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https://www.readbyqxmd.com/read/27914056/parallel-computational-protein-design
#1
Yichao Zhou, Bruce R Donald, Jianyang Zeng
Computational structure-based protein design (CSPD) is an important problem in computational biology, which aims to design or improve a prescribed protein function based on a protein structure template. It provides a practical tool for real-world protein engineering applications. A popular CSPD method that guarantees to find the global minimum energy solution (GMEC) is to combine both dead-end elimination (DEE) and A* tree search algorithms. However, in this framework, the A* search algorithm can run in exponential time in the worst case, which may become the computation bottleneck of large-scale computational protein design process...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914051/integration-of-molecular-dynamics-based-predictions-into-the-optimization-of-de-novo-protein-designs-limitations-and-benefits
#2
Henrique F Carvalho, Arménio J M Barbosa, Ana C A Roque, Olga Iranzo, Ricardo J F Branco
Recent advances in de novo protein design have gained considerable insight from the intrinsic dynamics of proteins, based on the integration of molecular dynamics simulations protocols on the state-of-the-art de novo protein design protocols used nowadays. With this protocol we illustrate how to set up and run a molecular dynamics simulation followed by a functional protein dynamics analysis. New users will be introduced to some useful open-source computational tools, including the GROMACS molecular dynamics simulation software package and ProDy for protein structural dynamics analysis...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27914032/on-measuring-advances-in-human-arts-one-step-at-a-time
#3
EDITORIAL
David F Albertini
No abstract text is available yet for this article.
December 2, 2016: Journal of Assisted Reproduction and Genetics
https://www.readbyqxmd.com/read/27913545/what-have-we-learned-from-large-population-studies-of-von-willebrand-disease
#4
Robert R Montgomery, Veronica H Flood
Von Willebrand factor (VWF) is a critical regulator of hemostatic processes, including collagen binding, platelet adhesion, and platelet aggregation. It also serves as a carrier protein to normalize plasma factor VIII synthesis, release, and survival. While VWF protein measurements by immunoassay are reasonably comparable between institutions, the measurement of VWF ristocetin cofactor activity (VWF:RCo) has significant variability. Other tests of VWF function, including collagen binding or platelet glycoprotein IIb-IIIa binding, are not universally available, yet these functional defects may cause major bleeding even with normal VWF antigen (VWF:Ag) and VWF:RCo assays...
December 2, 2016: Hematology—the Education Program of the American Society of Hematology
https://www.readbyqxmd.com/read/27913371/multiview-convolutional-neural-networks-for-multidocument-extractive-summarization
#5
Yong Zhang, Meng Joo Er, Rui Zhao, Mahardhika Pratama
Multidocument summarization has gained popularity in many real world applications because vital information can be extracted within a short time. Extractive summarization aims to generate a summary of a document or a set of documents by ranking sentences and the ranking results rely heavily on the quality of sentence features. However, almost all previous algorithms require hand-crafted features for sentence representation. In this paper, we leverage on word embedding to represent sentences so as to avoid the intensive labor in feature engineering...
November 28, 2016: IEEE Transactions on Cybernetics
https://www.readbyqxmd.com/read/27913362/learning-to-predict-eye-fixations-via-multiresolution-convolutional-neural-networks
#6
Nian Liu, Junwei Han, Tianming Liu, Xuelong Li
Eye movements in the case of freely viewing natural scenes are believed to be guided by local contrast, global contrast, and top-down visual factors. Although a lot of previous works have explored these three saliency cues for several years, there still exists much room for improvement on how to model them and integrate them effectively. This paper proposes a novel computation model to predict eye fixations, which adopts a multiresolution convolutional neural network (Mr-CNN) to infer these three types of saliency cues from raw image data simultaneously...
November 29, 2016: IEEE Transactions on Neural Networks and Learning Systems
https://www.readbyqxmd.com/read/27913356/a-framework-for-integrating-multiple-biological-networks-to-predict-microrna-disease-associations
#7
Wei Peng, Wei Lan, Zeng Yu, Jianxin Wang, Yi Pan
MicroRNAs have close relationship with human diseases. Therefore, identifying disease related MicroRNAs plays an important role in disease diagnosis, prognosis and therapy. However, designing an effective computational method which can make good use of various biological resources and correctly predict the associations between MicroRNA and disease is still a big challenge. Previous researchers have pointed out that there are complex relationships among microRNAs, diseases and environment factors. There are inter-relationships between microRNAs, diseases or environment factors based on their functional similarity or phenotype similarity or chemical structure similarity and so on...
