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Minimal pairs approach

Amit Raj Singh, Rony Granek
We study DNA denaturation by integrating elasticity - as described by the Gaussian network model - with bond binding energies, distinguishing between different base pairs and stacking energies. We use exact calculation, within the model, of the Helmholtz free-energy of any partial denaturation state, which implies that the entropy of all formed "bubbles" ("loops") is accounted for. Considering base pair bond removal single events, the bond designated for opening is chosen by minimizing the free-energy difference for the process, over all remaining base pair bonds...
October 14, 2016: Journal of Chemical Physics
Sudath Hapuarachchige, Dmitri Artemov
Click chemistry provides fast, convenient, versatile, and reliable chemical reactions that take place between pairs of functional groups of small molecules that can be purified without chromatographic methods. Due to the fast kinetics and low or no elimination of byproducts, click chemistry is a promising approach that is rapidly gaining acceptance in drug discovery, radiochemistry, bioconjugation, and nanoscience applications. Increasing use of click chemistry in synthetic procedures or as a bioconjugation technique in diagnostic imaging is occurring because click reactions are fast, provide a quantitative yield, and produce a minimal amount of nontoxic byproducts...
October 2016: Topics in Magnetic Resonance Imaging: TMRI
M-O Timsit, F Kleinclauss, M F Mamzer Bruneel, R Thuret
OBJECTIVES: To review ethical, legal and technical aspects of living kidney donor surgery. MATERIAL AND METHODS: An exhaustive systematic review of the scientific literature was performed in the Medline database ( and Embase ( using different associations of the following keywords: Donor nephrectomy; Kidney paired donation; Kidney transplantation; Laparoscopic nephrectomy; Living donor; Organs trafficking; Robotic assisted nephrectomy; Vaginal extraction...
October 6, 2016: Progrès en Urologie
Jonas Fredriksson, Viviane S de Paula, Ana Paula Valente, Fabio C L Almeida, Martin Billeter
We demonstrate for the first time a complete small protein characterization with the projection-decomposition approach, including full assignments as well as determination of the 3D fold. In TOCSY- and NOESY-type 4D experiments, pairing of signals from hydrogens and from their respective heavy atoms in decompositions represents a new problem. An approach, referred to as "DIADECOMP" (diagonal decomposition), is introduced to solve this problem; it consists of two separate decompositions of the input projections, differing in a 45° rotation of the spectral axes...
October 3, 2016: Journal of Magnetic Resonance
Shi Wang, Pingping Liu, Jia Lv, Yangping Li, Taoran Cheng, Lingling Zhang, Yu Xia, Hongzhen Sun, Xiaoli Hu, Zhenmin Bao
Isolength restriction site-associated DNA (isoRAD) sequencing is a very simple but powerful approach that was originally developed for genome-wide genotyping at minimal labor and cost, and it has recently extended its applicability to allow quantification of DNA methylation levels. The isoRAD method is distinct from other genotyping-by-sequencing (GBS) methods because of its use of special restriction enzymes to produce isolength tags (32-36 bp), and sequencing of these uniform tags can bring many benefits...
November 2016: Nature Protocols
Zijia Lin, Guiguang Ding, Jungong Han, Jianmin Wang
For efficiently retrieving nearest neighbors from large-scale multiview data, recently hashing methods are widely investigated, which can substantially improve query speeds. In this paper, we propose an effective probability-based semantics-preserving hashing (SePH) method to tackle the problem of cross-view retrieval. Considering the semantic consistency between views, SePH generates one unified hash code for all observed views of any instance. For training, SePH first transforms the given semantic affinities of training data into a probability distribution, and aims to approximate it with another one in Hamming space, via minimizing their Kullback-Leibler divergence...
September 29, 2016: IEEE Transactions on Cybernetics
Antonino Ditto, Giorgio Bogani, Fabio Martinelli, Mauro Signorelli, Valentina Chiappa, Cono Scaffa, Alice Indini, Umberto Leone Roberti Maggiore, Domenica Lorusso, Francesco Raspagliesi
STUDY OBJECTIVE: Growing evidence supports the safety of laparoscopic approach for patients affected by apparent early stage ovarian cancer (eEOC). However, no well-designed studies comparing laparoscopic (LS) and open surgical staging (OSS) are available. In the present investigation we aimed to provide a balanced long-term comparison between these two approaches. DESIGN: Retrospective study DESIGN CLASSIFICATION: Canadian Task Force classification II-2 SETTING: Tertiary Centre PATIENTS: Data of consecutive patients affected by eEOC who had LS were matched 1:1 with a cohort of patients undergoing OSS...
