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Global alignment

Gregory D M Potter, Debra J Skene, Josephine Arendt, Janet E Cade, Peter J Grant, Laura J Hardie
Circadian (∼ 24 hour) timing systems pervade all kingdoms of life, and temporally optimize behaviour and physiology in humans. Relatively recent changes to our environments, such as the introduction of artificial lighting, can disorganize the circadian system, from the level of the molecular clocks that regulate the timing of cellular activities to the level of synchronization between our daily cycles of behaviour and the solar day. Sleep/wake cycles are intertwined with the circadian system, and global trends indicate that these too are increasingly subject to disruption...
October 20, 2016: Endocrine Reviews
M C Burg, P Lunkenheimer, P Niederer, C Brune, K Redmann, M Smerup, U Spiegel, F Becker, D Maintz, W Heindel, R H Anderson
Purpose: There are ongoing arguments as to how cardiomyocytes are aggregated together within the ventricular walls. We used pneumatic distension through the coronary arteries to exaggerate the gaps between the aggregated cardiomyocytes, analyzing the pattern revealed using computed tomography, and validating our findings by histology. Methods: We distended 10 porcine hearts, arresting 4 in diastole by infusion of cardioplegic solutions, and 4 in systole by injection of barium chloride. Mural architecture was revealed by computed tomography, measuring also the angulations of the long chains of cardiomyocytes...
November 2016: RöFo: Fortschritte Auf Dem Gebiete der Röntgenstrahlen und der Nuklearmedizin
Udo A Ernst, Alina Schiffer, Malte Persike, Günter Meinhardt
Processing natural scenes requires the visual system to integrate local features into global object descriptions. To achieve coherent representations, the human brain uses statistical dependencies to guide weighting of local feature conjunctions. Pairwise interactions among feature detectors in early visual areas may form the early substrate of these local feature bindings. To investigate local interaction structures in visual cortex, we combined psychophysical experiments with computational modeling and natural scene analysis...
2016: Frontiers in Systems Neuroscience
Louis M Day, Subaraman Ramchandran, Cyrus M Jalai, Bassel G Diebo, Barthelemy Liabaud, Renaud Lafage, Themistocles Protopsaltis, Peter G Passias, Frank J Schwab, Shay Bess, Thomas J Errico, Virginie Lafage, Aaron J Buckland
STUDY DESIGN: Retrospective clinical and radiographic single-center study OBJECTIVE.: Assess simultaneous cervical spine and lower extremity compensatory changes with changes in thoracolumbar spinal alignment. SUMMARY OF BACKGROUND DATA: Full-body stereoradiographic imaging allows better understanding of reciprocal changes in cervical and lower extremity alignment in the setting of thoracolumbar malalignment. Few studies describe the simultaneous effect of alignment correction on these mechanisms...
October 17, 2016: Spine
Jan Bonhoeffer, Sonali Kochhar, Steven Hirschfeld, Paul T Heath, Christine E Jones, Jorgen Bauwens, Ángel Honrado, Ulrich Heininger, Flor M Muñoz, Linda Eckert, Mark Steinhoff, Steven Black, Michael Padula, Miriam Sturkenboom, Jim Buttery, Robert Pless, Patrick Zuber
Immunization in pregnancy provides a promising contribution to globally reducing neonatal and under-five childhood mortality and morbidity. Thorough assessment of benefits and risks for the primarily healthy pregnant women and their unborn babies is required. The GAIA project was formed in response to the call of the World Health Organization for a globally concerted approach to actively monitor the safety of vaccines and immunization in pregnancy programs. GAIA aims to improve the quality of outcome data from clinical vaccine trials in pregnant women with a specific focus on the needs and requirements for safety monitoring in LMIC...
October 14, 2016: Vaccine
Matthias Schuppler, Felix C Keber, Martin Kröger, Andreas R Bausch
Cells set up contractile actin arrays to drive various shape changes and to exert forces to their environment. To understand their assembly process, we present here a reconstituted contractile system, comprising F-actin and myosin II filaments, where we can control the local activation of myosin by light. By stimulating different symmetries, we show that the force balancing at the boundaries determine the shape changes as well as the dynamics of the global contraction. Spatially anisotropic attachment of initially isotropic networks leads to a self-organization of highly aligned contractile fibres, being reminiscent of the order formation in muscles or stress fibres...
