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https://www.readbyqxmd.com/read/28717961/determining-the-optimal-forensic-dna-analysis-procedure-following-investigation-of-sample-quality
#1
Ronny Hedell, Johannes Hedman, Petter Mostad
Crime scene traces of various types are routinely sent to forensic laboratories for analysis, generally with the aim of addressing questions about the source of the trace. The laboratory may choose to analyse the samples in different ways depending on the type and quality of the sample, the importance of the case and the cost and performance of the available analysis methods. Theoretically well-founded guidelines for the choice of analysis method are, however, lacking in most situations. In this paper, it is shown how such guidelines can be created using Bayesian decision theory...
July 17, 2017: International Journal of Legal Medicine
https://www.readbyqxmd.com/read/28706740/action-video-game-experience-related-to-altered-large-scale-white-matter-networks
#2
Diankun Gong, Weiyi Ma, Jinnan Gong, Hui He, Li Dong, Dan Zhang, Jianfu Li, Cheng Luo, Dezhong Yao
With action video games (AVGs) becoming increasingly popular worldwide, the cognitive benefits of AVG experience have attracted continuous research attention over the past two decades. Research has repeatedly shown that AVG experience can causally enhance cognitive ability and is related to neural plasticity in gray matter and functional networks in the brain. However, the relation between AVG experience and the plasticity of white matter (WM) network still remains unclear. WM network modulates the distribution of action potentials, coordinating the communication between brain regions and acting as the framework of neural networks...
2017: Neural Plasticity
https://www.readbyqxmd.com/read/28706301/a-haystack-heuristic-for-autoimmune-disease-biomarker-discovery-using-next-gen-immune-repertoire-sequencing-data
#3
Leonard Apeltsin, Shengzhi Wang, H-Christian von Büdingen, Marina Sirota
Large-scale DNA sequencing of immunological repertoires offers an opportunity for the discovery of novel biomarkers for autoimmune disease. Available bioinformatics techniques however, are not adequately suited for elucidating possible biomarker candidates from within large immunosequencing datasets due to unsatisfactory scalability and sensitivity. Here, we present the Haystack Heuristic, an algorithm customized to computationally extract disease-associated motifs from next-generation-sequenced repertoires by contrasting disease and healthy subjects...
July 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28705239/nap-the-network-analysis-profiler-a-web-tool-for-easier-topological-analysis-and-comparison-of-medium-scale-biological-networks
#4
Theodosios Theodosiou, Georgios Efstathiou, Nikolas Papanikolaou, Nikos C Kyrpides, Pantelis G Bagos, Ioannis Iliopoulos, Georgios A Pavlopoulos
OBJECTIVE: Nowadays, due to the technological advances of high-throughput techniques, Systems Biology has seen a tremendous growth of data generation. With network analysis, looking at biological systems at a higher level in order to better understand a system, its topology and the relationships between its components is of a great importance. Gene expression, signal transduction, protein/chemical interactions, biomedical literature co-occurrences, are few of the examples captured in biological network representations where nodes represent certain bioentities and edges represent the connections between them...
July 14, 2017: BMC Research Notes
https://www.readbyqxmd.com/read/28700698/suppressors-of-selection
#5
Fernando Alcalde Cuesta, Pablo González Sequeiros, Álvaro Lozano Rojo
Inspired by recent works on evolutionary graph theory, an area of growing interest in mathematical and computational biology, we present examples of undirected structures acting as suppressors of selection for any fitness value r > 1. This means that the average fixation probability of an advantageous mutant or invader individual placed at some node is strictly less than that of this individual placed in a well-mixed population. This leads the way to study more robust structures less prone to invasion, contrary to what happens with the amplifiers of selection where the fixation probability is increased on average for advantageous invader individuals...