November 29, 2016: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/27913351/adaptive-multispectral-demosaicking-based-on-frequency-domain-analysis-of-spectral-correlation
#8
Sunil Jaiswal, Lu Fang, Vinit Jakhetiya, Jiahao Pang, Klaus Mueller, Oscar C Au
Color filter array (CFA) interpolation, or 3-band demosaicking, is a process of interpolating the missing color samples in each band to reconstruct a full color image. In this paper, we are concerned with the challenging problem of multispectral demosaicking, where each band is significantly undersampled due to the increment in the number of bands. Specifically, we demonstrate a frequency-domain analysis of the subsampled color-difference signal and observe that the conventional assumption of highly correlated spectral bands for estimating undersampled components is not precise...
December 1, 2016: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
https://www.readbyqxmd.com/read/27913349/adaptive-cascade-regression-model-for-robust-face-alignment
#9
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/27913345/facial-age-estimation-with-age-difference
#10
Zhenzhen Hu, Yonggang Wen, Jianfeng Wang, Meng Wang, Richang Hong, Shuicheng Yan
Age estimation based on the human face remains a significant problem in computer vision and pattern recognition. In order to estimate an accurate age or age group of a facial image, most of the existing algorithms require a huge face data set attached with age labels. This imposes a constraint on the utilization of the immensely unlabeled or weakly labeled training data, e.g. the huge amount of human photos in the social networks. These images may provide no age label, but it is easily to derive the age difference for an image pair of the same person...
December 1, 2016: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
https://www.readbyqxmd.com/read/27912899/-art-on-art-off-the-expanding-horizon-of-arterial-grafting
#11
EDITORIAL
Saswata Deb, Stephen E Fremes
No abstract text is available yet for this article.
November 3, 2016: Journal of Thoracic and Cardiovascular Surgery
https://www.readbyqxmd.com/read/27911921/what-is-the-economic-burden-of-subsidized-hiv-aids-treatment-services-on-patients-in-nigeria-and-is-this-burden-catastrophic-to-households
#12
Enyi Etiaba, Obinna Onwujekwe, Kwasi Torpey, Benjamin Uzochukwu, Robert Chiegil
BACKGROUND: A gap in knowledge exists regarding the economic burden on households of subsidized anti-retroviral treatment (ART) programs in Nigeria. This is because patients also incur non-ART drug costs, which may constrain the delivery and utilisation of subsidized services. METHODS: An exit survey of adults (18+years) attending health facilities for HIV/AIDS treatment was conducted in three states in Nigeria (Adamawa, Akwa Ibom and Anambra). In the states, ART was fully subsidized but there were different payment modalities for other costs of treatment...
2016: PloS One
https://www.readbyqxmd.com/read/27911588/pulmonary-innate-immune-dysfunction-in-hiv
#13
Bashar S Staitieh, Eduardo E Egea, David M Guidot
The advent of anti-retroviral therapy (ART) has transformed infection by the type 1 human immunodeficiency virus (HIV) from a rapidly fatal disease to a chronic illness with excellent long-term survival rates. Although HIV primarily targets the adaptive arm of host immunity, it simultaneously impacts the innate immune system and has profound implications for lung health even when viral suppression is achieved with ART. The lung has evolved a unique array of innate immune defenses and the pathophysiological interactions between HIV and the pulmonary innate immune system deserve particular attention...
December 2, 2016: American Journal of Respiratory Cell and Molecular Biology
https://www.readbyqxmd.com/read/27911562/macroscopic-model-for-head-on-binary-droplet-collisions-in-a-gaseous-medium
#14
Jie Li
In this Letter, coalescence-bouncing transitions of head-on binary droplet collisions are predicted by a novel macroscopic model based entirely on fundamental laws of physics. By making use of the lubrication theory of Zhang and Law [Phys. Fluids 23, 042102 (2011)], we have modified the Navier-Stokes equations to accurately account for the rarefied nature of the interdroplet gas film. Through the disjoint pressure model, we have incorporated the intermolecular van der Waals forces. Our model does not use any adjustable (empirical) parameters...
November 18, 2016: Physical Review Letters
https://www.readbyqxmd.com/read/27911530/experimental-ten-photon-entanglement
#15
Xi-Lin Wang, Luo-Kan Chen, W Li, H-L Huang, C Liu, C Chen, Y-H Luo, Z-E Su, D Wu, Z-D Li, H Lu, Y Hu, X Jiang, C-Z Peng, L Li, N-L Liu, Yu-Ao Chen, Chao-Yang Lu, Jian-Wei Pan
We report the first experimental demonstration of quantum entanglement among ten spatially separated single photons. A near-optimal entangled photon-pair source was developed with simultaneously a source brightness of ∼12  MHz/W, a collection efficiency of ∼70%, and an indistinguishability of ∼91% between independent photons, which was used for a step-by-step engineering of multiphoton entanglement. Under a pump power of 0.57 W, the ten-photon count rate was increased by about 2 orders of magnitude compared to previous experiments, while maintaining a state fidelity sufficiently high for proving the genuine ten-particle entanglement...
