Flow-mediated dilation: can new approaches provide greater mechanistic insight into vascular dysfunction in preeclampsia and other diseases?

PubMed

Weissgerber, Tracey L

2014-11-01

Endothelial dysfunction is a key feature of preeclampsia and may contribute to increased cardiovascular disease risk years after pregnancy. Flow-mediated dilation (FMD) is a non-invasive endothelial function test that predicts cardiovascular event risk. New protocols allow researchers to measure three components of the FMD response: FMD, low flow-mediated constriction, and shear stimulus. This review encourages researchers to think beyond "low FMD" by examining how these three components may provide additional insights into the mechanisms and location of vascular dysfunction. The review then examines what FMD studies reveal about vascular dysfunction in preeclampsia while highlighting opportunities to gain greater mechanistic insight from new protocols. Studies using traditional protocols show that FMD is low in mid-pregnancy prior to preeclampsia, at diagnosis, and for 3 years post-partum. However, FMD returns to normal by 10 years post-partum. Studies using new protocols are needed to gain more mechanistic insight.

Brainstorming about next-generation computer-based documentation: an AMIA clinical working group survey.

PubMed

Johnson, Kevin B; Ravich, William J; Cowan, John A

2004-09-01

Computer-based software to record histories, physical exams, and progress or procedure notes, known as computer-based documentation (CBD) software, has been touted as an important addition to the electronic health record. The functionality of CBD systems has remained static over the past 30 years, which may have contributed to the limited adoption of these tools. Early users of this technology, who have tried multiple products, may have insight into important features to be considered in next-generation CBD systems. We conducted a cross-sectional, observational study of the clinical working group membership of the American Medical Informatics Association (AMIA) to generate a set of features that might improve adoption of next-generation systems. The study was conducted online over a 4-month period; 57% of the working group members completed the survey. As anticipated, CBD tool use was higher (53%) in this population than in the US physician offices. The most common methods of data entry employed keyboard and mouse, with agreement that these modalities worked well. Many respondents had experience with pre-printed data collection forms before interacting with a CBD system. Respondents noted that CBD improved their ability to document large amounts of information, allowed timely sharing of information, enhanced patient care, and enhanced medical information with other clinicians (all P < 0.001). Respondents also noted some important but absent features in CBD, including the ability to add images, get help, and generate billing information. The latest generation of CBD systems is being used successfully by early adopters, who find that these tools confer many advantages over the approaches to documentation that they replaced. These users provide insights that may improve successive generations of CBD tools. Additional surveys of CBD non-users and failed adopters will be necessary to provide other useful insights that can address barriers to the adoption of CBD by less computer literate physicians.

BioMon: A Google Earth Based Continuous Biomass Monitoring System (Demo Paper)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vatsavai, Raju

2009-01-01

We demonstrate a Google Earth based novel visualization system for continuous monitoring of biomass at regional and global scales. This system is integrated with a back-end spatiotemporal data mining system that continuously detects changes using high temporal resolution MODIS images. In addition to the visualization, we demonstrate novel query features of the system that provides insights into the current conditions of the landscape.

Structural and Mechanistic Insights into C-P Bond Hydrolysis by Phosphonoacetate Hydrolase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Agarwal, Vinayak; Borisova, Svetlana A.; Metcalf, William W.

2011-12-22

Bacteria have evolved pathways to metabolize phosphonates as a nutrient source for phosphorus. In Sinorhizobium meliloti 1021, 2-aminoethylphosphonate is catabolized to phosphonoacetate, which is converted to acetate and inorganic phosphate by phosphonoacetate hydrolase (PhnA). Here we present detailed biochemical and structural characterization of PhnA that provides insights into the mechanism of C-P bond cleavage. The 1.35 {angstrom} resolution crystal structure reveals a catalytic core similar to those of alkaline phosphatases and nucleotide pyrophosphatases but with notable differences, such as a longer metal-metal distance. Detailed structure-guided analysis of active site residues and four additional cocrystal structures with phosphonoacetate substrate, acetate, phosphonoformatemore » inhibitor, and a covalently bound transition state mimic provide insight into active site features that may facilitate cleavage of the C-P bond. These studies expand upon the array of reactions that can be catalyzed by enzymes of the alkaline phosphatase superfamily.« less

Feature-binding errors after eye movements and shifts of attention.

PubMed

Golomb, Julie D; L'heureux, Zara E; Kanwisher, Nancy

2014-05-01

When people move their eyes, the eye-centered (retinotopic) locations of objects must be updated to maintain world-centered (spatiotopic) stability. Here, we demonstrated that the attentional-updating process temporarily distorts the fundamental ability to bind object locations with their features. Subjects were simultaneously presented with four colors after a saccade-one in a precued spatiotopic target location-and were instructed to report the target's color using a color wheel. Subjects' reports were systematically shifted in color space toward the color of the distractor in the retinotopic location of the cue. Probabilistic modeling exposed both crude swapping errors and subtler feature mixing (as if the retinotopic color had blended into the spatiotopic percept). Additional experiments conducted without saccades revealed that the two types of errors stemmed from different attentional mechanisms (attention shifting vs. splitting). Feature mixing not only reflects a new perceptual phenomenon, but also provides novel insight into how attention is remapped across saccades.

Probing collective oscillation of d -orbital electrons at the nanoscale

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dhall, Rohan; Vigil-Fowler, Derek; Houston Dycus, J.

Here, we demonstrate that high energy electrons can be used to explore the collective oscillation of s, p, and d orbital electrons at the nanometer length scale. Using epitaxial AlGaN/AlN quantum wells as a test system, we observe the emergence of additional features in the loss spectrum with the increasing Ga content. A comparison of the observed spectra with ab-initio theory reveals that the origin of these spectral features lies in excitations of 3d-electrons contributed by Ga. We find that these modes differ in energy from the valence electron plasmons in Al1-xGaxN due to the different polarizabilities of the dmore » electrons. Finally, we study the dependence of observed spectral features on the Ga content, lending insights into the origin of these spectral features, and their coupling with electron-hole excitations.« less

Systems Analysis Programs for Hands-on Integrated Reliability Evaluations (SAPHIRE) Tutorial

DOE Office of Scientific and Technical Information (OSTI.GOV)

C. L. Smith; S. T. Beck; S. T. Wood

2008-08-01

The Systems Analysis Programs for Hands-on Integrated Reliability Evaluations (SAPHIRE) refers to a set of computer programs that were developed to create and analyze probabilistic risk assessment (PRAs). This volume is the tutorial manual for the SAPHIRE system. In this document, a series of lessons are provided that guide the user through basic steps common to most analyses preformed with SAPHIRE. The tutorial is divided into two major sections covering both basic and advanced features. The section covering basic topics contains lessons that lead the reader through development of a probabilistic hypothetical problem involving a vehicle accident, highlighting the program’smore » most fundamental features. The advanced features section contains additional lessons that expand on fundamental analysis features of SAPHIRE and provide insights into more complex analysis techniques. Together, these two elements provide an overview into the operation and capabilities of the SAPHIRE software.« less

Pathogenic features and characteristics of food borne pathogens biofilm: Biomass, viability and matrix.

PubMed

Lin, Shiqi; Yang, Ling; Chen, Gu; Li, Bing; Chen, Dingqiang; Li, Lin; Xu, Zhenbo

2017-10-01

Biofilm is a ubiquitous growth pattern of bacterial species survival but is notorious for its threat on public health and food contamination. Extensive studies of the biofilm structure, formation, quantification, quorum sensing system and underlying control strategies have been reported during the past decades. Insightful elucidation of the pathogenic features and characteristic of bacterial biofilm can facilitate in devising appropriate control strategies for biofilm eradication. Therefore, this review mainly summarized the pathogenic features of biofilms from food borne microorganisms, including the biomass (which could be quantified using crystal violet and fluorogenic dye Syto9 assays), viability (which could be determined by tetrazolium salts, fluorescein diacetate, resazurin staining and alamar blue assays) and matrix (which are commonly detected by dimethyl methylene blue and wheat germ agglutinin assays). In addition, three features were further compared with its particular benefits in specific application. Copyright © 2017 Elsevier Ltd. All rights reserved.

Dementia in the Oldest Old

PubMed Central

Bullain, Szófia S.; Corrada, María M.

2013-01-01

Purpose of Review: This article discusses some of the unique features of dementia in the oldest old, including some of the most common diagnostic challenges, and potential strategies to overcome them. Recent Findings: Advances include new insight into the role of common risk factors and the effects of multiple underlying neuropathologic features for dementia in the oldest old. In addition, this article contains the latest age-specific normative data for commonly used neuropsychological tests for the oldest old. Summary: The oldest old—people aged 90 years and older—are the fastest-growing segment of society and have the highest rates of dementia in the population. The risk factors, diagnostic challenges, and underlying neuropathologic features of dementia are strikingly different in the 90-years-and-older population compared to younger elderly. Special consideration of these unique features of dementia is necessary when evaluating oldest-old subjects with cognitive impairment. PMID:23558489

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kelly, J.R.; Duke, T.W.; Harwell, M.A.

Potential effects of oil drilling-fluid discharges upon Thalassia seagrass ecosystems were examined to provide general insights and raise ecotoxicological issues relevant to problems of addressing a priori, ecolgical effects of anthropogenic actions. Microcosm experiments have demonstrated effects upon both autotrophic and heterotrophic species, as well as the processes of primary productivity and decomposition. Significant ecological changes may result from disturbance effects related to the physical presence of higher particle loads, in addition to effects resulting from toxic features of drilling fluids.

Discriminative Nonlinear Analysis Operator Learning: When Cosparse Model Meets Image Classification.

PubMed

Wen, Zaidao; Hou, Biao; Jiao, Licheng

2017-05-03

Linear synthesis model based dictionary learning framework has achieved remarkable performances in image classification in the last decade. Behaved as a generative feature model, it however suffers from some intrinsic deficiencies. In this paper, we propose a novel parametric nonlinear analysis cosparse model (NACM) with which a unique feature vector will be much more efficiently extracted. Additionally, we derive a deep insight to demonstrate that NACM is capable of simultaneously learning the task adapted feature transformation and regularization to encode our preferences, domain prior knowledge and task oriented supervised information into the features. The proposed NACM is devoted to the classification task as a discriminative feature model and yield a novel discriminative nonlinear analysis operator learning framework (DNAOL). The theoretical analysis and experimental performances clearly demonstrate that DNAOL will not only achieve the better or at least competitive classification accuracies than the state-of-the-art algorithms but it can also dramatically reduce the time complexities in both training and testing phases.

Immunoglobulin M myeloma: evaluation of molecular features and cytokine expression.

PubMed

Konduri, Kartik; Sahota, Surinder S; Babbage, Gavin; Tong, Alex W; Kumar, Padmasini; Newman, Joseph T; Stone, Marvin J

2005-03-01

Immunoglobulin (Ig) M myeloma is a distinct entity with features of multiple myeloma (MM) and Waldenstrom's macroglobulinemia (WM). The malignant cells in IgM myeloma have a distinctive chromosomal translocation that differentiates them from WM. These cells are postgerminal-center in origin with isotype-switch transcripts. They appear to be arrested at a point of maturation between that of WM and MM. Preliminary data indicate that a pattern of osteoclast-activating factor and osteoprotegerin expression similar to that observed in classic MM is present in IgM myeloma. Additional studies on patients with this rare tumor may provide further insight into the pathogenesis of bone disease in plasma cell dyscrasias.

Learning representations for the early detection of sepsis with deep neural networks.

PubMed

Kam, Hye Jin; Kim, Ha Young

2017-10-01

Sepsis is one of the leading causes of death in intensive care unit patients. Early detection of sepsis is vital because mortality increases as the sepsis stage worsens. This study aimed to develop detection models for the early stage of sepsis using deep learning methodologies, and to compare the feasibility and performance of the new deep learning methodology with those of the regression method with conventional temporal feature extraction. Study group selection adhered to the InSight model. The results of the deep learning-based models and the InSight model were compared. With deep feedforward networks, the area under the ROC curve (AUC) of the models were 0.887 and 0.915 for the InSight and the new feature sets, respectively. For the model with the combined feature set, the AUC was the same as that of the basic feature set (0.915). For the long short-term memory model, only the basic feature set was applied and the AUC improved to 0.929 compared with the existing 0.887 of the InSight model. The contributions of this paper can be summarized in three ways: (i) improved performance without feature extraction using domain knowledge, (ii) verification of feature extraction capability of deep neural networks through comparison with reference features, and (iii) improved performance with feedforward neural networks using long short-term memory, a neural network architecture that can learn sequential patterns. Copyright © 2017 Elsevier Ltd. All rights reserved.

Widening the Heterogeneity of Leigh Syndrome: Clinical, Biochemical, and Neuroradiologic Features in a Patient Harboring a NDUFA10 Mutation.

