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https://www.readbyqxmd.com/read/29786557/the-gene-regulatory-network-of-mesc-differentiation-a-benchmark-for-reverse-engineering-methods
#1
Johannes Meisig, Nils Blüthgen
A large body of data have accumulated that characterize the gene regulatory network of stem cells. Yet, a comprehensive and integrative understanding of this complex network is lacking. Network reverse engineering methods that use transcriptome data to derive these networks may help to uncover the topology in an unbiased way. Many methods exist that use co-expression to reconstruct networks. However, it remains unclear how these methods perform in the context of stem cell differentiation, as most systematic assessments have been made for regulatory networks of unicellular organisms...
July 5, 2018: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/29786460/counterexample-driven-genetic-programming-heuristic-program-synthesis-from-formal-specifications
#2
Iwo Błądek, Krzysztof Krawiec, Jerry Swan
Conventional genetic programming (GP) can only guarantee that synthesized programs pass tests given by the provided input-output examples. The alternative to such test-based approach is synthesizing programs by formal specification, typically realized with exact, non-heuristic algorithms. In this paper, we build on our earlier study on Counterexample-Based Genetic Programming (CDGP), an evolutionary heuristic that synthesizes programs from formal specifications. The candidate programs in CDGP undergo formal verification with a Satisfiability Modulo Theory (SMT) solver, which results in counterexamples that are subsequently turned into tests and used to calculate fitness...
May 22, 2018: Evolutionary Computation
https://www.readbyqxmd.com/read/29786430/galaxygpcrloop-template-based-and-ab-initio-structure-sampling-of-the-extracellular-loops-of-g-protein-coupled-receptors
#3
Jonghun Won, Gyu Rie Lee, Hahnbeom Park, Chaok Seok
The second extracellular loops (ECL2s) of G-protein-coupled receptors (GPCRs) are often involved in GPCR functions, and their structures have important implications in drug discovery. However, structure prediction of ECL2 is difficult because of its long length and the structural diversity among different GPCRs. In this study, a new ECL2 conformational sampling method involving both template-based and ab initio sampling was developed. Inspired by observation of similar ECL2 structures of closely related GPCRs, a template-based sampling method employing loop structure templates selected from the structure database was developed...
May 22, 2018: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/29784844/incidences-of-pseudomonas-associated-ventilator-associated-pneumonia-within-studies-of-respiratory-tract-applications-of-polymyxin-testing-the-stoutenbeek-concurrency-postulates
#4
James C Hurley
Regimens containing topical polymyxin appear highly effective at preventing Ventilator-associated pneumonia (VAP) overall and more-so, gram negative VAP. However, Soutenbeek's postulates, that VAP incidences within studies of topical antibiotics would depend on the context of whether the component (control and intervention) groups of each study were concurrent versus non-concurrent, remain untested.The literature was searched for concurrent control (CC) versus non-concurrent control (NCC) designed studies of respiratory tract applications of topical polymyxin to mechanically ventilated (MV) patients that reported Pseudomonas associated Ventilator-associated pneumonia (PsVAP) incidences...
May 21, 2018: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/29782930/all-atom-four-body-knowledge-based-statistical-potential-to-distinguish-native-tertiary-rna-structures-from-nonnative-folds
#5
Majid Masso
Scientific breakthroughs in recent decades have uncovered the capability of RNA molecules to fulfill a wide array of structural, functional, and regulatory roles in living cells, leading to a concomitantly significant increase in both the number and diversity of experimentally determined RNA three-dimensional (3D) structures. Atomic coordinates from a representative training set of solved RNA structures, displaying low sequence and structure similarity, facilitate derivation of knowledge-based energy functions...
May 18, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/29782796/resolution-measurement-from-a-single-reconstructed-cryo-em-density-map-with-multi-scale-spectral-analysis
#6
Yu-Jiao Yang, Shuai Wang, Biao Zhang, Hong-Bin Shen
As a relatively new technology to solve the 3D structure of a protein or protein complex, the Single-Particle Reconstruction (SPR) of cryo-EM images shows much superiority and is in a rapidly developing stage. Resolution measurement in SPR, which evaluates the quality of a reconstructed 3D density map, plays a critical role for promoting methodology development of SPR and structural biology. Due to there is no benchmark map in a new structure generation, how to realize the resolution estimation of a new map is still an open problem...
