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Feature engineering

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https://www.readbyqxmd.com/read/28432128/do-the-microbiota-influence-vaccines-and-protective-immunity-to-pathogens-issues-of-sovereignty-federalism-and-points-testing-in-the-prokaryotic-and-eukaryotic-spaces-of-the-host-microbial-superorganism
#1
Andrew J Macpherson
In contrast to live attenuated vaccines, which are designed to induce immunity through a time-limited bloom in systemic tissues, the microbiota is a persistent feature of body surfaces, especially the intestine. The immune responses to the microbiota are idiosyncratic depending on the niche intimacy of different taxa and generally adapt the host to avoid overgrowth and maintain mutualism rather than to eliminate the organisms of that taxon. Both the microbiota and the host have so much molecular cross talk controlling each other, that the prokaryotic and the eukaryotic spaces of the host-microbial superorganism are federal rather than sovereign...
April 21, 2017: Cold Spring Harbor Perspectives in Biology
https://www.readbyqxmd.com/read/28432038/seeking-web-based-information-about-attention-deficit-hyperactivity-disorder-where-what-and-when
#2
Sara Rosenblum, Elad Yom-Tov
BACKGROUND: Attention Deficit Hyperactivity Disorder (ADHD) is a common neurodevelopmental disorder, prevalent among 2-10% of the population. OBJECTIVE: The objective of this study was to describe where, what, and when people search online for topics related to ADHD. METHODS: Data were collected from Microsoft's Bing search engine and from the community question and answer site, Yahoo Answers. The questions were analyzed based on keywords and using further statistical methods...
April 21, 2017: Journal of Medical Internet Research
https://www.readbyqxmd.com/read/28430426/the-rosetta-all-atom-energy-function-for-macromolecular-modeling-and-design
#3
Rebecca Faye Alford, Andrew Leaver-Fay, Jeliazko R Jeliazkov, Matthew J O'Meara, Frank P DiMaio, Hahnbeom Park, Maxim V Shapovalov, P Douglas Renfrew, Vikram Khipple Mulligan, Kalli Kappel, Jason W Labonte, Michael Steven Pacella, Richard Bonneau, Philip Bradley, Roland L Dunbrack, Rhiju Das, David Baker, Brian Kuhlman, Tanja Kortemme, Jeffrey J Gray
Over the past decade, the Rosetta biomolecular modeling suite has informed diverse biological questions and engineering challenges ranging from interpretation of low-resolution structural data to design of nanomaterials, protein therapeutics, and vaccines. Central to Rosetta's success is the energy function: a model parameterized from small molecule and X-ray crystal structure data used to approximate the energy associated with each biomolecule conformation. This paper describes the mathematical models and physical concepts that underlie the latest Rosetta Energy Function, REF15...
April 21, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28429845/following-nature-s-roadmap-folding-factors-from-plasma-cells-led-to-improvements-in-antibody-secretion-in-s-cerevisiae
#4
Essi V Koskela, Jorg C de Ruijter, Alexander D Frey
Therapeutic protein production in yeast is a reality in industry with an untapped potential to expand to more complex proteins, such as full-length antibodies. Despite multiple numerous engineering approaches, cellular limitations are preventing the use of Saccharomyces cerevisiae as the titers of recombinant antibodies are currently not competitive. Instead of a host specific approach, we demonstrate the possibility of adopting the features from native producers of antibodies, plasma cells, to improve antibody production in yeast...
April 21, 2017: Biotechnology Journal
https://www.readbyqxmd.com/read/28427327/analysis-of-transcriptome-data-reveals-multifactor-constraint-on-codon-usage-in-taenia-multiceps
#5
Xing Huang, Jing Xu, Lin Chen, Yu Wang, Xiaobin Gu, Xuerong Peng, Guangyou Yang
BACKGROUND: Codon usage bias (CUB) is an important evolutionary feature in genomes that has been widely observed in many organisms. However, the synonymous codon usage pattern in the genome of T. multiceps remains to be clarified. In this study, we analyzed the codon usage of T. multiceps based on the transcriptome data to reveal the constraint factors and to gain an improved understanding of the mechanisms that shape synonymous CUB. RESULTS: Analysis of a total of 8,620 annotated mRNA sequences from T...
