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https://www.readbyqxmd.com/read/28719743/machine-learning-on-samdi-mass-spectrometry-signal-to-noise-ratio-improves-peptide-array-designs
#1
Albert Yan Xue, Lindsey C Szymczak, Milan Mrksich, Neda Bagheri
Emerging peptide array technologies are able to profile molecular activities within cell lysates. However, the structural diversity of peptides leads to inherent differences in peptide signal to noise ratios (S/N). These complex effects can lead to potentially unrepresentative signal intensities and can bias subsequent analyses. Within mass spectrometry-based peptide technologies, the relation between a peptide's amino acid sequence and S/N remains largely non-quantitative. To address this challenge, we present a method to quantify and analyze mass spectrometry S/N of two peptide arrays, and we use this analysis to portray quality of data and to design future arrays for SAMDI mass spectrometry...
July 18, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28719722/learning-anatomy-through-thiel-vs-formalin-embalmed-cadavers-student-perceptions-of-embalming-methods-and-effect-on-functional-anatomy-knowledge
#2
Larissa Kennel, David M A Martin, Hannah Shaw, Tracey Wilkinson
Thiel-embalmed cadavers, which have been adopted for use in anatomy teaching in relatively few universities, show greater flexibility and color retention compared to formalin-embalmed cadavers, properties which might be considered advantageous for anatomy teaching. This study aimed to investigate student attitudes toward the dissection experience with Thiel- compared to formalin/ethanol-embalmed cadavers. It also aimed to determine if one embalming method is more advantageous in terms of learning functional anatomy through the comparison of student anterior forearm functional anatomy knowledge...
July 18, 2017: Anatomical Sciences Education
https://www.readbyqxmd.com/read/28719206/direct-quantum-dynamics-using-grid-based-wavefunction-propagation-and-machine-learned-potential-energy-surfaces
#3
Gareth W Richings, Scott Habershon
We describe a method for performing nuclear quantum dynamics calculations using standard, grid-based algorithms, including the multi configurational time-dependent Hartree (MCTDH) method, where the potential energy surface (PES) is calculated ``on-the-fly''. The method of Gaussian process regression (GPR) is used to construct a global representation of the PES using values of the energy at points distributed in molecular configuration space during the course of the wavepacket propagation. We demonstrate this direct dynamics approach for both an analytical PES function describing 3-dimensional proton transfer dynamics in malonaldehyde, and for 2- and 6-dimensional quantum dynamics simulations of proton transfer in salicylaldimine...
July 18, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28718848/label-free-high-throughput-holographic-screening-and-enumeration-of-tumor-cells-in-blood
#4
Dhananjay Kumar Singh, Caroline C Ahrens, Wei Li, Siva A Vanapalli
We introduce inline digital holographic microscopy (in-line DHM) as a label-free technique for detecting tumor cells in blood. The optimized DHM platform fingerprints every cell flowing through a microchannel at 10 000 cells per second, based on three features - size, maximum intensity and mean intensity. To identify tumor cells in a background of blood cells, we developed robust gating criteria using machine-learning approaches. We established classifiers from the features extracted from 100 000-cell training sets consisting of red blood cells, peripheral blood mononuclear cells and tumor cell lines...
July 18, 2017: Lab on a Chip
https://www.readbyqxmd.com/read/28718181/erythropoietin-for-cognitive-deficits-associated-with-schizophrenia-bipolar-disorder-and-major-depression-a-systematic-review
#5
Xian-Bin Li, Wei Zheng, Yu-Ping Ning, Dong-Bin Cai, Xin-Hu Yang, Gabor S Ungvari, Chee H Ng, Chuan-Yue Wang, Yu-Tao Xiang
Introduction The purpose of this study is to systematically review the efficacy and safety of adjunctive erythropoietin (EPO) in treating cognitive deficits associated with schizophrenia, bipolar disorder, and major depression based on randomized controlled trials (RCTs). Methods Two evaluators independently and systematically searched and selected studies, extracted data, and conducted quality assessment. Results Four RCTs with 144 patients (71 in the EPO group and 73 in the placebo group) met the study entry criteria...
