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https://www.readbyqxmd.com/read/29409442/semantic-annotation-of-consumer-health-questions
#1
Halil Kilicoglu, Asma Ben Abacha, Yassine Mrabet, Sonya E Shooshan, Laritza Rodriguez, Kate Masterton, Dina Demner-Fushman
BACKGROUND: Consumers increasingly use online resources for their health information needs. While current search engines can address these needs to some extent, they generally do not take into account that most health information needs are complex and can only fully be expressed in natural language. Consumer health question answering (QA) systems aim to fill this gap. A major challenge in developing consumer health QA systems is extracting relevant semantic content from the natural language questions (question understanding)...
February 6, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/29391424/large-scale-intact-glycopeptide-identification-by-mascot-database-search
#2
Ravi Chand Bollineni, Christian Jeffrey Koehler, Randi Elin Gislefoss, Jan Haug Anonsen, Bernd Thiede
Workflows capable of determining glycopeptides in large-scale are missing in the field of glycoproteomics. We present an approach for automated annotation of intact glycopeptide mass spectra. The steps in adopting the Mascot search engine for intact glycopeptide analysis included: (i) assigning one letter codes for monosaccharides, (ii) linearizing glycan sequences and (iii) preparing custom glycoprotein databases. Automated annotation of both N- and O-linked glycopeptides was proven using standard glycoproteins...
February 1, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29299837/brute-force-approach-for-mass-spectrometry-based-variant-peptide-identification-in-proteogenomics-without-personalized-genomic-data
#3
Mark V Ivanov, Anna A Lobas, Lev I Levitsky, Sergei A Moshkovskii, Mikhail V Gorshkov
In a proteogenomic approach based on tandem mass spectrometry analysis of proteolytic peptide mixtures, customized exome or RNA-seq databases are employed for identifying protein sequence variants. However, the problem of variant peptide identification without personalized genomic data is important for a variety of applications. Following the recent proposal by Chick et al. (Nat. Biotechnol. 33, 743-749, 2015) on the feasibility of such variant peptide search, we evaluated two available approaches based on the previously suggested "open" search and the "brute-force" strategy...
January 3, 2018: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/29216772/proteomic-cinderella-customized-analysis-of-bulky-ms-ms-data-in-one-night
#4
Olga Kiseleva, Ekaterina Poverennaya, Alexander Shargunov, Andrey Lisitsa
Proteomic challenges, stirred up by the advent of high-throughput technologies, produce large amount of MS data. Nowadays, the routine manual search does not satisfy the "speed" of modern science any longer. In our work, the necessity of single-thread analysis of bulky data emerged during interpretation of HepG2 proteome profiling results for proteoforms searching. We compared the contribution of each of the eight search engines (X!Tandem, MS-GF[Formula: see text], MS Amanda, MyriMatch, Comet, Tide, Andromeda, and OMSSA) integrated in an open-source graphical user interface SearchGUI ( http://searchgui...
November 13, 2017: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/29131300/engineered-scaffolds-and-cell-based-therapy-for-periodontal-regeneration
#5
Daniela Carmagnola, Mihai Tarce, Claudia Dellavia, Lia Rimondini, Elena M Varoni
BACKGROUND: The main objective of regenerative periodontal therapy is to completely restore the periodontal tissues lost. This review summarizes the most recent evidence in support of scaffold- and cell-based tissue engineering, which are expected to play a relevant role in next-generation periodontal regenerative therapy. METHODS: A literature search (PubMed database) was performed to analyze more recently updated articles regarding periodontal regeneration, scaffolds and cell-based technologies...
November 10, 2017: Journal of Applied Biomaterials & Functional Materials
https://www.readbyqxmd.com/read/29031638/dbgaps-a-comprehensive-database-of-genes-and-genetic-markers-associated-with-psoriasis-and-its-subtypes
#6
Shweta Aggarwal, Arnab Nayek, Dibyabhaba Pradhan, Rashi Verma, Monika Yadav, Kalaiarasan Ponnusamy, Arun Kumar Jain
Psoriasis is a systemic hyperproliferative inflammatory skin disorder, although rarely fatal but significantly reduces quality of life. Understanding the full genetic component of the disease association may provide insight into biological pathways as well as targets and biomarkers for diagnosis, prognosis and therapy. Studies related to psoriasis associated genes and genetic markers are scattered and not easily amendable to data-mining. To alleviate difficulties, we have developed dbGAPs an integrated knowledgebase representing a gateway to psoriasis associated genomic data...
