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Deep Web

Ilia Korvigo, Andrey Afanasyev, Nikolay Romashchenko, Mikhail Skoblov
Many automatic classifiers were introduced to aid inference of phenotypical effects of uncategorised nsSNVs (nonsynonymous Single Nucleotide Variations) in theoretical and medical applications. Lately, several meta-estimators have been proposed that combine different predictors, such as PolyPhen and SIFT, to integrate more information in a single score. Although many advances have been made in feature design and machine learning algorithms used, the shortage of high-quality reference data along with the bias towards intensively studied in vitro models call for improved generalisation ability in order to further increase classification accuracy and handle records with insufficient data...
2018: PloS One
Christien P Laber, Jonathan E Hunter, Filipa Carvalho, James R Collins, Elias J Hunter, Brittany M Schieler, Emmanuel Boss, Kuldeep More, Miguel Frada, Kimberlee Thamatrakoln, Christopher M Brown, Liti Haramaty, Justin Ossolinski, Helen Fredricks, Jozef I Nissimov, Rebecca Vandzura, Uri Sheyn, Yoav Lehahn, Robert J Chant, Ana M Martins, Marco J L Coolen, Assaf Vardi, Giacomo R DiTullio, Benjamin A S Van Mooy, Kay D Bidle
Marine phytoplankton account for approximately half of global primary productivity1 , making their fate an important driver of the marine carbon cycle. Viruses are thought to recycle more than one-quarter of oceanic photosynthetically fixed organic carbon2 , which can stimulate nutrient regeneration, primary production and upper ocean respiration2 via lytic infection and the 'virus shunt'. Ultimately, this limits the trophic transfer of carbon and energy to both higher food webs and the deep ocean2 . Using imagery taken by the Moderate Resolution Imaging Spectroradiometer (MODIS) onboard the Aqua satellite, along with a suite of diagnostic lipid- and gene-based molecular biomarkers, in situ optical sensors and sediment traps, we show that Coccolithovirus infections of mesoscale (~100 km) Emiliania huxleyi blooms in the North Atlantic are coupled with particle aggregation, high zooplankton grazing and greater downward vertical fluxes of both particulate organic and particulate inorganic carbon from the upper mixed layer...
March 12, 2018: Nature Microbiology
Ian M MacDonald, Pamela C Sieving
PURPOSE: To review the contributions to ophthalmic genetics through the American Journal of OphthalmologyDesign: Perspective. METHODS: A literature search to retrieve original articles, letters, editorials, and published lectures from 1966 to 2017, providing a 50 year review. Titles were excluded that gave no reference to genetics or presented findings related to a non-genetic ocular condition. RESULTS: From a search of the Scopus database, 719 articles were ascertained...
March 9, 2018: American Journal of Ophthalmology
Juan Ruano, Francisco Gómez-García, Jesús Gay-Mimbrera, Macarena Aguilar-Luque, José Luis Fernández-Rueda, Jesús Fernández-Chaichio, Patricia Alcalde-Mellado, Pedro J Carmona-Fernandez, Juan Luis Sanz-Cabanillas, Isabel Viguera-Guerra, Francisco Franco-García, Manuel Cárdenas-Aranzana, José Luis Hernández Romero, Marcelino Gonzalez-Padilla, Beatriz Isla-Tejera, Antonio Velez Garcia-Nieto
BACKGROUND: Epidemiology and the reporting characteristics of systematic reviews (SRs) and meta-analyses (MAs) are well known. However, no study has analyzed the influence of protocol features on the probability that a study's results will be finally reported, thereby indirectly assessing the reporting bias of International Prospective Register of Systematic Reviews (PROSPERO) registration records. OBJECTIVE: The objective of this study is to explore which factors are associated with a higher probability that results derived from a non-Cochrane PROSPERO registration record for a systematic review will be finally reported as an original article in a scientific journal...
March 9, 2018: Systematic Reviews
Tomoyasu Tachibana, Shin Kariya, Yorihisa Orita, Michihiro Nakada, Takuma Makino, Yasutoshi Komatsubara, Yuko Matsuyama, Yuto Naoi, Kazunori Nishizaki
OBJECTIVES: We reviewed surgical results of canal wall-down tympanoplasty (CWDT) with soft posterior meatal wall reconstruction (SWR) for acquired cholesteatoma (AC), and identified factors associated with surgical outcomes. METHODS: Results from 119 ears with AC (pars flaccida, n = 99; pars tensa, n = 20) that underwent CWDT with SWR were retrospectively reviewed. We defined postoperative balloon-like retraction (PBR) with web formation, which needed reoperation to clean accumulated cerumen, as postoperative deep retraction pocket (PDRP)...
March 8, 2018: Acta Oto-laryngologica
Andrew Adams, Carilynne Yarascavitch, Carlos Quiñonez, Amir Azarpazhooh
OBJECTIVE: This study aims to assess barriers to the use of deep sedation/general anesthesia (DS/GA) identified by dentists in Ontario. METHODS: An email invitation to a web-based survey was distributed to all licensed dentists and specialists who have provided an email address to the provincial regulator (n = 5507). Descriptive and regression analyses were performed to explore practice and demographic factors associated with the use of DS/GA. RESULTS: The response rate was 18...