July 17, 2017: Pharmacopsychiatry
https://www.readbyqxmd.com/read/28718087/speaking-two-languages-in-america-a-semantic-space-analysis-of-how-presidential-candidates-and-their-supporters-represent-abstract-political-concepts-differently
#6
Ping Li, Benjamin Schloss, D Jake Follmer
In this article we report a computational semantic analysis of the presidential candidates' speeches in the two major political parties in the USA. In Study One, we modeled the political semantic spaces as a function of party, candidate, and time of election, and findings revealed patterns of differences in the semantic representation of key political concepts and the changing landscapes in which the presidential candidates align or misalign with their parties in terms of the representation and organization of politically central concepts...
July 17, 2017: Behavior Research Methods
https://www.readbyqxmd.com/read/28717985/basic-echocardiography-for-undergraduate-students-a-comparison-of-different-peer-teaching-approaches
#7
G Gradl-Dietsch, A K Menon, A Gürsel, A Götzenich, N Hatam, A Aljalloud, S Schrading, F Hölzl, M Knobe
BACKGROUND: The aim of this study was to assess the impact of different teaching interventions in a peer-teaching environment on basic echocardiography skills and to examine the influence of gender on learning outcomes. METHODS: We randomly assigned 79 s year medical students (55 women, 24 men) to one of four groups: peer teaching (PT), peer teaching using Peyton's four-step approach (PPT), team based learning (TBL) and video-based learning (VBL). All groups received theoretical and practical hands-on training according to the different approaches...
July 17, 2017: European Journal of Trauma and Emergency Surgery: Official Publication of the European Trauma Society
https://www.readbyqxmd.com/read/28716785/imbuing-medical-professionalism-in-relation-to-safety-a-study-protocol-for-a-mixed-methods-intervention-focused-on-trialling-an-embedded-learning-approach-that-centres-on-the-use-of-a-custom-designed-board-game
#8
Marie Ward, Eilish McAuliffe, Éidín Ní Shé, Ann Duffy, Una Geary, Una Cunningham, Catherine Holland, Nick McDonald, Karen Egan, Christian Korpos
INTRODUCTION: Healthcare organisations have a responsibility for ensuring that the governance of workplace settings creates a culture that supports good professional practice. Encouraging such a culture needs to start from an understanding of the factors that make it difficult for health professionals to raise issues of concern in relation to patient safety. The focus of this study is to determine whether a customised education intervention, developed as part of the study, with interns and senior house officers (SHOs) can imbue a culture of medical professionalism in relation to patient safety and support junior doctors to raise issues of concern, while shaping a culture of responsiveness and learning...
July 17, 2017: BMJ Open
https://www.readbyqxmd.com/read/28716627/membrane-proteins-structures-a-review-on-computational-modeling-tools
#9
REVIEW
Jose G Almeida, Antonio J Preto, Panagiotis I Koukos, Alexandre M J J Bonvin, Irina S Moreira
BACKGROUND: Membrane proteins (MPs) play diverse and important functions in living organisms. They constitute 20% to 30% of the known bacterial, archaean and eukaryotic organisms' genomes. In humans, their importance is emphasized as they represent 50% of all known drug targets. Nevertheless, experimental determination of their three-dimensional (3D) structure has proven to be both time consuming and rather expensive, which has led to the development of computational algorithms to complement the available experimental methods and provide valuable insights...