PubMed

Minoia, Francesca; Bertamino, Marta; Picco, Paolo; Severino, Mariasavina; Rossi, Andrea; Fiorillo, Chiara; Minetti, Carlo; Nesti, Claudia; Santorelli, Filippo Maria; Di Rocco, Maja

2017-01-01

Leigh syndrome (LS) is an early-onset progressive neurodegenerative disorder, characterized by a wide clinical and genetic heterogeneity, and is the most frequent disorder of mitochondrial energy production in children. Beside its great variability in clinical, biochemical, and genetic features, LS is pathologically uniformly characterized by multifocal bilateral and symmetric spongiform degeneration of the basal ganglia, brainstem, thalamus, cerebellum, spinal cord, and optic nerves. Isolated complex I deficiency is the most common defect identified in Leigh syndrome. In 2011, the first child with a mutation of NDUFA10 gene, coding for an accessory subunits of complex I, was described. Here, we present an additional description of a child with Leigh syndrome harboring a homozygous mutation in NDUFA10, providing insights in clinical, biochemical, and neuroradiologic features for future earlier recognition.

Neocentromeres and epigenetically inherited features of centromeres

PubMed Central

Burrack, Laura S.; Berman, Judith

2012-01-01

Neocentromeres are ectopic sites where new functional kinetochores assemble and permit chromosome segregation. Neocentromeres usually form following genomic alterations that remove or disrupt centromere function. The ability to form neocentromeres is conserved in eukaryotes ranging from fungi to mammals. Neocentromeres that rescue chromosome fragments in cells with gross chromosomal rearrangements are found in several types of human cancers, and in patients with developmental disabilities. In this review, we discuss the importance of neocentromeres to human health and evaluate recently developed model systems to study neocentromere formation, maintenance, and function in chromosome segregation. Additionally, studies of neocentromeres provide insight into native centromeres; analysis of neocentromeres found in human clinical samples and induced in model organisms distinguishes features of centromeres that are dependent on centromere DNA from features that are epigenetically inherited together with the formation of a functional kinetochore. PMID:22723125

Automated Feature Identification and Classification Using Automated Feature Weighted Self Organizing Map (FWSOM)

NASA Astrophysics Data System (ADS)

Starkey, Andrew; Usman Ahmad, Aliyu; Hamdoun, Hassan

2017-10-01

This paper investigates the application of a novel method for classification called Feature Weighted Self Organizing Map (FWSOM) that analyses the topology information of a converged standard Self Organizing Map (SOM) to automatically guide the selection of important inputs during training for improved classification of data with redundant inputs, examined against two traditional approaches namely neural networks and Support Vector Machines (SVM) for the classification of EEG data as presented in previous work. In particular, the novel method looks to identify the features that are important for classification automatically, and in this way the important features can be used to improve the diagnostic ability of any of the above methods. The paper presents the results and shows how the automated identification of the important features successfully identified the important features in the dataset and how this results in an improvement of the classification results for all methods apart from linear discriminatory methods which cannot separate the underlying nonlinear relationship in the data. The FWSOM in addition to achieving higher classification accuracy has given insights into what features are important in the classification of each class (left and right-hand movements), and these are corroborated by already published work in this area.

Adult and juvenile dermatomyositis: are the distinct clinical features explained by our current understanding of serological subgroups and pathogenic mechanisms?

PubMed Central

2013-01-01

Adult and juvenile dermatomyositis share the hallmark features of pathognomic skin rash and muscle inflammation, but are heterogeneous disorders with a range of additional disease features and complications. The frequency of important clinical features such as calcinosis, interstitial lung disease and malignancy varies markedly between adult and juvenile disease. These differences may reflect different disease triggers between children and adults, but whilst various viral and other environmental triggers have been implicated, results are so far conflicting. Myositis-specific autoantibodies can be detected in both adults and children with idiopathic inflammatory myopathies. They are associated with specific disease phenotypes and complications, and divide patients into clinically homogenous subgroups. Interestingly, whilst the same autoantibodies are found in both adults and children, the disease features remain different within autoantibody subgroups, particularly with regard to life-threatening disease associations, such as malignancy and rapidly progressive interstitial lung disease. Our understanding of the mechanisms that underlie these differences is limited by a lack of studies directly comparing adults and children. Dermatomyositis is an autoimmune disease, which is believed to develop as a result of an environmental trigger in a genetically predisposed individual. Age-specific host immune responses and muscle physiology may be additional complicating factors that have significant impact on disease presentation. Further study into this area may produce new insights into disease pathogenesis. PMID:23566358

Numerical insight into the micromechanics of jet erosion of a cohesive granular material

NASA Astrophysics Data System (ADS)

Cuéllar, Pablo; Benseghier, Zeyd; Luu, Li-Hua; Bonelli, Stéphane; Delenne, Jean-Yves; Radjaï, Farhang; Philippe, Pierre

2017-06-01

Here we investigate the physical mechanisms behind the surface erosion of a cohesive granular soil induced by an impinging jet by means of numerical simulations coupling fluid and grains at the microscale. The 2D numerical model combines the Discrete Element and Lattice Boltzmann methods (DEM-LBM) and accounts for the granular cohesion with a contact model featuring a paraboloidal yield surface. Here we review first the hydrodynamical conditions imposed by the fluid jet on a solid granular packing, turning then the attention to the impact of cohesion on the erosion kinetics. Finally, the use of an additional subcritical debonding damage model based on the work of Silvani and co-workers provides a novel insight into the internal solicitation of the cohesive granular sample by the impinging jet.

A Statistical Analysis of Corona Topography: New Insights into Corona Formation and Evolution

NASA Technical Reports Server (NTRS)

Stofan, E. R.; Glaze, L. S.; Smrekar, S. E.; Baloga, S. M.

2003-01-01

Extensive mapping of the surface of Venus and continued analysis of Magellan data have allowed a more comprehensive survey of coronae to be conducted. Our updated corona database contains 514 features, an increase from the 326 coronae of the previous survey. We include a new set of 106 Type 2 or stealth coronae, which have a topographic rather than a fracture annulus. The large increase in the number of coronae over the 1992 survey results from several factors, including the use of the full Magellan data set and the addition of features identified as part of the systematic geologic mapping of Venus. Parameters of the population that we have analyzed to date include size and topography.

Emerging Insight into MAPK Inhibitors and Immunotherapy in Colorectal Cancer.

PubMed

Pancione, Massimo; Giordano, Guido; Parcesepe, Pietro; Cerulo, Luigi; Coppola, Luigi; Curatolo, Anais Del; Conciatori, Fabiana; Milella, Michele; Porras, Almudena

2017-01-01

Our understanding of the genetic and non-genetic molecular alterations associated with colorectal cancer (CRC) progression and therapy resistance has markedly expanded in the recent years. In addition to their effects on tumor biology, targeted therapies can have effects on host immune responses. However, the mechanisms by which immune cells organize tumor microenvironments to regulate T-cell activity need to be comprehensively defined. There is good evidence in the literature that alterations in different members of the MAPK superfamily (mainly ERKs and p38 MAPKs) modify the inflammatory response and antitumor immunity, enhancing metastatic features of the tumors. In addition, a plethora of alterations that emerge at relapse often converge on the activation of MAPKs, particularly, ERKs, which act in concert with other oncogenic signals to modulate cellular homeostasis and clonal evolution during targeted therapies. Herein, we discuss how this knowledge can be translated into drug development strategies aimed at increasing tumor antigenicity and antitumor immune responses. Insights from these studies could provide a framework for considering additional combinations of targeted therapies and immunotherapies for the treatment of CRC. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Imaging genetics approach to predict progression of Parkinson's diseases.

PubMed

Mansu Kim; Seong-Jin Son; Hyunjin Park

2017-07-01

Imaging genetics is a tool to extract genetic variants associated with both clinical phenotypes and imaging information. The approach can extract additional genetic variants compared to conventional approaches to better investigate various diseased conditions. Here, we applied imaging genetics to study Parkinson's disease (PD). We aimed to extract significant features derived from imaging genetics and neuroimaging. We built a regression model based on extracted significant features combining genetics and neuroimaging to better predict clinical scores of PD progression (i.e. MDS-UPDRS). Our model yielded high correlation (r = 0.697, p <; 0.001) and low root mean squared error (8.36) between predicted and actual MDS-UPDRS scores. Neuroimaging (from 123 I-Ioflupane SPECT) predictors of regression model were computed from independent component analysis approach. Genetic features were computed using image genetics approach based on identified neuroimaging features as intermediate phenotypes. Joint modeling of neuroimaging and genetics could provide complementary information and thus have the potential to provide further insight into the pathophysiology of PD. Our model included newly found neuroimaging features and genetic variants which need further investigation.

Fluid Mechanical Properties of Silkworm Fibroin Solutions

NASA Astrophysics Data System (ADS)

Matsumoto, Akira

2005-11-01

The aqueous solution behavior of silk fibroin is of interest due to the assembly and processing of this protein related to the spinning of protein fibers that exhibit remarkable mechanical properties. To gain insight into the origins of this functional feature, it is desired to determine how the protein behaves under a range of solution conditions. Pure fibroin at different concentrations in water was studied for surface tension, as a measure of surfactancy. In addition, shear induced changes on these solutions in terms of structure and morphology was also determined. Fibroin solutions exhibited shear rate-sensitive viscosity changes and precipitated at a critical shear rate where a dramatic increase of 75-150% of the initial value was observed along with a decrease in viscosity. In surface tension measurements, critical micelle concentrations were in the range of 3-4% w/v. The influence of additional factors, such as sericin protein, divalent and monovalent cations, and pH on the solution behavior in relation to structural and morphological features will also be described.

Extraction of Molecular Features through Exome to Transcriptome Alignment

PubMed Central

Mudvari, Prakriti; Kowsari, Kamran; Cole, Charles; Mazumder, Raja; Horvath, Anelia

2014-01-01

Integrative Next Generation Sequencing (NGS) DNA and RNA analyses have very recently become feasible, and the published to date studies have discovered critical disease implicated pathways, and diagnostic and therapeutic targets. A growing number of exomes, genomes and transcriptomes from the same individual are quickly accumulating, providing unique venues for mechanistic and regulatory features analysis, and, at the same time, requiring new exploration strategies. In this study, we have integrated variation and expression information of four NGS datasets from the same individual: normal and tumor breast exomes and transcriptomes. Focusing on SNPcentered variant allelic prevalence, we illustrate analytical algorithms that can be applied to extract or validate potential regulatory elements, such as expression or growth advantage, imprinting, loss of heterozygosity (LOH), somatic changes, and RNA editing. In addition, we point to some critical elements that might bias the output and recommend alternative measures to maximize the confidence of findings. The need for such strategies is especially recognized within the growing appreciation of the concept of systems biology: integrative exploration of genome and transcriptome features reveal mechanistic and regulatory insights that reach far beyond linear addition of the individual datasets. PMID:24791251

Peculiarities of Ionospheric Response to Solar Eruptive Events

NASA Astrophysics Data System (ADS)

Cadez, V. M.; Nina, A.

2013-05-01

Solar eruptive events such as flares and coronal mass ejections (CMEs) affect the terrestrial upper atmosphere, the magnetosphere and ionosphere in particular, through sudden impacts of additional X-ray radiation and by increased intensity of the solar wind. As a consequence, a variety perturbation features occur locally as well as globally in the plasma medium in space around the Earth. We study some of such transient phenomena taking place at low altitudes of the ionosphere (below 90 km) by monitoring and analyzing registered amplitude and phase time variations of VLF radio waves with given frequencies. The main object of this research is gaining an additional insight into the structure and physical properties of the lower ionosphere.