October 14, 2016: Nature Communications
Aaron M Fleming, Yun Ding, Anton Alenko, Cynthia J Burrows
Zika virus has emerged as a global concern because neither a vaccine nor antiviral compounds targeting it exist. A structure for the positive-sense RNA genome has not been established, leading us to look for potential G-quadruplex sequences (PQS) in the genome. The analysis identified >60 PQSs in the Zika genome. To minimize the PQS population, conserved sequences in the Flaviviridae family were found by sequence alignment, identifying seven PQSs in the prM, E, NS1, NS3, and NS5 genes. Next, alignment of 78 Zika strain genomes identified a unique PQS near the end of the 3'-UTR...
October 14, 2016: ACS Infectious Diseases
Jonathan J Powell, Timothy L Fitzgerald, Jiri Stiller, Paul J Berkman, Donald M Gardiner, John M Manners, Robert J Henry, Kemal Kazan
Bread wheat (Triticum aestivum L.) is an allopolyploid species containing three ancestral genomes. Therefore, three homoeologous copies exist for the majority of genes in the wheat genome. Whether different homoeologs are differentially expressed (homoeolog expression bias) in response to biotic and abiotic stresses is poorly understood. In this study, we applied a RNA-seq approach to analyze homoeolog-specific global gene expression patterns in wheat during infection by the fungal pathogen Fusarium pseudograminearum, which causes crown rot disease in cereals...
October 13, 2016: Plant Biotechnology Journal
Yang Zhang, Chenglin Zhao, Juan Meng, Shibao Li, Li Li
It is very important that the radar sensor network has autonomous capabilities such as self-managing, etc. Quite often, MIMO interference channels are applied to radar sensor networks, and for self-managing purpose, interference management in MIMO interference channels is critical. Interference alignment (IA) has the potential to dramatically improve system throughput by effectively mitigating interference in multi-user networks at high signal-to-noise (SNR). However, the implementation of IA predominantly relays on perfect and global channel state information (CSI) at all transceivers...
2016: EURASIP Journal on Wireless Communications and Networking
Tiffeny R Jimenez, Bernadette Sánchez, Susan D McMahon, Judah Viola
As we reflect on the founding vision of the field of community psychology in the United States, we assess our progress toward achieving, building upon, and refining this vision. We review early literature regarding the US vision of the field, provide a historical overview of education and training within the field, and provide recommendations to guide and strengthen our approach to education. Our recommendations include the following: (a) serve as a resource to communities, (b) promote a sense of community within our field, (c) diversify students, faculty, and leadership, (d) evaluate our efforts, (e) be current and relevant, (f) enhance the visibility and growth of our field, and (g) create globally minded and innovative CPists...
October 11, 2016: American Journal of Community Psychology
C A Reddy, A Patel, C P Gyawali
BACKGROUND: High-resolution manometry (HRM) categorizes esophageal motor processes into specific Chicago Classification (CC) diagnoses, but the clinical impact of these motor diagnoses on symptom burden remain unclear. METHODS: Two hundred and eleven subjects (56.8±1.0 years, 66.8% F) completed symptom questionnaires (GERDQ, Mayo dysphagia questionnaire [MDQ], visceral sensitivity index, short-form 36, dominant symptom index, and global symptom severity [GSS] on a 100-mm visual analog scale) prior to HRM...
October 9, 2016: Neurogastroenterology and Motility: the Official Journal of the European Gastrointestinal Motility Society
Susannah Hopkins Leisher, Zheyi Teoh, Hanna Reinebrant, Emma Allanson, Hannah Blencowe, Jan Jaap Erwich, J Frederik Frøen, Jason Gardosi, Sanne Gordijn, A Metin Gülmezoglu, Alexander E P Heazell, Fleurisca Korteweg, Joy Lawn, Elizabeth M McClure, Robert Pattinson, Gordon C S Smith, Ӧzge Tunçalp, Aleena M Wojcieszek, Vicki Flenady
BACKGROUND: Each year, about 5.3 million babies die in the perinatal period. Understanding of causes of death is critical for prevention, yet there is no globally acceptable classification system. Instead, many disparate systems have been developed and used. We aimed to identify all systems used or created between 2009 and 2014, with their key features, including extent of alignment with the International Classification of Diseases (ICD) and variation in features by region, to inform the World Health Organization's development of a new global approach to classifying perinatal deaths...
October 5, 2016: BMC Pregnancy and Childbirth
Hu Cao, Yonggang Lu
With the rapid growth of known protein 3D structures in number, how to efficiently compare protein structures becomes an essential and challenging problem in computational structural biology. At present, many protein structure alignment methods have been developed. Among all these methods, flexible structure alignment methods are shown to be superior to rigid structure alignment methods in identifying structure similarities between proteins, which have gone through conformational changes. It is also found that the methods based on aligned fragment pairs (AFPs) have a special advantage over other approaches in balancing global structure similarities and local structure similarities...
