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knowledge network

Jianming Luo, Yuetong Li, Jinli Xie, Lijuan Gao, Liu Liu, Shiyi Ou, Long Chen, Xichun Peng
Bacterial interactions in the biological network affect the growth of Bifidobacterium. In the present study, five habitats were constructed by changing animals, their health statuses and their diets. In each of these habitats, different networks of Bifidobacterium were outlined through correlation analysis of the 50 most dominant microbes. Thirty-eight bacterial genera directly correlated with the growth of Bifidobacterium, including 23 genera with a positive correlation and 15 genera with a negative correlation...
March 13, 2018: FEMS Microbiology Letters
Marguerite M Nyhan, Brent A Coull, Annelise J Blomberg, Carol L Z Vieira, Eric Garshick, Abdulaziz Aba, Pantel Vokonas, Diane R Gold, Joel Schwartz, Petros Koutrakis
BACKGROUND: The cardiovascular effects of low-level environmental radiation exposures are poorly understood. Although particulate matter (PM) has been linked to cardiovascular morbidity and mortality, and elevated blood pressure (BP), the properties promoting its toxicity remain uncertain. Addressing a knowledge gap, we evaluated whether BP increased with higher exposures to radioactive components of ambient PM, herein referred to as particle radioactivity (PR). METHODS AND RESULTS: We performed a repeated-measures analysis of 852 men to examine associations between PR exposure and BP using mixed-effects regression models...
March 15, 2018: Journal of the American Heart Association
Ellen V S Hessel, Yvonne C M Staal, Aldert H Piersma
Developmental neurotoxicity entails one of the most complex areas in toxicology. Animal studies provide only limited information as to human relevance. A multitude of alternative models have been developed over the years, providing insights into mechanisms of action. We give an overview of fundamental processes in neural tube formation, brain development and neural specification, aiming at illustrating complexity rather than comprehensiveness. We also give a flavor of the wealth of alternative methods in this area...
March 12, 2018: Toxicology and Applied Pharmacology
Shuchao Pang, Mehmet A Orgun, Zhezhou Yu
BACKGROUND AND OBJECTIVES: The traditional biomedical image retrieval methods as well as content-based image retrieval (CBIR) methods originally designed for non-biomedical images either only consider using pixel and low-level features to describe an image or use deep features to describe images but still leave a lot of room for improving both accuracy and efficiency. In this work, we propose a new approach, which exploits deep learning technology to extract the high-level and compact features from biomedical images...
May 2018: Computer Methods and Programs in Biomedicine
Piotr Chudzik, Somshubra Majumdar, Francesco Calivá, Bashir Al-Diri, Andrew Hunter
BACKROUND AND OBJECTIVES: Diabetic retinopathy is a microvascular complication of diabetes that can lead to sight loss if treated not early enough. Microaneurysms are the earliest clinical signs of diabetic retinopathy. This paper presents an automatic method for detecting microaneurysms in fundus photographies. METHODS: A novel patch-based fully convolutional neural network with batch normalization layers and Dice loss function is proposed. Compared to other methods that require up to five processing stages, it requires only three...
May 2018: Computer Methods and Programs in Biomedicine
Irene Navarro-Lobato, Lisa Genzel
Alternations of up and down can be seen across many different levels during sleep. Neural firing-rates, synaptic markers, molecular pathways, and gene expression all show differential up and down regulation across brain areas and sleep stages. And also the hallmarks of sleep - sleep stage specific oscillations - are characterized themselves by up and down as seen within the slow oscillation or theta cycles. In this review, we summarize the up and down of sleep covering molecules to electrophysiology and present different theories how this up and down could be regulated by the up and down of sleep oscillations...
March 12, 2018: Neurobiology of Learning and Memory
JoAnne S Richards
Follicular development and ovulation are complex development processes that are regulated by multiple, interacting pathways and cell types. The oocyte, cumulus cells, granulosa cells, and theca cells communicate to impact follicular development and ovulation. Many hormones and cytokines control intracellular regulatory networks and transcription factors, some of which are cell type specific. Molecular biology approaches and mutant mouse models have contributed immensely to our knowledge of what genes and signaling cascades impact each stage of follicular development and ovulation, and how the alteration of gene expression profiles and the activation of specific signaling pathways can impact ovarian cancer development in ovarian surface epithelial cells as well as granulosa cells...