A Semiquantitative Framework for Gene Regulatory Networks: Increasing the Time and Quantitative Resolution of Boolean Networks

PubMed Central

Kerkhofs, Johan; Geris, Liesbet

2015-01-01

Boolean models have been instrumental in predicting general features of gene networks and more recently also as explorative tools in specific biological applications. In this study we introduce a basic quantitative and a limited time resolution to a discrete (Boolean) framework. Quantitative resolution is improved through the employ of normalized variables in unison with an additive approach. Increased time resolution stems from the introduction of two distinct priority classes. Through the implementation of a previously published chondrocyte network and T helper cell network, we show that this addition of quantitative and time resolution broadens the scope of biological behaviour that can be captured by the models. Specifically, the quantitative resolution readily allows models to discern qualitative differences in dosage response to growth factors. The limited time resolution, in turn, can influence the reachability of attractors, delineating the likely long term system behaviour. Importantly, the information required for implementation of these features, such as the nature of an interaction, is typically obtainable from the literature. Nonetheless, a trade-off is always present between additional computational cost of this approach and the likelihood of extending the model’s scope. Indeed, in some cases the inclusion of these features does not yield additional insight. This framework, incorporating increased and readily available time and semi-quantitative resolution, can help in substantiating the litmus test of dynamics for gene networks, firstly by excluding unlikely dynamics and secondly by refining falsifiable predictions on qualitative behaviour. PMID:26067297

New perspectives in the treatment of body dysmorphic disorder

PubMed Central

Hong, Kevin; Nezgovorova, Vera; Hollander, Eric

2018-01-01

Body dysmorphic disorder (BDD) is a disabling illness with a high worldwide prevalence. Patients demonstrate a debilitating preoccupation with one or more perceived defects, often marked by poor insight or delusional convictions. Multiple studies have suggested that selective serotonin reuptake inhibitors and various cognitive behavioral therapy modalities are effective first-line treatments in decreasing BDD severity, relieving depressive symptoms, restoring insight, and increasing quality of life. Selective serotonin reuptake inhibitors have also recently been shown to be effective for relapse prevention. This review provides a comprehensive summary of the current understanding of BDD, including its clinical features, epidemiology, genetics, and current treatment modalities. Additional research is needed to fully elucidate the relationship between BDD and comorbid illnesses such as obsessive–compulsive-related disorders and depression and to develop therapies for refractory patients and those who have contraindications for pharmacological intervention. PMID:29636904

The relationship between insight and the level of expressed emotion in patients with obsessive-compulsive disorder.

PubMed

Ozkiris, Ayse; Essizoglu, Altan; Gulec, Gulcan; Aksaray, Gokay

2015-04-01

The aim of this study is firstly to compare the obsessive-compulsive disorder (OCD) patients with good insight and OCD patients with poor insight in terms of socio-demographic and clinical features; to investigate the relation between insight and the level of the expressed emotion (EE) in the patients; and lastly to specify the factors that predict level of insight. OCD patients with good insight and patients with poor insight were compared in terms of clinical features and the perceived EE level of the patients and the individuals that they live with in order to specify the factors that predict the insight level, and to investigate the relationship between insight level and EE. It was found that the total Expressed Emotion Scale, total Level of Expressed Emotion (LEE), LEE-Emotional Response and LEE-Tolerance/Expectation subscale scores of the group comprised of patients with poor insight are higher than the other group. The results also show that the duration of illness and Yale-Brown Obsessive Compulsive Scale (Y-BOCS) total score predict insight level. This study shows that the level of EE perceived by the patients with poor insight and the person that he/she lives with, is higher than the group with good insight. The studies that investigate the relationship between the factors of insight level and EE level, which are indicated to determine the level of the illness severity and its chronicity, will enable the researchers to understand the importance of the role of the family on the treatment processes of OCD.

Computational study of ibuprofen removal from water by adsorption in realistic activated carbons.

PubMed

Bahamon, Daniel; Carro, Leticia; Guri, Sonia; Vega, Lourdes F

2017-07-15

Molecular simulations using the Grand Canonical Monte Carlo (GCMC) method have been performed in order to obtain physical insights on how the interaction between ibuprofen (IBP) and activated carbons (ACs) in aqueous mixtures affects IBP removal from water by ACs. A nanoporous carbon model based on units of polyaromatic molecules with different number of rings, defects and polar-oxygenated sites is described. Individual effects of factors such as porous features and chemical heterogeneities in the adsorbents are investigated and quantified. Results are in good agreement with experimental adsorption data, highlightening the ability of GCMC simulation to describe the macroscopic adsorption performance in drug removal applications, while also providing additional insights into the IBP/water adsorption mechanism. The simulation results allow finding the optimal type of activated carbon material for separating this pollutant in water treatment. Copyright © 2017 Elsevier Inc. All rights reserved.

Genomic analyses of primitive, wild and cultivated citrus provide insights into asexual reproduction.

PubMed

Wang, Xia; Xu, Yuantao; Zhang, Siqi; Cao, Li; Huang, Yue; Cheng, Junfeng; Wu, Guizhi; Tian, Shilin; Chen, Chunli; Liu, Yan; Yu, Huiwen; Yang, Xiaoming; Lan, Hong; Wang, Nan; Wang, Lun; Xu, Jidi; Jiang, Xiaolin; Xie, Zongzhou; Tan, Meilian; Larkin, Robert M; Chen, Ling-Ling; Ma, Bin-Guang; Ruan, Yijun; Deng, Xiuxin; Xu, Qiang

2017-05-01

The emergence of apomixis-the transition from sexual to asexual reproduction-is a prominent feature of modern citrus. Here we de novo sequenced and comprehensively studied the genomes of four representative citrus species. Additionally, we sequenced 100 accessions of primitive, wild and cultivated citrus. Comparative population analysis suggested that genomic regions harboring energy- and reproduction-associated genes are probably under selection in cultivated citrus. We also narrowed the genetic locus responsible for citrus polyembryony, a form of apomixis, to an 80-kb region containing 11 candidate genes. One of these, CitRWP, is expressed at higher levels in ovules of polyembryonic cultivars. We found a miniature inverted-repeat transposable element insertion in the promoter region of CitRWP that cosegregated with polyembryony. This study provides new insights into citrus apomixis and constitutes a promising resource for the mining of agriculturally important genes.

The atmospheres of Saturn and Titan in the near-infrared: First results of Cassini/Vims

USGS Publications Warehouse

Baines, K.H.; Momary, T.W.; Buratti, B.J.; Matson, D.L.; Nelson, R.M.; Drossart, P.; Sicardy, B.; Formisano, V.; Bellucci, G.; Coradini, A.; Griffith, C.; Brown, R.H.; Bibring, J.-P.; Langevin, Y.; Capaccioni, F.; Cerroni, P.; Clark, R.N.; Combes, M.; Cruikshank, D.P.; Jaumann, R.; McCordt, T.B.; Mennella, V.; Nicholson, P.D.; Sotin, Christophe

2006-01-01

The wide spectral coverage and extensive spatial, temporal, and phase-angle mapping capabilities of the Visual Infrared Mapping Spectrometer (VIMS) onboard the Cassini-Huygens Orbiter are producing fundamental new insights into the nature of the atmospheres of Saturn and Titan. For both bodies, VIMS maps over time and solar phase angles provide information for a multitude of atmospheric constituents and aerosol layers, providing new insights into atmospheric structure and dynamical and chemical processes. For Saturn, salient early results include evidence for phosphine depletion in relatively dark and less cloudy belts at temperate and mid-latitudes compared to the relatively bright and cloudier Equatorial Region, consistent with traditional theories of belts being regions of relative downwelling. Additional Saturn results include (1) the mapping of enhanced trace gas absorptions at the south pole, and (2) the first high phase-angle, high-spatial-resolution imagery of CH4 fluorescence. An additional fundamental new result is the first nighttime near-infrared mapping of Saturn, clearly showing discrete meteorological features relatively deep in the atmosphere beneath the planet's sunlit haze and cloud layers, thus revealing a new dynamical regime at depth where vertical dynamics is relatively more important than zonal dynamics in determining cloud morphology. Zonal wind measurements at deeper levels than previously available are achieved by tracking these features over multiple days, thereby providing measurements of zonal wind shears within Saturn's troposphere when compared to cloudtop movements measured in reflected sunlight. For Titan, initial results include (1) the first detection and mapping of thermal emission spectra of CO, CO2, and CH3D on Titan's nightside limb, (2) the mapping of CH4 fluorescence over the dayside bright limb, extending to ??? 750 km altitude, (3) wind measurements of ???0.5 ms-1, favoring prograde, from the movement of a persistent (multiple months) south polar cloud near 88??S latitude, and (4) the imaging of two transient mid-southern-latitude cloud features. ?? Springer Science+Business Media, Inc. 2006.

Interactive Exploration and Analysis of Large-Scale Simulations Using Topology-Based Data Segmentation.

PubMed

Bremer, Peer-Timo; Weber, Gunther; Tierny, Julien; Pascucci, Valerio; Day, Marcus S; Bell, John B

2011-09-01

Large-scale simulations are increasingly being used to study complex scientific and engineering phenomena. As a result, advanced visualization and data analysis are also becoming an integral part of the scientific process. Often, a key step in extracting insight from these large simulations involves the definition, extraction, and evaluation of features in the space and time coordinates of the solution. However, in many applications, these features involve a range of parameters and decisions that will affect the quality and direction of the analysis. Examples include particular level sets of a specific scalar field, or local inequalities between derived quantities. A critical step in the analysis is to understand how these arbitrary parameters/decisions impact the statistical properties of the features, since such a characterization will help to evaluate the conclusions of the analysis as a whole. We present a new topological framework that in a single-pass extracts and encodes entire families of possible features definitions as well as their statistical properties. For each time step we construct a hierarchical merge tree a highly compact, yet flexible feature representation. While this data structure is more than two orders of magnitude smaller than the raw simulation data it allows us to extract a set of features for any given parameter selection in a postprocessing step. Furthermore, we augment the trees with additional attributes making it possible to gather a large number of useful global, local, as well as conditional statistic that would otherwise be extremely difficult to compile. We also use this representation to create tracking graphs that describe the temporal evolution of the features over time. Our system provides a linked-view interface to explore the time-evolution of the graph interactively alongside the segmentation, thus making it possible to perform extensive data analysis in a very efficient manner. We demonstrate our framework by extracting and analyzing burning cells from a large-scale turbulent combustion simulation. In particular, we show how the statistical analysis enabled by our techniques provides new insight into the combustion process.

Hemipteran Mitochondrial Genomes: Features, Structures and Implications for Phylogeny

PubMed Central

Wang, Yuan; Chen, Jing; Jiang, Li-Yun; Qiao, Ge-Xia

2015-01-01

The study of Hemipteran mitochondrial genomes (mitogenomes) began with the Chagas disease vector, Triatoma dimidiata, in 2001. At present, 90 complete Hemipteran mitogenomes have been sequenced and annotated. This review examines the history of Hemipteran mitogenomes research and summarizes the main features of them including genome organization, nucleotide composition, protein-coding genes, tRNAs and rRNAs, and non-coding regions. Special attention is given to the comparative analysis of repeat regions. Gene rearrangements are an additional data type for a few families, and most mitogenomes are arranged in the same order to the proposed ancestral insect. We also discuss and provide insights on the phylogenetic analyses of a variety of taxonomic levels. This review is expected to further expand our understanding of research in this field and serve as a valuable reference resource. PMID:26039239

Morphological characteristics of motile plants for dynamic motion

NASA Astrophysics Data System (ADS)

Song, Kahye; Yeom, Eunseop; Kim, Kiwoong; Lee, Sang Joon

2014-11-01

Most plants have been considered as non-motile organisms. However, plants move in response to environmental changes for survival. In addition, some species drive dynamic motions in a short period of time. Mimosa pudica is a plant that rapidly shrinks its body in response to external stimuli. It has specialized organs that are omnidirectionally activated due to morphological features. In addition, scales of pinecone open or close up depending on humidity for efficient seed release. A number of previous studies on the dynamic motion of plants have been investigated in a biochemical point of view. In this study, the morphological characteristics of those motile organs were investigated by using X-ray CT and micro-imaging techniques. The results show that the dynamic motions of motile plants are supported by structural features related with water transport. These studies would provide new insight for better understanding the moving mechanism of motile plant in morphological point of view. This research was financially supported by the Creative Research Initiative of the Ministry of Science, ICT and Future Planning (MSIP) and the National Research Foundation (NRF) of Korea (Grant Number: 2008-0061991).

Bidirectional holographic codes and sub-AdS locality

NASA Astrophysics Data System (ADS)

Yang, Zhao; Hayden, Patrick; Qi, Xiaoliang

Tensor networks implementing quantum error correcting codes have recently been used as toy models of the holographic duality which explicitly realize some of the more puzzling features of the AdS/CFT correspondence. These models reproduce the Ryu-Takayanagi entropy formula for boundary intervals, and allow bulk operators to be mapped to the boundary in a redundant fashion. These exactly solvable, explicit models have provided valuable insight but nonetheless suffer from many deficiencies, some of which we attempt to address in this talk. We propose a new class of tensor network models that subsume the earlier advances and, in addition, incorporate additional features of holographic duality, including: (1) a holographic interpretation of all boundary states, not just those in a ''code'' subspace, (2) a set of bulk states playing the role of ''classical geometries'' which reproduce the Ryu-Takayanagi formula for boundary intervals, (3) a bulk gauge symmetry analogous to diffeomorphism invariance in gravitational theories, (4) emergent bulk locality for sufficiently sparse excitations, and the ability to describe geometry at sub-AdS resolutions or even flat space. David and Lucile Packard Foundation.