October 1, 2016: Journal of Minimally Invasive Gynecology
Kenneth K Mugwanya, Craig W Hendrix, Nelly R Mugo, Mark Marzinke, Elly T Katabira, Kenneth Ngure, Nulu B Semiyaga, Grace John-Stewart, Timothy R Muwonge, Gabriel Muthuri, Andy Stergachis, Connie L Celum, Jared M Baeten
BACKGROUND: As pre-exposure prophylaxis (PrEP) becomes more widely used in heterosexual populations, an important consideration is its safety in infants who are breastfed by women taking PrEP. We investigated whether tenofovir and emtricitabine are excreted into breast milk and then absorbed by the breastfeeding infant in clinically significant concentrations when used as PrEP by lactating women. METHODS AND FINDINGS: We conducted a prospective short-term, open-label study of daily oral emtricitabine-tenofovir disoproxil fumarate PrEP among 50 HIV-uninfected breastfeeding African mother-infant pairs between 1-24 wk postpartum (ClinicalTrials...
September 2016: PLoS Medicine
Mathias Scharinger, Ulrike Domahs, Elise Klein, Frank Domahs
Research in auditory neuroscience illustrated the importance of superior temporal sulcus (STS) for speech sound processing. However, evidence for abstract processing beyond the level of phonetics in STS has remained elusive. In this study, we follow an underspecification approach according to which the phonological representation of vowels is based on the presence vs. absence of abstract features. We hypothesized that phonological mismatch in a same/different task is governed by underspecification: A less specified vowel in second position of same/different minimal pairs (e...
September 23, 2016: Brain and Language
Scott D Kennedy
Knowledge of RNA secondary structure is often sufficient to identify relationships between the structure of RNA and processing pathways, and the design of therapeutics. Nuclear magnetic resonance (NMR) can identify types of nucleotide base pairs and the sequence, thus limiting possible secondary structures. Because NMR experiments, like chemical mapping, are performed in solution, not in single crystals, experiments can be initiated as soon as the biomolecule is expressed and purified. This chapter summarizes NMR methods that permit rapid identification of RNA secondary structure, information that can be used as supplements to chemical mapping, and/or as preliminary steps required for 3D structure determination...
2016: Methods in Molecular Biology
Veronika Pilařová, Mumtaz Sultani, Kristine Skoglund Ask, Lucie Nováková, Stig Pedersen-Bjergaard, Astrid Gjelstad
The new microextraction technique named parallel artificial liquid membrane extraction (PALME) was introduced as an alternative approach to liquid-liquid extraction of charged analytes from aqueous samples. The concept is based on extraction of analytes across a supported liquid membrane sustained in the pores of a thin polymeric membrane, a well-known extraction principle also used in hollow fiber liquid-phase microextraction (HF-LPME). However, the new PALME technique offers a more user-friendly setup in which the supported liquid membrane is incorporated in a 96 well plate system...
September 14, 2016: Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences
Rüdiger Lange, Bernhard Voss, Victoria Kehl, Domenico Mazzitelli, Peter Tassani-Prell, Thomas Günther
BACKGROUND: Mitral valve (MV) repair through a right minithoracotomy (RT) is technically more demanding than through a median sternotomy (MS) and has been cited for a higher rate of reoperation, increased postoperative bleeding, thromboembolic events, poor visualization, and longer operative times. Randomized studies are not available, however, and specific characteristics of patients who undergo operation with either technique are usually highly different. Therefore, a propensity matching study was performed to reduce selection bias...
September 9, 2016: Annals of Thoracic Surgery
Jay Thomas Sutliffe, Joel Harvey Fuhrman, Mary Jo Carnot, Raena Marie Beetham, Madison Sarah Peddy
UNLABELLED: conduct interventions for health promotion and disease prevention to ameliorate chronic risk factors for disease, such as for cardiovascular disease (CVD). Likewise, nutrient-dense, plant-rich (NDPR) dietary patterns have been shown to be effective at preventing and improving chronic-disease conditions, including CVD. Objective • The study's aim was to determine the feasibility and effectiveness of an NDPR dietary intervention for worksites to lower CVD risk factors. Design • The study was a 6-wk pilot intervention using a pretest and posttest design...
