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https://www.readbyqxmd.com/read/28441476/sboldesigner-2-an-intuitive-tool-for-structural-genetic-design
#1
Michael Zhang, James Alastair McLaughlin, Anil Wipat, Chris J Myers
As the Synthetic Biology Open Language (SBOL) data and visual standards gain acceptance for describing genetic designs in a detailed and reproducible way, there is an increasing need for an intuitive sequence editor tool that biologists can use that supports these standards. This paper describes SBOLDesigner 2, a genetic design automation (GDA) tool that natively supports both the SBOL data model (Version 2.1) and SBOL Visual (Version 1.0). This software is enabled to fetch and store parts and designs from SBOL repositories, such as SynBioHub...
April 25, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28440948/novel-reduction-sensitive-micellar-nanoparticles-assembled-from-rituximab-doxorubicin-conjugates-as-smart-and-intuitive-drug-delivery-systems-for-the-treatment-of-non-hodgkin-s-lymphoma
#2
Huabin Yin, Tong Meng, Ling Shu, Min Mao, Lei Zhou, Haiyan Chen, Dianwen Song
In this study, a novel reduction-sensitive drug delivery system, the Rituximab-Doxorubicin (RTX-DOX) micellar nanoparticle (RDMN), was specially designed for targeted delivery and release of DOX in Non-Hodgkin's Lymphoma (NHL) cells. The RDMN was fabricated by self-assembling of amphiphilic RTX-DOX conjugates (RDCs), which were synthesized by conjugating the hydrophilic Fab fragments of RTX (an anti-CD20 monoclonal antibody) and hydrophobic DOXs by a reduction-responsive linker, 3-(2-Pyridyldithio) propionyl hydrazide (PDPH)...
April 25, 2017: Chemical Biology & Drug Design
https://www.readbyqxmd.com/read/28438154/network-based-analysis-reveals-novel-gene-signatures-in-peripheral-blood-of-patients-with-chronic-obstructive-pulmonary-disease
#3
Ma'en Obeidat, Yunlong Nie, Virginia Chen, Casey P Shannon, Anand Kumar Andiappan, Bernett Lee, Olaf Rotzschke, Peter J Castaldi, Craig P Hersh, Nick Fishbane, Raymond T Ng, Bruce McManus, Bruce E Miller, Stephen Rennard, Peter D Paré, Don D Sin
BACKGROUND: Chronic obstructive pulmonary disease (COPD) is currently the third leading cause of death and there is a huge unmet clinical need to identify disease biomarkers in peripheral blood. Compared to gene level differential expression approaches to identify gene signatures, network analyses provide a biologically intuitive approach which leverages the co-expression patterns in the transcriptome to identify modules of co-expressed genes. METHODS: A weighted gene co-expression network analysis (WGCNA) was applied to peripheral blood transcriptome from 238 COPD subjects to discover co-expressed gene modules...
April 24, 2017: Respiratory Research
https://www.readbyqxmd.com/read/28437367/-effective-requesting-a-scoping-review-of-the-literature-on-asking-families-to-consent-to-organ-and-tissue-donation
#4
Jennifer A Chandler, Matthew Connors, Giles Holland, Sam D Shemie
BACKGROUND: Families are often asked to consent to the donation of their deceased relative's organs or tissues. These end-of-life conversations are important because they affect consent rates as well as the psychological impact of the decision for families. This scoping review of the literature on requesting family consent was prepared to support of the development of leading practice recommendations for end-of-life conversations with families of potential donors. A scoping review maps research activity in a field across a range of commentary and empirical study designs but does not attempt meta-synthesis of empirical data or quality assessment...
May 2017: Transplantation
https://www.readbyqxmd.com/read/28436922/the-feasibility-of-manual-parameter-tuning-for-deformable-breast-mr-image-registration-from-a-multi-objective-optimization-perspective
#5
Kleopatra Pirpinia, Peter Bosman, Claudette Loo, Gonneke Winter-Warnars, Natasja Janssen, Astrid Scholten, Jan-Jakob Sonke, Marcel van Herk, Tanja Alderliesten
Deformable image registration is typically formulated as an optimization problem involving a linearly weighted combination of terms that correspond to objectives of interest (e.g., similarity, deformation magnitude). The weights, along with multiple other parameters, need to be manually tuned for each application, a task currently mainly addressed via trial-and-error approaches. Such approaches can only be successful if there is a sensible interplay between parameters, objectives, and desired registration outcome...
April 24, 2017: Physics in Medicine and Biology
https://www.readbyqxmd.com/read/28436868/high-order-local-pooling-and-encoding-gaussians-over-a-dictionary-of-gaussians
#6
Peihua Li, Hui Zeng, Qilong Wang, Simon Shiu, Lei Zhang
Local pooling (LP) in configuration (feature) space proposed by Boureau et al. explicitly restricts similar features to be aggregated, which can preserve as much discriminative information as possible. At the time it appeared, this method combined with sparse coding achieved competitive classification results with only a small dictionary. However, its performance lags far behind state-of-the-art results as only zero-order information is exploited. Inspired by the success of high-order statistical information in existing advanced feature coding or pooling methods, we make an attempt to address the limitation of LP...