October 6, 2016: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
Jasper J Koehorst, Edoardo Saccenti, Peter J Schaap, Vitor A P Martins Dos Santos, Maria Suarez-Diez
A functional comparative genome analysis is essential to understand the mechanisms underlying bacterial evolution and adaptation. Detection of functional orthologs using standard global sequence similarity methods faces several problems; the need for defining arbitrary acceptance thresholds for similarity and alignment length, lateral gene acquisition and the high computational cost for finding bi-directional best matches at a large scale. We investigated the use of protein domain architectures for large scale functional comparative analysis as an alternative method...
2016: F1000Research
Lejla Zunic, Doncho Donev
Higher education in Europe and in the Balkan's countries is undergoing major reforms. The Bologna Process was a major reform created with the claimed goal of providing responses to issues such as the public responsibility for higher education and research, higher education governance, the social dimension of higher education and research, and the values and roles of higher education and research in modern, globalized, and increasingly complex societies with the most demanding qualification needs. Changes in the curricula, modernization of facilities and their alignment with the programs of other European universities, employment of a larger number of assistants, especially in the clinical courses at our universities are necessary...
July 24, 2016: Materia Socio-medica
Patrick B F O'Connor, Dmitry E Andreev, Pavel V Baranov
Ribosome profiling (Ribo-seq), a promising technology for exploring ribosome decoding rates, is characterized by the presence of infrequent high peaks in ribosome footprint density and by long alignment gaps. Here, to reduce the impact of data heterogeneity we introduce a simple normalization method, Ribo-seq Unit Step Transformation (RUST). RUST is robust and outperforms other normalization techniques in the presence of heterogeneous noise. We illustrate how RUST can be used for identifying mRNA sequence features that affect ribosome footprint densities globally...
October 4, 2016: Nature Communications
Eike Quilling, Kevin Dadaczynski, Merle Müller
BACKGROUND: Childhood and adolescent overweight can still be seen as a global public health problem. Based on our socioeconomic understanding, overweight is the result of a complex interplay of a diverse array of factors acting on different levels. Hence, in addition to individual level determinants overweight prevention should also address environmental related factors as part of a holistic and integrated setting approach. OBJECTIVE: This paper aims to discuss the setting approach with regard to overweight prevention in childhood and adolescence...
September 30, 2016: Bundesgesundheitsblatt, Gesundheitsforschung, Gesundheitsschutz
Chris A Dejong, Gregory M Chen, Haoxin Li, Chad W Johnston, Mclean R Edwards, Philip N Rees, Michael A Skinnider, Andrew L H Webster, Nathan A Magarvey
Polyketides (PKs) and nonribosomal peptides (NRPs) are profoundly important natural products, forming the foundations of many therapeutic regimes. Decades of research have revealed over 11,000 PK and NRP structures, and genome sequencing is uncovering new PK and NRP gene clusters at an unprecedented rate. However, only ∼10% of PK and NRPs are currently associated with gene clusters, and it is unclear how many of these orphan gene clusters encode previously isolated molecules. Therefore, to efficiently guide the discovery of new molecules, we must first systematically de-orphan emergent gene clusters from genomes...
October 3, 2016: Nature Chemical Biology
Dmytro Guzenko, Sergei V Strelkov
MOTIVATION: Modern algorithms for de novo prediction of protein structures typically output multiple full-length models (decoys) rather than a single solution. Subsequent clustering of such decoys is used both to gauge the success of the modelling and to decide on the most native-like conformation. At the same time, partial protein models are sufficient for some applications such as crystallographic phasing by molecular replacement (MR) in particular, provided these models represent a certain part of the target structure with reasonable accuracy...
September 30, 2016: Bioinformatics
Linnea K Honeker, Robert A Root, Jon Chorover, Raina M Maier
Metal(loid)-contamination of the environment due to anthropogenic activities is a global problem. Understanding the fate of contaminants requires elucidation of biotic and abiotic factors that influence metal(loid) speciation from molecular to field scales. Improved methods are needed to assess micro-scale processes, such as those occurring at biogeochemical interfaces between plant tissues, microbial cells, and metal(loid)s. Here we present an advanced method that combines fluorescence in situ hybridization (FISH) with synchrotron-based multiple-energy micro-focused X-ray fluorescence microprobe imaging (ME μXRF) to examine colocalization of bacteria and metal(loid)s on root surfaces of plants used to phytostabilize metalliferous mine tailings...
September 29, 2016: Journal of Microbiological Methods
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