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https://www.readbyqxmd.com/read/27914058/osprey-predicts-resistance-mutations-using-positive-and-negative-computational-protein-design
#1
Adegoke Ojewole, Anna Lowegard, Pablo Gainza, Stephanie M Reeve, Ivelin Georgiev, Amy C Anderson, Bruce R Donald
Drug resistance in protein targets is an increasingly common phenomenon that reduces the efficacy of both existing and new antibiotics. However, knowledge of future resistance mutations during pre-clinical phases of drug development would enable the design of novel antibiotics that are robust against not only known resistant mutants, but also against those that have not yet been clinically observed. Computational structure-based protein design (CSPD) is a transformative field that enables the prediction of protein sequences with desired biochemical properties such as binding affinity and specificity to a target...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27913989/cost-effectiveness-analysis-of-isavuconazole-vs-voriconazole-as-first-line-treatment-for-invasive-aspergillosis
#2
Rachel Harrington, Edward Lee, Hongbo Yang, Jin Wei, Andrew Messali, Nkechi Azie, Eric Q Wu, James Spalding
INTRODUCTION: Invasive aspergillosis (IA) is associated with a significant clinical and economic burden. The phase III SECURE trial demonstrated non-inferiority in clinical efficacy between isavuconazole and voriconazole. No studies have evaluated the cost-effectiveness of isavuconazole compared to voriconazole. The objective of this study was to evaluate the costs and cost-effectiveness of isavuconazole vs. voriconazole for the first-line treatment of IA from the US hospital perspective...
December 2, 2016: Advances in Therapy
https://www.readbyqxmd.com/read/27913967/the-texture-of-causal-construals-domain-specific-biases-shape-causal-inferences-from-discourse
#3
Brent Strickland, Ike Silver, Frank C Keil
We conducted five sets of experiments asking whether psychological and physical events are construed in broadly different manners concerning the underlying textures of their causes. In Experiments 1a-1d, we found a robust tendency to estimate fewer causes (but not effects) for psychological than for physical events; Experiment 2 showed a similar pattern of results when participants were asked to generate hypothetical causes and effects; Experiment 3 revealed a greater tendency to ascribe linear chains of causes (but not effects) to physical events; Experiment 4 showed that the expectation of linear chains was related to intuitions about deterministic processes; and Experiment 5 showed that simply framing a given ambiguous event in psychological versus physical terms is sufficient to induce changes in the patterns of causal inferences...
December 2, 2016: Memory & Cognition
https://www.readbyqxmd.com/read/27913961/prediction-of-postoperative-clinical-recovery-of-drop-foot-attributable-to-lumbar-degenerative-diseases-via-a-bayesian-network
#4
Shota Takenaka, Hiroyuki Aono
BACKGROUND: Drop foot resulting from degenerative lumbar diseases can impair activities of daily living. Therefore, predictors of recovery of this symptom have been investigated using univariate or/and multivariate analyses. However, the conclusions have been somewhat controversial. Bayesian network models, which are graphic and intuitive to the clinician, may facilitate understanding of the prognosis of drop foot resulting from degenerative lumbar diseases. QUESTIONS/PURPOSES: (1) To show a layered correlation among predictors of recovery from drop foot resulting from degenerative lumbar diseases; and (2) to develop support tools for clinical decisions to treat drop foot resulting from lumbar degenerative diseases...
December 2, 2016: Clinical Orthopaedics and related Research
https://www.readbyqxmd.com/read/27913833/tight-repulsion-linkage-between-sr36-and-sr39-was-revealed-by-genetic-cytogenetic-and-molecular-analyses
#5
Bosco Chemayek, Urmil K Bansal, Naeela Qureshi, Peng Zhang, William W Wagoire, Harbans S Bariana
The shortening of Aegilops speltoides segment did not facilitate recombination between stem rust resistance genes Sr36 and Sr39 . Robustness of marker rwgs28 for marker-assisted selection of Sr39 was demonstrated. Stem rust resistance genes Sr39 and Sr36 were transferred from Aegilops speltoides and Triticum timopheevii, respectively, to chromosome 2B of wheat. Genetic stocks RL6082 and RWG1 carrying Sr39 on a large and a shortened Ae. speltoides segments, respectively, and the Sr36-carrying Australian wheat cultivar Cook were used in this study...
