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https://www.readbyqxmd.com/read/28732007/a-data-driven-modeling-approach-to-identify-disease-specific-multi-organ-networks-driving-physiological-dysregulation
#1
Warren D Anderson, Danielle DeCicco, James S Schwaber, Rajanikanth Vadigepalli
Multiple physiological systems interact throughout the development of a complex disease. Knowledge of the dynamics and connectivity of interactions across physiological systems could facilitate the prevention or mitigation of organ damage underlying complex diseases, many of which are currently refractory to available therapeutics (e.g., hypertension). We studied the regulatory interactions operating within and across organs throughout disease development by integrating in vivo analysis of gene expression dynamics with a reverse engineering approach to infer data-driven dynamic network models of multi-organ gene regulatory influences...
July 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28731267/heuristic-knowledge-based-planning-for-single-isocenter-stereotactic-radiosurgery-to-multiple-brain-metastases
#2
Benjamin P Ziemer, Parag Sanghvi, Jona Hattangadi-Gluth, Kevin L Moore
PURPOSE: Single-isocenter, volumetric modulated arc therapy (VMAT) stereotactic radiosurgery (SRS) for multiple brain metastases (multi-mets) can deliver highly conformal dose distributions and reduce overall patient treatment time compared to other techniques. However, treatment planning for multi-met cases is highly complex due to variability in numbers and sizes of brain metastases, as well as their relative proximity to organs-at-risk (OARs). The purpose of this study was to automate the VMAT planning of multi-met cases through a knowledge-based planning (KBP) approach that adapts single target SRS dose predictions to multiple target predictions...
July 21, 2017: Medical Physics
https://www.readbyqxmd.com/read/28731040/er-stress-and-the-unfolded-protein-response-in-neurodegeneration
#3
REVIEW
Claudio Hetz, Smita Saxena
The clinical manifestation of neurodegenerative diseases is initiated by the selective alteration in the functionality of distinct neuronal populations. The pathology of many neurodegenerative diseases includes accumulation of misfolded proteins in the brain. In physiological conditions, the proteostasis network maintains normal protein folding, trafficking and degradation; alterations in this network - particularly disturbances to the function of endoplasmic reticulum (ER) - are thought to contribute to abnormal protein aggregation...
July 21, 2017: Nature Reviews. Neurology
https://www.readbyqxmd.com/read/28729899/evolutionary-loss-of-melanogenesis-in-the-tunicate-molgula-occulta
#4
Claudia Racioppi, Maria Carmen Valoroso, Ugo Coppola, Elijah K Lowe, C Titus Brown, Billie J Swalla, Lionel Christiaen, Alberto Stolfi, Filomena Ristoratore
BACKGROUND: Analyzing close species with diverse developmental modes is instrumental for investigating the evolutionary significance of physiological, anatomical and behavioral features at a molecular level. Many examples of trait loss are known in metazoan populations living in dark environments. Tunicates are the closest living relatives of vertebrates and typically present a lifecycle with distinct motile larval and sessile adult stages. The nervous system of the motile larva contains melanized cells associated with geotactic and light-sensing organs...
2017: EvoDevo
https://www.readbyqxmd.com/read/28729161/the-neural-basis-of-precise-visual-short-term-memory-for-complex-recognisable-objects
#5
Michele Veldsman, Daniel J Mitchell, Rhodri Cusack
Recent evidence suggests that visual short-term memory (VSTM) capacity estimated using simple objects, such as colours and oriented bars, may not generalise well to more naturalistic stimuli. More visual detail can be stored in VSTM when complex, recognisable objects are maintained compared to simple objects. It is not yet known if it is recognisability that enhances memory precision, nor whether maintenance of recognisable objects is achieved with the same network of brain regions supporting maintenance of simple objects...
July 17, 2017: NeuroImage
https://www.readbyqxmd.com/read/28720701/de-novo-peptide-sequencing-by-deep-learning
#6
Ngoc Hieu Tran, Xianglilan Zhang, Lei Xin, Baozhen Shan, Ming Li
De novo peptide sequencing from tandem MS data is the key technology in proteomics for the characterization of proteins, especially for new sequences, such as mAbs. In this study, we propose a deep neural network model, DeepNovo, for de novo peptide sequencing. DeepNovo architecture combines recent advances in convolutional neural networks and recurrent neural networks to learn features of tandem mass spectra, fragment ions, and sequence patterns of peptides. The networks are further integrated with local dynamic programming to solve the complex optimization task of de novo sequencing...
July 18, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28709281/how-the-fittest-compete-for-leadership-a-tale-of-tails
#7
J M Luck, A Mehta
We investigate how leaders emerge as a consequence of the competitive dynamics between coupled papers in a model citation network. Every paper is allocated an initial fitness depending on its intrinsic quality. Its fitness then involves dynamically as a consequence of the competition between itself and all the other papers in the field. It picks up citations as a result of this adaptive dynamics, becoming a leader if it has the highest citation count at a given time. Extensive analytical and numerical investigations of this model suggest the existence of a universal phase diagram, divided into regions of weak and strong coupling...