April 20, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28426134/metastasis-detection-from-whole-slide-images-using-local-features-and-random-forests
#6
Mira Valkonen, Kimmo Kartasalo, Kaisa Liimatainen, Matti Nykter, Leena Latonen, Pekka Ruusuvuori
Digital pathology has led to a demand for automated detection of regions of interest, such as cancerous tissue, from scanned whole slide images. With accurate methods using image analysis and machine learning, significant speed-up, and savings in costs through increased throughput in histological assessment could be achieved. This article describes a machine learning approach for detection of cancerous tissue from scanned whole slide images. Our method is based on feature engineering and supervised learning with a random forest model...
April 20, 2017: Cytometry. Part A: the Journal of the International Society for Analytical Cytology
https://www.readbyqxmd.com/read/28423779/fast-and-efficient-feature-engineering-for-multi-cohort-analysis-of-ehr-data
#7
Michal Ozery-Flato, Chen Yanover, Assaf Gottlieb, Omer Weissbrod, Naama Parush Shear-Yashuv, Yaara Goldschmidt
We present a framework for feature engineering, tailored for longitudinal structured data, such as electronic health records (EHRs). To fast-track feature engineering and extraction, the framework combines general-use plug-in extractors, a multi-cohort management mechanism, and modular memoization. Using this framework, we rapidly extracted thousands of features from diverse and large healthcare data sources in multiple projects.
2017: Studies in Health Technology and Informatics
https://www.readbyqxmd.com/read/28423767/querying-ehrs-with-a-semantic-and-entity-oriented-query-language
#8
Romain Lelong, Lina Soualmia, Badisse Dahamna, Nicolas Griffon, Stéfan J Darmoni
While the digitization of medical documents has greatly expanded during the past decade, health information retrieval has become a great challenge to address many issues in medical research. Information retrieval in electronic health records (EHR) should also reduce the difficult tasks of manual information retrieval from records in paper format or computer. The aim of this article was to present the features of a semantic search engine implemented in EHRs. A flexible, scalable and entity-oriented query language tool is proposed...
2017: Studies in Health Technology and Informatics
https://www.readbyqxmd.com/read/28423276/supramolecular-%C3%AE-sheets-stabilized-protein-nanocarriers-for-drug-delivery-and-gene-transfection
#9
Yuan Ping, Dawei Ding, Ricardo Almeida Neves Sampayo Ramos, Harini Mohanram, Kanagavel Deepankumar, Jianqing Gao, Guping Tang, Ali Miserez
Suckerin proteins, recently discovered in the sucker ring teeth of squids, represent a family of promising structural biomacromolecules that can form supramolecular networks stabilized by nanoconfined β-sheets. Exploiting this feature as well as their specific amino acid composition, we demonstrate that artificial suckerin-19 (S-19) can be engineered into nanocarriers for efficient drug delivery and gene transfection in vitro and in vivo. First, we demonstrated that S-19 is self-assembled into β-sheet stabilized nanoparticles with controlled particle sizes of 100-200 nm that are able to encapsulate hydrophobic drugs for pH-dependent release in vitro, and that could effectively inhibit tumor growth in vivo...
April 19, 2017: ACS Nano
https://www.readbyqxmd.com/read/28419941/pamam-generation-4-incorporated-gelatin-3d-matrix-as-an-improved-dermal-substitute-for-skin-tissue-engineering
#10
Somnath Maji, Tarun Agarwal, Tapas Kumar Maiti
The study explored the prospects of PAMAM (generation 4) applicability in gelatin based scaffolds for skin tissue engineering. The effect of PAMAM on physico-chemical and biological characteristics of gelatin scaffolds was evaluated. Gelatin scaffolds (with/without PAMAM) were prepared by lyophilization, chemically crosslinked by glutaraldehyde and characterized for their morphology (pore size), chemical features (bond nature), water adsorption, biodegradation and biological compatibility. The study demonstrated that addition of PAMAM did not significantly alter the pore size distribution or porosity of the scaffolds...
