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https://www.readbyqxmd.com/read/28644616/importance-of-a-fully-anharmonic-treatment-of-equilibrium-isotope-fractionation-properties-of-dissolved-ionic-species-as-evidenced-by-li-aq
#1
Romain Dupuis, Magali Benoit, Mark E Tuckerman, Merlin Méheut
Equilibrium fractionation of stable isotopes is critically important in fields ranging from chemistry, including medicinal chemistry, electrochemistry, geochemistry, and nuclear chemistry, to environmental science. The dearth of reliable estimates of equilibrium fractionation factors, from experiment or from natural observations, has created a need for accurate computational approaches. Because isotope fractionation is a purely quantum mechanical phenomenon, exact calculation of fractionation factors is nontrivial...
June 23, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28644431/an-in-vitro-study-on-the-efficacy-of-removing-calcium-hydroxide-from-curved-root-canal-systems-in-root-canal-therapy
#2
Ying Wang, Li-Yang Guo, Hong-Zhi Fang, Wen-Ling Zou, Ying-Ming Yang, Yuan Gao, Hui Yang, Tao Hu
To compare the efficacy of various irrigants (citric acid, ethylenediaminetetraacetic acid (EDTA) and NaOCl) and techniques in removing Ca(OH)2 in two types of curved root canal systems, simulated root canals with specific curvatures were used to investigate the effects of different irrigants and instruments on Ca(OH)2 removal. The optimal methods were verified on extracted human teeth. Simulated root canals were assigned to one of two groups based on the irrigation solution: 10% citric acid or 2.5% NaOCl. Each group was divided into four subgroups according to the technique used to remove Ca(OH)2...
June 23, 2017: International Journal of Oral Science
https://www.readbyqxmd.com/read/28642491/a-cross-species-approach-to-identify-transcriptional-regulators-exemplified-for-dnajc22-and-hnf4a
#3
A C Aschenbrenner, K Bassler, M Brondolin, L Bonaguro, P Carrera, K Klee, T Ulas, J L Schultze, M Hoch
There is an enormous need to make better use of the ever increasing wealth of publicly available genomic information and to utilize the tremendous progress in computational approaches in the life sciences. Transcriptional regulation of protein-coding genes is a major mechanism of controlling cellular functions. However, the myriad of transcription factors potentially controlling transcription of any given gene makes it often difficult to quickly identify the biological relevant transcription factors. Here, we report on the identification of Hnf4a as a major transcription factor of the so far unstudied DnaJ heat shock protein family (Hsp40) member C22 (Dnajc22)...
June 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28641485/microarray-based-gene-expression-analysis-for-veterinary-pathologists-a-review
#4
Barbara B Raddatz, Ingo Spitzbarth, Katja A Matheis, Arno Kalkuhl, Ulrich Deschl, Wolfgang Baumgärtner, Reiner Ulrich
High-throughput, genome-wide transcriptome analysis is now commonly used in all fields of life science research and is on the cusp of medical and veterinary diagnostic application. Transcriptomic methods such as microarrays and next-generation sequencing generate enormous amounts of data. The pathogenetic expertise acquired from understanding of general pathology provides veterinary pathologists with a profound background, which is essential in translating transcriptomic data into meaningful biological knowledge, thereby leading to a better understanding of underlying disease mechanisms...
January 1, 2017: Veterinary Pathology
https://www.readbyqxmd.com/read/28640806/good-enough-practices-in-scientific-computing
#5
Greg Wilson, Jennifer Bryan, Karen Cranston, Justin Kitzes, Lex Nederbragt, Tracy K Teal
Computers are now essential in all branches of science, but most researchers are never taught the equivalent of basic lab skills for research computing. As a result, data can get lost, analyses can take much longer than necessary, and researchers are limited in how effectively they can work with software and data. Computing workflows need to follow the same practices as lab projects and notebooks, with organized data, documented steps, and the project structured for reproducibility, but researchers new to computing often don't know where to start...
June 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28640634/structure-prediction-for-surface-induced-phases-of-organic-monolayers-overcoming-the-combinatorial-bottleneck
#6
Veronika Obersteiner, Michael Scherbela, Lukas Hörmann, Daniel Wegner, Oliver T Hofmann
Structure determination and prediction pose a major challenge to computational material science, demanding efficient global structure search techniques tailored to identify promising and relevant candidates. A major bottleneck is the fact that, due to the many combinatorial possibilities, there are too many possible geometries to be sampled exhaustively. Here, an innovative computational approach to overcome this problem is presented, that explores the potential energy landscape of commensurate organic/inorganic interfaces where the orientation and conformation of the molecules in the tightly packed layer is close to a favorable geometry adopted by isolated molecules on the surface...