June 2017: Physical Review. E
https://www.readbyqxmd.com/read/28704963/challenges-in-wireless-system-integration-as-enablers-for-indoor-context-aware-environments
#8
Peio López-Iturri, Erik Aguirre, Leyre Azpilicueta, José Javier Astrain, Jesús Villandangos, Francisco Falcone
The advent of fully interactive environments within Smart Cities and Smart Regions requires the use of multiple wireless systems. In the case of user-device interaction, which finds multiple applications such as Ambient Assisted Living, Intelligent Transportation Systems or Smart Grids, among others, large amount of transceivers are employed in order to achieve anytime, anyplace and any device connectivity. The resulting combination of heterogeneous wireless network exhibits fundamental limitations derived from Coverage/Capacity relations, as a function of required Quality of Service parameters, required bit rate, energy restrictions and adaptive modulation and coding schemes...
July 12, 2017: Sensors
https://www.readbyqxmd.com/read/28703114/inhibition-of-perk-dependent-pro-adaptive-signaling-pathway-as-a-promising-approach-for-cancer-treatment
#9
Wioletta Rozpędek, Dariusz Pytel, Łukasz Dziki, Alicja Nowak, Adam Dziki, J Alan Diehl, Ireneusz Majsterek
Endoplasmic Reticulum (ER) is an organelle that is vital for cell growth and maintenance of homeostasis. Recent studies have reported that numerous human diseases, including cancer, are strictly connected to disruption of ER homeostasis. In order to counteract adverse intracellular conditions, cancer cells induce protein kinase R (PKR)-like endoplasmic reticulum kinase (PERK)-dependent, pro-adaptive unfolded protein response (UPR) signaling branches. If ER stress is severe or prolonged, pro-adaptive signaling networks are insufficient, resulting in apoptotic cell death of cancer cells...
June 30, 2017: Polski Przeglad Chirurgiczny
https://www.readbyqxmd.com/read/28698475/pedestrian-detection-based-on-adaptive-selection-of-visible-light-or-far-infrared-light-camera-image-by-fuzzy-inference-system-and-convolutional-neural-network-based-verification
#10
Jin Kyu Kang, Hyung Gil Hong, Kang Ryoung Park
A number of studies have been conducted to enhance the pedestrian detection accuracy of intelligent surveillance systems. However, detecting pedestrians under outdoor conditions is a challenging problem due to the varying lighting, shadows, and occlusions. In recent times, a growing number of studies have been performed on visible light camera-based pedestrian detection systems using a convolutional neural network (CNN) in order to make the pedestrian detection process more resilient to such conditions. However, visible light cameras still cannot detect pedestrians during nighttime, and are easily affected by shadows and lighting...
July 8, 2017: Sensors
https://www.readbyqxmd.com/read/28694848/epiaco-a-method-for-identifying-epistasis-based-on-ant-colony-optimization-algorithm
#11
Yingxia Sun, Junliang Shang, Jin-Xing Liu, Shengjun Li, Chun-Hou Zheng
BACKGROUND: Identifying epistasis or epistatic interactions, which refer to nonlinear interaction effects of single nucleotide polymorphisms (SNPs), is essential to understand disease susceptibility and to detect genetic architectures underlying complex diseases. Though many works have been done for identifying epistatic interactions, due to their methodological and computational challenges, the algorithmic development is still ongoing. RESULTS: In this study, a method epiACO is proposed to identify epistatic interactions, which based on ant colony optimization algorithm...
2017: BioData Mining
https://www.readbyqxmd.com/read/28694337/targeted-memory-reactivation-during-sleep-adaptively-promotes-the-strengthening-or-weakening-of-overlapping-memories
#12
J P Oyarzún, J Morís, D Luque, R de Diego-Balaguer, L Fuentemilla
System memory consolidation is conceptualized as an active process whereby newly encoded memory representations are strengthened through selective memory reactivation during sleep. However, our learning experience is highly overlapping in content (i.e., shares common elements), and memories of these events are organized in an intricate network of overlapping associated events. It remains to be explored whether and how selective memory reactivation during sleep has an impact on these overlapping memories acquired during awake time...
July 10, 2017: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/28690511/neurotessmesh-a-tool-for-the-generation-and-visualization-of-neuron-meshes-and-adaptive-on-the-fly-refinement
#13
Juan J Garcia-Cantero, Juan P Brito, Susana Mata, Sofia Bayona, Luis Pastor
Gaining a better understanding of the human brain continues to be one of the greatest challenges for science, largely because of the overwhelming complexity of the brain and the difficulty of analyzing the features and behavior of dense neural networks. Regarding analysis, 3D visualization has proven to be a useful tool for the evaluation of complex systems. However, the large number of neurons in non-trivial circuits, together with their intricate geometry, makes the visualization of a neuronal scenario an extremely challenging computational problem...