October 12, 2017: Genomics
https://www.readbyqxmd.com/read/28969593/biocarian-search-engine-for-exploratory-searches-in-heterogeneous-biological-databases
#7
Nazar Zaki, Chandana Tennakoon
BACKGROUND: There are a large number of biological databases publicly available for scientists in the web. Also, there are many private databases generated in the course of research projects. These databases are in a wide variety of formats. Web standards have evolved in the recent times and semantic web technologies are now available to interconnect diverse and heterogeneous sources of data. Therefore, integration and querying of biological databases can be facilitated by techniques used in semantic web...
October 2, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28939228/reputation-management-and-content-control-an-analysis-of-radiation-oncologists-digital-identities
#8
Arpan V Prabhu, Christopher Kim, Eison De Guzman, Eric Zhao, Evan Madill, Jonathan Cohen, David R Hansberry, Nitin Agarwal, Dwight E Heron, Sushil Beriwal
INTRODUCTION: Google is the most popular search engine in the United States, and patients are increasingly relying on online webpages to seek information about individual physicians. This study aims to characterize what patients find when they search for radiation oncologists online. METHODS AND MATERIALS: The Centers for Medicare and Medicaid Services (CMS) Physician Comparable Downloadable File was used to identify all Medicare-participating radiation oncologists in the United States and Puerto Rico...
August 19, 2017: International Journal of Radiation Oncology, Biology, Physics
https://www.readbyqxmd.com/read/28919368/a-comparison-of-clinical-follow-up-of-different-total-temporomandibular-joint-replacement-prostheses-a-systematic-review-and-meta-analysis
#9
REVIEW
Luxiang Zou, Dongmei He, Edward Ellis
PURPOSE: There are different total temporomandibular joint (TMJ) prostheses on the market but no comparison of their efficacy. The purpose of this meta-analysis was to evaluate the effectiveness of different TMJ replacement (TJR) systems. MATERIALS AND METHODS: A systematic review and meta-analysis was performed using the PubMed, Embase, Medline, and Cochrane Library search engines in May 2017 to identify qualified studies. Outcome measurements were changes in maximal incisal opening (MIO), pain, dietary limitations, and functional deficiencies from before to after TJR...
August 24, 2017: Journal of Oral and Maxillofacial Surgery
https://www.readbyqxmd.com/read/28705213/the-therapeutic-landscape-of-hiv-1-via-genome-editing
#10
REVIEW
Alexander Kwarteng, Samuel Terkper Ahuno, Godwin Kwakye-Nuako
Current treatment for HIV-1 largely relies on chemotherapy through the administration of antiretroviral drugs. While the search for anti-HIV-1 vaccine remain elusive, the use of highly active antiretroviral therapies (HAART) have been far-reaching and has changed HIV-1 into a manageable chronic infection. There is compelling evidence, including several side-effects of ARTs, suggesting that eradication of HIV-1 cannot depend solely on antiretrovirals. Gene therapy, an expanding treatment strategy, using RNA interference (RNAi) and programmable nucleases such as meganuclease, zinc finger nuclease (ZFN), transcription activator-like effector nuclease (TALEN), and clustered regularly interspaced short palindromic repeats/CRISPR-associated proteins (CRISPR-Cas9) are transforming the therapeutic landscape of HIV-1...