June 22, 2017: Nano Letters
https://www.readbyqxmd.com/read/28637405/molecular-dynamics-simulations-challenges-and-opportunities-a-biologist-s-prospective
#7
Indu Kumari, Padmani Sandhu, Mushtaq Ahmed, Yusuf Akhter
Molecular dynamics (MD) is a computational technique which is used to study biomolecules in virtual environment. Each of the constituent atoms represents a particle and hence the biomolecule embodies a multi-particle mechanical system analyzed within a simulation box during MD analysis. The potential energies of the atoms are explained by a mathematical expression consisting of different forces and space parameters. There are various software and force fields that have been developed for MD studies of the biomolecules...
June 21, 2017: Current Protein & Peptide Science
https://www.readbyqxmd.com/read/28636619/what-do-computer-scientists-tweet-analyzing-the-link-sharing-practice-on-twitter
#8
Marco Schmitt, Robert Jäschke
Twitter communication has permeated every sphere of society. To highlight and share small pieces of information with possibly vast audiences or small circles of the interested has some value in almost any aspect of social life. But what is the value exactly for a scientific field? We perform a comprehensive study of computer scientists using Twitter and their tweeting behavior concerning the sharing of web links. Discerning the domains, hosts and individual web pages being tweeted and the differences between computer scientists and a Twitter sample enables us to look in depth at the Twitter-based information sharing practices of a scientific community...
2017: PloS One
https://www.readbyqxmd.com/read/28635155/representation-and-computation-in-cognitive-models
#9
Kenneth D Forbus, Chen Liang, Irina Rabkina
One of the central issues in cognitive science is the nature of human representations. We argue that symbolic representations are essential for capturing human cognitive capabilities. We start by examining some common misconceptions found in discussions of representations and models. Next we examine evidence that symbolic representations are essential for capturing human cognitive capabilities, drawing on the analogy literature. Then we examine fundamental limitations of feature vectors and other distributed representations that, despite their recent successes on various practical problems, suggest that they are insufficient to capture many aspects of human cognition...
June 21, 2017: Topics in Cognitive Science
https://www.readbyqxmd.com/read/28633344/pheno4j-a-gene-to-phenotype-graph-database
#10
Sajid Mughal, Ismail Moghul, Jing Yu, Tristan Clark, David S Gregory, Nikolas Pontikos
Summary: Efficient storage and querying of large amounts of genetic and phenotypic data is crucial to contemporary clinical genetic research. This introduces computational challenges for classical relational databases, due to the sparsity and sheer volume of the data. Our Java based solution loads annotated genetic variants and well phenotyped patients into a graph database to allow fast efficient storage and querying of large volumes of structured genetic and phenotypic data. This abstracts technical problems away and lets researchers focus on the science rather than the implementation...
June 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28632436/development-of-computer-algorithm-for-editing-of-next-generation-sequencing-metagenome-data
#11
Radhika Khanna, Sangeeta Mittal, Sujata Mohanty
The successful implementation of the advanced sequencing technology, the next generation sequencing (NGS) motivates scientists from diverse fields of biological research especially from genomics and transcriptomics in generating large genomic data set to make their analysis more robust and come up with strong inference. However, exploiting this huge genomic data set becomes a challenge for the molecular biologists. To corroborate this problem, computational software and hardware are being developed in parallel and become an integral part of life science...
June 20, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/28631633/significance-of-vascular-endothelial-growth-factor-and-cd31-and-morphometric-analysis-of-microvessel-density-by-cd31-receptor-expression-as-an-adjuvant-tool-in-diagnosis-of-psoriatic-lesions-of-skin
#12
Nitika Chawla, Sant Prakash Kataria, Kamal Aggarwal, Pardeep Chauhan, Dinesh Kumar
BACKGROUND: Pathogenesis of psoriasis is a debated issue. Several mechanisms have been proposed to identify the etiology and pathogenesis so that specific treatments can be given to patients with psoriasis. AIMS: (1) To compare pattern and distribution of vascular endothelial growth factor (VEGF) and CD31 in patients with psoriasis and other psoriasiform lesions of skin. (2) To study the correlation between VEGF and CD31 expression, clinical severity, and histopathology of psoriasiform lesions of skin...
April 2017: Indian Journal of Pathology & Microbiology
https://www.readbyqxmd.com/read/28630968/designing-self-powered-materials-systems-that-perform-pattern-recognition
#13
Yan Fang, Victor V Yashin, Steven P Levitan, Anna C Balazs
Inspired by the advances in both materials and computer science, we describe efforts to design "materials that compute" where the material and the computer are the same entity. Using theory and simulation, we devise systems that integrate the behavior of self-oscillating gels and fundamental concepts from oscillator-based computing. We specifically focus on gels that undergo the Belousov-Zhabotinsky (BZ) reaction and thus exhibit self-sustained oscillations. In our models, we couple the BZ gel to an overlaying piezoelectric (PZ) cantilever to create a BZ-PZ unit...