April 19, 2017: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
https://www.readbyqxmd.com/read/28436506/electrostatic-interactions-between-ions-near-thomas-fermi-substrates-and-the-surface-energy-of-ionic-crystals-at-imperfect-metals
#7
V Kaiser, J Comtet, A Niguès, A Siria, B Coasne, L Bocquet
The electrostatic interaction between two charged particles is strongly modified in the vicinity of a metal. This situation is usually accounted for by the celebrated image charges approach, which was further extended to account for the electronic screening properties of the metal at the level of the Thomas-Fermi description. In this paper we build upon a previous approach [M. A. Vorotyntsev and A. A. Kornyshev, Zh. Eksp. Teor. Fiz., 1980, 78(3), 1008-1019] and successive works to calculate the 1-body and 2-body electrostatic energy of ions near a metal in terms of the Thomas-Fermi screening length...
April 24, 2017: Faraday Discussions
https://www.readbyqxmd.com/read/28433037/directed-motion-from-particle-size-oscillations-inside-an-asymmetric-channel
#8
Yurii A Makhnovskii, Sheh-Yi Sheu, Dah-Yen Yang, Sheng Hsien Lin
The motion of a spherical Brownian particle in an asymmetric periodic channel is considered. Under an external periodic stimulus, the particle switches between two states with different particle radius, every half-period. Using Brownian dynamics simulations, we show that the particle size oscillation, combined with the asymmetry of the channel, induces a drift along the channel axis, directed towards the steeper wall of the channel. The oscillation of the particle size is accompanied by a time variation of the space accessible to the particle and by an oscillation of its diffusion coefficient...
April 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28432008/turkish-version-of-the-intuitive-eating-scale-2-validity-and-reliability-among-university-students
#9
Murat Bas, Kezban Esen Karaca, Duygu Saglam, Gozde Arıtıcı, Ecem Cengiz, Selen Köksal, Aylin Hasbay Buyukkaragoz
Intuitive Eating is defined as "the dynamic process-integrating attunement of mind, body, and food". The purpose of this study was, therefore, adapt the IES-2 to the Turkish language and reliability and validity of IES-2 among Turkish populations. We also examined the instrument's internal consistency and test-retest reliability and analysed the relationships between the IES-2 and several variables so as to evaluate the convergent and discriminant validity. Three hundred seventy-seven undergraduate and postgraduate women and men between the ages of 19-31 years (mean 22...
April 18, 2017: Appetite
https://www.readbyqxmd.com/read/28431680/two-paradigms-for-religious-representation-the-physicist-and-the-playground-a-reply-to-levy
#10
Neil Van Leeuwen
In an earlier issue, I argue (2014) that psychology and epistemology should distinguish religious credence from factual belief. These are distinct cognitive attitudes. Levy (2017) rejects this distinction, arguing that both religious and factual "beliefs" are subject to "shifting" on the basis of fluency and "intuitiveness." Levy's theory, however, (1) is out of keeping with much research in cognitive science of religion and (2) misrepresents the notion of factual belief employed in my theory. So his claims don't undermine my distinction...
April 18, 2017: Cognition
https://www.readbyqxmd.com/read/28430994/personhood-and-natural-kinds-why-cognitive-status-need-not-affect-moral-status
#11
Joseph Vukov
Lockean accounts of personhood propose that an individual is a person just in case that individual is characterized by some advanced cognitive capacity. On these accounts, human beings with severe cognitive impairment are not persons. Some accept this result-I do not. In this paper, I therefore advance and defend an account of personhood that secures personhood for human beings who are cognitively impaired. On the account for which I argue, an individual is a person just in case that individual belongs to a natural kind that is normally characterized by advanced cognitive capacities...
April 19, 2017: Journal of Medicine and Philosophy
https://www.readbyqxmd.com/read/28430042/control-without-controllers-toward-a-distributed-neuroscience-of-executive-control
#12
Benjamin R Eisenreich, Rei Akaishi, Benjamin Y Hayden
Executive control refers to the regulation of cognition and behavior by mental processes and is a hallmark of higher cognition. Most approaches to understanding its mechanisms begin with the assumption that our brains have anatomically segregated and functionally specialized control modules. The modular approach is intuitive: Control is conceptually distinct from basic mental processing, so an organization that reifies that distinction makes sense. An alternative approach sees executive control as self-organizing principles of a distributed organization...
April 21, 2017: Journal of Cognitive Neuroscience
https://www.readbyqxmd.com/read/28429925/robot-assisted-laparoendoscopic-single-site-versus-mini-laparoscopic-pyeloplasty-a-comparison-of-perioperative-functional-and-cosmetic-results
#13
Cristian Fiori, Riccardo Bertolo, Matteo Manfredi, Fabrizio Mele, Daniele Amparore, Giovanni Cattaneo, Ivano Morra, Roberto M Scarpa, Francesco Porpiglia
BACKGROUND: New approaches have been developed to further reduce the invasiveness of laparoscopic pyeloplasty (P) as treatment for uretero-pelvic junction obstruction (UPJO). Aim of the study was to compare perioperative, functional and cosmetic results of mini-laparoscopic (mL-P) versus robot-assisted laparoendoscopic single-site P (rLESS-P). METHODS: Since April 2009 to June 2010, 12 adult patients with primary UPJO, BMI<25 and no previous abdominal surgeries were enrolled undergoing mLP (3-mm instruments only)...