September 2016: Alternative Therapies in Health and Medicine
Olga V Matveeva, Yury D Nechipurenko, Evgeniy Riabenko, Chikako Ragan, Nafisa N Nazipova, Aleksey Y Ogurtsov, Svetlana A Shabalina
MOTIVATION: Target-specific hybridization depends on oligo-probe characteristics that improve hybridization specificity and minimize genome-wide cross-hybridization. Interplay between specific hybridization and genome-wide cross-hybridization has been insufficiently studied, despite its crucial role in efficient probe design and in data analysis. RESULTS: In this study, we defined hybridization specificity as a ratio between oligo target-specific hybridization and oligo genome-wide cross-hybridization...
September 1, 2016: Bioinformatics
Ehsan Haghshenas, Faraz Hach, S Cenk Sahinalp, Cedric Chauve
MOTIVATION: Second generation sequencing technologies paved the way to an exceptional increase in the number of sequenced genomes, both prokaryotic and eukaryotic. However, short reads are difficult to assemble and often lead to highly fragmented assemblies. The recent developments in long reads sequencing methods offer a promising way to address this issue. However, so far long reads are characterized by a high error rate, and assembling from long reads require a high depth of coverage...
September 1, 2016: Bioinformatics
Sudipto Dolui, Ze Wang, Russell T Shinohara, David A Wolk, John A Detre
PURPOSE: To propose and validate Structural Correlation-based Outlier REjection (SCORE), a novel algorithm for removal of artifacts arising from outlier control-label pairs in 2D arterial spin labeling (ASL) data. MATERIALS AND METHODS: The proposed method was assessed with respect to other state-of-the-art ASL signal processing approaches using 2D pulsed ASL data obtained with a 3T Siemens scanner from the Alzheimer's Disease Neuroimaging Initiative (ADNI) database...
August 29, 2016: Journal of Magnetic Resonance Imaging: JMRI
Mun-Gwan Hong, Woojoo Lee, Peter Nilsson, Yudi Pawitan, Jochen M Schwenk
Enhanced by the growing number of biobanks, biomarker studies can now be performed with reasonable statistical power by using large sets of samples. Antibody-based proteomics by means of suspension bead arrays offers one attractive approach to analyze serum, plasma, or CSF samples for such studies in microtiter plates. To expand measurements beyond single batches, with either 96 or 384 samples per plate, suitable normalization methods are required to minimize the variation between plates. Here we propose two normalization approaches utilizing MA coordinates...
October 7, 2016: Journal of Proteome Research
Allison M Borges, Jinyi Kuang, Hannah Milhorn, Richard Yi
Applied to delay discounting data, Area-Under-the-Curve (AUC) provides an atheoretical index of the rate of delay discounting. The conventional method of calculating AUC, by summing the areas of the trapezoids formed by successive delay-indifference point pairings, does not account for the fact that most delay discounting tasks scale delay pseudoexponentially, that is, time intervals between delays typically get larger as delays get longer. This results in a disproportionate contribution of indifference points at long delays to the total AUC, with minimal contribution from indifference points at short delays...
September 2016: Journal of the Experimental Analysis of Behavior
(no author information available yet)
"Universal design provides a blueprint for maximum inclusion of all people" [7]. This statement is now nearly 20 years old. The present collection of papers from the 3rd International Conference on Universal Design (UD 2016) is testament to the fact that Universal Design is now benefitting from a climate that is more knowledgeable about, and possibly more accommodating of, individual differences between people. However, there are still many open issues, and much to be learnt from exchanging experiences between all stakeholders interested in Universal Design, be they policy makers, practitioners or researchers...
2016: Studies in Health Technology and Informatics
Alicia C Bunger, Rebecca Lengnick-Hall
BACKGROUND: Collaborative learning models were designed to support quality improvements, such as innovation implementation by promoting communication within organizational teams. Yet the effect of collaborative learning approaches on organizational team communication during implementation is untested. PURPOSE: The aim of this study was to explore change in communication patterns within teams from children's mental health organizations during a year-long learning collaborative focused on implementing a new treatment...
August 15, 2016: Health Care Management Review
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