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https://www.readbyqxmd.com/read/27908126/communication-multipole-approximations-of-distant-pair-energies-in-local-correlation-methods-with-pair-natural-orbitals
#1
Hans-Joachim Werner
The accuracy of multipole approximations for distant pair energies in local second-order Møller-Plesset perturbation theory (LMP2) as introduced by Hetzer et al. [Chem. Phys. Lett. 290, 143 (1998)] is investigated for three chemical reactions involving molecules with up to 92 atoms. Various iterative and non-iterative approaches are compared, using different energy thresholds for distant pair selection. It is demonstrated that the simple non-iterative dipole-dipole approximation, which has been used in several recent pair natural orbitals (PNO)-LMP2 and PNO-LCCSD (local coupled-cluster with singles and doubles) methods, may underestimate the distant pair energies by up to 50% and can lead to significant errors in relative energies, unless very tight thresholds are used...
November 28, 2016: Journal of Chemical Physics
https://www.readbyqxmd.com/read/27897128/defining-the-limits-of-endoscopic-access-to-internal-auditory-canal
#2
Adam Master, Mickie Hamiter, Maura Cosetti
OBJECTIVE: To quantify surgical access to the internal auditory canal (IAC) using an exclusively endoscopic transcanal approach (EETA) and investigate surgically relevant relationships with neurovascular and osseous landmarks of the temporal bone. MATERIALS AND METHODS: Anatomical dissection of two paired temporal bones and 15 unpaired temporal bones was performed using an exclusively endoscopic approach to IAC. The dissection proceeded until the cerebellopontine angle (CPA) could be accessed...
November 28, 2016: Journal of International Advanced Otology
https://www.readbyqxmd.com/read/27887873/a-rapid-method-for-detecting-propionibacterium-acnes-in-surgical-biopsy-specimens-from-the-shoulder
#3
Scott Holmes, Ana M Pena Diaz, George S Athwal, Kenneth J Faber, David B O'Gorman
BACKGROUND: Propionibacterium (P) acnes infection of the shoulder after arthroplasty is a common and serious complication. Current detection methods for P acnes involve anaerobic cultures that require prolonged incubation periods (typically 7-14 days). We have developed a polymerase chain reaction (PCR)-restriction fragment length polymorphism (RFLP) approach that sensitively and specifically identifies P acnes in tissue specimens within a 24-hour period. METHODS: Primers were designed to amplify a unique region of the 16S rRNA gene in P acnes that contained a unique HaeIII restriction enzyme site...
November 22, 2016: Journal of Shoulder and Elbow Surgery
https://www.readbyqxmd.com/read/27884202/extending-colonic-mucosal-microbiome-analysis-assessment-of-colonic-lavage-as-a-proxy-for-endoscopic-colonic-biopsies
#4
Euan Watt, Matthew R Gemmell, Susan Berry, Mark Glaire, Freda Farquharson, Petra Louis, Graeme I Murray, Emad El-Omar, Georgina L Hold
BACKGROUND: Sequencing-based analysis has become a well-established approach to deciphering the composition of the gut microbiota. However, due to the complexity of accessing sufficient material from colonoscopic biopsy samples, most studies have focused on faecal microbiota analysis, even though it is recognised that differences exist between the microbial composition of colonic biopsies and faecal samples. We determined the suitability of colonic lavage samples to see if it had comparable microbial diversity composition to colonic biopsies as they are without the limitations associated with sample size...
November 25, 2016: Microbiome
https://www.readbyqxmd.com/read/27861202/novel-approaches-to-early-detection-of-endometrial-cancer
#5
Madhu Bagaria, Emily Shields, Jamie N Bakkum-Gamez
PURPOSE OF REVIEW: Detection of endometrial cancer at an early stage leads to better oncologic outcomes. To date, a screening test for endometrial cancer does not exist. RECENT FINDINGS: Evolving knowledge of molecular changes involved in endometrial cancer carcinogenesis paired with sensitive and high-throughput technological advancements are a promising combination that can be leveraged to detect tumor DNA and proteins. These molecular biomarkers can be identified in biospecimens collected via minimally invasive and noninvasive approaches...
November 17, 2016: Current Opinion in Obstetrics & Gynecology
https://www.readbyqxmd.com/read/27846853/dgca-a-comprehensive-r-package-for-differential-gene-correlation-analysis
#6
Andrew T McKenzie, Igor Katsyv, Won-Min Song, Minghui Wang, Bin Zhang
BACKGROUND: Dissecting the regulatory relationships between genes is a critical step towards building accurate predictive models of biological systems. A powerful approach towards this end is to systematically study the differences in correlation between gene pairs in more than one distinct condition. RESULTS: In this study we develop an R package, DGCA (for Differential Gene Correlation Analysis), which offers a suite of tools for computing and analyzing differential correlations between gene pairs across multiple conditions...