December 2, 2016: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/27913617/evaluating-sequence-based-genomic-prediction-with-an-efficient-new-simulator
#6
Miguel Pérez-Enciso, Natalia Forneris, Gustavo de Los Campos, Andrés Legarra
The vast amount of sequence data to analyze complex traits is posing new challenges in terms of analysis and interpretation of the results. Although simulation is a fundamental tool to investigate the reliability of genomic analyses and to optimize experimental design, existing software cannot simulate complete genomes realistically. To remedy this, we have developed a new strategy (Sequence Based Virtual Breeding, SBVB) that consists of using real sequence data and simulating new offspring genomes and phenotypes in a very efficient and flexible manner...
December 2, 2016: Genetics
https://www.readbyqxmd.com/read/27913593/higher-heart-rate-variability-is-associated-with-vmpfc-activity-and-increased-resistance-to-temptation-in-dietary-self-control-challenges
#7
Silvia U Maier, Todd A Hare
: Higher levels of self-control in decision making have been linked to better psychosocial and physical health. A similar link to health outcomes has been reported for heart rate variability (HRV), a marker of physiological flexibility. Here, we sought to link these two, largely separate, research domains by testing the hypothesis that greater HRV would be associated with better dietary self-control in humans. Specifically, we examined whether total HRV at sedentary rest (measured as the standard deviation of normal-to-normal intervals, SDNN) can serve as a biomarker for the neurophysiological adaptability that putatively underlies self-controlled behavior...
December 2, 2016: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/27913590/control-of-spike-transfer-at-hippocampal-mossy-fiber-synapses-in-vivo-by-gabaa-and-gabab-receptor-mediated-inhibition
#8
Stefano Zucca, Marilena Griguoli, Meryl Malézieux, Noëlle Grosjean, Mario Carta, Christophe Mulle
: Despite extensive studies in hippocampal slices and incentive from computational theories, the synaptic mechanisms underlying information transfer at mossy fiber (mf) connections between the dentate gyrus (DG) and CA3 neurons in vivo are still elusive. Here we used an optogenetic approach in mice to selectively target and control the activity of DG granule cells (GCs) while performing whole cell and juxtacellular recordings of CA3 neurons in vivo In CA3 pyramidal cells (PCs), mf-CA3 synaptic responses consisted predominantly of an inhibitory postsynaptic potential (IPSP) at low stimulation frequency (0...
December 2, 2016: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/27913477/the-value-of-quality-of-life-assessment-in-chronic-myeloid-leukemia-patients-receiving-tyrosine-kinase-inhibitors
#9
Fabio Efficace, Laura Cannella
The development of the oral tyrosine kinase inhibitors (TKIs) to treat chronic myeloid leukemia (CML) is one of the great triumphs of cancer research. Although the efficacy of TKIs has dramatically improved the disease-specific overall survival rate, the prevalence of CML is increasing worldwide. Currently, CML patients receive prolonged (even lifelong) treatment, and over the last decade, clinical decision making has become challenging. Therefore, consideration of the effects of TKI therapies on patients' quality of life (QoL) and symptom burden (ie, patient-reported outcomes [PROs]) is now critical to more robustly inform patient care and improve health care quality...
December 2, 2016: Hematology—the Education Program of the American Society of Hematology
https://www.readbyqxmd.com/read/27913368/content-driven-associative-memories-for-color-image-patterns
#10
Mingming Li, Shuzhi Sam Ge, Tong Heng Lee
This paper presents a novel content-driven associative memory (CDAM) to associate large-scale color images based on the subjects that represent the images' content. Compared to traditional associative memories, CDAM inherits their tolerance to random noise in images and possesses greater robustness against correlated noise that distorts an image's spatial contextual structure. A three-layer recurrent neural tensor network (RNTN) is designed as the network model of CDAM. Multiple salient objects detection algorithm and partial radial basis function (PRBF) kernel are proposed for subject determination and content-driven association, respectively...