April 5, 2017: Colloids and Surfaces. B, Biointerfaces
https://www.readbyqxmd.com/read/28416788/characteristics-of-arabic-websites-with-information-on-autism
#11
Fahad M Alnemary, Faisal M Alnemary, Abdulrahman S Alamri, Yassar A Alamri
OBJECTIVE: To explore the characteristics of Arabic websites with information on autism spectrum disorder (ASD). METHODS: The word autism in Arabic was entered into 2 popular search engines in September 2013 to locate the top 80 websites featuring the term. Websites were sorted using 10 characteristics, previously used to evaluate the characteristics of English websites with information on ASD. RESULTS: Most websites were registered using a ...
April 2017: Neurosciences: the Official Journal of the Pan Arab Union of Neurological Sciences
https://www.readbyqxmd.com/read/28416141/multiplexed-engineering-and-analysis-of-combinatorial-enhancer-activity-in-single-cells
#12
Shiqi Xie, Jialei Duan, Boxun Li, Pei Zhou, Gary C Hon
The study of enhancers has been hampered by the scarcity of methods to systematically quantify their endogenous activity. We develop Mosaic-seq to systematically perturb enhancers and measure their endogenous activities at single-cell resolution. Mosaic-seq uses a CRISPR barcoding system to jointly measure a cell's transcriptome and its sgRNA modulators, thus quantifying the effects of dCas9-KRAB-mediated enhancer repression in single cells. Applying Mosaic-seq to 71 constituent enhancers from 15 super-enhancers, our analysis of 51,448 sgRNA-induced transcriptomes finds that only a small number of constituents are major effectors of target gene expression...
April 20, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28415542/bladder-smooth-muscle-cells-on-electrospun-poly-%C3%AE%C2%B5-caprolactone-poly-l-lactic-acid-scaffold-promote-bladder-regeneration-in-a-canine-model
#13
Nasser Shakhssalim, Masoud Soleimani, Mohammad M Dehghan, Javad Rasouli, Masoud Taghizadeh-Jahed, Peyman M Torbati, Mohammad Naji
Engineering of urinary bladder has been the focus of numerous studies in recent decade. Novel biomaterials, innovative fabrication methods and various modification processes of scaffolds are the critical issues to find supportive matrices. Supportive characteristics of electrospun PCL/PLLA nano-scaffold for bladder augmentation in canine model and the role of bladder cells in regeneration process were appraised. Electrospun PCL/PLLA was fabricated by co-electrospinning of PCL and PLLA. Bladder cells were isolated and transduced with lentiviral particles encoding eGFP and JRed proteins...
June 1, 2017: Materials Science & Engineering. C, Materials for Biological Applications
https://www.readbyqxmd.com/read/28415397/surface-modified-bioresorbable-electrospun-scaffolds-for-improving-hemocompatibility-of-vascular-grafts
#14
Pablo C Caracciolo, María Isabel Rial-Hermida, Florencia Montini-Ballarin, Gustavo A Abraham, Angel Concheiro, Carmen Alvarez-Lorenzo
The replacement of small-diameter vessels is one of the main challenges in tissue engineering. Moreover, the surface modification of small-diameter vascular grafts (SDVG) is a key factor in the success of the therapy due to their increased thrombogenicity and infection susceptibility caused by the lack of a functional endothelium. In this work, electrospun scaffolds were prepared from blends of poly(L-lactic acid) (PLLA) and segmented polyurethane (PHD) with a composition designed to perform as SDVG inner layer...
June 1, 2017: Materials Science & Engineering. C, Materials for Biological Applications
https://www.readbyqxmd.com/read/28415315/rectification-and-one-way-street-for-the-energy-current-in-boundary-driven-asymmetric-quantum-spin-chains
#15
Emmanuel Pereira
Motivated by the demand for efficient quantum devices to engineer energy transport, we analyze some inhomogeneous quantum spin systems, including XXZ chains, with magnetization baths at the ends. With a goal of finding general properties, we study the effects of suitable transformations on the boundary-driven Lindblad master equation associated with the dynamics of the systems. For asymmetric models with target polarization at the edges or twisted XY boundary gradients, we show the properties of the steady state, which establish the features of the energy current irrespective of the system size and the regime of transport...
