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Global alignment

Maureen Mackintosh, Julius Mugwagwa, Geoffrey Banda, Paula Tibandebage, Jires Tunguhole, Samuel Wangwe, Mercy Karimi Njeru
The benefits of local production of pharmaceuticals in Africa for local access to medicines and to effective treatment remain contested. There is scepticism among health systems experts internationally that production of pharmaceuticals in sub-Saharan Africa (SSA) can provide competitive prices, quality and reliability of supply. Meanwhile low-income African populations continue to suffer poor access to a broad range of medicines, despite major international funding efforts. A current wave of pharmaceutical industry investment in SSA is associated with active African government promotion of pharmaceuticals as a key sector in industrialization strategies...
March 19, 2018: Health Policy and Planning
Peter G Passias, Samantha R Horn, Nicholas J Frangella, Gregory W Poorman, Dennis Vasquez-Montes, Bassel G Diebo, Cole A Bortz, Frank A Segreto, John Y Moon, Peter L Zhou, Shaleen Vira, Akhila Sure, Bryan Beaubrun, Jared C Tishelman, Subaraman Ramchandran, Cyrus M Jalai, Wesley Bronson, Charles Wang, Virginie Lafage, Aaron J Buckland, Thomas J Errico
BACKGROUND: Prior studies have built a foundation for understanding compensation in adult spinal deformity (ASD) patients using full-body stereographic assessments. These mechanisms, in relation to age-adjusted alignment targets, have yet to be fully studied. The aim of this study is to assess lower limb compensatory mechanisms of patients failing to meet age-adjusted alignment goals. METHODS: ASD patients >40 y/o with full body baseline and follow-up radiographs were included...
March 16, 2018: World Neurosurgery
Xin Yu, Fatih Porikli
We tackle the challenge of constructing 64 pixels for each individual pixel of a thumbnail face image. We show that such an aggressive super-resolution objective can be attained by taking advantage of the global context and making the best use of the prior information portrayed by the image class. Our input image is so small (e.g., pixels) that it can be considered as a patch of itself. Thus, conventional patch-matching-based super-resolution solutions are unsuitable. In order to enhance the resolution while enforcing the global context, we incorporate a pixel-wise appearance similarity objective into a deconvolutional neural network, which allows efficient learning of mappings between low-resolution input images and their high-resolution counterparts in the training data set...
June 2018: IEEE Transactions on Image Processing: a Publication of the IEEE Signal Processing Society
Supratik Banerjee, Alexei G Kritsuk
Three-dimensional, compressible, magnetohydrodynamic turbulence of an isothermal, self-gravitating fluid is analyzed using two-point statistics in the asymptotic limit of large Reynolds numbers (both kinetic and magnetic). Following an alternative formulation proposed by Banerjee and Galtier [Phys. Rev. E 93, 033120 (2016)2470-004510.1103/PhysRevE.93.033120; J. Phys. A: Math. Theor. 50, 015501 (2017)1751-811310.1088/1751-8113/50/1/015501], an exact relation has been derived for the total energy transfer. This approach results in a simpler relation expressed entirely in terms of mixed second-order structure functions...
February 2018: Physical Review. E
Sen Wang, Xinxin Zuo, Chao Du, Runxiao Wang, Jiangbin Zheng, Ruigang Yang
This paper deals with the 3D reconstruction problem for dynamic non-rigid objects with a single RGB-D sensor. It is a challenging task as we consider the almost inevitable accumulation error issue in some previous sequential fusion methods and also the possible failure of surface tracking in a long sequence. Therefore, we propose a global non-rigid registration framework and tackle the drifting problem via an explicit loop closure. Our novel scheme starts with a fusion step to get multiple partial scans from the input sequence, followed by a pairwise non-rigid registration and loop detection step to obtain correspondences between neighboring partial pieces and those pieces that form a loop...
March 16, 2018: Sensors
Loïc Peter, Marcel Tella-Amo, Dzhoshkun Ismail Shakir, George Attilakos, Ruwan Wimalasundera, Jan Deprest, Sébastien Ourselin, Tom Vercauteren
PURPOSE: The standard clinical treatment of Twin-to-Twin transfusion syndrome consists in the photo-coagulation of undesired anastomoses located on the placenta which are responsible to a blood transfer between the two twins. While being the standard of care procedure, fetoscopy suffers from a limited field-of-view of the placenta resulting in missed anastomoses. To facilitate the task of the clinician, building a global map of the placenta providing a larger overview of the vascular network is highly desired...