November 29, 2016: IEEE Transactions on Cybernetics
https://www.readbyqxmd.com/read/27913358/conformational-sampling-of-a-biomolecular-rugged-energy-landscape
#11
Jakub Rydzewski, Rafal Jakubowski, Giuseppe Nicosia, Wieslaw Nowak
The protein structure refinement using conformational sampling is important in hitherto protein studies. In this paper we examined the protein structure refinement by means of potential energy minimization using immune computing as a method of sampling conformations. The method was tested on the x-ray structure and 30 decoys of the mutant of [Leu]Enkephalin, a paradigmatic example of the biomolecular multiple-minima problem. In order to score the refined conformations, we used a standard potential energy function with the OPLSAA force field...
December 1, 2016: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/27913349/adaptive-cascade-regression-model-for-robust-face-alignment
#12
Qingshan Liu, Jiankang Deng, Jing Yang, Guangcan Liu, Dacheng Tao
Cascade regression is a popular face alignment approach, and it has achieved good performances on the wild databases. However, it depends heavily on local features in estimating reliable landmark locations and therefore suffers from corrupted images, such as images with occlusion, which often exists in real-world face images. In this paper, we present a new adaptive cascade regression model for robust face alignment. In each iteration, the shape-indexed appearance is introduced to estimate the occlusion level of each landmark, and each landmark is then weighted according to its estimated occlusion level...
December 1, 2016: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
https://www.readbyqxmd.com/read/27913346/automatic-design-of-high-sensitivity-color-filter-arrays-with-panchromatic-pixels
#13
Jia Li, Chenyan Bai, Zhouchen Lin, Jian Yu
In most of existing digital cameras, color images have to be reconstructed from raw images which only have one color sensed at each pixel, as their imaging sensors are covered by color filter arrays (CFAs). At each pixel a CFA usually allows only a portion of the light spectrum to pass through and thereby reduces the light sensitivity of pixels. To address this issue, previous works have explored adding panchromatic pixels into CFAs. However, almost all existing methods assign panchromatic pixels empirically, making the designed CFAs prone to aliasing artifacts...
December 1, 2016: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
https://www.readbyqxmd.com/read/27913331/lamb-wave-multitouch-ultrasonic-touchscreen
#14
Kamyar Firouzi, Amin Nikoozadeh, Thomas E Carver, Butrus Pierre T Khuri-Yakub
Touchscreen sensors are widely used in many devices such as smart phones, tablets, and laptops with diverse applications. We present the design, analysis, and implementation of an ultrasonic touchscreen system that utilizes the interaction of transient Lamb waves with objects in contact with the screen. It attempts to improve on the existing ultrasound technologies, with the potential of addressing some of the weaknesses of the dominant technologies, such as the capacitive or resistive ones. Compared with the existing ultrasonic and acoustic modalities, among other advantages, it provides the capability of detecting several simultaneous touch points and also a more robust performance...
December 2016: IEEE Transactions on Ultrasonics, Ferroelectrics, and Frequency Control
https://www.readbyqxmd.com/read/27913324/beamforming-through-regularized-inverse-problems-in-ultrasound-medical-imaging
#15
Teodora Szasz, Adrian Basarab, Denis Kouame
Beamforming (BF) in ultrasound (US) imaging has significant impact on the quality of the final image, controlling its resolution and contrast. Despite its low spatial resolution and contrast, delay-and-sum (DAS) is still extensively used nowadays in clinical applications, due to its real-time capabilities. The most common alternatives are minimum variance (MV) method and its variants, which overcome the drawbacks of DAS, at the cost of higher computational complexity that limits its utilization in real-time applications...