June 20, 2017: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/28630033/trust-and-credibility-in-web-based-health-information-a-review-and-agenda-for-future-research
#14
Laura Sbaffi, Jennifer Rowley
BACKGROUND: Internet sources are becoming increasingly important in seeking health information, such that they may have a significant effect on health care decisions and outcomes. Hence, given the wide range of different sources of Web-based health information (WHI) from different organizations and individuals, it is important to understand how information seekers evaluate and select the sources that they use, and more specifically, how they assess their credibility and trustworthiness...
June 19, 2017: Journal of Medical Internet Research
https://www.readbyqxmd.com/read/28628732/understanding-neurophobia-reasons-behind-impaired-understanding-and-learning-of-neuroanatomy-in-cross-disciplinary-healthcare-students
#15
Muhammad Asim Javaid, Shelly Chakraborty, John F Cryan, Harriët Schellekens, André Toulouse
Recent studies have highlighted a fear or difficulty with the study and understanding of neuroanatomy among medical and healthcare students. This has been linked with a diminished confidence of clinical practitioners and students to manage patients with neurological conditions. The underlying reasons for this difficulty have been queried among a broad cohort of medical, dental, occupational therapy, and speech and language sciences students. Direct evidence of the students' perception regarding specific difficulties associated with learning neuroanatomy has been provided and some of the measures required to address these issues have been identified...
June 19, 2017: Anatomical Sciences Education
https://www.readbyqxmd.com/read/28626895/khat-chewing-habit-produces-a-significant-adverse-effect-on%C3%A2-periodontal-oral-health-a-systematic-review-and-meta-analysis
#16
REVIEW
M S Al-Akhali, E A Al-Moraissi
Although there is a general agreement that a khat chewing habit produces clinicopathological changes in the oral mucosa. However there is no reliable evidence of the effects of a khat chewing habit on the periodontal tissues. Thus, authors aimed to investigate the influence of khat chewing habits on periodontal, oral health, by comparing khat chewers to non-chewers in respect of gingival recession, periodontal pocketing depth and loss of attachment. A systematic review and meta-analysis were conducted based on the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines...
June 18, 2017: Journal of Periodontal Research
https://www.readbyqxmd.com/read/28626813/hallucinations-as-top-down-effects-on-perception
#17
Albert R Powers, Megan Kelley, Philip R Corlett
The problem of whether and how information is integrated across hierarchical brain networks embodies a fundamental tension in contemporary cognitive neuroscience, and by extension, cognitive neuropsychiatry. Indeed, the penetrability of perceptual processes in a 'top-down' manner by higher-level cognition-a natural extension of hierarchical models of perception-may contradict a strictly modular view of mental organization. Furthermore, some in the cognitive science community have challenged cognitive penetration as an unlikely, if not impossible, process...
September 2016: Biological Psychiatry: Cognitive Neuroscience and Neuroimaging
https://www.readbyqxmd.com/read/28621740/a-multi-disciplinary-approach-to-remote-sensing-through-low-cost-uavs
#18
Gabriela Calvario, Basilio Sierra, Teresa E Alarcón, Carmen Hernandez, Oscar Dalmau
The use of Unmanned Aerial Vehicles (UAVs) based on remote sensing has generated low cost monitoring, since the data can be acquired quickly and easily. This paper reports the experience related to agave crop analysis with a low cost UAV. The data were processed by traditional photogrammetric flow and data extraction techniques were applied to extract new layers and separate the agave plants from weeds and other elements of the environment. Our proposal combines elements of photogrammetry, computer vision, data mining, geomatics and computer science...
June 16, 2017: Sensors
https://www.readbyqxmd.com/read/28621324/marginal-bone-loss-around-non-submerged-implants-is-associated-with-salivary-microbiome-during-bone-healing
#19
Xiao-Bo Duan, Ting-Xi Wu, Yu-Chen Guo, Xue-Dong Zhou, Yi-Ling Lei, Xin Xu, An-Chun Mo, Yong-Yue Wang, Quan Yuan
Marginal bone loss during bone healing exists around non-submerged dental implants. The aim of this study was to identify the relationship between different degrees of marginal bone loss during bone healing and the salivary microbiome. One hundred patients were recruited, and marginal bone loss around their implants was measured using cone beam computed tomography during a 3-month healing period. The patients were divided into three groups according to the severity of marginal bone loss. Saliva samples were collected from all subjected and were analysed using 16S MiSeq sequencing...
June 16, 2017: International Journal of Oral Science
https://www.readbyqxmd.com/read/28621323/a-robust-methodology-for-the-quantitative-assessment-of-the-rat-jawbone-microstructure
#20
Marissa Chatterjee, Fernanda Faot, Cassia Correa, Joke Duyck, Ignace Naert, Katleen Vandamme
Micro-computed tomography can be applied for the assessment of the micro-architectural characteristics of the cortical and trabecular bones in either physiological or disease conditions. However, reports often lack a detailed description of the methodological steps used to analyse these images, such as the volumes of interest, the algorithms used for image filtration, the approach used for image segmentation, and the bone parameters quantified, thereby making it difficult to compare or reproduce the studies...
June 16, 2017: International Journal of Oral Science
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