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https://www.readbyqxmd.com/read/29779153/intraoperative-stent-segmentation-in-x-ray-fluoroscopy-for-endovascular-aortic-repair
#1
Katharina Breininger, Shadi Albarqouni, Tanja Kurzendorfer, Marcus Pfister, Markus Kowarschik, Andreas Maier
PURPOSE: Fusion of preoperative data with intraoperative X-ray images has proven the potential to reduce radiation exposure and contrast agent, especially for complex endovascular aortic repair (EVAR). Due to patient movement and introduced devices that deform the vasculature, the fusion can become inaccurate. This is usually detected by comparing the preoperative information with the contrasted vessel. To avoid repeated use of iodine, comparison with an implanted stent can be used to adjust the fusion...
May 19, 2018: International Journal of Computer Assisted Radiology and Surgery
https://www.readbyqxmd.com/read/29778931/monitoring-tool-usage-in-surgery-videos-using-boosted-convolutional-and-recurrent-neural-networks
#2
Hassan Al Hajj, Mathieu Lamard, Pierre-Henri Conze, Béatrice Cochener, Gwenolé Quellec
This paper investigates the automatic monitoring of tool usage during a surgery, with potential applications in report generation, surgical training and real-time decision support. Two surgeries are considered: cataract surgery, the most common surgical procedure, and cholecystectomy, one of the most common digestive surgeries. Tool usage is monitored in videos recorded either through a microscope (cataract surgery) or an endoscope (cholecystectomy). Following state-of-the-art video analysis solutions, each frame of the video is analyzed by convolutional neural networks (CNNs) whose outputs are fed to recurrent neural networks (RNNs) in order to take temporal relationships between events into account...
May 9, 2018: Medical Image Analysis
https://www.readbyqxmd.com/read/29778908/mammalian-target-of-rapamycin-complex-2-signaling-in-obese-women-changes-after-bariatric-surgery
#3
Marcela Augusta de Souza Pinhel, Carolina Ferreira Nicoletti, Natalia Yumi Noronha, Bruno Affonso Parenti de Oliveira, Cristiana Cortes-Oliveira, Wilson Salgado, Wilson Araujo da Silva, Doroteia Rossi Silva Souza, Julio Sergio Marchini, Carla Barbosa Nonino
OBJECTIVES: After bariatric surgery, modifications to signaling pathway networks including those of the metabolic regulator called mammalian or mechanistic target of rapamycin (mTOR) may lead to molecular alterations related to energy source availability, systemic nutrients, and catabolic and anabolic cellular processes. This study aimed to identify gene expression changes with regard to the mTOR complex 2 subunit signaling pathway in obese patients before and after bariatric surgery...
March 21, 2018: Nutrition
https://www.readbyqxmd.com/read/29778837/defining-host-responses-during-systemic-bacterial-infection-through-construction-of-a-murine-organ-proteome-atlas
#4
John D Lapek, Robert H Mills, Jacob M Wozniak, Anaamika Campeau, Ronnie H Fang, Xiaoli Wei, Kirsten van de Groep, Araceli Perez-Lopez, Nina M van Sorge, Manuela Raffatellu, Rob Knight, Liangfang Zhang, David J Gonzalez
Group A Streptococcus (GAS) remains one of the top 10 deadliest human pathogens worldwide despite its sensitivity to penicillin. Although the most common GAS infection is pharyngitis (strep throat), it also causes life-threatening systemic infections. A series of complex networks between host and pathogen drive invasive infections, which have not been comprehensively mapped. Attempting to map these interactions, we examined organ-level protein dynamics using a mouse model of systemic GAS infection. We quantified over 11,000 proteins, defining organ-specific markers for all analyzed tissues...