2017: Frontiers in Neuroinformatics
https://www.readbyqxmd.com/read/28687663/a-module-for-rac-temporal-signal-integration-revealed-with-optogenetics
#14
Brian R Graziano, Delquin Gong, Karen E Anderson, Anne Pipathsouk, Anna R Goldberg, Orion D Weiner
Sensory systems use adaptation to measure changes in signaling inputs rather than absolute levels of signaling inputs. Adaptation enables eukaryotic cells to directionally migrate over a large dynamic range of chemoattractant. Because of complex feedback interactions and redundancy, it has been difficult to define the portion or portions of eukaryotic chemotactic signaling networks that generate adaptation and identify the regulators of this process. In this study, we use a combination of optogenetic intracellular inputs, CRISPR-based knockouts, and pharmacological perturbations to probe the basis of neutrophil adaptation...
July 7, 2017: Journal of Cell Biology
https://www.readbyqxmd.com/read/28686801/exposure-to-complex-environments-results-in-more-sparse-representations-of-space-in-the-hippocampus
#15
David K Bilkey, Kirsten R Cheyne, Michael J Eckert, Xiaodong Lu, Shoaib Chowdhury, Paul F Worley, James E Crandall, Wickliffe C Abraham
The neural circuitry mediating sensory and motor representations is adaptively tuned by an animal's interaction with its environment. Similarly, higher order representations such as spatial memories can be modified by exposure to a complex environment (CE), but in this case the changes in brain circuitry that mediate the effect are less well understood. Here we show that prolonged CE exposure was associated with increased selectivity of CA1 "place cells" to a particular recording arena compared to a social control (SC) group...
July 7, 2017: Hippocampus
https://www.readbyqxmd.com/read/28682235/topological-analysis-of-multicellular-complexity-in-the-plant-hypocotyl
#16
Matthew Db Jackson, Hao Xu, Salva Duran-Nebreda, Petra Stamm, George W Bassel
Multicellularity arose as a result of adaptive advantages conferred to complex cellular assemblies. The arrangement of cells within organs endows higher-order functionality through a structure-function relationship, though the organizational properties of these multicellular configurations remain poorly understood. We investigated the topological properties of complex organ architecture by digitally capturing global cellular interactions in the plant embryonic stem (hypocotyl), and analyzing these using quantitative network analysis...
July 6, 2017: ELife
https://www.readbyqxmd.com/read/28680391/the-role-of-the-multifunctional-bag3-protein-in-cellular-protein-quality-control-and-in-disease
#17
REVIEW
Elisabeth Stürner, Christian Behl
In neurons, but also in all other cells the complex proteostasis network is monitored and tightly regulated by the cellular protein quality control (PQC) system. Beyond folding of newly synthesized polypeptides and their refolding upon misfolding the PQC also manages the disposal of aberrant proteins either by the ubiquitin-proteasome machinery or by the autophagic-lysosomal system. Aggregated proteins are primarily degraded by a process termed selective macroautophagy (or aggrephagy). One such recently discovered selective macroautophagy pathway is mediated by the multifunctional HSP70 co-chaperone BAG3 (BCL-2-associated athanogene 3)...
2017: Frontiers in Molecular Neuroscience
https://www.readbyqxmd.com/read/28679232/behavioral-synchronization-induced-by-epidemic-spread-in-complex-networks
#18
Mengfeng Sun, Yijun Lou, Jinqiao Duan, Xinchu Fu
During the spread of an epidemic, individuals in realistic networks may exhibit collective behaviors. In order to characterize this kind of phenomenon and explore the correlation between collective behaviors and epidemic spread, in this paper, we construct several mathematical models (including without delay, with a coupling delay, and with double delays) of epidemic synchronization by applying the adaptive feedback motivated by real observations. By using Lyapunov function methods, we obtain the conditions for local and global stability of these epidemic synchronization models...
June 2017: Chaos
https://www.readbyqxmd.com/read/28677638/unsupervised-fault-diagnosis-of-a-gear-transmission-chain-using-a-deep-belief-network
#19
Jun He, Shixi Yang, Chunbiao Gan
Artificial intelligence (AI) techniques, which can effectively analyze massive amounts of fault data and automatically provide accurate diagnosis results, have been widely applied to fault diagnosis of rotating machinery. Conventional AI methods are applied using features selected by a human operator, which are manually extracted based on diagnostic techniques and field expertise. However, developing robust features for each diagnostic purpose is often labour-intensive and time-consuming, and the features extracted for one specific task may be unsuitable for others...
July 4, 2017: Sensors
https://www.readbyqxmd.com/read/28674733/micrornas-modulate-core-clock-gene-expression-in-pancreatic-islets-during-early-postnatal-life-in-rats
#20
Cécile Jacovetti, Adriana Rodriguez-Trejo, Claudiane Guay, Jonathan Sobel, Sonia Gattesco, Volodymyr Petrenko, Camille Saini, Charna Dibner, Romano Regazzi
AIMS/HYPOTHESIS: Evidence continues to emerge detailing a fine-tuning of the regulation of metabolic processes and energy homeostasis by cell-autonomous circadian clocks. Pancreatic beta cell functional maturation occurs after birth and implies transcriptional changes triggered by a shift in the nutritional supply that occurs at weaning, enabling the adaptation of insulin secretion. So far, the developmental timing and exact mechanisms involved in the initiation of the circadian clock in the growing pancreatic islets have never been addressed...
July 4, 2017: Diabetologia
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