July 14, 2017: AIDS Research and Therapy
https://www.readbyqxmd.com/read/28673978/unearthing-a-sesterterpene-biosynthetic-repertoire-in-the-brassicaceae-through-genome-mining-reveals-convergent-evolution
#11
Ancheng C Huang, Satria A Kautsar, Young J Hong, Marnix H Medema, Andrew D Bond, Dean J Tantillo, Anne Osbourn
Sesterterpenoids are a rare terpene class harboring untapped chemodiversity and bioactivities. Their structural diversity originates primarily from the scaffold-generating sesterterpene synthases (STSs). In fungi, all six known STSs are bifunctional, containing C-terminal trans-prenyltransferase (PT) and N-terminal terpene synthase (TPS) domains. In plants, two colocalized PT and TPS gene pairs from Arabidopsis thaliana were recently reported to synthesize sesterterpenes. However, the landscape of PT and TPS genes in plant genomes is unclear...
July 18, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28657187/an-insight-into-the-deep-web-why-it-matters-for-addiction-psychiatry
#12
Laura Orsolini, Duccio Papanti, John Corkery, Fabrizio Schifano
OBJECTIVE: Nowadays, the web is rapidly spreading, playing a significant role in the marketing or sale or distribution of "quasi" legal drugs, hence facilitating continuous changes in drug scenarios. The easily renewable and anarchic online drug-market is gradually transforming indeed the drug market itself, from a "street" to a "virtual" one, with customers being able to shop with a relative anonymity in a 24-hr marketplace. The hidden "deep web" is facilitating this phenomenon. The paper aims at providing an overview to mental health's and addiction's professionals on current knowledge about prodrug activities on the deep web...
May 2017: Human Psychopharmacology
https://www.readbyqxmd.com/read/28641282/health-related-genetic-direct-to-consumer-tests-in-the-german-setting-the-available-offer-and-the-potential-implications-for-a-solidarily-financed-health-care-system
#13
Marika Plöthner, Mike Klora, Daniel Rudolph, Johann-Matthias Graf von der Schulenburg
BACKGROUND: The global genetic direct-to-consumer (DTC) market will reach a volume of USD 230 billion in 2018. The expenditures for this genetic analysis are borne by the customer, whereas consequential costs may arise for a solidarily financed system. In a first step, it is essential to gain an overview of the currently available offer in the German setting. METHODS: In April 2016, we conducted a systematic internet search in the Google search engine. In November 2016, we updated the information of the webpages in terms of country, language, types of health-related tests, additional offer of non-health-related DTC test, information about sensitivity and specificity, certification and accreditation, costs as well as reference to German Act on Genetic Testing...
2017: Public Health Genomics
https://www.readbyqxmd.com/read/28609391/promotion-and-marketing-of-bioidentical-hormone-therapy-on-the-internet-a-content-analysis-of-websites
#14
Nese Yuksel, Laetitia Treseng, Bushra Malik, Ubaka Ogbogu
OBJECTIVE: To evaluate the quality of information presented and claims made on websites offering bioidentical hormone therapy (BHT) products or services. METHODS: A quantitative content analysis was completed on 100 websites promoting or offering BHT products or services. Websites were identified through Google search engine from September to October 2013. Search terms included "bioidentical hormone therapy" or "bioidentical progesterone," accompanied by "purchase or buy," "service," or "doctors...
October 2017: Menopause: the Journal of the North American Menopause Society
https://www.readbyqxmd.com/read/28575964/scaffolds-for-bone-tissue-engineering-state-of-the-art-and-new-perspectives
#15
REVIEW
Livia Roseti, Valentina Parisi, Mauro Petretta, Carola Cavallo, Giovanna Desando, Isabella Bartolotti, Brunella Grigolo
This review is intended to give a state of the art description of scaffold-based strategies utilized in Bone Tissue Engineering. Numerous scaffolds have been tested in the orthopedic field with the aim of improving cell viability, attachment, proliferation and homing, osteogenic differentiation, vascularization, host integration and load bearing. The main traits that characterize a scaffold suitable for bone regeneration concerning its biological requirements, structural features, composition, and types of fabrication are described in detail...