May 21, 2018: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/29782536/fungal-type-carbohydrate-binding-modules-from-the-coccolithophore-emiliania-huxleyi-show-binding-affinity-to-cellulose-and-chitin
#7
Bart J M Rooijakkers, Martina S Ikonen, Markus B Linder
Six fungal-type cellulose binding domains were found in the genome of the coccolithophore Emiliania huxleyi and cloned and expressed in Escherichia coli. Sequence comparison indicate high similarity to fungal cellulose binding domains, raising the question of why these domains exist in coccolithophores. The proteins were tested for binding with cellulose and chitin as ligands, which resulted in the identification of two functional carbohydrate binding modules: EHUX2 and EHUX4. Compared to benchmark fungal cellulose binding domain Cel7A-CBM1 from Trichoderma reesei, these proteins showed slightly lower binding to birch and bacterial cellulose, but were more efficient chitin binders...
2018: PloS One
https://www.readbyqxmd.com/read/29782491/community-based-benchmarking-improves-spike-rate-inference-from-two-photon-calcium-imaging-data
#8
Philipp Berens, Jeremy Freeman, Thomas Deneux, Nicolay Chenkov, Thomas McColgan, Artur Speiser, Jakob H Macke, Srinivas C Turaga, Patrick Mineault, Peter Rupprecht, Stephan Gerhard, Rainer W Friedrich, Johannes Friedrich, Liam Paninski, Marius Pachitariu, Kenneth D Harris, Ben Bolte, Timothy A Machado, Dario Ringach, Jasmine Stone, Luke E Rogerson, Nicolas J Sofroniew, Jacob Reimer, Emmanouil Froudarakis, Thomas Euler, Miroslav Román Rosón, Lucas Theis, Andreas S Tolias, Matthias Bethge
In recent years, two-photon calcium imaging has become a standard tool to probe the function of neural circuits and to study computations in neuronal populations. However, the acquired signal is only an indirect measurement of neural activity due to the comparatively slow dynamics of fluorescent calcium indicators. Different algorithms for estimating spike rates from noisy calcium measurements have been proposed in the past, but it is an open question how far performance can be improved. Here, we report the results of the spikefinder challenge, launched to catalyze the development of new spike rate inference algorithms through crowd-sourcing...
May 21, 2018: PLoS Computational Biology
https://www.readbyqxmd.com/read/29781821/basic-science-and-clinical-application-of-reamed-sources-for-autogenous-bone-graft-harvest
#9
Thomas F Higgins, Lucas S Marchand
Autologous bone graft remains the only clinically available source of graft material with osteogenic, osteoinductive, and osteoconductive properties. Although iliac crest autologous bone graft has long served as the benchmark, reamed autogenous bone graft offers several advantages. Reamed autograft has a biochemical and cellular profile that is at least equivalent, and perhaps superior, to that of iliac crest autograft. In addition, larger volumes of reamed autograft can be obtained via less-invasive techniques, giving surgeons an accessible source of mesenchymal stem cells that can be reliably and repeatedly harvested...
May 16, 2018: Journal of the American Academy of Orthopaedic Surgeons
https://www.readbyqxmd.com/read/29781362/the-era-of-the-large-databases-outcomes-after-gastroesophageal-surgery-according-to-nsqip-nis-and-ncdb-databases-systematic-literature-review
#10
Gabriela Batista Rodríguez, Andrea Balla, Sonia Fernández-Ananín, Carmen Balagué, Eduard M Targarona
BACKGROUND: The term big data refers to databases that include large amounts of information used in various areas of knowledge. Currently, there are large databases that allow the evaluation of postoperative evolution, such as the American College of Surgeons National Surgical Quality Improvement Program (ACS-NSQIP), the Healthcare Cost and Utilization Project (HCUP) National Inpatient Sample (NIS), and the National Cancer Database (NCDB). The aim of this review was to evaluate the clinical impact of information obtained from these registries regarding gastroesophageal surgery...