Bidirectional holographic codes and sub-AdS locality

NASA Astrophysics Data System (ADS)

Yang, Zhao; Hayden, Patrick; Qi, Xiao-Liang

2016-01-01

Tensor networks implementing quantum error correcting codes have recently been used to construct toy models of holographic duality explicitly realizing some of the more puzzling features of the AdS/CFT correspondence. These models reproduce the Ryu-Takayanagi entropy formula for boundary intervals, and allow bulk operators to be mapped to the boundary in a redundant fashion. These exactly solvable, explicit models have provided valuable insight but nonetheless suffer from many deficiencies, some of which we attempt to address in this article. We propose a new class of tensor network models that subsume the earlier advances and, in addition, incorporate additional features of holographic duality, including: (1) a holographic interpretation of all boundary states, not just those in a "code" subspace, (2) a set of bulk states playing the role of "classical geometries" which reproduce the Ryu-Takayanagi formula for boundary intervals, (3) a bulk gauge symmetry analogous to diffeomorphism invariance in gravitational theories, (4) emergent bulk locality for sufficiently sparse excitations, and (5) the ability to describe geometry at sub-AdS resolutions or even flat space.

Exploring the Design and Role of Mobile Apps for Healthcare Providers to Find Teratogenic Information

PubMed Central

Lie, Lily; Shetty, Vishwas; Gupta, Karan; Polifka, Janine E; Markham, Glen; Albee, Sarah; Collins, Carol; Hsieh, Gary

2017-01-01

Healthcare providers (HCPs) caring for pregnant patients often need information on drug risks to the embryo or fetus, but such complex information takes time to find and is difficult to convey on an app. In this work, we first surveyed 167 HCPs to understand their current teratogen information-seeking practices to help inform our general design goals. Using the insights gained, we then designed a prototype of a mobile app and tested it with 22 HCPs. We learned that HCP ’s information needs in this context can be grouped into 3 types: to understand, to decide, and to explain. Different sets of information and features may be needed to support these different needs. Further, while some HCPs had concerns about appearing unprofessional and unknowledgeable when using the app in front of patients, many did not. They noted that incorporating mobile information apps into practice improves information access, can help signal care and technology-savviness, in addition to providing an opportunity to engage and educate patients. Implications for design and additional features for reference apps for HCPs are discussed. PMID:29854178

Empathy and moral emotions in post-apartheid South Africa: an fMRI investigation.

PubMed

Fourie, Melike M; Stein, Dan J; Solms, Mark; Gobodo-Madikizela, Pumla; Decety, Jean

2017-06-01

Moral emotions elicited in response to others' suffering are mediated by empathy and affect how we respond to their pain. South Africa provides a unique opportunity to study group processes given its racially divided past. The present study seeks insights into aspects of the moral brain by investigating behavioral and functional MRI responses of White and Black South Africans who lived through apartheid to in- and out-group physical and social pain. Whereas the physical pain task featured faces expressing dynamic suffering, the social pain task featured victims of apartheid violence from the South African Truth and Reconciliation Commission to elicit heartfelt emotion. Black participants' behavioral responses were suggestive of in-group favoritism, whereas White participants' responses were apparently egalitarian. However, all participants showed significant in-group biases in activation in the amygdala (physical pain), as well as areas involved in mental state representation, including the precuneus, temporoparietal junction (TPJ) and frontal pole (physical and social pain). Additionally, Black participants reacted with heightened moral indignation to own-race suffering, whereas White participants reacted with heightened shame to Black suffering, which was associated with blunted neural empathic responding. These findings provide ecologically valid insights into some behavioral and brain processes involved in complex moral situations. © The Author (2017). Published by Oxford University Press.

Virus-host interactions: insights from the replication cycle of the large Paramecium bursaria chlorella virus.

PubMed

Milrot, Elad; Mutsafi, Yael; Fridmann-Sirkis, Yael; Shimoni, Eyal; Rechav, Katya; Gurnon, James R; Van Etten, James L; Minsky, Abraham

2016-01-01

The increasing interest in cytoplasmic factories generated by eukaryotic-infecting viruses stems from the realization that these highly ordered assemblies may contribute fundamental novel insights to the functional significance of order in cellular biology. Here, we report the formation process and structural features of the cytoplasmic factories of the large dsDNA virus Paramecium bursaria chlorella virus 1 (PBCV-1). By combining diverse imaging techniques, including scanning transmission electron microscopy tomography and focused ion beam technologies, we show that the architecture and mode of formation of PBCV-1 factories are significantly different from those generated by their evolutionary relatives Vaccinia and Mimivirus. Specifically, PBCV-1 factories consist of a network of single membrane bilayers acting as capsid templates in the central region, and viral genomes spread throughout the host cytoplasm but excluded from the membrane-containing sites. In sharp contrast, factories generated by Mimivirus have viral genomes in their core, with membrane biogenesis region located at their periphery. Yet, all viral factories appear to share structural features that are essential for their function. In addition, our studies support the notion that PBCV-1 infection, which was recently reported to result in significant pathological outcomes in humans and mice, proceeds through a bacteriophage-like infection pathway. © 2015 John Wiley & Sons Ltd.

Analysis of intracerebral EEG recordings of epileptic spikes: insights from a neural network model

PubMed Central

Demont-Guignard, Sophie; Benquet, Pascal; Gerber, Urs; Wendling, Fabrice

2009-01-01

The pathophysiological interpretation of EEG signals recorded with depth electrodes (i.e. local field potentials, LFPs) during interictal (between seizures) or ictal (during seizures) periods is fundamental in the pre-surgical evaluation of patients with drug-resistant epilepsy. Our objective was to explain specific shape features of interictal spikes in the hippocampus (observed in LFPs) in terms of cell and network-related parameters of neuronal circuits that generate these events. We developed a neural network model based on “minimal” but biologically-relevant neuron models interconnected through GABAergic and glutamatergic synapses that reproduces the main physiological features of the CA1 subfield. Simulated LFPs were obtained by solving the forward problem (dipole theory) from networks including a large number (~3000) of cells. Insertion of appropriate parameters allowed the model to simulate events that closely resemble actual epileptic spikes. Moreover, the shape of the early fast component (‘spike’) and the late slow component (‘negative wave’) was linked to the relative contribution of glutamatergic and GABAergic synaptic currents in pyramidal cells. In addition, the model provides insights about the sensitivity of electrode localization with respect to recorded tissue volume and about the relationship between the LFP and the intracellular activity of principal cells and interneurons represented in the network. PMID:19651549

Empathy and moral emotions in post-apartheid South Africa: an fMRI investigation

PubMed Central

Stein, Dan J.; Solms, Mark; Gobodo-Madikizela, Pumla; Decety, Jean

2017-01-01

Abstract Moral emotions elicited in response to others’ suffering are mediated by empathy and affect how we respond to their pain. South Africa provides a unique opportunity to study group processes given its racially divided past. The present study seeks insights into aspects of the moral brain by investigating behavioral and functional MRI responses of White and Black South Africans who lived through apartheid to in- and out-group physical and social pain. Whereas the physical pain task featured faces expressing dynamic suffering, the social pain task featured victims of apartheid violence from the South African Truth and Reconciliation Commission to elicit heartfelt emotion. Black participants’ behavioral responses were suggestive of in-group favoritism, whereas White participants’ responses were apparently egalitarian. However, all participants showed significant in-group biases in activation in the amygdala (physical pain), as well as areas involved in mental state representation, including the precuneus, temporoparietal junction (TPJ) and frontal pole (physical and social pain). Additionally, Black participants reacted with heightened moral indignation to own-race suffering, whereas White participants reacted with heightened shame to Black suffering, which was associated with blunted neural empathic responding. These findings provide ecologically valid insights into some behavioral and brain processes involved in complex moral situations. PMID:28338783

Insight: An ontology-based integrated database and analysis platform for epilepsy self-management research.

PubMed

Sahoo, Satya S; Ramesh, Priya; Welter, Elisabeth; Bukach, Ashley; Valdez, Joshua; Tatsuoka, Curtis; Bamps, Yvan; Stoll, Shelley; Jobst, Barbara C; Sajatovic, Martha

2016-10-01

We present Insight as an integrated database and analysis platform for epilepsy self-management research as part of the national Managing Epilepsy Well Network. Insight is the only available informatics platform for accessing and analyzing integrated data from multiple epilepsy self-management research studies with several new data management features and user-friendly functionalities. The features of Insight include, (1) use of Common Data Elements defined by members of the research community and an epilepsy domain ontology for data integration and querying, (2) visualization tools to support real time exploration of data distribution across research studies, and (3) an interactive visual query interface for provenance-enabled research cohort identification. The Insight platform contains data from five completed epilepsy self-management research studies covering various categories of data, including depression, quality of life, seizure frequency, and socioeconomic information. The data represents over 400 participants with 7552 data points. The Insight data exploration and cohort identification query interface has been developed using Ruby on Rails Web technology and open source Web Ontology Language Application Programming Interface to support ontology-based reasoning. We have developed an efficient ontology management module that automatically updates the ontology mappings each time a new version of the Epilepsy and Seizure Ontology is released. The Insight platform features a Role-based Access Control module to authenticate and effectively manage user access to different research studies. User access to Insight is managed by the Managing Epilepsy Well Network database steering committee consisting of representatives of all current collaborating centers of the Managing Epilepsy Well Network. New research studies are being continuously added to the Insight database and the size as well as the unique coverage of the dataset allows investigators to conduct aggregate data analysis that will inform the next generation of epilepsy self-management studies. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

A System-Level Pathway-Phenotype Association Analysis Using Synthetic Feature Random Forest

PubMed Central

Pan, Qinxin; Hu, Ting; Malley, James D.; Andrew, Angeline S.; Karagas, Margaret R.; Moore, Jason H.

2015-01-01

As the cost of genome-wide genotyping decreases, the number of genome-wide association studies (GWAS) has increased considerably. However, the transition from GWAS findings to the underlying biology of various phenotypes remains challenging. As a result, due to its system-level interpretability, pathway analysis has become a popular tool for gaining insights on the underlying biology from high-throughput genetic association data. In pathway analyses, gene sets representing particular biological processes are tested for significant associations with a given phenotype. Most existing pathway analysis approaches rely on single-marker statistics and assume that pathways are independent of each other. As biological systems are driven by complex biomolecular interactions, embracing the complex relationships between single-nucleotide polymorphisms (SNPs) and pathways needs to be addressed. To incorporate the complexity of gene-gene interactions and pathway-pathway relationships, we propose a system-level pathway analysis approach, synthetic feature random forest (SF-RF), which is designed to detect pathway-phenotype associations without making assumptions about the relationships among SNPs or pathways. In our approach, the genotypes of SNPs in a particular pathway are aggregated into a synthetic feature representing that pathway via Random Forest (RF). Multiple synthetic features are analyzed using RF simultaneously and the significance of a synthetic feature indicates the significance of the corresponding pathway. We further complement SF-RF with pathway-based Statistical Epistasis Network (SEN) analysis that evaluates interactions among pathways. By investigating the pathway SEN, we hope to gain additional insights into the genetic mechanisms contributing to the pathway-phenotype association. We apply SF-RF to a population-based genetic study of bladder cancer and further investigate the mechanisms that help explain the pathway-phenotype associations using SEN. The bladder cancer associated pathways we found are both consistent with existing biological knowledge and reveal novel and plausible hypotheses for future biological validations. PMID:24535726

Association between insight, cognitive insight, positive symptoms and violence in patients with schizophrenia.

PubMed

Ekinci, Okan; Ekinci, Asli

2013-04-01

Violence is a significant clinical and public concern and is a frequent occurrence in patients with schizophrenia. The relationship between insight and violence remains controversial. In addition, there is a lack of research on insight, cognitive insight, demographic and psychopathologic variables in violent versus nonviolent schizophrenia patients. We aimed to compare insight, cognitive insight, psychopathological and demographic variables in violent and nonviolent subjects suffering from schizophrenia. In addition, we aimed to determine the demographic and clinical predictors of violent behaviour in patients with schizophrenia. We recruited 133 schizophrenic patients without concomitant substance abuse or axis II disorder. Diagnoses were based on the SCID-I and SCID-II. Violent behaviours were assessed using the Overt Aggression Scale. Insight and cognitive insight were assessed with the Scale to Assess Unawareness of Mental Disorder and the Beck Cognitive Insight Scale, respectively. We compared 47 patients with violent schizophrenia with 86 nonviolent patients. Non-violent patients had more severe depression, lower scores on positive symptoms, better clinical insight, more self-reflectivity and higher R-C index scores than did violent patients. In addition, history of violence, lower self-reflectiveness, worse clinical insight and delusion severity were significant predictors of violence in schizophrenia. The present study suggests that the inclusion of insight and cognitive insight may increase the prediction of violence in this population. In addition, clinicians should consider using non-pharmacological techniques that are based on cognitive behaviour therapy and enhance insight, particularly cognitive insight, among patients with schizophrenia who exhibit violent behaviour.

Immunology of the Uterine and Vaginal Mucosae.