November 15, 2016: BMC Systems Biology
https://www.readbyqxmd.com/read/27826778/comparison-of-single-and-multi-incision-minimally-invasive-esophagectomy-mie-for-treating-esophageal-cancer-a-propensity-matched-study
#7
Jang-Ming Lee, Shang-Chi Chen, Shun-Mao Yang, Ying-Fan Tseng, Pei-Wen Yang, Pei-Ming Huang
OBJECTIVE: To compare the perioperative outcome of minimally invasive (MIE) esophagectomy performed with a single- or a multi-incision in treating esophageal cancer. METHOD: Patients with esophageal cancer who underwent MIE from 2006 to 2016 were evaluated. A 3-4-cm incision was created in both the thoracoscopic and the laparoscopic phases during the single-incision MIE procedures. A propensity-matched comparison was made between the two groups of patients. RESULTS: We analyzed a total of 48 pairs of patients with propensity-matched from the cohort of 360 patients undergoing MIE during 2006-2015...
November 8, 2016: Surgical Endoscopy
https://www.readbyqxmd.com/read/27824584/making-trillion-correlations-feasible-in-feature-grouping-and-selection
#8
Yiteng Zhai, Yew-Soon Ong, Ivor W Tsang
Today, modern databases with "Big Dimensionality" are experiencing a growing trend. Existing approaches that require the calculations of pairwise feature correlations in their algorithmic designs have scored miserably on such databases, since computing the full correlation matrix (i.e., square of dimensionality in size) is computationally very intensive (i.e., million features would translate to trillion correlations). This poses a notable challenge that has received much lesser attention in the field of machine learning and data mining research...
December 2016: IEEE Transactions on Pattern Analysis and Machine Intelligence
https://www.readbyqxmd.com/read/27797688/cannabis-involvement-and-nonsuicidal-self-injury-a-discordant-twin-approach
#9
Lauren R Few, Julia D Grant, Elliot C Nelson, Timothy J Trull, Richard A Grucza, Kathleen K Bucholz, Karin J H Verweij, Nicholas G Martin, Dixie J Statham, Pamela A F Madden, Andrew C Heath, Michael T Lynskey, Arpana Agrawal
OBJECTIVE: Cannabis use, particularly at an early age, has been linked to suicidal thoughts and behavior, but minimal work has examined the association between cannabis use and lifetime nonsuicidal self-injury (NSSI). The current study aims to characterize the overlap between lifetime and early cannabis use and NSSI and to examine genetic and environmental mechanisms of this association. METHOD: Adult male and female twins from the Australian Twin Registry (N = 9,583) were used to examine the odds of NSSI associated with lifetime cannabis use and early cannabis use (i...
November 2016: Journal of Studies on Alcohol and Drugs
https://www.readbyqxmd.com/read/27787783/a-two-step-approach-for-longitudinal-registration-of-retinal-images
#10
Sajib Kumar Saha, Di Xiao, Shaun Frost, Yogesan Kanagasingam
This paper presents a novel two step approach for longitudinal (over time) registration of retinal images. Longitudinal registration is an important preliminary step to analyse longitudinal changes on the retina including disease progression. While potential overlap and minimal geometric distortion are likely in longitudinal images, identification of reliable features over time is a potential challenge for longitudinal registration. Relying on the widely accepted phenomenon that retinal vessels are more reliable over time, the proposed method aims to accurately match bifurcation and cross-over points between different timestamp images...
December 2016: Journal of Medical Systems
https://www.readbyqxmd.com/read/27782499/sufficient-minimal-model-for-dna-denaturation-integration-of-harmonic-scalar-elasticity-and-bond-energies
#11
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
https://www.readbyqxmd.com/read/27748712/click-chemistry-in-the-development-of-contrast-agents-for-magnetic-resonance-imaging
#12
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
https://www.readbyqxmd.com/read/27720629/-living-kidney-donation
#13
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 (http://www.ncbi.nlm.nih.gov) and Embase (http://www.embase.com) 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
https://www.readbyqxmd.com/read/27718459/diadecomp-a-new-approach-to-analyze-decompositions-from-projection-spectroscopy
#14
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
https://www.readbyqxmd.com/read/27711051/serial-sequencing-of-isolength-rad-tags-for-cost-efficient-genome-wide-profiling-of-genetic-and-epigenetic-variations
#15
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
https://www.readbyqxmd.com/read/27705870/cross-view-retrieval-via-probability-based-semantics-preserving-hashing
#16
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
https://www.readbyqxmd.com/read/27702704/minimally-invasive-surgical-staging-for-ovarian-carcinoma-a-propensity-matched-comparison-with-traditional-open-surgery
#17
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
https://www.readbyqxmd.com/read/27676257/pre-exposure-prophylaxis-use-by-breastfeeding-hiv-uninfected-women-a-prospective-short-term-study-of-antiretroviral-excretion-in-breast-milk-and-infant-absorption
#18
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
https://www.readbyqxmd.com/read/27669107/mental-representations-of-vowel-features-asymmetrically-modulate-activity-in-superior-temporal-sulcus
#19
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
https://www.readbyqxmd.com/read/27665604/nmr-methods-for-characterization-of-rna-secondary-structure
#20
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
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