May 1, 2018: Surgical Innovation
https://www.readbyqxmd.com/read/29780432/-in-silico-toxicology-comprehensive-benchmarking-of-multi-label-classification-methods-applied-to-chemical-toxicity-data
#11
REVIEW
Arwa B Raies, Vladimir B Bajic
One goal of toxicity testing, among others, is identifying harmful effects of chemicals. Given the high demand for toxicity tests, it is necessary to conduct these tests for multiple toxicity endpoints for the same compound. Current computational toxicology methods aim at developing models mainly to predict a single toxicity endpoint. When chemicals cause several toxicity effects, one model is generated to predict toxicity for each endpoint, which can be labor and computationally intensive when the number of toxicity endpoints is large...
May 2018: Wiley Interdisciplinary Reviews. Computational Molecular Science
https://www.readbyqxmd.com/read/29780043/-propose-for-the-benchmark-dose-bd-for-the-optimization-of-protection-in-medical-exposure-in-general-radiography
#12
Hiroshi Watanabe, Masashi Seki, Masahiro Nitta, Itsuki Serita, Yoshiaki Maehara, Hideaki Okura, Tomofumi Murakami, Kazuyuki Yamamoto, Tsutomu Sato, Ryuto Tajima
The goal of this research was to create the most appropriate index dose for the optimization of protection in medical exposure in general radiography in Kanagawa prefecture. We distributed questionnaires to 272 medical institutions in Kanagawa prefecture. The investigation period was from October 2015 to February 2016. Entrance surface dose (ESD) was used as the index dose. Investigated regions in general radiography were the adult chest, adult abdomen, and infant chest (anterior-posterior projections for all regions)...
2018: Nihon Hoshasen Gijutsu Gakkai Zasshi
https://www.readbyqxmd.com/read/29779891/fixation-and-spread-of-somatic-mutations-in-adult-human-colonic-epithelium
#13
Anna M Nicholson, Cora Olpe, Alice Hoyle, Ann-Sofie Thorsen, Teja Rus, Mathilde Colombé, Roxanne Brunton-Sim, Richard Kemp, Kate Marks, Phil Quirke, Shalini Malhotra, Rogier Ten Hoopen, Ashraf Ibrahim, Cecilia Lindskog, Meagan B Myers, Barbara Parsons, Simon Tavaré, Mark Wilkinson, Edward Morrissey, Douglas J Winton
We investigated the means and timing by which mutations become fixed in the human colonic epithelium by visualizing somatic clones and mathematical inference. Fixation requires two sequential steps. First, one of approximately seven active stem cells residing within each colonic crypt has to be mutated. Second, the mutated stem cell has to replace neighbors to populate the entire crypt in a process that takes several years. Subsequent clonal expansion due to crypt fission is infrequent for neutral mutations (around 0...
May 11, 2018: Cell Stem Cell
https://www.readbyqxmd.com/read/29779683/strabismus-strabismus-surgery-and-reoperation-rate-in-the-united-states-analysis-from-the-iris-registry
#14
Michael X Repka, Flora Lum, Bhavya Burugapalli
PURPOSE: To describe the rates of strabismus, strabismus surgery, and strabismus surgery reoperations among all age groups in the United States. DESIGN: Retrospective analysis of electronic health record data. PARTICIPANTS: Patients from the IRIS (Intelligent Research in Sight) Registry. METHODS: Description of the types and rates of strabismus and strabismus surgery from 2013 to 2016 with subgroups by age, sex, race/ethnicity, and region of the United States...
May 17, 2018: Ophthalmology
https://www.readbyqxmd.com/read/29778434/implementation-of-multimodal-infection-control-and-hand-hygiene-strategies-in-acute-care-hospitals-in-greece-a-cross-sectional-benchmarking-survey
#15
Evangelos I Kritsotakis, Eirini Astrinaki, Argyri Messaritaki, Achilleas Gikas
BACKGROUND: In this first attempt to suggest achievable standards for improvement in hospital infection prevention and control (IPC) in Greece, we assessed main IPC structure and process indicators emphasizing hand hygiene. METHODS: Acute-care hospitals across the country participated in a cross-sectional survey by completing the World Health Organization Hand Hygiene Self-assessment Framework (HHSAF) and by providing hospital-level IPC indicators. RESULTS: Seventeen hospitals completed the survey, comprising 14% of the country's public hospitals...