2018: Vitamins and Hormones
Sara Sigismund, Giorgio Scita
An explosive growth in knowledge, in the last two decades, has conferred a new dimension to the process of endocytosis. Endocytic circuitries have come into focus as a pervasive system that controls virtual all aspects of cell biology. A few years ago, we proposed the term 'endocytic matrix' to define a cellular network of signalling wiring that is at the core of the cellular blueprint. A primary role of the endocytic matrix is the delivery of space-resolved and time-resolved signals to the cell in an interpretable format, and, as such, it has profound consequences on polarized cellular and supra-cellular functions, first and foremost, cell motility...
March 12, 2018: Current Opinion in Cell Biology
Alessandra Livigni, Laura O'Hara, Marta E Polak, Tim Angus, Derek W Wright, Lee B Smith, Tom C Freeman
A major endeavor of systems biology is the construction of graphical and computational models of biological pathways as a means to better understand their structure and function. Here, we present a protocol for a biologist-friendly graphical modeling scheme that facilitates the construction of detailed network diagrams, summarizing the components of a biological pathway (such as proteins and biochemicals) and illustrating how they interact. These diagrams can then be used to simulate activity flow through a pathway, thereby modeling its dynamic behavior...
April 2018: Nature Protocols
Morgan Lawley, Jessica W Wu, Victor M Navas-López, Hien Q Huynh, Matthew W Carroll, Min Chen, Pavel Medvedev, Andrew S Day, Séamus Hussey, Rotem Sigall-Boneh, Arie Levine, Eytan Wine
OBJECTIVES: Exclusive enteral nutrition (EEN) is an effective induction treatment for pediatric Crohn disease. Given the center-based variation in use and diversity in practice we constructed a survey aimed at sharing experience and strategies in administering EEN, stimulating further research, and optimizing therapy. METHODS: This survey was constructed after consultation with experts and designed to address key knowledge gaps. The survey was disseminated through the Paediatric IBD Porto Group of ESPGHAN, Canadian Children IBD Network, selective experts, and was sent twice through the PEDGI-BB...
March 14, 2018: Journal of Pediatric Gastroenterology and Nutrition
Sara L Ackerman, Gato Gourley, Gem Le, Pamela Williams, Jinoos Yazdany, Urmimala Sarkar
OBJECTIVE: The aim of the study was to develop standards for tracking patient safety gaps in ambulatory care in safety net health systems. METHODS: Leaders from five California safety net health systems were invited to participate in a modified Delphi process sponsored by the Safety Promotion Action Research and Knowledge Network (SPARKNet) and the California Safety Net Institute in 2016. During each of the three Delphi rounds, the feasibility and validity of 13 proposed patient safety measures were discussed and prioritized...
March 14, 2018: Journal of Patient Safety
Marc N Jarczok, Corina Aguilar-Raab, Julian Koenig, Michael Kaess, Jeremy C Borniger, Randy J Nelson, Martica Hall, Beate Ditzen, Julian F Thayer, Joachim E Fischer
INTRODUCTION: Successful regulation of emotional states is positively associated to mental health, while difficulties in regulating emotions are negatively associated to overall mental health and in particular associated with anxiety or depression symptoms. A key structure associated to socio-emotional regulatory processes is the central autonomic network. Activity in this structure is associated to vagal activity can be indexed noninvasively and simply by measures of peripheral cardiac autonomic modulations such as heart rate variability...
March 15, 2018: Chronobiology International
Alana Grech, Emmanuel Hanert, Len McKenzie, Michael Rasheed, Christopher Thomas, Samantha Tol, Mingzhu Wang, Michelle Waycott, Jolan Wolter, Rob Coles
The rate of exchange, or connectivity, among populations effects their ability to recover after disturbance events. However, there is limited information on the extent to which populations are connected or how multiple disturbances affect connectivity, especially in coastal and marine ecosystems. We used network analysis and the outputs of a biophysical model to measure potential functional connectivity and predict the impact of multiple disturbances on seagrasses in the central Great Barrier Reef World Heritage Area (GBRWHA), Australia...
March 15, 2018: Global Change Biology
Leland J Dunwoodie, William L Poehlman, Stephen P Ficklin, Frank Alexander Feltus
Tumors exhibit complex patterns of aberrant gene expression. Using a knowledge-independent, noise-reducing gene co-expression network construction software called KINC, we created multiple RNAseq-based gene co-expression networks relevant to brain and glioblastoma biology. In this report, we describe the discovery and validation of a glioblastoma-specific gene module that contains 22 co-expressed genes. The genes are upregulated in glioblastoma relative to normal brain and lower grade glioma samples; they are also hypo-methylated in glioblastoma relative to lower grade glioma tumors...