PubMed

Zhou, Jordan Z; Way, Sing Sing; Chen, Kang

2018-04-01

Along with the maintenance of symbiotic mutualism with commensal microbes and protection against invasive infections common to all mucosal barrier tissues, female reproductive tissues have additional, unique tasks that include dynamic cyclic cellular turnover in menstruation and immunological tolerance to genetically foreign fetal antigens in pregnancy. Here we review current knowledge on distinct features of the immune cells in female reproductive tissue with regard to antimicrobial host defense and adaptations to accommodate the fetus during pregnancy. Outstanding areas for future research to obtain new functional insights on this enigmatic mucosal barrier are also highlighted. Copyright © 2018 Elsevier Ltd. All rights reserved.

Some spectral and spatial characteristics of LANDSAT data

NASA Technical Reports Server (NTRS)

1982-01-01

Activities are provided for: (1) developing insight into the way in which the LANDSAT MSS produces multispectral data; (2) promoting understanding of what a "pixel" means in a LANDSAT image and the implications of the term "mixed pixel"; (3) explaining the concept of spectral signatures; (4) deriving a simple signature for a class or feature by analysis: of the four band images; (5) understanding the production of false color composites; (6) appreciating the use of color additive techniques; (7) preparing Diazo images; and (8) making quick visual identifications of major land cover types by their characteristic gray tones or colors in LANDSAT images.

Premotor and non-motor features of Parkinson’s disease

PubMed Central

Goldman, Jennifer G.; Postuma, Ron

2014-01-01

Purpose of review This review highlights recent advances in premotor and non-motor features in Parkinson’s disease, focusing on these issues in the context of prodromal and early stage Parkinson’s disease. Recent findings While Parkinson’s disease patients experience a wide range of non-motor symptoms throughout the disease course, studies demonstrate that non-motor features are not solely a late manifestation. Indeed, disturbances of smell, sleep, mood, and gastrointestinal function may herald Parkinson’s disease or related synucleinopathies and precede these neurodegenerative conditions by 5 or more years. In addition, other non-motor symptoms such as cognitive impairment are now recognized in incident or de novo Parkinson’s disease cohorts. Many of these non-motor features reflect disturbances in non-dopaminergic systems and early involvement of peripheral and central nervous systems including olfactory, enteric, and brainstem neurons as in Braak’s proposed pathological staging of Parkinson’s disease. Current research focuses on identifying potential biomarkers that may detect persons at risk for Parkinson’s disease and permit early intervention with neuroprotective or disease-modifying therapeutics. Summary Recent studies provide new insights on the frequency, pathophysiology, and importance of non-motor features in Parkinson’s disease as well as the recognition that these non-motor symptoms occur in premotor, early, and later phases of Parkinson’s disease. PMID:24978368

Obsessive-compulsive skin disorders: a novel classification based on degree of insight.

PubMed

Zhu, Tian Hao; Nakamura, Mio; Farahnik, Benjamin; Abrouk, Michael; Reichenberg, Jason; Bhutani, Tina; Koo, John

2017-06-01

Individuals with obsessive-compulsive features frequently visit dermatologists for complaints of the skin, hair or nails, and often progress towards a chronic relapsing course due to the challenge associated with accurate diagnosis and management of their psychiatric symptoms. The current DSM-5 formally recognizes body dysmorphic disorder, trichotillomania, neurotic excoriation and body focused repetitive behavior disorder as psychodermatological disorders belonging to the category of Obsessive-Compulsive and Related Disorders. However there is evidence that other relevant skin diseases such as delusions of parasitosis, dermatitis artefacta, contamination dermatitis, AIDS phobia, trichotemnomania and even lichen simplex chronicus possess prominent obsessive-compulsive characteristics that do not necessarily fit the full diagnostic criteria of the DSM-5. Therefore, to increase dermatologists' awareness of this unique group of skin disorders with OCD features, we propose a novel classification system called Obsessive-Compulsive Insight Continuum. Under this new classification system, obsessive-compulsive skin manifestations are categorized along a continuum based on degree of insight, from minimal insight with delusional obsessions to good insight with minimal obsessions. Understanding the level of insight is thus an important first step for clinicians who routinely interact with these patients.

Detection of Interictal Discharges With Convolutional Neural Networks Using Discrete Ordered Multichannel Intracranial EEG.

PubMed

Antoniades, Andreas; Spyrou, Loukianos; Martin-Lopez, David; Valentin, Antonio; Alarcon, Gonzalo; Sanei, Saeid; Cheong Took, Clive

2017-12-01

Detection algorithms for electroencephalography (EEG) data, especially in the field of interictal epileptiform discharge (IED) detection, have traditionally employed handcrafted features, which utilized specific characteristics of neural responses. Although these algorithms achieve high accuracy, mere detection of an IED holds little clinical significance. In this paper, we consider deep learning for epileptic subjects to accommodate automatic feature generation from intracranial EEG data, while also providing clinical insight. Convolutional neural networks are trained in a subject independent fashion to demonstrate how meaningful features are automatically learned in a hierarchical process. We illustrate how the convolved filters in the deepest layers provide insight toward the different types of IEDs within the group, as confirmed by our expert clinicians. The morphology of the IEDs found in filters can help evaluate the treatment of a patient. To improve the learning of the deep model, moderately different score classes are utilized as opposed to binary IED and non-IED labels. The resulting model achieves state-of-the-art classification performance and is also invariant to time differences between the IEDs. This paper suggests that deep learning is suitable for automatic feature generation from intracranial EEG data, while also providing insight into the data.

LncRNA, a new component of expanding RNA-protein regulatory network important for animal sperm development.

PubMed

Zhang, Chenwang; Gao, Liuze; Xu, Eugene Yujun

2016-11-01

Spermatogenesis is one of the fundamental processes of sexual reproduction, present in almost all metazoan animals. Like many other reproductive traits, developmental features and traits of spermatogenesis are under strong selective pressure to change, both at morphological and underlying molecular levels. Yet evidence suggests that some fundamental features of spermatogenesis may be ancient and conserved among metazoan species. Identifying the underlying conserved molecular mechanisms could reveal core components of metazoan spermatogenic machinery and provide novel insight into causes of human infertility. Conserved RNA-binding proteins and their interacting RNA network emerge to be a common theme important for animal sperm development. We review research on the recent addition to the RNA family - Long non-coding RNA (lncRNA) and its roles in spermatogenesis in the context of the expanding RNA-protein network. Copyright © 2016 Elsevier Ltd. All rights reserved.

New Insights into Shape Memory Alloy Bimorph Actuators Formed by Electron Beam Evaporation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sun, Hao; Nykypanchuk, Dmytro

In order to create shape memory alloy (SMA) bimorph microactuators with high-precision features, a novel fabrication process combined with electron beam (E-beam) evaporation, lift-off resist and isotropic XeF2 dry etching method was developed. To examine the effect of E-beam deposition and annealing process on nitinol (NiTi) characteristics, the NiTi thin film samples with different deposition rate and overflow conditions during annealing process were investigated. With the characterizations using scanning electron microscope and x-ray diffraction, the results indicated that low E-beam deposition rate and argon employed annealing process could benefit the formation of NiTi crystalline structure. In addition, SMA bimorph microactuatorsmore » with high-precision features as small as 5 microns were successfully fabricated. Furthermore, the thermomechanical performance was experimentally verified and compared with finite element analysis simulation results.« less

Sentinel-3A Views Ocean Variability More Accurately at Finer Resolution

NASA Astrophysics Data System (ADS)

Heslop, E. E.; Sánchez-Román, A.; Pascual, A.; Rodríguez, D.; Reeve, K. A.; Faugère, Y.; Raynal, M.

2017-12-01

This is the first multiplatform evaluation involving data from the new Sentinel-3A altimeter. An experiment was undertaken in the Algerian Basin, employing an ocean glider and a ship mission, along the same track and synchronous with an overpass of the Sentinel-3A mission. This provided three independent views of the ocean velocity field, along a section that encompassed three different oceanographic regimes. The results demonstrate the capacity of Sentinel-3A to retrieve fine-scale oceanographic features ( 20 km). The intercomparison with in situ platforms showed a significant improvement, order 30% in resolution and 42% in velocity accuracy using a synthetic aperture radar mode with respect to lower-resolution mode of conventional altimetry. In addition, the three-platform view provided valuable insight into the variability of evolving oceanographic features, in an area of the Mediterranean that remains chronically under sampled.

Unsymmetric Mono- and Dinuclear Platinum(IV) Complexes Featuring an Ethylene Glycol Moiety: Synthesis, Characterization, and Biological Activity

PubMed Central

Pichler, Verena; Heffeter, Petra; Valiahdi, Seied M.; Kowol, Christian R.; Egger, Alexander; Berger, Walter; Jakupec, Michael A.; Galanski, Markus; Keppler, Bernhard K.

2014-01-01

Eight novel mononuclear and two dinuclear platinum(IV) complexes were synthesized and characterized by elemental analysis, one- and two-dimensional NMR spectroscopy, mass spectrometry, and reversed-phase HPLC (log kw) and in one case by X-ray diffraction. Cytotoxicity of the compounds was studied in three human cancer cell lines (CH1, SW480, and A549) by means of the MTT assay, featuring IC50 values to the low micromolar range. Furthermore a selected set of compounds was investigated in additional cancer cell lines (P31 and P31/cis, A2780 and A2780/cis, SW1573, 2R120, and 2R160) with regard to their resistance patterns, offering a distinctly different scheme compared to cisplatin. To gain further insights into the mode of action, drug uptake, DNA synthesis inhibition, cell cycle effects, and induction of apoptosis were determined for two characteristic substances. PMID:23194425

Using Consumer Electronics and Apps in Industrial Environments - Development of a Framework for Dynamic Feature Deployment and Extension by Using Apps on Field Devices

NASA Astrophysics Data System (ADS)

Schmitt, Mathias

2014-12-01

The aim of this paper is to give a preliminary insight regarding the current work in the field of mobile interaction in industrial environments by using established interaction technologies and metaphors from the consumer goods industry. The major objective is the development and implementation of a holistic app-framework, which enables dynamic feature deployment and extension by using mobile apps on industrial field devices. As a result, field device functionalities can be updated and adapted effectively in accordance with well-known appconcepts from consumer electronics to comply with the urgent requirements of more flexible and changeable factory systems of the future. In addition, a much more user-friendly and utilizable interaction with field devices can be realized. Proprietary software solutions and device-stationary user interfaces can be overcome and replaced by uniform, cross-vendor solutions

Health insurance exchanges of past and present offer examples of features that could attract small-business customers.

PubMed

Gardiner, Terry

2012-02-01

The Affordable Care Act calls on states to create health insurance exchanges serving small businesses by 2014. These exchanges will allow small-business owners to pool their buying power, have more choices of health plans, and buy affordable health insurance. However, creating an exchange that appeals to small-business owners poses several challenges. Past and current exchanges provide valuable insights into the role exchanges can play, services they can offer, and design features that can make them successful. For example, states should allow insurance brokers to provide employers with advice and analysis regarding plans offered in the exchanges. Exchanges should also provide services to ease enrollment, such as a single application for all of the plans they offer, and make additional benefits, such as wellness programs, available on a stand-alone basis or within insurance plans.

Sequential structural damage diagnosis algorithm using a change point detection method

NASA Astrophysics Data System (ADS)

Noh, H.; Rajagopal, R.; Kiremidjian, A. S.

2013-11-01

This paper introduces a damage diagnosis algorithm for civil structures that uses a sequential change point detection method. The general change point detection method uses the known pre- and post-damage feature distributions to perform a sequential hypothesis test. In practice, however, the post-damage distribution is unlikely to be known a priori, unless we are looking for a known specific type of damage. Therefore, we introduce an additional algorithm that estimates and updates this distribution as data are collected using the maximum likelihood and the Bayesian methods. We also applied an approximate method to reduce the computation load and memory requirement associated with the estimation. The algorithm is validated using a set of experimental data collected from a four-story steel special moment-resisting frame and multiple sets of simulated data. Various features of different dimensions have been explored, and the algorithm was able to identify damage, particularly when it uses multidimensional damage sensitive features and lower false alarm rates, with a known post-damage feature distribution. For unknown feature distribution cases, the post-damage distribution was consistently estimated and the detection delays were only a few time steps longer than the delays from the general method that assumes we know the post-damage feature distribution. We confirmed that the Bayesian method is particularly efficient in declaring damage with minimal memory requirement, but the maximum likelihood method provides an insightful heuristic approach.