April 28, 2018: Cell Systems
https://www.readbyqxmd.com/read/29778836/interrogation-of-mammalian-protein-complex-structure-function-and-membership-using-genome-scale-fitness-screens
#5
Joshua Pan, Robin M Meyers, Brittany C Michel, Nazar Mashtalir, Ann E Sizemore, Jonathan N Wells, Seth H Cassel, Francisca Vazquez, Barbara A Weir, William C Hahn, Joseph A Marsh, Aviad Tsherniak, Cigall Kadoch
Protein complexes are assemblies of subunits that have co-evolved to execute one or many coordinated functions in the cellular environment. Functional annotation of mammalian protein complexes is critical to understanding biological processes, as well as disease mechanisms. Here, we used genetic co-essentiality derived from genome-scale RNAi- and CRISPR-Cas9-based fitness screens performed across hundreds of human cancer cell lines to assign measures of functional similarity. From these measures, we systematically built and characterized functional similarity networks that recapitulate known structural and functional features of well-studied protein complexes and resolve novel functional modules within complexes lacking structural resolution, such as the mammalian SWI/SNF complex...
May 14, 2018: Cell Systems
https://www.readbyqxmd.com/read/29778791/evolutionary-transitions-in-controls-reconcile-adaptation-with-continuity-of-evolution
#6
REVIEW
Alexander V Badyaev
Evolution proceeds by accumulating functional solutions, necessarily forming an uninterrupted lineage from past solutions of ancestors to the current design of extant forms. At the population level, this process requires an organismal architecture in which the maintenance of local adaptation does not preclude the ability to innovate in the same traits and their continuous evolution. Representing complex traits as networks enables us to visualize a fundamental principle that resolves tension between adaptation and continuous evolution: phenotypic states encompassing adaptations traverse the continuous multi-layered landscape of past physical, developmental and functional associations among traits...
May 17, 2018: Seminars in Cell & Developmental Biology
https://www.readbyqxmd.com/read/29778716/the-hematopoietic-stem-cell-niche-what-s-so-special-about-bone
#7
REVIEW
Benjamin J Frisch
Hematopoietic stem cells (HSCs) require a supportive microenvironment to regulate their function and produce sufficient hematopoietic cells over the lifetime of an individual. With the exception of fish, all vertebrates, including mammals, maintain HSCs in a complex niche within the bone marrow. Several bone specific cellular populations have been implicated as components of the HSC niche and are part of a complex network that regulates HSC functions. However, the full extent of interactions within the HSC niche, and the role of individual cell populations remain to be fully elucidated...
May 17, 2018: Bone
https://www.readbyqxmd.com/read/29778258/new-treatments-have-changed-the-game-hepatitis-c-treatment-in-primary-care
#8
REVIEW
Shelley N Facente, Katie Burk, Kelly Eagen, Elise S Mara, Aaron A Smith, Colleen S Lynch
In the pre-direct-acting antiviral era, hepatitis C virus (HCV) treatments were complex and largely managed by hepatologists, gastroenterologists, and infectious disease physicians. As direct-acting antivirals have driven up demand for treatment, the relative scarcity of these specialists has created a bottleneck effect, resulting in only a fraction of HCV-infected individuals offered treatment. The San Francisco Health Network is a safety net system of care. Its intervention was designed to be sustainable and scalable; with minimal time commitments for training providers, primary care-based HCV treatment increased 3-fold in a period of just over 3 years...
June 2018: Infectious Disease Clinics of North America
https://www.readbyqxmd.com/read/29777828/mutual-connectivity-analysis-of-resting-state-functional-mri-data-with-local-models
#9
Adora M DSouza, Anas Z Abidin, Udaysankar Chockanathan, Giovanni Schifitto, Axel Wismüller
Functional connectivity analysis of functional MRI (fMRI) can represent brain networks and reveal insights into interactions amongst different brain regions. However, most connectivity analysis approaches adopted in practice are linear and non-directional. In this paper, we demonstrate the advantage of a data-driven, directed connectivity analysis approach called Mutual Connectivity Analysis using Local Models (MCA-LM) that approximates connectivity by modeling nonlinear dependencies of signal interaction, over more conventionally used approaches, such as Pearson's and partial correlation, Patel's conditional dependence measures, etcetera...
