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https://www.readbyqxmd.com/read/27913340/efficient-3d-reconstruction-in-ultrasound-elastography-via-a-sparse-iteration-based-on-markov-random-fields
#1
Atul Ingle, Tomy Varghese, William Sethares
Percutaneous needle-based liver ablation procedures are becoming increasingly common for treatment of small isolated tumors in hepatocellular carcinoma patients who are not candidates for surgery. Rapid three dimensional visualization of liver ablations has potential clinical value because it can enable interventional radiologists to plan and execute needle-based ablation procedures with real time feedback. Ensuring the right volume of tissue is ablated is desirable to avoid recurrence of tumors from residual untreated cancerous cells...
November 29, 2016: IEEE Transactions on Ultrasonics, Ferroelectrics, and Frequency Control
https://www.readbyqxmd.com/read/27911809/unique-attributes-of-cyanobacterial-metabolism-revealed-by-improved-genome-scale-metabolic-modeling-and-essential-gene-analysis
#2
Jared T Broddrick, Benjamin E Rubin, David G Welkie, Niu Du, Nathan Mih, Spencer Diamond, Jenny J Lee, Susan S Golden, Bernhard O Palsson
The model cyanobacterium, Synechococcus elongatus PCC 7942, is a genetically tractable obligate phototroph that is being developed for the bioproduction of high-value chemicals. Genome-scale models (GEMs) have been successfully used to assess and engineer cellular metabolism; however, GEMs of phototrophic metabolism have been limited by the lack of experimental datasets for model validation and the challenges of incorporating photon uptake. Here, we develop a GEM of metabolism in S. elongatus using random barcode transposon site sequencing (RB-TnSeq) essential gene and physiological data specific to photoautotrophic metabolism...
December 1, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27910837/accurate-and-efficient-representation-of-intramolecular-energy-in-ab-initio-generation-of-crystal-structures-i-adaptive-local-approximate-models
#3
Isaac Sugden, Claire S Adjiman, Constantinos C Pantelides
The global search stage of crystal structure prediction (CSP) methods requires a fine balance between accuracy and computational cost, particularly for the study of large flexible molecules. A major improvement in the accuracy and cost of the intramolecular energy function used in the CrystalPredictor II [Habgood et al. (2015). J. Chem. Theory Comput. 11, 1957-1969] program is presented, where the most efficient use of computational effort is ensured via the use of adaptive local approximate model (LAM) placement...
December 1, 2016: Acta Crystallographica Section B, Structural Science, Crystal Engineering and Materials
https://www.readbyqxmd.com/read/27910069/lkb1-as-a-tumor-suppressor-in-uterine-cancer-mouse-models-and-translational-studies
#4
Christopher G Peña, Diego H Castrillón
The LKB1 tumor suppressor was identified in 1998 as the gene mutated in the Peutz-Jeghers Syndrome (PJS), a hereditary cancer predisposition characterized by gastrointestinal polyposis and a high incidence of cancers, particularly carcinomas, at a variety of anatomic sites including the gastrointestinal tract, lung, and female reproductive tract. Women with PJS have a high incidence of carcinomas of the uterine corpus (endometrium) and cervix. The LKB1 gene is also somatically mutated in human cancers arising at these sites...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/27905091/recent-advances-of-molecular-toolbox-construction-expand-pichia-pastoris-in-synthetic-biology-applications
#5
REVIEW
Zhen Kang, Hao Huang, Yunfeng Zhang, Guocheng Du, Jian Chen
Pichia pastoris: (reclassified as Komagataella phaffii), a methylotrophic yeast strain has been widely used for heterologous protein production because of its unique advantages, such as readily achievable high-density fermentation, tractable genetic modifications and typical eukaryotic post-translational modifications. More recently, P. pastoris as a metabolic pathway engineering platform has also gained much attention. In this mini-review, we addressed recent advances of molecular toolboxes, including synthetic promoters, signal peptides, and genome engineering tools that established for P...