2017: PloS One
https://www.readbyqxmd.com/read/28695358/retained-executive-abilities-in-mild-cognitive-impairment-are-associated-with-increased-white-matter-network-connectivity
#6
Danielle C Farrar, Asim Z Mian, Andrew E Budson, Mark B Moss, Bang Bon Koo, Ronald J Killiany
PURPOSE: To describe structural network differences in individuals with mild cognitive impairment (MCI) with high versus low executive abilities, as reflected by measures of white matter connectivity using diffusion tensor imaging (DTI). MATERIALS AND METHODS: This was a retrospective, cross-sectional study. Of the 128 participants from the Alzheimer's Disease Neuroimaging Initiative database who had both a DTI scan as well as a diagnosis of MCI, we used an executive function score to classify the top 15 scoring patients as high executive ability, and the bottom-scoring 16 patients as low executive ability...
July 10, 2017: European Radiology
https://www.readbyqxmd.com/read/28694044/more-randomized-and-resilient-in-the-topological-properties-of-functional-brain-networks-in-patients-with-major-depressive-disorder
#7
Huaizhou Li, Haiyan Zhou, Yang Yang, Haiyuan Wang, Ning Zhong
Previous studies have reported the enhanced randomization of functional brain networks in patients with major depressive disorder (MDD). However, little is known about the changes of key nodal attributes for randomization, the resilience of network, and the clinical significance of the alterations. In this study, we collected the resting-state functional MRI data from 19 MDD patients and 19 healthy control (HC) individuals. Graph theory analysis showed that decreases were found in the small-worldness, clustering coefficient, local efficiency, and characteristic path length (i...
July 7, 2017: Journal of Clinical Neuroscience: Official Journal of the Neurosurgical Society of Australasia
https://www.readbyqxmd.com/read/28692887/electron-magnetic-resonance-data-on-high-spin-mn-iii-s-2-ions-in-porphyrinic-and-salen-complexes-modeled-by-microscopic-spin-hamiltonian-approach
#8
Krzysztof Tadyszak, Czesław Rudowicz, Hitoshi Ohta, Takahiro Sakurai
The spin Hamiltonian (SH) parameters experimentally determined by EMR (EPR) may be corroborated or otherwise using various theoretical modeling approaches. To this end semiempirical modeling is carried out for high-spin (S=2) manganese (III) 3d(4) ions in complex of tetraphenylporphyrinato manganese (III) chloride (MnTPPCl). This modeling utilizes the microscopic spin Hamiltonians (MSH) approach developed for the 3d(4) and 3d(6) ions with spin S=2 at orthorhombic and tetragonal symmetry sites in crystals, which exhibit an orbital singlet ground state...
June 28, 2017: Journal of Inorganic Biochemistry
https://www.readbyqxmd.com/read/28691806/automatic-assignment-of-methyl-nmr-spectra-of-supramolecular-machines-using-graph-theory
#9
Iva Pritišanac, Matteo T Degiacomi, T Reid Alderson, Marta G Carneiro, Eiso Ab, Gregg Siegal, Andrew J Baldwin
Methyl groups are powerful probes for the analysis of structure, dynamics and function of supramolecular assemblies, using both solution- and solid-state NMR. Widespread application of the methodology has been limited due to the challenges associated with assigning spectral resonances to specific locations within a biomolecule. Here, we present Methyl Assignment by Graph Matching (MAGMA), for the automatic assignment of methyl resonances. A graph matching protocol examines all possibilities for each resonance in order to determine an exact assignment that includes a complete description of any ambiguity...
July 10, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28690424/generating-subtour-elimination-constraints-for-the-tsp-from-pure-integer-solutions
#10
Ulrich Pferschy, Rostislav Staněk
The traveling salesman problem (TSP) is one of the most prominent combinatorial optimization problems. Given a complete graph [Formula: see text] and non-negative distances d for every edge, the TSP asks for a shortest tour through all vertices with respect to the distances d. The method of choice for solving the TSP to optimality is a branch and cut approach. Usually the integrality constraints are relaxed first and all separation processes to identify violated inequalities are done on fractional solutions...