April 20, 2017: Minerva Urologica e Nefrologica, the Italian Journal of Urology and Nephrology
https://www.readbyqxmd.com/read/28426791/correction-cctop-an-intuitive-flexible-and-reliable-crispr-cas9-target-prediction-tool
#14
Manuel Stemmer, Thomas Thumberger, Maria Del Sol Keyer, Joachim Wittbrodt, Juan L Mateo
[This corrects the article DOI: 10.1371/journal.pone.0124633.].
2017: PloS One
https://www.readbyqxmd.com/read/28425452/estimating-the-irreversible-pressure-drop-across-a-stenosis-by-quantifying-turbulence-production-using-4d-flow-mri
#15
Hojin Ha, Jonas Lantz, Magnus Ziegler, Belen Casas, Matts Karlsson, Petter Dyverfeldt, Tino Ebbers
The pressure drop across a stenotic vessel is an important parameter in medicine, providing a commonly used and intuitive metric for evaluating the severity of the stenosis. However, non-invasive estimation of the pressure drop under pathological conditions has remained difficult. This study demonstrates a novel method to quantify the irreversible pressure drop across a stenosis using 4D Flow MRI by calculating the total turbulence production of the flow. Simulation MRI acquisitions showed that the energy lost to turbulence production can be accurately quantified with 4D Flow MRI within a range of practical spatial resolutions (1-3 mm; regression slope = 0...
April 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28425112/beyond-guidelines-discretionary-practice-in-face-to-face-triage-nursing
#16
Lars E F Johannessen
This article draws on ethnographic data from a Norwegian emergency primary care clinic (EPCC) to explore nurses' discretionary application of guidelines. Specifically, it analyses nurses' discretionary use of the Manchester Triage System (MTS) when performing face-to-face triage, that is, assessing the urgency of patients' complaints. The analysis shows how nurses assessed patients at odds with MTS prescriptions by collecting supplementary data, engaging in differential diagnostic and holistic reasoning, relying on emotion and intuition, and allowing colleagues and patients to influence their reasoning...
April 20, 2017: Sociology of Health & Illness
https://www.readbyqxmd.com/read/28424642/response-commentary-incubation-and-intuition-in-creative-problem-solving
#17
COMMENT
Kenneth J Gilhooly
No abstract text is available yet for this article.
2017: Frontiers in Psychology
https://www.readbyqxmd.com/read/28422179/heritability-maps-of-human-face-morphology-through-large-scale-automated-three-dimensional-phenotyping
#18
Dimosthenis Tsagkrasoulis, Pirro Hysi, Tim Spector, Giovanni Montana
The human face is a complex trait under strong genetic control, as evidenced by the striking visual similarity between twins. Nevertheless, heritability estimates of facial traits have often been surprisingly low or difficult to replicate. Furthermore, the construction of facial phenotypes that correspond to naturally perceived facial features remains largely a mystery. We present here a large-scale heritability study of face geometry that aims to address these issues. High-resolution, three-dimensional facial models have been acquired on a cohort of 952 twins recruited from the TwinsUK registry, and processed through a novel landmarking workflow, GESSA (Geodesic Ensemble Surface Sampling Algorithm)...
April 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28422088/clustering-by-fast-search-and-merge-of-local-density-peaks-for-gene-expression-microarray-data
#19
Rashid Mehmood, Saeed El-Ashram, Rongfang Bie, Hussain Dawood, Anton Kos
Clustering is an unsupervised approach to classify elements based on their similarity, and it is used to find the intrinsic patterns of data. There are enormous applications of clustering in bioinformatics, pattern recognition, and astronomy. This paper presents a clustering approach based on the idea that density wise single or multiple connected regions make a cluster, in which density maxima point represents the center of the corresponding density region. More precisely, our approach firstly finds the local density regions and subsequently merges the density connected regions to form the meaningful clusters...
April 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28421706/generative-topographic-mapping-of-conformational-space
#20
Dragos Horvath, Igor Baskin, Gilles Marcou, Alexandre Varnek
Herein, Generative Topographic Mapping (GTM) was challenged to produce planar projections of the high-dimensional conformational space of complex molecules (the 1LE1 peptide). GTM is a probability-based mapping strategy, and its capacity to support property prediction models serves to objectively assess map quality (in terms of regression statistics). The properties to predict were total, non-bonded and contact energies, surface area and fingerprint darkness. Map building and selection was controlled by a previously introduced evolutionary strategy allowed to choose the best-suited conformational descriptors, options including classical terms and novel atom-centric autocorrellograms...
April 19, 2017: Molecular Informatics
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