January 2017: World Journal of Microbiology & Biotechnology
https://www.readbyqxmd.com/read/27904993/molecular-mechanisms-of-heart-failure-insights-from-drosophila
#6
Shasha Zhu, Zhe Han, Yan Luo, Yulin Chen, Qun Zeng, Xiushan Wu, Wuzhou Yuan
Heart failure places an enormous burden on health and economic systems worldwide. It is a complex disease that is profoundly influenced by both genetic and environmental factors. Neither the molecular mechanisms underlying heart failure nor effective prevention strategies are fully understood. Fortunately, relevant aspects of human heart failure can be experimentally studied in tractable model animals, including the fruit fly, Drosophila, allowing the in vivo application of powerful and sophisticated molecular genetic and physiological approaches...
December 1, 2016: Heart Failure Reviews
https://www.readbyqxmd.com/read/27904877/lifestyles-through-expenditures-a-case-based-approach-to-saving
#7
Lisa A Keister, Richard Benton, James Moody
Treating people as cases that are proximate in a behavior space-representing lifestyles-rather than as markers of single variables has a long history in sociology. Yet, because it is difficult to find analytically tractable ways to implement this idea, this approach is rarely used. We take seriously the idea that people are whole packages, and we use household spending to identify groups who occupy similar positions in social space. Using detailed data on household consumption, we identify eight positions that are clearly similar in lifestyle...
2016: Sociological Science
https://www.readbyqxmd.com/read/27903772/diverse-activities-of-viral-cis-acting-rna-regulatory-elements-revealed-using-multi-color-long-term-single-cell-imaging
#8
Ginger M Pocock, Laraine L Zimdars, Ming Yuan, Kevin W Eliceiri, Paul Ahlquist, Nathan M Sherer
Cis-acting RNA structural elements govern crucial aspects of viral gene expression. How these structures and other post-transcriptional signals affect RNA trafficking and translation in the context of single cells is poorly understood. Herein we describe a multi-color, long-term (>24 h) imaging strategy for measuring integrated aspects of viral RNA regulatory control in individual cells. We apply this strategy to demonstrate differential mRNA trafficking behaviors governed by RNA elements derived from three retroviruses (HIV-1, murine leukemia virus, and Mason-Pfizer monkey virus), two hepadnaviruses (hepatitis B virus and woodchuck hepatitis virus) and an intron-retaining transcript encoded by the cellular NXF1 gene...
November 30, 2016: Molecular Biology of the Cell
https://www.readbyqxmd.com/read/27902356/luciferase-tagged-wild-type-and-tropism-deficient-mouse-cytomegaloviruses-reveal-early-dynamics-of-host-colonization-following-peripheral-challenge
#9
Helen Farrell, Martha Oliveira, Kate Macdonald, Joseph Yunis, Michael Mach, Kimberley Bruce, Philip Stevenson, Rhonda Cardin, Nicholas Davis-Poynter
Cytomegaloviruses (CMVs) establish persistent, systemic infections and cause disease by maternal-fetal transfer, suggesting that their dissemination is a key target for anti-viral intervention. Late clinical presentation has meant that human CMV dissemination is not well understood. Murine CMV provides a tractable model. Whole mouse imaging of virus-expressed luciferase has proved a useful way to track systemic infections. MCMV, in which the abundant lytic gene M78 was luciferase tagged via a self-cleaving peptide (M78-LUC), allowed serial, unbiased imaging of systemic and peripheral infection without significant virus attenuation...
October 26, 2016: Journal of General Virology
https://www.readbyqxmd.com/read/27887565/genomic-evaluation-by-including-dominance-effects-and-inbreeding-depression-for-purebred-and-crossbred-performance-with-an-application-in-pigs
#10
Tao Xiang, Ole Fredslund Christensen, Zulma Gladis Vitezica, Andres Legarra
BACKGROUND: Improved performance of crossbred animals is partly due to heterosis. One of the major genetic bases of heterosis is dominance, but it is seldom used in pedigree-based genetic evaluation of livestock. Recently, a trivariate genomic best linear unbiased prediction (GBLUP) model including dominance was developed, which can distinguish purebreds from crossbred animals explicitly. The objectives of this study were: (1) methodological, to show that inclusion of marker-based inbreeding accounts for directional dominance and inbreeding depression in purebred and crossbred animals, to revisit variance components of additive and dominance genetic effects using this model, and to develop marker-based estimators of genetic correlations between purebred and crossbred animals and of correlations of allele substitution effects between breeds; (2) to evaluate the impact of accounting for dominance effects and inbreeding depression on predictive ability for total number of piglets born (TNB) in a pig dataset composed of two purebred populations and their crossbreds...