July 14, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28716018/prediction-of-extubation-readiness-in-extremely-preterm-infants-by-the-automated-analysis-of-cardiorespiratory-behavior-study-protocol
#10
Wissam Shalish, Lara J Kanbar, Smita Rao, Carlos A Robles-Rubio, Lajos Kovacs, Sanjay Chawla, Martin Keszler, Doina Precup, Karen Brown, Robert E Kearney, Guilherme M Sant'Anna
BACKGROUND: Extremely preterm infants (≤ 28 weeks gestation) commonly require endotracheal intubation and mechanical ventilation (MV) to maintain adequate oxygenation and gas exchange. Given that MV is independently associated with important adverse outcomes, efforts should be made to limit its duration. However, current methods for determining extubation readiness are inaccurate and a significant number of infants fail extubation and require reintubation, an intervention that may be associated with increased morbidities...
July 17, 2017: BMC Pediatrics
https://www.readbyqxmd.com/read/28715685/metabolic-profile-study-of-7-8-dihydroxyflavone-in-monkey-plasma-using-high-performance-liquid-chromatography-tandem-mass-spectrometry
#11
Taoping Sun, Sijing Chen, Hao Huang, Tianqing Li, Wei Yang, Liegang Liu
7, 8-Dihydroxyflavone, as a high-affinity tropomyosin-receptor-kinase B agonist, can mimic the physiological actions of brain-derived neurotrophic factor and exert a variety of neurological actions in numerous models including Parkinsońs disease, depression, learning and memory. Nonetheless, a limited number of studies have been focused on its metabolism in mammal and no methodology has been reported for the determination of 7, 8-DHF and its metabolites. Herein, we developed a rapid, sensitive and accurate method using high performance liquid chromatography-tandem mass spectroscopy for the determination of 7, 8-DHF and its metabolites in monkey plasma...
July 4, 2017: Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences
https://www.readbyqxmd.com/read/28715336/combination-of-supervised-and-unsupervised-approaches-for-mirna-target-prediction
#12
Nafiseh Sedaghat, Mahmood Fathy, Mohammad Hossein Modarressi, Ali Shojaie
MicroRNAs (miRNAs) are short non-coding RNAs which target mRNAs by binding to them and regulating their expression. Involvement of miRNAs has been discovered in many diseases, so it is fruitful to investigate the miRNAs and their targets to develop new therapeutic ways by designing anti-miRNA oligonucleotides. There are various computational methods to predict the target genes, however, their precisions are not good enough. In this paper, we apply a two-step approach to refine the results of sequence-based prediction algorithms...
July 13, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28715326/joint-multi-leaf-segmentation-alignment-and-tracking-from-fluorescence-plant-videos
#13
Xi Yin, Xiaoming Liu, Jin Chen, David M Kramer
This paper proposes a novel framework for fluorescence plant video processing. The plant research community is interested in the leaf-level photosynthetic analysis within a plant. A prerequisite for such analysis is to segment all leaves, estimate their structures, and track them over time. We identify this as a joint multi-leaf segmentation, alignment, and tracking problem. First, leaf segmentation and alignment are applied on the last frame of a plant video to find a number of well-aligned leaf candidates...
July 17, 2017: IEEE Transactions on Pattern Analysis and Machine Intelligence
https://www.readbyqxmd.com/read/28715325/inference-based-similarity-search-in-randomized-montgomery-domains-for-privacy-preserving-biometric-identification
#14
Yi Wang, Jianwu Wan, Jun Guo, Yiu-Ming Cheung, Pong C Yuen
Similarity search is essential to many important applications and often involves searching at scale on high-dimensional data based on their similarity to a query. In biometric applications, recent vulnerability studies have shown that adversarial machine learning can compromise biometric recognition systems by exploiting the biometric similarity information. Existing methods for biometric privacy protection are in general based on pairwise matching of secured biometric templates and have inherent limitations in search efficiency and scalability...
July 14, 2017: IEEE Transactions on Pattern Analysis and Machine Intelligence
https://www.readbyqxmd.com/read/28715261/social-media-use-and-conduct-problems-in-emerging-adults
#15
Victoria L Galica, Anna Vannucci, Kaitlin M Flannery, Christine McCauley Ohannessian
Social media use has become pervasive in the lives of emerging adults. Although social media may provide individuals with positive opportunities for communication and learning, social media sites also may provide an outlet for youth conduct problems, such as bullying, harassment, and intentional hostility and aggression toward others. Yet, the relationship between social media use and conduct problems remains unclear. This study investigated the association between conduct disorder (CD) symptoms before age 15 and social media use during emerging adulthood in a large, nationally representative sample...