May 16, 2018: American Journal of Infection Control
https://www.readbyqxmd.com/read/29778066/transport-of-trace-organic-compounds-through-novel-forward-osmosis-membranes-role-of-membrane-properties-and-the-draw-solution
#16
Marc Sauchelli, Giuseppe Pellegrino, Arnout D'Haese, Ignasi Rodríguez-Roda, Wolfgang Gernjak
Forward osmosis (FO) offers to be a very promising technology for the removal of trace organic compounds (TrOCs) from contaminated wastewater, and with the recent developments in FO membranes, the effect of both a higher water flux and reverse salt flux on the rejection of TrOCs needs to be explored. In this study two novel thin-film composite (TFC) membranes with greater water permeability and selectivity than the benchmark cellulose tri-acetate (CTA) membrane were compared at bench-scale in terms of TrOCs permeability...
May 5, 2018: Water Research
https://www.readbyqxmd.com/read/29777986/predicting-of-the-refractive-index-of-haemoglobin-using-the-hybrid-ga-svr-approach
#17
Tajudeen A Oyehan, Ibrahim O Alade, Aliyu Bagudu, Kazeem O Sulaiman, Sunday O Olatunji, Tawfik A Saleh
The optical properties of blood play crucial roles in medical diagnostics and treatment, and in the design of new medical devices. Haemoglobin is a vital constituent of the blood whose optical properties affect all of the optical properties of human blood. The refractive index of haemoglobin has been reported to strongly depend on its concentration which is a function of the physiology of biological cells. This makes the refractive index of haemoglobin an essential non-invasive bio-marker of diseases. Unfortunately, the complexity of blood tissue makes it challenging to experimentally measure the refractive index of haemoglobin...
April 30, 2018: Computers in Biology and Medicine
https://www.readbyqxmd.com/read/29777595/a-ring-based-compensator-imrt-system-optimized-for-low-and-middle-income-countries-design-and-treatment-planning-study
#18
Jonathon Van Schelt, Daniel Smith, Nicholas Fong, Dolla Toomeh, Patricia A Sponseller, Derek W Brown, Meghan W Macomber, Nina A Mayr, Shilpen Patel, Adam Shulman, G V Subrahmanyam, K Govindarajan, Eric C Ford
PURPOSE: We propose a novel compensator-based IMRT system designed to provide a simple, reliable, and cost-effective adjunct technology, with the goal of expanding global access to advanced radiotherapy techniques. The system would employ easily-reusable tungsten bead compensators that operate independent of a gantry (e.g. mounted in a ring around the patient). Thereby the system can be retrofitted to existing linac and cobalt teletherapy units. This study explores the quality of treatment plans from the proposed system and the dependence on associated design parameters...
May 19, 2018: Medical Physics
https://www.readbyqxmd.com/read/29776590/batch-process-fault-detection-and-identification-based-on-discriminant-global-preserving-kernel-slow-feature-analysis
#19
Hanyuan Zhang, Xuemin Tian, Xiaogang Deng, Yuping Cao
As an attractive nonlinear dynamic data analysis tool, global preserving kernel slow feature analysis (GKSFA) has achieved great success in extracting the high nonlinearity and inherently time-varying dynamics of batch process. However, GKSFA is an unsupervised feature extraction method and lacks the ability to utilize batch process class label information, which may not offer the most effective means for dealing with batch process monitoring. To overcome this problem, we propose a novel batch process monitoring method based on the modified GKSFA, referred to as discriminant global preserving kernel slow feature analysis (DGKSFA), by closely integrating discriminant analysis and GKSFA...
May 16, 2018: ISA Transactions
https://www.readbyqxmd.com/read/29776137/numerical-simulation-of-three-component-multiphase-flows-at-high-density-and-viscosity-ratios-using-lattice-boltzmann-methods
#20
Reza Haghani Hassan Abadi, Abbas Fakhari, Mohammad Hassan Rahimian
In this paper, we propose a multiphase lattice Boltzmann model for numerical simulation of ternary flows at high density and viscosity ratios free from spurious velocities. The proposed scheme, which is based on the phase-field modeling, employs the Cahn-Hilliard theory to track the interfaces among three different fluid components. Several benchmarks, such as the spreading of a liquid lens, binary droplets, and head-on collision of two droplets in binary- and ternary-fluid systems, are conducted to assess the reliability and accuracy of the model...
March 2018: Physical Review. E
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