May 16, 2018: NeuroImage
https://www.readbyqxmd.com/read/29777385/changes-in-selection-intensity-on-the-mitogenome-of-subterranean-and-fossorial-rodents-respective-to-aboveground-species
#10
William Corrêa Tavares, Hector N Seuánez
Several rodent lineages independently acquired the ability to dig complex networks of tunnels where fossorial and subterranean species spend part or their whole life, respectively. Their underground lifestyles imposed harsh physiological demands, presumably triggering strong selective pressures on genes involved in energy metabolism like those coding for mitochondrial proteins. Moreover, underground lifestyles must have increased inbreeding and susceptibility to population bottlenecks as well as restricted migration, leading to small effective population size (Ne ) that, in turn, must have reduced the effectiveness of selection...
May 18, 2018: Mammalian Genome: Official Journal of the International Mammalian Genome Society
https://www.readbyqxmd.com/read/29777200/a-map-of-the-pgc-1%C3%AE-and-nt-pgc-1%C3%AE-regulated-transcriptional-network-in-brown-adipose-tissue
#11
Ji Suk Chang, Sujoy Ghosh, Susan Newman, J Michael Salbaum
Transcriptional coactivator PGC-1α and its splice variant NT-PGC-1α play crucial roles in regulating cold-induced thermogenesis in brown adipose tissue (BAT). PGC-1α and NT-PGC-1α are highly induced by cold in BAT and subsequently bind to and coactivate many transcription factors to regulate expression of genes involved in mitochondrial biogenesis, fatty acid oxidation, respiration and thermogenesis. To identify the complete repertoire of PGC-1α and NT-PGC-1α target genes in BAT, we analyzed genome-wide DNA-binding and gene expression profiles...
May 18, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29777175/artificial-intelligence-in-radiology
#12
REVIEW
Ahmed Hosny, Chintan Parmar, John Quackenbush, Lawrence H Schwartz, Hugo J W L Aerts
Artificial intelligence (AI) algorithms, particularly deep learning, have demonstrated remarkable progress in image-recognition tasks. Methods ranging from convolutional neural networks to variational autoencoders have found myriad applications in the medical image analysis field, propelling it forward at a rapid pace. Historically, in radiology practice, trained physicians visually assessed medical images for the detection, characterization and monitoring of diseases. AI methods excel at automatically recognizing complex patterns in imaging data and providing quantitative, rather than qualitative, assessments of radiographic characteristics...
May 17, 2018: Nature Reviews. Cancer
https://www.readbyqxmd.com/read/29777110/using-network-analysis-for-the-prediction-of-treatment-dropout-in-patients-with-mood-and-anxiety-disorders-a-methodological-proof-of-concept-study
#13
Wolfgang Lutz, Brian Schwartz, Stefan G Hofmann, Aaron J Fisher, Kristin Husen, Julian A Rubel
There are large health, societal, and economic costs associated with attrition from psychological services. The recently emerged, innovative statistical tool of complex network analysis was used in the present proof-of-concept study to improve the prediction of attrition. Fifty-eight patients undergoing psychological treatment for mood or anxiety disorders were assessed using Ecological Momentary Assessments four times a day for two weeks before treatment (3,248 measurements). Multilevel vector autoregressive models were employed to compute dynamic symptom networks...
May 18, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29776967/multicentre-study-of-maternal-and-neonatal-outcomes-in-individuals-with-prader-willi-syndrome
#14
Preeti Singh, Ranim Mahmoud, June-Anne Gold, Jennifer L Miller, Elizabeth Roof, Roy Tamura, Elisabeth Dykens, Merlin G Butler, Dan J Driscoll, Virginia Kimonis
INTRODUCTION: Prader-Willi syndrome (PWS) is a complex genetic disorder associated with three different genetic subtypes: deletion of the paternal copy of 15q11-q13, maternal UPD for chromosome 15 and imprinting defect. Patients are typically diagnosed because of neonatal hypotonia, dysmorphism and feeding difficulties; however, data on the prenatal features of PWS are limited. OBJECTIVE: The aim of the study was to identify and compare frequencies of prenatal and neonatal clinical features of PWS among the three genetic subtypes...