March 15, 2018: International Journal of Computer Assisted Radiology and Surgery
Ryan B Scott, Jason Samaha, Ron Chrisley, Zoltan Dienes
While theories of consciousness differ substantially, the 'conscious access hypothesis', which aligns consciousness with the global accessibility of information across cortical regions, is present in many of the prevailing frameworks. This account holds that consciousness is necessary to integrate information arising from independent functions such as the specialist processing required by different senses. We directly tested this account by evaluating the potential for associative learning between novel pairs of subliminal stimuli presented in different sensory modalities...
March 12, 2018: Cognition
Brittney N Keel, Warren M Snelling
Ongoing developments and cost decreases in next-generation sequencing (NGS) technologies have led to an increase in their application, which has greatly enhanced the fields of genetics and genomics. Mapping sequence reads onto a reference genome is a fundamental step in the analysis of NGS data. Efficient alignment of the reads onto the reference genome with high accuracy is very important because it determines the global quality of downstream analyses. In this study, we evaluate the performance of three Burrows-Wheeler transform-based mappers, BWA, Bowtie2, and HISAT2, in the context of paired-end Illumina whole-genome sequencing of livestock, using simulated sequence data sets with varying sequence read lengths, insert sizes, and levels of genomic coverage, as well as five real data sets...
2018: Frontiers in Genetics
Chengxin Zhang, Wei Zheng, Peter L Freddolino, Yang Zhang
Homology-based transferal remains the major approach to computational protein function annotations, but it becomes increasingly unreliable when the sequence identity between query and template decreases below 30%. We propose a novel pipeline, MetaGO, to deduce Gene Ontology attributes of proteins by combining sequence homology-based annotation with low-resolution structure prediction and comparison, and partner's-homology based protein-protein network mapping. The pipeline was tested on a large-scale set of 1000 non-redundant proteins from the CAFA3 experiment...
March 10, 2018: Journal of Molecular Biology
Hyewon Lee, Marta Lomazzi, Aimee Lee, Raman Bedi
Oral diseases are a neglected epidemic affecting all ages globally and can substantially impact overall health and well-being. Even though most oral diseases are preventable and share major risk factors with other non-communicable diseases, integration of oral health into public health systems is still limited in both clinical and health policy perspectives. This Viewpoint aims to highlight oral health from a global health perspective, calling for all public health leaders to advocate for oral health of all...
March 12, 2018: Journal of Public Health Policy
'Ale'alani Dudoit, Matthew Iacchei, Richard R Coleman, Michelle R Gaither, William E Browne, Brian W Bowen, Robert J Toonen
The banded coral shrimp, Stenopus hispidus (Crustacea: Decapoda: Stenopodidea) is a popular marine ornamental species with a circumtropical distribution. The planktonic larval stage lasts ∼120-253 days, indicating considerable dispersal potential, but few studies have investigated genetic connectivity on a global scale in marine invertebrates. To resolve patterns of divergence and phylogeography of S. hispidus , we surveyed 525 bp of mitochondrial cytochrome c oxidase subunit I (COI) from 198 individuals sampled at 10 locations across ∼27,000 km of the species range...
2018: PeerJ
Rajiv Gandhi Govindaraj, Michal Brylinski
BACKGROUND: Detecting similar ligand-binding sites in globally unrelated proteins has a wide range of applications in modern drug discovery, including drug repurposing, the prediction of side effects, and drug-target interactions. Although a number of techniques to compare binding pockets have been developed, this problem still poses significant challenges. RESULTS: We evaluate the performance of three algorithms to calculate similarities between ligand-binding sites, APoc, SiteEngine, and G-LoSA...
March 9, 2018: BMC Bioinformatics
Aditi Jain, Jafar Hasan, Perumal Arumugam Desingu, Nagalingam R Sundaresan, Kaushik Chatterjee
Neonatal cardiomyocytes cultured on flat surfaces are commonly used as a model to study cardiac failure of diverse origin. A major drawback of such a system is that the cardiomyocytes do not exhibit alignment, organization and calcium transients, similar to the native heart. Therefore, there is a need to develop in vitro platforms that recapitulate the cellular microenvironment of the murine heart as organotypic models to study cardiovascular diseases. In this study, we report an engineered platform that mimics cardiac cell organization and function of the heart...