Assessing the impact of representational and contextual problem features on student use of right-hand rules

NASA Astrophysics Data System (ADS)

Kustusch, Mary Bridget

2016-06-01

Students in introductory physics struggle with vector algebra and these challenges are often associated with contextual and representational features of the problems. Performance on problems about cross product direction is particularly poor and some research suggests that this may be primarily due to misapplied right-hand rules. However, few studies have had the resolution to explore student use of right-hand rules in detail. This study reviews literature in several disciplines, including spatial cognition, to identify ten contextual and representational problem features that are most likely to influence performance on problems requiring a right-hand rule. Two quantitative measures of performance (correctness and response time) and two qualitative measures (methods used and type of errors made) were used to explore the impact of these problem features on student performance. Quantitative results are consistent with expectations from the literature, but reveal that some features (such as the type of reasoning required and the physical awkwardness of using a right-hand rule) have a greater impact than others (such as whether the vectors are placed together or separate). Additional insight is gained by the qualitative analysis, including identifying sources of difficulty not previously discussed in the literature and revealing that the use of supplemental methods, such as physically rotating the paper, can mitigate errors associated with certain features.

Subgraph augmented non-negative tensor factorization (SANTF) for modeling clinical narrative text

PubMed Central

Xin, Yu; Hochberg, Ephraim; Joshi, Rohit; Uzuner, Ozlem; Szolovits, Peter

2015-01-01

Objective Extracting medical knowledge from electronic medical records requires automated approaches to combat scalability limitations and selection biases. However, existing machine learning approaches are often regarded by clinicians as black boxes. Moreover, training data for these automated approaches at often sparsely annotated at best. The authors target unsupervised learning for modeling clinical narrative text, aiming at improving both accuracy and interpretability. Methods The authors introduce a novel framework named subgraph augmented non-negative tensor factorization (SANTF). In addition to relying on atomic features (e.g., words in clinical narrative text), SANTF automatically mines higher-order features (e.g., relations of lymphoid cells expressing antigens) from clinical narrative text by converting sentences into a graph representation and identifying important subgraphs. The authors compose a tensor using patients, higher-order features, and atomic features as its respective modes. We then apply non-negative tensor factorization to cluster patients, and simultaneously identify latent groups of higher-order features that link to patient clusters, as in clinical guidelines where a panel of immunophenotypic features and laboratory results are used to specify diagnostic criteria. Results and Conclusion SANTF demonstrated over 10% improvement in averaged F-measure on patient clustering compared to widely used non-negative matrix factorization (NMF) and k-means clustering methods. Multiple baselines were established by modeling patient data using patient-by-features matrices with different feature configurations and then performing NMF or k-means to cluster patients. Feature analysis identified latent groups of higher-order features that lead to medical insights. We also found that the latent groups of atomic features help to better correlate the latent groups of higher-order features. PMID:25862765

Insights into Mutation Effect in Three Poikiloderma with Neutropenia Patients by Transcript Analysis and Disease Evolution of Reported Patients with the Same Pathogenic Variants.

PubMed

Colombo, Elisa A; Elcioglu, Nursel H; Graziano, Claudio; Farinelli, Pamela; Di Fede, Elisabetta; Neri, Iria; Facchini, Elena; Greco, Mariangela; Gervasini, Cristina; Larizza, Lidia

2018-05-16

Poikiloderma with neutropenia (PN) is a genodermatosis currently described in 77 patients, all presenting with early-onset poikiloderma, neutropenia, and several additional signs. Biallelic loss-of-function mutations in USB1 gene are detected in all molecularly tested patients but genotype-phenotype correlation remains elusive. Cancer predisposition is recognized among PN features and pathogenic variants found in patients who developed early in life myelodysplasia (n = 12), acute myeloid leukemia (n = 2), and squamous cell carcinoma (n = 2) should be kept into account in management and follow-up of novel patients. This will hopefully allow achieving data clustered on specific mutations relevant to oncological surveillance of the carrier patients. We describe the clinical features of three unreported PN patients and characterize their USB1 pathogenic variants by transcript analysis to get insights into the effect on the overall phenotype and disease evolution. A Turkish boy is homozygous for the c.531delA deletion, a recurrent mutation in Turkey; an adult Italian male is compound heterozygous for two nonsense mutations, c.243G>A and c.541C>T, while an Italian boy is homozygous for the splicing c.683_693+1del variant. The identified mutations have already been reported in PN patients who developed hematologic or skin cancer. Aberrant mRNAs of all four mutated alleles could be identified confirming that transcripts of USB1 main isoform either carrying stop codons or mis-spliced may at least partially escape nonsense-mediated decay. Our study addresses the need of gathering insights on genotype-phenotype correlations in newly described PN patients, by transcript analysis and information on disease evolution of reported patients with the same pathogenic variants.

The Porifera Ontology (PORO): enhancing sponge systematics with an anatomy ontology.

PubMed

Thacker, Robert W; Díaz, Maria Cristina; Kerner, Adeline; Vignes-Lebbe, Régine; Segerdell, Erik; Haendel, Melissa A; Mungall, Christopher J

2014-01-01

Porifera (sponges) are ancient basal metazoans that lack organs. They provide insight into key evolutionary transitions, such as the emergence of multicellularity and the nervous system. In addition, their ability to synthesize unusual compounds offers potential biotechnical applications. However, much of the knowledge of these organisms has not previously been codified in a machine-readable way using modern web standards. The Porifera Ontology is intended as a standardized coding system for sponge anatomical features currently used in systematics. The ontology is available from http://purl.obolibrary.org/obo/poro.owl, or from the project homepage http://porifera-ontology.googlecode.com/. The version referred to in this manuscript is permanently available from http://purl.obolibrary.org/obo/poro/releases/2014-03-06/. By standardizing character representations, we hope to facilitate more rapid description and identification of sponge taxa, to allow integration with other evolutionary database systems, and to perform character mapping across the major clades of sponges to better understand the evolution of morphological features. Future applications of the ontology will focus on creating (1) ontology-based species descriptions; (2) taxonomic keys that use the nested terms of the ontology to more quickly facilitate species identifications; and (3) methods to map anatomical characters onto molecular phylogenies of sponges. In addition to modern taxa, the ontology is being extended to include features of fossil taxa.

Celluloid devils: a research study of male nurses in feature films.

PubMed

Stanley, David

2012-11-01

To report a study of how male nurses are portrayed in feature films. It was hypothesized that male nurses are frequently portrayed negatively or stereotypically in the film media, potentially having a negative impact on male nurse recruitment and the public's perception of male nurses. An interpretive, qualitative methodology guided by insights into hegemonic masculinity and structured around a set of collective case studies (films) was used to examine the portrayal of male nurses in feature films made in the Western world from 1900 to 2007. Over 36,000 feature film synopses were reviewed (via CINAHL, ProQuest and relevant movie-specific literature) for the keyword 'nurse' and 'nursing' with an additional search for films from 1900 to 2010 for the word 'male nurse'. Identified films were labelled as 'cases' and analysed collectively to determine key attributes related to men in nursing and explore them for the emergence of concepts and themes related to the image of male nurses in films. A total of 13 relevant cases (feature films) were identified with 12 being made in the USA. Most films portrayed male nurses negatively and in ways opposed to hegemonic masculinity, as effeminate, homosexual, homicidal, corrupt or incompetent. Few film images of male nurses show them in traditional masculine roles or as clinically competent or self-confident professionals.   Feature films predominantly portray male nurses negatively. Given the popularity of feature films, there may be negative effects on recruitment and on the public's perception of male nurses. © 2012 Blackwell Publishing Ltd.

Geological and Structural Patterns on Titan Enhanced Through Cassini's SAR PCA and High-Resolution Radiometry

NASA Astrophysics Data System (ADS)

Paganelli, F.; Schubert, G.; Lopes, R. M. C.; Malaska, M.; Le Gall, A. A.; Kirk, R. L.

2016-12-01

The current SAR data coverage on Titan encompasses several areas in which multiple radar passes are present and overlapping, providing additional information to aid the interpretation of geological and structural features. We exploit the different combinations of look direction and variable incidence angle to examine Cassini Synthetic Aperture RADAR (SAR) data using the Principal Component Analysis (PCA) technique and high-resolution radiometry, as a tool to aid in the interpretation of geological and structural features. Look direction and variable incidence angle is of particular importance in the analysis of variance in the images, which aid in the perception and identification of geological and structural features, as extensively demonstrated in Earth and planetary examples. The PCA enhancement technique uses projected non-ortho-rectified SAR imagery in order to maintain the inherent differences in scattering and geometric properties due to the different look directions, while enhancing the geometry of surface features. The PC2 component provides a stereo view of the areas in which complex surface features and structural patterns can be enhanced and outlined. We focus on several areas of interest, in older and recently acquired flybys, in which evidence of geological and structural features can be enhanced and outlined in the PC1 and PC2 components. Results of this technique provide enhanced geometry and insights into the interpretation of the observed geological and structural features, thus allowing a better understanding towards the geology and tectonics on Titan.

From dots to doughnuts: Two-dimensionally confined deposition of polyelectrolytes on block copolymer templates

DOE PAGES

Oded, Meirav; Kelly, Stephen T.; Gilles, Mary K.; ...

2016-07-05

The combination of block copolymer templating with electrostatic self-assembly provides a simple and robust method for creating nano-patterned polyelectrolyte multilayers over large areas. The deposition of the first polyelectrolyte layer provides important insights on the initial stages of multilayer buildup. Here, we focus on two-dimensionally confined “dots” patterns afforded by block copolymer films featuring hexagonally-packed cylinders that are oriented normal to the substrate. Rendering the cylinder caps positively charged enables the selective deposition of negatively charged polyelectrolytes on them under salt-free conditions. The initially formed polyelectrolyte nanostructures adopt a toroidal (“doughnut”) shape, which results from retraction of dangling polyelectrolyte segmentsmore » into the “dots” upon drying. With increasing exposure time to the polyelectrolyte solution, the final shape of the deposited polyelectrolyte transitions from a doughnut to a hemisphere. In conclusion, these insights would enable the creation of patterned polyelectrolyte multilayers with increased control over adsorption selectivity of the additional incoming polyelectrolytes.« less

From dots to doughnuts: Two-dimensionally confined deposition of polyelectrolytes on block copolymer templates

DOE Office of Scientific and Technical Information (OSTI.GOV)

Oded, Meirav; Kelly, Stephen T.; Gilles, Mary K.

The combination of block copolymer templating with electrostatic self-assembly provides a simple and robust method for creating nano-patterned polyelectrolyte multilayers over large areas. The deposition of the first polyelectrolyte layer provides important insights on the initial stages of multilayer buildup. Here, we focus on two-dimensionally confined “dots” patterns afforded by block copolymer films featuring hexagonally-packed cylinders that are oriented normal to the substrate. Rendering the cylinder caps positively charged enables the selective deposition of negatively charged polyelectrolytes on them under salt-free conditions. The initially formed polyelectrolyte nanostructures adopt a toroidal (“doughnut”) shape, which results from retraction of dangling polyelectrolyte segmentsmore » into the “dots” upon drying. With increasing exposure time to the polyelectrolyte solution, the final shape of the deposited polyelectrolyte transitions from a doughnut to a hemisphere. In conclusion, these insights would enable the creation of patterned polyelectrolyte multilayers with increased control over adsorption selectivity of the additional incoming polyelectrolytes.« less

SimpleITK Image-Analysis Notebooks: a Collaborative Environment for Education and Reproducible Research.

PubMed

Yaniv, Ziv; Lowekamp, Bradley C; Johnson, Hans J; Beare, Richard

2018-06-01

Modern scientific endeavors increasingly require team collaborations to construct and interpret complex computational workflows. This work describes an image-analysis environment that supports the use of computational tools that facilitate reproducible research and support scientists with varying levels of software development skills. The Jupyter notebook web application is the basis of an environment that enables flexible, well-documented, and reproducible workflows via literate programming. Image-analysis software development is made accessible to scientists with varying levels of programming experience via the use of the SimpleITK toolkit, a simplified interface to the Insight Segmentation and Registration Toolkit. Additional features of the development environment include user friendly data sharing using online data repositories and a testing framework that facilitates code maintenance. SimpleITK provides a large number of examples illustrating educational and research-oriented image analysis workflows for free download from GitHub under an Apache 2.0 license: github.com/InsightSoftwareConsortium/SimpleITK-Notebooks .

Exploiting the epigenome to control cancer promoting gene expression programs

PubMed Central

Brien, Gerard L.; Valerio, Daria G.; Armstrong, Scott A.

2016-01-01

Summary The epigenome is a key determinant of transcriptional output. Perturbations within the epigenome are thought to be a key feature of many, perhaps all cancers, and it is now clear that epigenetic changes are instrumental in cancer development. The inherent reversibility of these changes makes them attractive targets for therapeutic manipulation and a number of small molecules targeting chromatin-based mechanisms are currently in clinical trials. In this perspective we discuss how understanding the cancer epigenome is providing insights into disease pathogenesis and informing drug development. We also highlight additional opportunities to further unlock the therapeutic potential within the cancer epigenome. PMID:27070701

The impact of insight in a first-episode mania with psychosis population on outcome at 18 months.