February 16, 2018: Oncotarget
Yiran Ao, Qin Zhao, Kai Yang, Gang Zheng, Xiaoqing Lv, Xiaoli Su
Clock genes are the core of the circadian rhythms in the human body and are important in regulating normal physiological functions. To date, research has indicated that the clock gene, period circadian clock 2 ( PER2 ), is downregulated in numerous types of cancer, and that it is associated with cancer occurrence and progression via the regulation of various downstream cell cycle genes. However, it remains unclear whether the decreased expression of PER2 influences the expression of other clock genes in cancer cells...
April 2018: Oncology Letters
Homero San-Juan-Vergara, Eduardo Zurek, Nadim J Ajami, Christian Mogollon, Mario Peña, Ivan Portnoy, Jorge I Vélez, Christian Cadena-Cruz, Yirys Diaz-Olmos, Leidy Hurtado-Gómez, Silvana Sanchez-Sit, Danitza Hernández, Irina Urruchurtu, Pierina Di-Ruggiero, Ella Guardo-García, Nury Torres, Oscar Vidal-Orjuela, Diego Viasus, Joseph F Petrosino, Guillermo Cervantes-Acosta
HIV infection has a tremendous impact on the immune system's proper functioning. The mucosa-associated lymphoid tissue (MALT) is significantly disarrayed during HIV infection. Compositional changes in the gut microbiota might contribute to the mucosal barrier disruption, and consequently to microbial translocation. We performed an observational, cross-sectional study aimed at evaluating changes in the fecal microbiota of HIV-infected individuals from Colombia. We analyzed the fecal microbiota of 37 individuals via 16S rRNA gene sequencing; 25 HIV-infected patients and 12 control (non-infected) individuals, which were similar in body mass index, age, gender balance and socioeconomic status...
March 14, 2018: Scientific Reports
François Ancien, Fabrizio Pucci, Maxime Godfroid, Marianne Rooman
The classification of human genetic variants into deleterious and neutral is a challenging issue, whose complexity is rooted in the large variety of biophysical mechanisms that can be responsible for disease conditions. For non-synonymous mutations in structured proteins, one of these is the protein stability change, which can lead to loss of protein structure or function. We developed a stability-driven knowledge-based classifier that uses protein structure, artificial neural networks and solvent accessibility-dependent combinations of statistical potentials to predict whether destabilizing or stabilizing mutations are disease-causing...
March 14, 2018: Scientific Reports
Antonella Succurro, Oliver Ebenhöh
Understanding microbial ecosystems means unlocking the path toward a deeper knowledge of the fundamental mechanisms of life. Engineered microbial communities are also extremely relevant to tackling some of today's grand societal challenges. Advanced meta-omics experimental techniques provide crucial insights into microbial communities, but have been so far mostly used for descriptive, exploratory approaches to answer the initial 'who is there?' QUESTION: An ecosystem is a complex network of dynamic spatio-temporal interactions among organisms as well as between organisms and the environment...
March 14, 2018: Biochemical Society Transactions
Jennifer L Guthrie, Clare Kong, David Roth, Danielle Jorgensen, Mabel Rodrigues, Patrick Tang, Maichael Thejoe, Kevin Elwood, Victoria J Cook, James Johnston, Jennifer L Gardy
Prospective universal genotyping of tuberculosis (TB) isolates is used by many laboratories to detect clusters of cases and inform contact investigations. Prior to universal genotyping, most TB prevention programs genotyped isolates on request only, relying on requests from public health professionals whose knowledge of a patient's clinical, demographic, and epidemiological characteristics suggested potential transmission. To justify the switch from on-request to universal genotyping - particularly in the public health domain, with its limited resources and competing priorities - it is important to demonstrate the additional benefit provided by a universal genotyping program...
March 14, 2018: Journal of Clinical Microbiology
H P E M Spitters, L A M van de Goor, C Juel Lau, P Sandu, L Eklund Karlsson, J Jansen, J A M van Oers
Since public health problems are complex and the related policies need to address a wide range of sectors, cross-sectoral collaboration is beneficial. One intervention focusing on stimulating collaboration is a 'policy game'. The focus on specific problems facilitates relationships between the stakeholders and stimulates cross-sectoral policymaking. The present study explores stakeholders' learning experiences with respect to the collaboration process in public health policymaking. This was achieved via their game participation, carried out in real-life stakeholder networks in the Netherlands, Denmark and Romania...
March 1, 2018: Journal of Public Health
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