December 2016: IEEE Transactions on Ultrasonics, Ferroelectrics, and Frequency Control
https://www.readbyqxmd.com/read/27913322/automatic-detection-and-classification-of-high-frequency-oscillations-in-depth-eeg-signals
#16
Nisrine Jrad, Amar Kachenoura, Isabelle Merlet, Fabrice Bartolomei, Anca Nica, Arnaud Biraben, Fabrice Wendling
GOAL: Interictal High Frequency Oscillations (HFOs [30-600 Hz]) have proven to be relevant biomarkers in epilepsy. In this paper, four categories of HFOs are considered: Gamma ([30- 80 Hz]), High-Gamma ([80-120 Hz]), Ripples ([120-250 Hz]) and Fast-Ripples ([250-600 Hz]). A universal detector of the four types of HFOs is proposed. It has the advantages of i) classifying HFOs, and thus being robust to inter- and intra-subject variability; ii) rejecting artefacts, thus being specific. METHODS: Gabor atoms are tuned to cover the physiological bands...
November 29, 2016: IEEE Transactions on Bio-medical Engineering
https://www.readbyqxmd.com/read/27913321/deterioration-of-r-wave-detection-in-pathology-and-noise-a-comprehensive-analysis-using-simultaneous-truth-and-performance-level-estimation
#17
Muhammad Kashif, Stephan Jonas, Thomas Deserno
OBJECTIVE: For long-term electrocardiography (ECG) recordings, accurate R-wave detection is essential. Several algorithms have been proposed but not yet compared on large, noisy, or pathological data, since manual ground truth establishment is impossible on such large data. METHODS: We apply the simultaneous truth and performance level estimation (STAPLE) method to ECG signals comparing 9 R-wave detectors: Pan & Tompkins (1985), Chernenko (2007), Arzeno et al. (2008), Manikandan et al...
December 1, 2016: IEEE Transactions on Bio-medical Engineering
https://www.readbyqxmd.com/read/27913294/sleep-mediated-memory-consolidation-depends-on-the-level-of-integration-at-encoding
#18
Lea Himmer, Elias Müller, Steffen Gais, Monika Schönauer
There is robust evidence that sleep facilitates declarative memory consolidation. Integration of newly acquired memories into existing neocortical knowledge networks has been proposed to underlie this effect. Here, we test whether sleep affects memory retention for word-picture associations differently when it was learned explicitly or using a fast mapping strategy. Fast mapping is an incidental form of learning that references new information to existing knowledge and possibly allows neocortical integration already during encoding...
November 29, 2016: Neurobiology of Learning and Memory
https://www.readbyqxmd.com/read/27913216/spatiotopic-updating-across-saccades-revealed-by-spatially-specific-fmri-adaptation
#19
Scott L Fairhall, Jens Schwarzbach, Angelika Lingnau, Martijn Gerbrand Van Koningsbruggen, David Melcher
Brain representations of visual space are predominantly eye-centred (retinotopic) yet our experience of the world is largely world-centred (spatiotopic). A long-standing question is how the brain creates continuity between these reference frames across successive eye movements (saccades). Here we use functional magnetic resonance imaging (fMRI) to address whether spatially specific repetition suppression (RS) is evident during trans-saccadic perception. We presented two successive Gabor patches (S1 and S2) in either the upper or lower visual field, left or right of fixation...
November 29, 2016: NeuroImage
https://www.readbyqxmd.com/read/27913168/fermentative-production-of-high-titer-citric-acid-from-corn-stover-feedstock-after-dry-dilute-acid-pretreatment-and-biodetoxification
#20
Ping-Ping Zhou, Jiao Meng, Jie Bao
The aim of this work is to study the citric acid fermentation by a robust strain Aspergillus niger SIIM M288 using corn stover feedstock after dry dilute sulfuric acid pretreatment and biodetoxification. Citric acid at 100.04g/L with the yield of 94.11% was obtained, which are comparable to the starch or sucrose based citric acid fermentation. No free wastewater was generated in the overall process from the pretreatment to citric acid fermentation. Abundant divalent metal ions as well as high titer of potassium, phosphate, and nitrogen were found in corn stover hydrolysate...
November 15, 2016: Bioresource Technology
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