November 25, 2016: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/27885283/induced-protein-degradation-an-emerging-drug-discovery-paradigm
#11
Ashton C Lai, Craig M Crews
Small-molecule drug discovery has traditionally focused on occupancy of a binding site that directly affects protein function, and this approach typically precludes targeting proteins that lack such amenable sites. Furthermore, high systemic drug exposures may be needed to maintain sufficient target inhibition in vivo, increasing the risk of undesirable off-target effects. Induced protein degradation is an alternative approach that is event-driven: upon drug binding, the target protein is tagged for elimination...
November 25, 2016: Nature Reviews. Drug Discovery
https://www.readbyqxmd.com/read/27881803/inferring-animal-social-networks-and-leadership-applications-for-passive-monitoring-arrays
#12
David M P Jacoby, Yannis P Papastamatiou, Robin Freeman
Analyses of animal social networks have frequently benefited from techniques derived from other disciplines. Recently, machine learning algorithms have been adopted to infer social associations from time-series data gathered using remote, telemetry systems situated at provisioning sites. We adapt and modify existing inference methods to reveal the underlying social structure of wide-ranging marine predators moving through spatial arrays of passive acoustic receivers. From six months of tracking data for grey reef sharks (Carcharhinus amblyrhynchos) at Palmyra atoll in the Pacific Ocean, we demonstrate that some individuals emerge as leaders within the population and that this behavioural coordination is predicted by both sex and the duration of co-occurrences between conspecifics...
November 2016: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/27881766/bridging-the-gap-parkour-athletes-provide-new-insights-into-locomotion-energetics-of-arboreal-apes
#13
Lewis G Halsey, Samuel R L Coward, Susannah K S Thorpe
The tree canopy is an energetically challenging environment to traverse. Along with compliant vegetation, gaps in the canopy can prove energetically costly if they force a route-extending detour. Arboreal apes exhibit diverse locomotion strategies, including for gap crossing. Which one they employ in any given scenario may be influenced by the energy costs to do so, which are affected by the details of the immediate environment in combination with their body size. Measuring energetics of arboreal apes is not tractable; thus our knowledge in this area is limited...
November 2016: Biology Letters
https://www.readbyqxmd.com/read/27881166/using-the-social-amoeba-dictyostelium-to-study-the-functions-of-proteins-linked-to-neuronal-ceroid-lipofuscinosis
#14
REVIEW
Robert J Huber
Neuronal ceroid lipofuscinosis (NCL), also known as Batten disease, is a debilitating neurological disorder that affects both children and adults. Thirteen genetically distinct genes have been identified that when mutated, result in abnormal lysosomal function and an excessive accumulation of ceroid lipofuscin in neurons, as well as other cell types outside of the central nervous system. The NCL family of proteins is comprised of lysosomal enzymes (PPT1/CLN1, TPP1/CLN2, CTSD/CLN10, CTSF/CLN13), proteins that peripherally associate with membranes (DNAJC5/CLN4, KCTD7/CLN14), a soluble lysosomal protein (CLN5), a protein present in the secretory pathway (PGRN/CLN11), and several proteins that display different subcellular localizations (CLN3, CLN6, MFSD8/CLN7, CLN8, ATP13A2/CLN12)...
November 24, 2016: Journal of Biomedical Science
https://www.readbyqxmd.com/read/27879267/pifithrin-%C3%A2%C2%B5-prevents-cisplatin-induced-chemobrain-by-preserving-neuronal-mitochondrial-function
#15
Gabriel S Chiu, Magdalena A Maj, Sahar Rizvi, Robert Dantzer, Elisabeth G Vichaya, Geoffroy Laumet, Annemieke Kavelaars, Cobi J Heijnen
Cognitive impairment termed chemobrain is a common neurotoxicity associated with chemotherapy treatment, affecting an estimated 78% of patients. Prompted by the hypothesis that neuronal mitochondrial dysfunction underlies chemotherapy-induced cognitive impairment (CICI), we explored the efficacy of administering the small molecule pifithrin (PFT)-µ, an inhibitor of mitochondrial p53 accumulation, in preventing CICI. Male C57BL/6J mice injected with cisplatin +/- PFT-µ for two 5-day cycles were assessed for cognitive function using novel object/place recognition and alternation in a Y-maze...