2017: Cent Eur J Oper Res
https://www.readbyqxmd.com/read/28689700/surrounding-control-of-nonlinear-multi-agent-systems-with-non-identical-agents
#11
Shamisa Shoja, Mahdi Baradarannia, Farzad Hashemzadeh, Mohammadali Badamchizadeh, Peyman Bagheri
In this paper, the surrounding control problem of a group of non-identical agents is considered, where a team of followers achieves an equidistant distributed formation to surround a team of moving leaders. An adaptive design method is presented for multi-agent systems where the dynamics of agents are supposed to be nonlinear with unknown parameters. First, an estimator for the center of the leaders is introduced. Then, two distributed adaptive controllers based on the estimated center are proposed for each follower...
July 7, 2017: ISA Transactions
https://www.readbyqxmd.com/read/28680817/mvp-an-open-source-preprocessor-for-cleaning-duplicate-records-and-missing-values-in-mass-spectrometry-data
#12
Geunho Lee, Hyun Beom Lee, Byung Hwa Jung, Hojung Nam
Mass spectrometry (MS) data are used to analyze biological phenomena based on chemical species. However, these data often contain unexpected duplicate records and missing values due to technical or biological factors. These 'dirty data' problems increase the difficulty of performing MS analyses because they lead to performance degradation when statistical or machine-learning tests are applied to the data. Thus, we have developed missing values preprocessor (mvp), an open-source software for preprocessing data that might include duplicate records and missing values...
July 2017: FEBS Open Bio
https://www.readbyqxmd.com/read/28675389/topologically-convergent-and-divergent-functional-connectivity-patterns-in-unmedicated-unipolar-depression-and-bipolar-disorder
#13
Y Wang, J Wang, Y Jia, S Zhong, M Zhong, Y Sun, M Niu, L Zhao, L Zhao, J Pan, L Huang, R Huang
Bipolar disorder (BD), particularly BD II, is frequently misdiagnosed as unipolar depression (UD), leading to inappropriate treatment and poor clinical outcomes. Although depressive symptoms may be expressed similarly in UD and BD, the similarities and differences in the architecture of brain functional networks between the two disorders are still unknown. In this study, we hypothesized that UD and BD II patients would show convergent and divergent patterns of disrupted topological organization of the functional connectome, especially in the default mode network (DMN) and the limbic network...
July 4, 2017: Translational Psychiatry
https://www.readbyqxmd.com/read/28673634/orthogonality-measurements-for-multidimensional-chromatography-in-three-and-higher-dimensional-separations
#14
Mark R Schure, Joe M Davis
Orthogonality metrics (OMs) for three and higher dimensional separations are proposed as extensions of previously developed OMs, which were used to evaluate the zone utilization of two-dimensional (2D) separations. These OMs include correlation coefficients, dimensionality, information theory metrics and convex-hull metrics. In a number of these cases, lower dimensional subspace metrics exist and can be readily calculated. The metrics are used to interpret previously generated experimental data. The experimental datasets are derived from Gilar's peptide data, now modified to be three dimensional (3D), and a comprehensive 3D chromatogram from Moore and Jorgenson...
June 13, 2017: Journal of Chromatography. A
https://www.readbyqxmd.com/read/28667481/disrupted-topological-organization-of-brain-structural-network-associated-with-prior-overt-hepatic-encephalopathy-in-cirrhotic-patients
#15
Hua-Jun Chen, Hai-Bin Shi, Long-Feng Jiang, Lan Li, Rong Chen
OBJECTIVES: To investigate structural brain connectome alterations in cirrhotic patients with prior overt hepatic encephalopathy (OHE). METHODS: Seventeen cirrhotic patients with prior OHE (prior-OHE), 18 cirrhotic patients without prior OHE (non-prior-OHE) and 18 healthy controls (HC) underwent diffusion tensor imaging. Neurocognitive functioning was assessed with Psychometric Hepatic Encephalopathy Score (PHES). Using a probabilistic fibre tracking approach, we depicted the whole-brain structural network as a connectivity matrix of 90 regions (derived from the Automated Anatomic Labeling atlas)...