July 2017: Journal—Canadian Dental Association, Journal de L'Association Dentaire Canadienne
Nan Jiang, Gui-Qiu Zhao, Jing Lin, Li-Ting Hu, Cheng-Ye Che, Qian Wang, Qiang Xu, Cui Li, Jie Zhang
AIM: To conduct a systematic review and quantitative Meta-analysis of the efficacy and safety of combined surgery for the eyes with coexisting cataract and open angle glaucoma. METHODS: We performed a systematic search of the related literature in the Cochrane Library, PubMed, EMBASE, Web of Science databases, CNKI, CBM and Wan Fang databases, with no limitations on language or publication date. The primary efficacy estimate was identified by weighted mean difference of the percentage of intraocular pressure reduction (IOPR%) from baseline to end-point, the percentage of number of glaucoma medications reduction from pre- to post-operation, and the secondary efficacy evaluations were performed by odds ratio (OR) and 95% confidence interval (CI) for complete and qualified success rate...
2018: International Journal of Ophthalmology
Saad Ahmed Alkahtani, Pramod S Kunwar, Mostafa Jalilifar, Samaneh Rashidi, Ali Yadollahpour
Ultrasound (US) waves have been recently developed for the treatment of different chronic wounds with promising therapeutic outcomes. However, the clinical efficacy of these techniques is still not fully understood and standard guidelines on dose ranges and possible side effects should be determined. This paper aims to comprehensively review the recent advances in US techniques for chronic wound treatment, their therapeutic efficacies, and clinical considerations and challenges. The databases of PubMed (1985-2017), EMBASE (1985-2017), Web of Sciences (1985-2017), Cochrane central library (1990-2017), and Google Scholar (1980-2017) were searched using the set terms...
December 15, 2017: Curēus
César Domínguez, Jónathan Heras, Eloy Mata, Vico Pascual
BACKGROUND: Fungi have diverse biotechnological applications in, among others, agriculture, bioenergy generation, or remediation of polluted soil and water. In this context, culture media based on color change in response to degradation of dyes are particularly relevant; but measuring dye decolorisation of fungal strains mainly relies on a visual and semiquantitative classification of color intensity changes. Such a classification is a subjective, time-consuming and difficult to reproduce process...
February 27, 2018: BMC Bioinformatics
Stephen A Jackson, Lisa Crossman, Eduardo L Almeida, Lekha Menon Margassery, Jonathan Kennedy, Alan D W Dobson
The genus Streptomyces produces secondary metabolic compounds that are rich in biological activity. Many of these compounds are genetically encoded by large secondary metabolism biosynthetic gene clusters (smBGCs) such as polyketide synthases (PKS) and non-ribosomal peptide synthetases (NRPS) which are modular and can be highly repetitive. Due to the repeats, these gene clusters can be difficult to resolve using short read next generation datasets and are often quite poorly predicted using standard approaches...
February 20, 2018: Marine Drugs
Roongroj Bhidayasiri, Onanong Jitkritsadakul, Joseph H Friedman, Stanley Fahn
BACKGROUND: Management of tardive syndromes (TS) is challenging, with only a few evidence-based therapeutic algorithms reported in the American Academy of Neurology (AAN) guideline in 2013. OBJECTIVE: To update the evidence-based recommendations and provide a practical treatment algorithm for management of TS by addressing 5 questions: 1) Is withdrawal of dopamine receptor blocking agents (DRBAs) an effective TS treatment? 2) Does switching from typical to atypical DRBAs reduce TS symptoms? 3) What is the efficacy of pharmacologic agents in treating TS? 4) Do patients with TS benefit from chemodenervation with botulinum toxin? 5) Do patients with TS benefit from surgical therapy? METHODS: Systematic reviews were conducted by searching PsycINFO, Ovid MEDLINE, PubMed, EMBASE, Web of Science and Cochrane for articles published between 2012 and 2017 to identify new evidence published after the 2013 AAN guidelines...
February 5, 2018: Journal of the Neurological Sciences
Thomas W Carver
OBJECTIVE: Surgical critical care (SCC) fellows are expected to receive training in critical care ultrasound (CCUS) but training is sporadic and there is no standardized curriculum to guide educators. Previous studies show wide variation in CCUS training during fellowship across specialties but SCC has been underrepresented. This study was performed to assess SCC program directors' views regarding CCUS during fellowship training. DESIGN: Adult SCC program directors were surveyed regarding the role of CCUS in fellowship training...
February 12, 2018: Journal of Surgical Education
Raza-Ur Rahman, Abhivyakti Gautam, Jörn Bethune, Abdul Sattar, Maksims Fiosins, Daniel Sumner Magruder, Vincenzo Capece, Orr Shomroni, Stefan Bonn
BACKGROUND: Small RNA molecules play important roles in many biological processes and their dysregulation or dysfunction can cause disease. The current method of choice for genome-wide sRNA expression profiling is deep sequencing. RESULTS: Here we present Oasis 2, which is a new main release of the Oasis web application for the detection, differential expression, and classification of small RNAs in deep sequencing data. Compared to its predecessor Oasis, Oasis 2 features a novel and speed-optimized sRNA detection module that supports the identification of small RNAs in any organism with higher accuracy...