November 22, 2016: Cancer Research
https://www.readbyqxmd.com/read/27875209/jacobi-fiber-surfaces-for-bivariate-reeb-space-computation
#16
Julien Tierny, Hamish Carr
This paper presents an efficient algorithm for the computation of the Reeb space of an input bivariate piecewise linear scalar function f defined on a tetrahedral mesh. By extending and generalizing algorithmic concepts from the univariate case to the bivariate one, we report the first practical, output-sensitive algorithm for the exact computation of such a Reeb space. The algorithm starts by identifying the Jacobi set of f, the bivariate analogs of critical points in the univariate case. Next, the Reeb space is computed by segmenting the input mesh along the new notion of Jacobi Fiber Surfaces, the bivariate analog of critical contours in the univariate case...
January 2017: IEEE Transactions on Visualization and Computer Graphics
https://www.readbyqxmd.com/read/27873256/cell-based-fluorescent-screen-to-identify-inhibitors-of-bacterial-translation-initiation
#17
Federica Briani
A strategy that can be applied to the research of new molecules with antibacterial activity is to look for inhibitors of essential bacterial processes within large collections of chemically heterogeneous compounds. The implementation of this approach requires the development of proper assays aimed at the identification of molecules interfering with specific cell pathways and potentially applicable to the high throughput analysis of large chemical library. Here, I describe a fluorescence-based whole-cell assay in Escherichia coli devised to find inhibitors of the translation initiation pathway...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27872098/systematic-drug-screening-identifies-tractable-targeted-combination-therapies-in-triple-negative-breast-cancer
#18
Vikram B Wali, Casey G Langdon, Matthew A Held, James T Platt, Gauri A Patwardhan, Anton Safonov, Bilge Aktas, Lajos Pusztai, David F Stern, Christos Hatzis
Triple-negative breast cancer (TNBC) remains an aggressive disease without effective targeted therapies. In this study, we addressed this challenge by testing 128 FDA-approved or investigational drugs as either single agents or in 768 pairwise drug combinations in TNBC cell lines to identify synergistic combinations tractable to clinical translation. Medium-throughput results were scrutinized and extensively analyzed for sensitivity patterns, synergy, anticancer activity and validation in low-throughput experiments...
November 21, 2016: Cancer Research
https://www.readbyqxmd.com/read/27870213/unexpected-sex-specific-post-reproductive-lifespan-in-the-free-living-nematode-pristionchus-exspectatus
#19
Cameron J Weadick, Ralf J Sommer
Patterns of senescence (or aging) can vary among life history traits and between the sexes, providing an opportunity to study variation in the aging process within a single species. We previously found that females of the nematode Pristionchus exspectatus outlive males by a substantial margin under laboratory conditions. Here, we show that sex-specific reproductive senescence unfolds in the opposite direction in this species, resulting in a prolonged period of female-specific post-reproductive survival: females lost the ability to reproduce at approximately 4...
December 2016: Evolution & Development
https://www.readbyqxmd.com/read/27866798/long-distance-descending-spinal-neurons-ensure-quadrupedal-locomotor-stability
#20
Ludwig Ruder, Aya Takeoka, Silvia Arber
Locomotion is an essential animal behavior used for translocation. The spinal cord acts as key executing center, but how it coordinates many body parts located across distance remains poorly understood. Here we employed mouse genetic and viral approaches to reveal organizational principles of long-projecting spinal circuits and their role in quadrupedal locomotion. Using neurotransmitter identity, developmental origin, and projection patterns as criteria, we uncover that spinal segments controlling forelimbs and hindlimbs are bidirectionally connected by symmetrically organized direct synaptic pathways that encompass multiple genetically tractable neuronal subpopulations...
November 16, 2016: Neuron
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