June 30, 2017: European Radiology
https://www.readbyqxmd.com/read/28666764/evolutionary-dynamics-and-the-evolution-of-multiplayer-cooperation-in-a-subdivided-population
#16
Karan Pattni, Mark Broom, Jan Rychtář
The classical models of evolution have been developed to incorporate structured populations using evolutionary graph theory and, more recently, a new framework has been developed to allow for more flexible population structures which potentially change through time and can accommodate multiplayer games with variable group sizes. In this paper we extend this work in three key ways. Firstly by developing a complete set of evolutionary dynamics so that the range of dynamic processes used in classical evolutionary graph theory can be applied...
June 28, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28666351/brain-networks-predict-metabolism-diagnosis-and-prognosis-at-the-bedside-in-disorders-of-consciousness
#17
Srivas Chennu, Jitka Annen, Sarah Wannez, Aurore Thibaut, Camille Chatelle, Helena Cassol, Géraldine Martens, Caroline Schnakers, Olivia Gosseries, David Menon, Steven Laureys
Recent advances in functional neuroimaging have demonstrated novel potential for informing diagnosis and prognosis in the unresponsive wakeful syndrome and minimally conscious states. However, these technologies come with considerable expense and difficulty, limiting the possibility of wider clinical application in patients. Here, we show that high density electroencephalography, collected from 104 patients measured at rest, can provide valuable information about brain connectivity that correlates with behaviour and functional neuroimaging...
June 27, 2017: Brain: a Journal of Neurology
https://www.readbyqxmd.com/read/28657905/methods-of-minimizing-doses-incurred-by-external-exposure-while-moving-in-radiation-hazardous-areas
#18
Konstantin Chizhov, Malgorzata K Sneve, Sergey Shinkarev, Alexander Tsovyanov, Graham Smith, Aleksander Krasnoschekov, Aleksander Kosnikov, Igor Kemsky, Victor Kryuchkov
Radiation doses received by workers during their movement within areas contaminated as a result of events and activities, leading to emergency or existing exposure situations, may provide a substantial contribution to total external exposure during remediation work. This paper describes an approach to minimize worker external exposure in these circumstances, based on graph theory. The paper describes several tasks, including: searching for a route with the lowest dose, searching for an optimal bypass with a given set of control points and searching for the optimal road network coverage...
June 28, 2017: Journal of Radiological Protection: Official Journal of the Society for Radiological Protection
https://www.readbyqxmd.com/read/28657774/integrative-structural-brain-network-analysis-in-diffusion-tensor-imaging
#19
Moo K Chung, Jamie L Hanson, Nagesh Adluru, Andrew L Alexander, Richard J Davidson, Seth D Pollak
In diffusion tensor imaging, structural connectivity between brain regions is often measured by the number of white matter fiber tracts connecting them. Other features such as the length of tracts or fractional anisotropy (FA) are also used in measuring the strength of connectivity. In this study, we investigated the effects of incorporating the number of tracts, the tract length, and FA values into the connectivity model. Using various node-degree-based graph theory features, the three connectivity models are compared...
June 28, 2017: Brain Connectivity
https://www.readbyqxmd.com/read/28657334/large-scale-network-analysis-of-whole-brain-resting-state-functional-connectivity-in-spinal-cord-injury-a-comparative-study
#20
Mayank Kaushal, Akinwunmi Oni-Orisan, Gang Chen, Wenjun Li, Jack Leschke, Doug Ward, Benjamin Kalinosky, Matthew Budde, Brain Schmit, Shi-Jiang Li, Vaishnavi Muqeet, Shekar Kurpad
BACKGROUND: Network analysis based on graph theory depicts the brain as a complex network that allows for inspection of overall brain connectivity pattern and calculation of quantifiable network metrics. To date, large-scale network analysis has not been applied to resting-state functional networks in complete spinal cord injury (SCI) patients. OBJECTIVE: To characterize modular reorganization of whole brain into constituent nodes and compare network metrics between SCI and control subjects...
June 28, 2017: Brain Connectivity
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