February 14, 2018: BMC Bioinformatics
Peng Xiu, Fei Chai, Enrique N Curchitser, Frederic S Castruccio
Coastal upwelling ecosystems are among the most productive ecosystems in the world, meaning that their response to climate change is of critical importance. Our understanding of climate change impacts on marine ecosystems is largely limited to the open ocean, mainly because coastal upwelling is poorly reproduced by current earth system models. Here, a high-resolution model is used to examine the response of nutrients and plankton dynamics to future climate change in the California Current System (CCS). The results show increased upwelling intensity associated with stronger alongshore winds in the coastal region, and enhanced upper-ocean stratification in both the CCS and open ocean...
February 12, 2018: Scientific Reports
Jiansheng Wu, Qiuming Zhang, Weijian Wu, Tao Pang, Haifeng Hu, Wallace K B Chan, Xiaoyan Ke, Yang Zhang, Jonathan Wren
Motivation: Precise assessment of ligand bioactivities (including IC50, EC50, Ki, Kd, etc.) is essential for virtual screening and lead compound identification. However, not all ligands have experimentally-determined activities. In particular, many G protein-coupled receptors (GPCRs), which are the largest integral membrane protein family and represent targets of nearly 40% drugs on the market, lack published experimental data about ligand interactions. Computational methods with the ability to accurately predict the bioactivity of ligands can help efficiently address this problem...
February 8, 2018: Bioinformatics
Yadong Shi, Wanyin Shi, Liang Chen, Jianping Gu
To review the clinical evidence for ultrasound-accelerated catheter-directed thrombolysis (UACDT) using the EKOS system in the treatment of deep vein thrombosis (DVT) in terms of case selection, procedural outcomes, clinical outcomes and safety outcomes. A systematic literature search strategy was used to identify the use of the EKOS system in the treatment of DVT using the following electronic databases: MEDLINE, EMBASE, the Cochrane databases and the Web of Science. The references in the relevant literature were also screened...
February 7, 2018: Journal of Thrombosis and Thrombolysis
Lele Liao, You Chen, Qi Tang, Yi-Yue Chen, Wan-Chun Wang
BACKGROUND: The efficacy of tranexamic acid (TXA) plus drain-clamping in reducing blood loss after total knee arthroplasty (TKA) is controversial. This meta-analysis aimed to identify whether combined tranexamic acid and drain-clamping was superior to TXA alone, drain clamping alone and control treatments. METHODS: We searched the PubMed, EMBASE, Web of Science and Google databases and the Cochrane Database of Systematic Reviews. Patients prepared for primary TKA and who underwent TXA plus drain-clamping for blood loss were included in this meta-analysis...
February 3, 2018: International Journal of Surgery
Violetta La Cono, Gioachino Ruggeri, Maurizio Azzaro, Francesca Crisafi, Franco Decembrini, Renata Denaro, Gina La Spada, Giovanna Maimone, Luis S Monticelli, Francesco Smedile, Laura Giuliano, Michail M Yakimov
Covering two-thirds of our planet, the global deep ocean plays a central role in supporting life on Earth. Among other processes, this biggest ecosystem buffers the rise of atmospheric CO2. Despite carbon sequestration in the deep ocean has been known for a long time, microbial activity in the meso- and bathypelagic realm via the "assimilation of bicarbonate in the dark" (ABD) has only recently been described in more details. Based on recent findings, this process seems primarily the result of chemosynthetic and anaplerotic reactions driven by different groups of deep-sea prokaryoplankton...
2018: Frontiers in Microbiology
Judith C Lin, Janelle M Crutchfield, Dana K Zurawski, Courtney Stevens
OBJECTIVE: Using secured videoconferencing technologies, telemedicine may replace traditional clinic visits, save patients' time and travel, and improve use of limited surgeon and facility resources. We report our initial experience of the remote clinical encounter (RCE) by evaluating vascular surgery patients. METHODS: In this proof-of-concept pilot study, we conducted telemedicine evaluations of vascular patients at a tertiary care institution from October 2015 to August 2016...
February 1, 2018: Journal of Vascular Surgery
M Akdeniz, T Tomova-Simitchieva, G Dobos, U Blume-Peytavi, J Kottner
BACKGROUND: Associations between daily amounts of drinking water and skin hydration and skin physiology receive increasingly attention in the daily life and in clinical practice. However, there is a lack of evidence of dermatological benefits from drinking increased amounts of water. MATERIALS AND METHODS: Pubmed and Web of Science were searched without any restrictions of publication dates. References of included papers and related reviews were checked. Eligibility criteria were primary intervention and observational studies investigating the effects of fluid intake on skin properties in English, German, Spanish or Portuguese language, including subjects being healthy and 18+ years...
February 2, 2018: Skin Research and Technology
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