November 18, 2016: Physical Review Letters
https://www.readbyqxmd.com/read/27911140/effect-of-secondary-preventive-therapy-on-recurrence-of-tuberculosis-in-hiv-infected-individuals-a-systematic-review
#16
Wassilis Sc Bruins, Frank van Leth
Human immunodeficiency virus (HIV)-infected individuals successfully treated for tuberculosis (TB) remain at risk of recurrence of the disease, especially in high TB incidence settings. We performed a systematic review, investigating whether secondary preventive therapy (sPT) with anti-TB drugs (preventive therapy in former TB patients with treatment success) is an effective strategy to prevent recurrence of TB in this patient group. We searched the databases PubMed, Cochrane Library, EMBASE, Web of Science and Google Scholar using the keywords HIV-infections, HIV, human immunodeficiency virus, AIDS, isoniazid, isoniazid preventive therapy (IPT), tuberculosis, TB, recurrence and recurrent disease, resulting in 253 potential publications...
December 2, 2016: Infectious Diseases
https://www.readbyqxmd.com/read/27911122/an-update-on-the-use-of-cerebrospinal-fluid-analysis-as-a-diagnostic-tool-in-multiple-sclerosis
#17
Matteo Gastaldi, Elisabetta Zardini, Diego Franciotta
Intrathecal B-lymphocyte activation is a hallmark of multiple sclerosis (MS), a multi-factorial inflammatory-demyelinating disease of the central nervous system. Such activation has a counterpart in the cerebrospinal fluid (CSF) oligoclonal IgG bands (OCB), whose diagnostic role in MS has been downgraded within the current McDonald's criteria. With a theoretico-practical approach, the authors review the physiopathological basis of the CSF dynamics, and the state-of-the-art of routine CSF analysis and CSF biomarkers in MS...
December 2, 2016: Expert Review of Molecular Diagnostics
https://www.readbyqxmd.com/read/27911037/decoding-the-molecular-basis-for-the-population-mechanism-of-the-triplet-phototoxic-precursors-in-uva-light-activated-pyrimidine-anticancer-drugs
#18
Lara Martínez-Fernández, Giovanni Granucci, Marvin Pollum, Carlos Crespo-Hernández, Maurizio Persico, Ines Corral Perez
Photosensitization of DNA by thionucleosides is a promising photo-chemotherapeutic treatment option for a variety of malignancies. DNA metabolization of thiated prodrugs can lead to cell death upon exposure to a low dose of UVA light. The exact mechanisms of thionucleoside phototoxicity are still not fully understood. In this work, we have combined femtosecond broadband transient absorption experiments with state-of-the-art molecular simulations to provide mechanistic insights for the ultrafast and efficient population of the triplet-state in the UVA-activated pyrimidine anticancer drug: 4-thiothymine...
December 2, 2016: Chemistry: a European Journal
https://www.readbyqxmd.com/read/27911036/properties-of-embryoid-bodies
#19
REVIEW
Joshua M Brickman, Palle Serup
Embryoid bodies (EBs) have been popular in vitro differentiation models for pluripotent stem cells for more than five decades. Initially, defined as aggregates formed by embryonal carcinoma cells, EBs gained more prominence after the derivation of karyotypically normal embryonic stem cells from early mouse blastocysts. In many cases, formation of EBs constitutes an important initial step in directed differentiation protocols aimed at generated specific cell types from undifferentiated stem cells. Indeed state-of-the-art protocols for directed differentiation of cardiomyocytes still rely on this initial EB step...
December 2, 2016: Wiley Interdisciplinary Reviews. Developmental Biology
https://www.readbyqxmd.com/read/27910941/rapid-mapping-of-polarization-switching-through-complete-information-acquisition
#20
Suhas Somnath, Alex Belianinov, Sergei V Kalinin, Stephen Jesse
Polarization switching in ferroelectric and multiferroic materials underpins a broad range of current and emergent applications, ranging from random access memories to field-effect transistors, and tunnelling devices. Switching in these materials is exquisitely sensitive to local defects and microstructure on the nanometre scale, necessitating spatially resolved high-resolution studies of these phenomena. Classical piezoresponse force microscopy and spectroscopy, although providing necessary spatial resolution, are fundamentally limited in data acquisition rates and energy resolution...
December 2, 2016: Nature Communications
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