PubMed

Smith, Leo T; Shelton, Clare L; Berk, Michael; Hasty, Melissa K; Cotton, Sue M; Henry, Lisa; Daglas, Rothanthi; Gentle, Ellen; McGorry, Patrick D; Macneil, Craig A; Conus, Philippe

2014-01-01

To explore whether poor initial insight during a first episode of mania with psychotic features was predictive of poor psychosocial and clinical outcomes at 18 months. Secondary analysis was performed on data collected during an 8-week RCT comparing the efficacy of olanzapine versus chlorpromazine as an adjunct to lithium, and at 18-month follow-up. 74 participants were divided into three groups (no insight, partial insight, and full insight) according to the insight item from the Young Mania Rating Scale (YMRS). Differences between these three groups were examined at baseline and at 18 months on measures of symptoms (YMRS, HAMD-21, and CGI-S), and social and occupational functioning (SOFAS). Baseline differences between the three groups were determined using general linear models and chi-squared analyses. Group differences from baseline to 18-month follow-up were determined using repeated measures general linear models. At baseline there were significant differences between the three insight groups in terms of mania and functioning, but at 18 months all groups had improved significantly in terms of psychopathology, mania, depression and social and occupational functioning. There were no significant differences between the three groups at study completion with respect to these domains. The study was limited by the lack of availability of a more detailed rating scale for insight, and it did not account for the duration of untreated psychosis (DUI). Poor initial insight during a first episode of mania with psychotic features does not predict poor clinical and psychosocial outcome at 18 months. Crown Copyright © 2014. Published by Elsevier B.V. All rights reserved.

Children's Books in Review. Books That Give Cultural Insights.

ERIC Educational Resources Information Center

Winfield, Evelyn T.

1992-01-01

Presents a selection of children's books that feature a variety of topics and literary representations with insight into other cultures. The books focus on foods, historical events, reliance on the environment, folktales, family experiences, community heritage, words and phrases, and linguistic eccentricities. (SM)

Positron emission tomography to assess hypoxia and perfusion in lung cancer

PubMed Central

Verwer, Eline E; Boellaard, Ronald; van der Veldt, Astrid AM

2014-01-01

In lung cancer, tumor hypoxia is a characteristic feature, which is associated with a poor prognosis and resistance to both radiation therapy and chemotherapy. As the development of tumor hypoxia is associated with decreased perfusion, perfusion measurements provide more insight into the relation between hypoxia and perfusion in malignant tumors. Positron emission tomography (PET) is a highly sensitive nuclear imaging technique that is suited for non-invasive in vivo monitoring of dynamic processes including hypoxia and its associated parameter perfusion. The PET technique enables quantitative assessment of hypoxia and perfusion in tumors. To this end, consecutive PET scans can be performed in one scan session. Using different hypoxia tracers, PET imaging may provide insight into the prognostic significance of hypoxia and perfusion in lung cancer. In addition, PET studies may play an important role in various stages of personalized medicine, as these may help to select patients for specific treatments including radiation therapy, hypoxia modifying therapies, and antiangiogenic strategies. In addition, specific PET tracers can be applied for monitoring therapy. The present review provides an overview of the clinical applications of PET to measure hypoxia and perfusion in lung cancer. Available PET tracers and their characteristics as well as the applications of combined hypoxia and perfusion PET imaging are discussed. PMID:25493221

True-Triaxial Experimental Study of the Evolutionary Features of the Acoustic Emissions and Sounds of Rockburst Processes

NASA Astrophysics Data System (ADS)

Su, Guoshao; Shi, Yanjiong; Feng, Xiating; Jiang, Jianqing; Zhang, Jie; Jiang, Quan

2018-02-01

Rockbursts are markedly characterized by the ejection of rock fragments from host rocks at certain speeds. The rockburst process is always accompanied by acoustic signals that include acoustic emissions (AE) and sounds. A deep insight into the evolutionary features of AE and sound signals is important to improve the accuracy of rockburst prediction. To investigate the evolutionary features of AE and sound signals, rockburst tests on granite rock specimens under true-triaxial loading conditions were performed using an improved rockburst testing system, and the AE and sounds during rockburst development were recorded and analyzed. The results show that the evolutionary features of the AE and sound signals were obvious and similar. On the eve of a rockburst, a `quiescent period' could be observed in both the evolutionary process of the AE hits and the sound waveform. Furthermore, the time-dependent fractal dimensions of the AE hits and sound amplitude both showed a tendency to continuously decrease on the eve of the rockbursts. In addition, on the eve of the rockbursts, the main frequency of the AE and sound signals both showed decreasing trends, and the frequency spectrum distributions were both characterized by low amplitudes, wide frequency bands and multiple peak shapes. Thus, the evolutionary features of sound signals on the eve of rockbursts, as well as that of AE signals, can be used as beneficial information for rockburst prediction.

Gestures and Insight in Advanced Mathematical Thinking

ERIC Educational Resources Information Center

Yoon, Caroline; Thomas, Michael O. J.; Dreyfus, Tommy

2011-01-01

What role do gestures play in advanced mathematical thinking? We argue that the role of gestures goes beyond merely communicating thought and supporting understanding--in some cases, gestures can help generate new mathematical insights. Gestures feature prominently in a case study of two participants working on a sequence of calculus activities.…

'TIME': A Web Application for Obtaining Insights into Microbial Ecology Using Longitudinal Microbiome Data.

PubMed

Baksi, Krishanu D; Kuntal, Bhusan K; Mande, Sharmila S

2018-01-01

Realization of the importance of microbiome studies, coupled with the decreasing sequencing cost, has led to the exponential growth of microbiome data. A number of these microbiome studies have focused on understanding changes in the microbial community over time. Such longitudinal microbiome studies have the potential to offer unique insights pertaining to the microbial social networks as well as their responses to perturbations. In this communication, we introduce a web based framework called 'TIME' (Temporal Insights into Microbial Ecology'), developed specifically to obtain meaningful insights from microbiome time series data. The TIME web-server is designed to accept a wide range of popular formats as input with options to preprocess and filter the data. Multiple samples, defined by a series of longitudinal time points along with their metadata information, can be compared in order to interactively visualize the temporal variations. In addition to standard microbiome data analytics, the web server implements popular time series analysis methods like Dynamic time warping, Granger causality and Dickey Fuller test to generate interactive layouts for facilitating easy biological inferences. Apart from this, a new metric for comparing metagenomic time series data has been introduced to effectively visualize the similarities/differences in the trends of the resident microbial groups. Augmenting the visualizations with the stationarity information pertaining to the microbial groups is utilized to predict the microbial competition as well as community structure. Additionally, the 'causality graph analysis' module incorporated in TIME allows predicting taxa that might have a higher influence on community structure in different conditions. TIME also allows users to easily identify potential taxonomic markers from a longitudinal microbiome analysis. We illustrate the utility of the web-server features on a few published time series microbiome data and demonstrate the ease with which it can be used to perform complex analysis.

Image Feature Types and Their Predictions of Aesthetic Preference and Naturalness

PubMed Central

Ibarra, Frank F.; Kardan, Omid; Hunter, MaryCarol R.; Kotabe, Hiroki P.; Meyer, Francisco A. C.; Berman, Marc G.

2017-01-01

Previous research has investigated ways to quantify visual information of a scene in terms of a visual processing hierarchy, i.e., making sense of visual environment by segmentation and integration of elementary sensory input. Guided by this research, studies have developed categories for low-level visual features (e.g., edges, colors), high-level visual features (scene-level entities that convey semantic information such as objects), and how models of those features predict aesthetic preference and naturalness. For example, in Kardan et al. (2015a), 52 participants provided aesthetic preference and naturalness ratings, which are used in the current study, for 307 images of mixed natural and urban content. Kardan et al. (2015a) then developed a model using low-level features to predict aesthetic preference and naturalness and could do so with high accuracy. What has yet to be explored is the ability of higher-level visual features (e.g., horizon line position relative to viewer, geometry of building distribution relative to visual access) to predict aesthetic preference and naturalness of scenes, and whether higher-level features mediate some of the association between the low-level features and aesthetic preference or naturalness. In this study we investigated these relationships and found that low- and high- level features explain 68.4% of the variance in aesthetic preference ratings and 88.7% of the variance in naturalness ratings. Additionally, several high-level features mediated the relationship between the low-level visual features and aaesthetic preference. In a multiple mediation analysis, the high-level feature mediators accounted for over 50% of the variance in predicting aesthetic preference. These results show that high-level visual features play a prominent role predicting aesthetic preference, but do not completely eliminate the predictive power of the low-level visual features. These strong predictors provide powerful insights for future research relating to landscape and urban design with the aim of maximizing subjective well-being, which could lead to improved health outcomes on a larger scale. PMID:28503158

Human listeners provide insights into echo features used by dolphins (Tursiops truncatus) to discriminate among objects.

PubMed

Delong, Caroline M; Au, Whitlow W L; Harley, Heidi E; Roitblat, Herbert L; Pytka, Lisa

2007-08-01

Echolocating bottlenose dolphins (Tursiops truncatus) discriminate between objects on the basis of the echoes reflected by the objects. However, it is not clear which echo features are important for object discrimination. To gain insight into the salient features, the authors had a dolphin perform a match-to-sample task and then presented human listeners with echoes from the same objects used in the dolphin's task. In 2 experiments, human listeners performed as well or better than the dolphin at discriminating objects, and they reported the salient acoustic cues. The error patterns of the humans and the dolphin were compared to determine which acoustic features were likely to have been used by the dolphin. The results indicate that the dolphin did not appear to use overall echo amplitude, but that it attended to the pattern of changes in the echoes across different object orientations. Human listeners can quickly identify salient combinations of echo features that permit object discrimination, which can be used to generate hypotheses that can be tested using dolphins as subjects.

Human listening studies reveal insights into object features extracted by echolocating dolphins

NASA Astrophysics Data System (ADS)

Delong, Caroline M.; Au, Whitlow W. L.; Roitblat, Herbert L.

2004-05-01

Echolocating dolphins extract object feature information from the acoustic parameters of object echoes. However, little is known about which object features are salient to dolphins or how they extract those features. To gain insight into how dolphins might be extracting feature information, human listeners were presented with echoes from objects used in a dolphin echoic-visual cross-modal matching task. Human participants performed a task similar to the one the dolphin had performed; however, echoic samples consisting of 23-echo trains were presented via headphones. The participants listened to the echoic sample and then visually selected the correct object from among three alternatives. The participants performed as well as or better than the dolphin (M=88.0% correct), and reported using a combination of acoustic cues to extract object features (e.g., loudness, pitch, timbre). Participants frequently reported using the pattern of aural changes in the echoes across the echo train to identify the shape and structure of the objects (e.g., peaks in loudness or pitch). It is likely that dolphins also attend to the pattern of changes across echoes as objects are echolocated from different angles.

Gene family innovation, conservation and loss on the animal stem lineage.

PubMed

Richter, Daniel J; Fozouni, Parinaz; Eisen, Michael; King, Nicole

2018-05-31

Choanoflagellates, the closest living relatives of animals, can provide unique insights into the changes in gene content that preceded the origin of animals. However, only two choanoflagellate genomes are currently available, providing poor coverage of their diversity. We sequenced transcriptomes of 19 additional choanoflagellate species to produce a comprehensive reconstruction of the gains and losses that shaped the ancestral animal gene repertoire. We identified ~1,944 gene families that originated on the animal stem lineage, of which only 39 are conserved across all animals in our study. In addition, ~372 gene families previously thought to be animal-specific, including Notch, Delta, and homologs of the animal Toll-like receptor genes, instead evolved prior to the animal-choanoflagellate divergence. Our findings contribute to an increasingly detailed portrait of the gene families that defined the biology of the Urmetazoan and that may underpin core features of extant animals. © 2018, Richter et al.

Insight, Neurocognition, and Schizophrenia: Predictive Value of the Wisconsin Card Sorting Test

PubMed Central

Yanos, Philip T.

2013-01-01

Lack of insight in schizophrenia is a key feature of the illness and is associated with both positive and negative clinical outcomes. Previous research supports that neurocognitive dysfunction is related to lack of insight, but studies have not examined how neurocognition relates to change in insight over time. Therefore, the current study sought to understand how performance on the Wisconsin Card Sorting Test (WCST) differed between participants with varying degrees of change in insight over a 6-month period. Fifty-two patients with schizophrenia or schizoaffective disorder were administered the WCST and Positive and Negative Syndrome Scale (PANSS) at baseline, and the PANSS was again administered at a 6-month follow-up assessment. Results indicated that while neurocognition was related to insight at baseline, it was not related to subsequent change in insight. The implications of findings for conceptualization and assessment of insight are discussed. PMID:24303216

Insight in pediatric obsessive-compulsive disorder: associations with clinical presentation.