May 18, 2018: Journal of Medical Genetics
https://www.readbyqxmd.com/read/29776332/telnet-a-database-for-human-and-yeast-genes-involved-in-telomere-maintenance
#15
Delia M Braun, Inn Chung, Nick Kepper, Katharina I Deeg, Karsten Rippe
BACKGROUND: The ends of linear chromosomes, the telomeres, comprise repetitive DNA sequences in complex with proteins that protects them from being processed by the DNA repair machinery. Cancer cells need to counteract the shortening of telomere repeats during replication for their unlimited proliferation by reactivating the reverse transcriptase telomerase or by using the alternative lengthening of telomeres (ALT) pathway. The different telomere maintenance (TM) mechanisms appear to involve hundreds of proteins but their telomere repeat length related activities are only partly understood...
May 18, 2018: BMC Genetics
https://www.readbyqxmd.com/read/29776185/master-stability-functions-reveal-diffusion-driven-pattern-formation-in-networks
#16
Andreas Brechtel, Philipp Gramlich, Daniel Ritterskamp, Barbara Drossel, Thilo Gross
We study diffusion-driven pattern formation in networks of networks, a class of multilayer systems, where different layers have the same topology, but different internal dynamics. Agents are assumed to disperse within a layer by undergoing random walks, while they can be created or destroyed by reactions between or within a layer. We show that the stability of homogeneous steady states can be analyzed with a master stability function approach that reveals a deep analogy between pattern formation in networks and pattern formation in continuous space...
March 2018: Physical Review. E
https://www.readbyqxmd.com/read/29776179/geometric-evolution-of-complex-networks-with-degree-correlations
#17
Charles Murphy, Antoine Allard, Edward Laurence, Guillaume St-Onge, Louis J Dubé
We present a general class of geometric network growth mechanisms by homogeneous attachment in which the links created at a given time t are distributed homogeneously between a new node and the existing nodes selected uniformly. This is achieved by creating links between nodes uniformly distributed in a homogeneous metric space according to a Fermi-Dirac connection probability with inverse temperature β and general time-dependent chemical potential μ(t). The chemical potential limits the spatial extent of newly created links...
March 2018: Physical Review. E
https://www.readbyqxmd.com/read/29776160/universal-principles-governing-multiple-random-searchers-on-complex-networks-the-logarithmic-growth-pattern-and-the-harmonic-law
#18
Tongfeng Weng, Jie Zhang, Michael Small, Bahareh Harandizadeh, Pan Hui
We propose a unified framework to evaluate and quantify the search time of multiple random searchers traversing independently and concurrently on complex networks. We find that the intriguing behaviors of multiple random searchers are governed by two basic principles-the logarithmic growth pattern and the harmonic law. Specifically, the logarithmic growth pattern characterizes how the search time increases with the number of targets, while the harmonic law explores how the search time of multiple random searchers varies relative to that needed by individual searchers...
March 2018: Physical Review. E
https://www.readbyqxmd.com/read/29776147/sparse-dynamical-boltzmann-machine-for-reconstructing-complex-networks-with-binary-dynamics
#19
Yu-Zhong Chen, Ying-Cheng Lai
Revealing the structure and dynamics of complex networked systems from observed data is a problem of current interest. Is it possible to develop a completely data-driven framework to decipher the network structure and different types of dynamical processes on complex networks? We develop a model named sparse dynamical Boltzmann machine (SDBM) as a structural estimator for complex networks that host binary dynamical processes. The SDBM attains its topology according to that of the original system and is capable of simulating the original binary dynamical process...
March 2018: Physical Review. E
https://www.readbyqxmd.com/read/29776111/star-polymers-as-unit-cells-for-coarse-graining-cross-linked-networks
#20
Taras Y Molotilin, Salim R Maduar, Olga I Vinogradova
Reducing the complexity of cross-linked polymer networks by preserving their main macroscale properties is key to understanding them, and a crucial issue is to relate individual properties of the polymer constituents to those of the reduced network. Here we study polymer networks in a good solvent, by considering star polymers as their unit elements, and first quantify the interaction between their centers of masses. We then reduce the complexity of a network by replacing sets of its bridged star polymers by equivalent effective soft particles with dense cores...
March 2018: Physical Review. E
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