February 27, 2018: Colloids and Surfaces. B, Biointerfaces
Tao T Le, Charles G Prober
New digital platforms are transforming learning in higher education and providing high-quality education content at little or no cost. Educators can now reach large, even global audiences. Yet, many medical schools continue to develop and maintain custom but duplicative curricular content despite having limited faculty and financial resources. In addition, medical students are faced with a multitude of potentially unaligned curricula driven by the school, national licensing exams, and the students' own perceived clinical training needs...
March 6, 2018: Academic Medicine: Journal of the Association of American Medical Colleges
Martin Lindegren, Ben G Holt, Brian R MacKenzie, Carsten Rahbek
The global loss of biodiversity threatens unique biota and the functioning and services of ecosystems essential for human wellbeing. To safeguard biodiversity and ecosystem services, designating protected areas is crucial; yet the extent to which the existing placement of protection is aligned to meet these conservation priorities is questionable, especially in the oceans. Here we investigate and compare global patterns of multiple biodiversity components (taxonomic, phylogenetic and functional), ecosystem services and human impacts, with the coverage of marine protected areas across a nested spatial scale...
March 6, 2018: Scientific Reports
Max S Riley, Lawrence G Lenke, Todd M Chapman, Brenda A Sides, Kathy M Blanke, Michael P Kelly
BACKGROUND: Short-term studies have shown improved outcomes and alignment after posterior vertebral column resection for severe spinal deformity. Our goal was to report long-term changes in radiographic and health-related quality-of-life measures in a consecutive series of pediatric and adult patients undergoing posterior vertebral column resection with a minimum follow-up of 5 years. METHODS: We reviewed all patients undergoing posterior vertebral column resection by a single surgeon prior to January 1, 2010, at a single institution...
March 7, 2018: Journal of Bone and Joint Surgery. American Volume
C Jamsranjav, R S Reid, M E Fernández-Giménez, A Tsevlee, B Yadamsuren, M Heiner
Livestock-caused rangeland degradation remains a major policy concern globally and the subject of widespread scientific study. This concern persists in part because it is difficult to isolate the effects of livestock from climate and other factors that influence ecosystem conditions. Further, degradation studies seldom use multiple plant and soil indicators linked to a clear definition of and ecologically grounded framework for degradation assessment that distinguishes different levels of degradation. Here, we integrate two globally applicable rangeland degradation frameworks and apply them to a broad-scale empirical data set for the country of Mongolia...
March 6, 2018: Ecological Applications: a Publication of the Ecological Society of America
Hajime Suzuki, Masahiro Kasahara
BACKGROUND: The read length of single-molecule DNA sequencers is reaching 1 Mb. Popular alignment software tools widely used for analyzing such long reads often take advantage of single-instruction multiple-data (SIMD) operations to accelerate calculation of dynamic programming (DP) matrices in the Smith-Waterman-Gotoh (SWG) algorithm with a fixed alignment start position at the origin. Nonetheless, 16-bit or 32-bit integers are necessary for storing the values in a DP matrix when sequences to be aligned are long; this situation hampers the use of the full SIMD width of modern processors...
February 19, 2018: BMC Bioinformatics
Ye Li, Lei Chen, Jun Zhou, Xiurong Su, Taiwu Li
The gelsolin family proteins are best known for involvement in cytoskeletal rearrangement by controlling actin organization during a variety of cellular processes. Previously, a 1962 bp cDNA encoding a 41.7 kDa protein with three gelsolin-like domains (G domains) from Dendrorhynchus zhejiangensis was identified and named as DzGSN. In this study, the sequence and function of a novel member of the gelsolin family proteins from D. zhejiangensis have been analyzed. Sequence alignment indicates that DzGSN is highly homologous to human gelsolin (35% identity) and human CapG (36% identity)...
March 2, 2018: Protein Journal
Riccardo Barzaghi, Noemi Emanuela Cazzaniga, Carlo Iapige De Gaetani, Livio Pinto, Vincenza Tornatore
Global Navigation Satellite Systems (GNSS) receivers are nowadays commonly used in monitoring applications, e.g., in estimating crustal and infrastructure displacements. This is basically due to the recent improvements in GNSS instruments and methodologies that allow high-precision positioning, 24 h availability and semiautomatic data processing. In this paper, GNSS-estimated displacements on a dam structure have been analyzed and compared with pendulum data. This study has been carried out for the Eleonora D'Arborea (Cantoniera) dam, which is in Sardinia...
March 2, 2018: Sensors
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