therefore developed NOREVA to enable performance evaluation of various normalization methods from multiple perspectives...
May 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28522849/carcinopred-el-novel-models-for-predicting-the-carcinogenicity-of-chemicals-using-molecular-fingerprints-and-ensemble-learning-methods
#20
Li Zhang, Haixin Ai, Wen Chen, Zimo Yin, Huan Hu, Junfeng Zhu, Jian Zhao, Qi Zhao, Hongsheng Liu
Carcinogenicity refers to a highly toxic end point of certain chemicals, and has become an important issue in the drug development process. In this study, three novel ensemble classification models, namely Ensemble SVM, Ensemble RF, and Ensemble XGBoost, were developed to predict carcinogenicity of chemicals using seven types of molecular fingerprints and three machine learning methods based on a dataset containing 1003 diverse compounds with rat carcinogenicity. Among these three models, Ensemble XGBoost is found to be the best, giving an average accuracy of 70...
May 18, 2017: Scientific Reports
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