September 1, 2017: Materials Science & Engineering. C, Materials for Biological Applications
https://www.readbyqxmd.com/read/28431546/health-care-public-reporting-utilization-user-clusters-web-trails-and-usage-barriers-on-germany-s-public-reporting-portal-weisse-liste-de
#16
Christoph Pross, Lars-Henrik Averdunk, Josip Stjepanovic, Reinhard Busse, Alexander Geissler
BACKGROUND: Quality of care public reporting provides structural, process and outcome information to facilitate hospital choice and strengthen quality competition. Yet, evidence indicates that patients rarely use this information in their decision-making, due to limited awareness of the data and complex and conflicting information. While there is enthusiasm among policy makers for public reporting, clinicians and researchers doubt its overall impact. Almost no study has analyzed how users behave on public reporting portals, which information they seek out and when they abort their search...
April 21, 2017: BMC Medical Informatics and Decision Making
https://www.readbyqxmd.com/read/28317049/programming-and-runtime-support-to-blaze-fpga-accelerator-deployment-at-datacenter-scale
#17
Muhuan Huang, Di Wu, Cody Hao Yu, Zhenman Fang, Matteo Interlandi, Tyson Condie, Jason Cong
With the end of CPU core scaling due to dark silicon limitations, customized accelerators on FPGAs have gained increased attention in modern datacenters due to their lower power, high performance and energy efficiency. Evidenced by Microsoft's FPGA deployment in its Bing search engine and Intel's 16.7 billion acquisition of Altera, integrating FPGAs into datacenters is considered one of the most promising approaches to sustain future datacenter growth. However, it is quite challenging for existing big data computing systems-like Apache Spark and Hadoop-to access the performance and energy benefits of FPGA accelerators...
October 2016: Proceedings of the ... ACM Symposium on Cloud Computing [electronic Resource]: SOCC ... ... SoCC (Conference)
https://www.readbyqxmd.com/read/28314988/polymeric-micelles-as-mighty-nanocarriers-for-cancer-gene-therapy-a-review
#18
REVIEW
Mahsa Yousefpour Marzbali, Ahmad Yari Khosroushahi
PURPOSE: Gene therapy has shown extensive potential to treat human diseases occurring from the defection of genes like various types of cancers. The cationic polymers, as non-viral gene carriers, offer the ability to engineer carrier systems having customized features that can be adapted to suit any system. Upon polymeric micelle systems' core-shell structure, micelles can create the capacity to load genes/gene-drugs into the different micelle compartments, respectively. METHODS: The search will be managed in Pubmed, Medline, Cochrane library, Embase and Proquest for articles related to polymeric micelle-based gene delivery in order to cancer gene therapy using the accommodative search terms...
April 2017: Cancer Chemotherapy and Pharmacology
https://www.readbyqxmd.com/read/28231323/even-good-bots-fight-the-case-of-wikipedia
#19
Milena Tsvetkova, Ruth García-Gavilanes, Luciano Floridi, Taha Yasseri
In recent years, there has been a huge increase in the number of bots online, varying from Web crawlers for search engines, to chatbots for online customer service, spambots on social media, and content-editing bots in online collaboration communities. The online world has turned into an ecosystem of bots. However, our knowledge of how these automated agents are interacting with each other is rather poor. Bots are predictable automatons that do not have the capacity for emotions, meaning-making, creativity, and sociality and it is hence natural to expect interactions between bots to be relatively predictable and uneventful...
2017: PloS One
https://www.readbyqxmd.com/read/28145767/examining-guidelines-for-school-based-breakfast-programs-in-canada-a-systematic-review-of-the-grey-literature
#20
Katelyn M Godin, Sharon I Kirkpatrick, Rhona M Hanning, Jackie Stapleton, Scott T Leatherdale
School breakfast programs are widespread and serve varying objectives regarding youth health promotion. Evidence-based guidelines for breakfast programs may be important in maximizing their effectiveness related to student outcomes, yet it is unclear what is available in Canada. A systematic review was conducted to identify and compare Canadian guidelines related to breakfast programs. Data sources included grey literature databases, customized search engines, targeted websites, and content expert consultations...
June 1, 2017: Canadian Journal of Dietetic Practice and Research
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