March 2017: Physical Review. E
https://www.readbyqxmd.com/read/28415214/stochastic-thermodynamics-for-ising-chain-and-symmetric-exclusion-process
#16
R Toral, C Van den Broeck, D Escaff, Katja Lindenberg
We verify the finite-time fluctuation theorem for a linear Ising chain in contact with heat reservoirs at its ends. Analytic results are derived for a chain consisting of two spins. The system can be mapped onto a model for particle transport, namely, the symmetric exclusion process in contact with thermal and particle reservoirs. We modify the symmetric exclusion process to represent a thermal engine and reproduce universal features of the efficiency at maximum power.
March 2017: Physical Review. E
https://www.readbyqxmd.com/read/28414657/death-by-propofol
#17
James H Diaz, Alan David Kaye
Since its introduction in 1986, propofol ( two, 6-diisopropylphenol) , an intravenous sedative-hypnotic agent, has been utilized for the induction and maintenance of general anesthesia and conscious sedation in over 80 percent of cases; largely replacing thiopental ( sodium pentothal) over a decade ago. Unrestricted as a controlled substance, propofol's abuse potential emerged quickly and was highlighted by the death of pop singer, Michael Jackson, in 2009. In order to assess the epidemiological features of fatal propofol abuse, a descriptive analysis of the scientific literature was conducted using Internet search engines...
March 2017: Journal of the Louisiana State Medical Society: Official Organ of the Louisiana State Medical Society
https://www.readbyqxmd.com/read/28414373/superlensing-microscope-objective-lens
#18
Bing Yan, Zengbo Wang, Alan L Parker, Yu-Kun Lai, P John Thomas, Liyang Yue, James N Monks
Conventional microscope objective lenses are diffraction limited; they cannot resolve subdiffraction features of a size smaller than 250-300 nm under white lighting condition. New innovations are required to overcome this limitation. In this paper, we propose and demonstrate a new superlensing objective lens that possesses a resolution of 100 nm, which is a two-times resolution improvement over conventional objectives. This is accomplished by integrating a conventional microscope objective lens with a superlensing microsphere lens using a customized lens adaptor...
April 10, 2017: Applied Optics
https://www.readbyqxmd.com/read/28414316/tuning-crystallization-pathways-through-sequence-engineering-of-biomimetic-polymers
#19
Xiang Ma, Shuai Zhang, Fang Jiao, Christina J Newcomb, Yuliang Zhang, Arushi Prakash, Zhihao Liao, Marcel D Baer, Christopher J Mundy, James Pfaendtner, Aleksandr Noy, Chun-Long Chen, James J De Yoreo
Two-step nucleation pathways in which disordered, amorphous, or dense liquid states precede the appearance of crystalline phases have been reported for a wide range of materials, but the dynamics of such pathways are poorly understood. Moreover, whether these pathways are general features of crystallizing systems or a consequence of system-specific structural details that select for direct versus two-step processes is unknown. Using atomic force microscopy to directly observe crystallization of sequence-defined polymers, we show that crystallization pathways are indeed sequence dependent...
April 17, 2017: Nature Materials
https://www.readbyqxmd.com/read/28414197/engineering-of-a-self-adjuvanted-itep-delivered-ctl-vaccine
#20
Shuyun Dong, Tiefeng Xu, Peng Wang, Peng Zhao, Mingnan Chen
Cytotoxic T lymphocyte (CTL) epitope peptide-based vaccines are widely used in cancer and infectious disease therapy. We previously generated an immune-tolerant elastin-like polypeptides (iTEPs)-based carrier to deliver a peptide CTL vaccine and enhance the efficiency of the vaccine. To further optimize the vaccine carrier, we intended to potentiate its function by designing an iTEP-based carrier that was able to deliver adjuvant and a vaccine epitope as one molecule. Thus, we fused a 9-mer H100, a peptide derived from the high-mobility group box 1 protein (HMGB1) that could induce activation of dendritic cells (DCs), with an iTEP polymer to generate a new iTEP polymer named H100-iTEP...
April 17, 2017: Acta Pharmacologica Sinica
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