July 2017: Cyberpsychology, Behavior and Social Networking
https://www.readbyqxmd.com/read/28715259/teaching-principal-components-using-correlations
#16
Peter H Westfall, Andrea L Arias, Larry V Fulton
Introducing principal components (PCs) to students is difficult. First, the matrix algebra and mathematical maximization lemmas are daunting, especially for students in the social and behavioral sciences. Second, the standard motivation involving variance maximization subject to unit length constraint does not directly connect to the "variance explained" interpretation. Third, the unit length and uncorrelatedness constraints of the standard motivation do not allow re-scaling or oblique rotations, which are common in practice...
July 17, 2017: Multivariate Behavioral Research
https://www.readbyqxmd.com/read/28715190/chemical-topic-modeling-exploring-molecular-datasets-using-a-common-text-mining-approach
#17
Nadine Schneider, Nikolas Fechner, Gregory A Landrum, Nikolaus Stiefl
Big data is one of the key transformative factors which are increasingly influencing all aspects of modern life. Although this transformation brings vast opportunities it also generates novel challenges, not the least of which is organizing and searching this data deluge. The field of medicinal chemistry is not different: more and more data are being generated, for instance by technologies such as DNA encoded libraries, peptide libraries, text mining of large literature corpora, and new in silico enumeration methods...
July 17, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28715094/drosophila-mutants-lacking-octopamine-exhibit-impairment-in-aversive-olfactory-associative-learning
#18
Konstantin G Iliadi, Natalia Iliadi, Gabrielle L Boulianne
Octopamine is a biogenic amine in invertebrates that is considered a functional homolog of vertebrate norepinephrine, acting as a neurotransmitter, neuromodulator and neurohormone. Octopamine regulates many physiological processes such as metabolism, reproduction and different types of behaviour including learning and memory. Previous studies in insects led to the notion that acquisition of an olfactory memory depends on the octopaminergic system during appetitive (reward-based) learning, but not in the case of aversive (punishment-based) learning...
July 17, 2017: European Journal of Neuroscience
https://www.readbyqxmd.com/read/28715090/learning-based-automated-segmentation-of-the-carotid-artery-vessel-wall-in-dual-sequence-mri-using-subdivision-surface-fitting
#19
Shan Gao, Ronald Van't Klooster, Pieter H Kitslaar, Bram F Coolen, Alexandra M van den Berg, Loek P Smits, Rahil Shahzad, Denis P Shamonin, Patrick J H de Koning, Aart J Nederveen, Rob J van der Geest
PURPOSE: The quantification of vessel wall morphology and plaque burden requires vessel segmentation, which is generally performed by manual delineations. The purpose of our work is to develop and evaluate a new 3D model-based approach for carotid artery wall segmentation from dual-sequence MRI. METHODS: The proposed method segments the lumen and outer wall surfaces including the bifurcation region by fitting a subdivision surface constructed hierarchical-tree model to the image data...
July 17, 2017: Medical Physics
https://www.readbyqxmd.com/read/28714821/leaving-the-lecture-behind-putting-pubmed-instruction-into-the-hands-of-the-students
#20
Rose L Turner, Andrea M Ketchum, Melissa A Ratajeski, Charles B Wessel
This column describes the development of a one-shot PubMed instruction class for medical students at a health sciences library. Background information on the objective is presented and discussed in the context of educational practice literature. The new course design centers on a guided group method of instruction in order to integrate more active learning. Surveyed students reported that the method was an effective way to learn how to search PubMed and that they preferred it to a traditional lecture. Pros and cons of the method are offered for other health sciences libraries interested in presenting PubMed instruction in a similar manner...
July 2017: Medical Reference Services Quarterly
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