PubMed

Storch, Eric A; Milsom, Vanessa A; Merlo, Lisa J; Larson, Michael; Geffken, Gary R; Jacob, Marni L; Murphy, Tanya K; Goodman, Wayne K

2008-08-15

Insight has emerged as a significant treatment outcome predictor in adult obsessive-compulsive disorder (OCD), with some suggesting that OCD with poor insight represents a distinct clinical subtype. Despite its clinical relevance, limited data exist on insight in pediatric OCD patients. The present study investigated the relation between poor insight and clinical characteristics among children and adolescents with OCD (N=78, ages 6-20 years). Forty-five percent of the sample (n=35) was considered to have low levels of insight into their symptoms, as determined by clinician rating on item 11 of the Children's Yale-Brown Obsessive-Compulsive Scale. Pearson product-moment correlations showed a significant, inverse relation between insight and OCD severity. Relative to the high insight group, parents of patients with low insight reported higher levels of OCD-related impairment and family accommodation. These findings suggest that OCD with poor insight may represent a distinct clinical feature that may require more intensive and multimodal treatment approaches.

Measurement of Surface Composition for the Icy Galilean Moons Via Neutral and Ion Mass Spectrometry from Orbit with JIMO

NASA Technical Reports Server (NTRS)

Wong, M.; Berthelier, J.; Carlson, R.; Cooper, J.; Johnson, R.; Jurac, S.; Leblanc, F.; Shematovich, V.

2003-01-01

In this paper, we will provide insights into mass spectrometer requirements. In addition, we will describe the modeling of the neutrals ejected from likely surface materials and their ionization rates in the Jovian environment. We will use such models to connect the mass spectra measurements of the freshly formed ions to surface composition. We will also discuss what possible compositional signatures are for endogenic materials other than water ice. Finally, since a goal is to identify material composition with surface features, we will describe the transport of neutrals ejected from the surface prior to detection by either an ion or neutral mass spectrometer.

A Multidimensional Reappraisal of Language in Autism: Insights from a Discourse Analytic Study

ERIC Educational Resources Information Center

Sterponi, Laura; de Kirby, Kenton

2016-01-01

In this article, we leverage theoretical insights and methodological guidelines of discourse analytic scholarship to re-examine language phenomena typically associated with autism. Through empirical analysis of the verbal behavior of three children with autism, we engage the question of how prototypical features of autistic language--notably…

Administrator Responses to Financial Incentives: Insights from a TIF Program

ERIC Educational Resources Information Center

King Rice, Jennifer; Malen, Betty; Jackson, Cara; Hoyer, Kathleen Mulvaney

2017-01-01

This article provides evidence and generates insights about the power of financial rewards to motivate school administrators and the design features that influence their motivational potency. The multi-year mixed-methods study is grounded in expectancy and goal setting theories that suggest (a) awards must be salient and sizable enough to appeal…

Modeling Spoken Word Recognition Performance by Pediatric Cochlear Implant Users using Feature Identification

PubMed Central

Frisch, Stefan A.; Pisoni, David B.

2012-01-01

Objective Computational simulations were carried out to evaluate the appropriateness of several psycholinguistic theories of spoken word recognition for children who use cochlear implants. These models also investigate the interrelations of commonly used measures of closed-set and open-set tests of speech perception. Design A software simulation of phoneme recognition performance was developed that uses feature identification scores as input. Two simulations of lexical access were developed. In one, early phoneme decisions are used in a lexical search to find the best matching candidate. In the second, phoneme decisions are made only when lexical access occurs. Simulated phoneme and word identification performance was then applied to behavioral data from the Phonetically Balanced Kindergarten test and Lexical Neighborhood Test of open-set word recognition. Simulations of performance were evaluated for children with prelingual sensorineural hearing loss who use cochlear implants with the MPEAK or SPEAK coding strategies. Results Open-set word recognition performance can be successfully predicted using feature identification scores. In addition, we observed no qualitative differences in performance between children using MPEAK and SPEAK, suggesting that both groups of children process spoken words similarly despite differences in input. Word recognition ability was best predicted in the model in which phoneme decisions were delayed until lexical access. Conclusions Closed-set feature identification and open-set word recognition focus on different, but related, levels of language processing. Additional insight for clinical intervention may be achieved by collecting both types of data. The most successful model of performance is consistent with current psycholinguistic theories of spoken word recognition. Thus it appears that the cognitive process of spoken word recognition is fundamentally the same for pediatric cochlear implant users and children and adults with normal hearing. PMID:11132784

Integrating the patient portal into the health management work ecosystem: user acceptance of a novel prototype

PubMed Central

Eschler, Jordan; Meas, Perry Lin; Lozano, Paula; McClure, Jennifer B.; Ralston, James D.; Pratt, Wanda

2016-01-01

People with a chronic illness must manage a myriad of tasks to support their health. Online patient portals can provide vital information and support in managing health tasks through notification and reminder features. However, little is known about the efficacy of these features in managing health tasks via the portal. To elicit feedback about reminder and notification features in patient portals, we employed a patient-centered approach to design new features for managing health tasks within an existing portal tool. We tested three iteratively designed prototypes with 19 patients and caregivers. Our findings provide insights into users’ attitudes, behavior, and motivations in portal use. Design implications based on these insights include: (1) building on positive aspects of clinician relationships to enhance engagement with the portal; (2) using face-to-face visits to promote clinician collaboration in portal use; and (3) allowing customization of portal modules to support tasks based on user roles. PMID:28269850

Integrating the patient portal into the health management work ecosystem: user acceptance of a novel prototype.

PubMed

Eschler, Jordan; Meas, Perry Lin; Lozano, Paula; McClure, Jennifer B; Ralston, James D; Pratt, Wanda

2016-01-01

People with a chronic illness must manage a myriad of tasks to support their health. Online patient portals can provide vital information and support in managing health tasks through notification and reminder features. However, little is known about the efficacy of these features in managing health tasks via the portal. To elicit feedback about reminder and notification features in patient portals, we employed a patient-centered approach to design new features for managing health tasks within an existing portal tool. We tested three iteratively designed prototypes with 19 patients and caregivers. Our findings provide insights into users' attitudes, behavior, and motivations in portal use. Design implications based on these insights include: (1) building on positive aspects of clinician relationships to enhance engagement with the portal; (2) using face-to-face visits to promote clinician collaboration in portal use; and (3) allowing customization of portal modules to support tasks based on user roles.

Historical perspective: eponyms of vascular radiology.

PubMed

DiPoce, Jason; Jimenez, Guillermo; Weintraub, Joshua

2014-01-01

Eponyms are ubiquitous throughout the medical literature, especially the radiology lexicon. In particular, vascular radiology is replete with dozens of eponyms named after pathologic and anatomic features and various medical devices. Several disease processes are known exclusively by their eponyms or by both their eponyms and their descriptive names. Although some authors advocate abandoning eponyms in favor of more descriptive terms, the established history and common use of eponyms make it unlikely that they will disappear from the vocabulary. Radiologists should be familiar with both the eponymous and descriptive names of disease processes to ensure effective communication and prevent erroneous identification. Study of these eponyms provides information about these disease processes and other medical knowledge for use in daily practice. In addition, biographic information about the pertinent physicians can yield insights into the sometimes surprising origins of these eponyms. The authors provide biographic sketches of these physicians and discuss the clinical relevance of the anatomic features, malformations, and syndromes that bear their names. ©RSNA, 2014.

The Power of Materials Science Tools for Gaining Insights into Organic Semiconductors

NASA Astrophysics Data System (ADS)

Treat, Neil D.; Westacott, Paul; Stingelin, Natalie

2015-07-01

The structure of organic semiconductors can be complex because features from the molecular level (such as molecular conformation) to the micrometer scale (such as the volume fraction and composition of phases, phase distribution, and domain size) contribute to the definition of the optoelectronic landscape of the final architectures and, hence, to device performance. As a consequence, a detailed understanding of how to manipulate molecular ordering, e.g., through knowledge of relevant phase transitions, of the solidification process, of relevant solidification mechanisms, and of kinetic factors, is required to induce the desired optoelectronic response. In this review, we discuss relevant structural features of single-component and multicomponent systems; provide a case study of the multifaceted structure that polymer:fullerene systems can adopt; and highlight relevant solidification mechanisms such as nucleation and growth, liquid-liquid phase separation, and spinodal decomposition. In addition, cocrystal formation, solid solutions, and eutectic systems are treated and their relevance within the optoelectronic area emphasized.

Imposed, ordered dust structures and other plasma features in a strongly magnetized plasma

NASA Astrophysics Data System (ADS)

Thomas, Edward; Leblanc, Spencer; Lynch, Brian; Konopka, Uwe; Merlino, Robert; Rosenberg, Marlene

2015-11-01

The Magnetized Dusty Plasma Experiment (MDPX) device has been in operation for just over one year. In that time, the MDPX device has been operating using a uniform magnetic field configuration up to 3.0 Tesla and has successfully produced plasmas and dusty plasmas at high magnetic fields. In these experimental studies, we have made observations of a new type of imposed, ordered structure in a dusty plasma at magnetic fields above 1 T. These dusty plasma structures are shown to scale inversely with neutral pressure and are shown to reflect the spatial structure of a wire mesh placed in the plasma. Additionally, recent measurements have been made that give insights into the effective potential that establishes the ordered structures in the plasma. In this presentation, we report on details of the imposed, ordered dusty plasma structure as well as filamentary features that also appear in the plasma and modify the confinement of the dusty plasma. This work is supported with funding from the NSF and Department of Energy.

Sustainability Literacy of Older People in Retirement Villages

PubMed Central

Xia, Bo; Zuo, Jian; Skitmore, Martin; Buys, Laurie; Hu, Xin

2014-01-01

With many developed countries experiencing the aging of the population, older people play a large role in contributing to environmental problems but also to environmental solutions. The purpose of this research is to understand the awareness and behavior of current older people living in retirement villages towards sustainability development. To achieve this, a sustainability literacy survey was conducted with 65 older residents of a private retirement village located 10 Km outside the Brisbane, Australia's central business district (CBD). Most of residents recognized the importance of environment protection and would like to lead a more environmentally friendly lifestyle. In addition, the majority were willing to pay higher prices for a living environment with sustainable features. The importance of positive social communications was emphasized with most residents having established good relationships with others in the village. The findings provide an important insight into consumer perspectives regarding the sustainable features that should and can be incorporated into the village planning and development. PMID:25587448

In silico identification of potent pancreatic triacylglycerol lipase inhibitors from traditional Chinese medicine.

PubMed

Chen, Kuan-Yu; Chang, Su-Sen; Chen, Calvin Yu-Chian

2012-01-01

Pancreatic triacylglycerol lipase (PNLIP) are primary lipases that are critical for triacylglyceride digestion in human. Since reduced metabolism of triacylglyceride might be a plausible concept for weight loss, we screened for potential PNLIP inhibitors from traditional Chinese medicine (TCM) with the aim to identify weight loss candidate compounds. TCM candidates Aurantiamide, Cnidiadin, and 2-hexadecenoic acid exhibited higher Dock Scores than the commercial drug Orlistat, and were also predicted to have inhibitory characteristics against PNLIP using constructed MLR (R(2) = 0.8664) and SVM (R(2) = 0.9030) models. Molecular dynamics indicated that the TCM-PNLIP complexes formed were stable. We identified that the PNLIP binding site has several residues that can serve as anchors, and a hydrophobic corridor that provides additional stability to the complex. Aurantiamide, Cnidiadin, and 2-hexadecenoic acid all have features that correspond to these binding site features, indicating their potential as candidates for PNLIP inhibitors. The information presented in this study may provide helpful insights to designing novel weight-control drugs.

The Student Volunteer Army: a 'repeat emergent' emergency response organisation.

PubMed

Carlton, Sally; Mills, Colleen E

2017-10-01

This paper seeks to contribute to understanding of the factors associated with an effective emergent emergency response organisation and to provide new insights into this understudied area. It examines, through an analysis of a range of textual resources, the emergence and re-emergence of the Student Volunteer Army (SVA) during the devastating earthquakes in Canterbury, New Zealand, in 2010-11. This evaluation is conducted in relation to the four key features of an effective emergency response organisation: adaptability; direction; leadership; and communication. In addition, the paper aims to further understanding of 'emergency entrepreneurship' and thus of the values and strategies that underpin social entrepreneur organisations in times of normalcy. The paper concludes that the unique position of the SVA as a 'repeat emergent' emergency response organisation enabled it to innovate continually and to improve repeatedly its systems, relationships, and image, such that it exhibited features common to emergent and established emergency response organisations. © 2017 The Author(s). Disasters © Overseas Development Institute, 2017.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yuan, Ke; De Andrade, Vincent; Feng, Zhange

The presence of impurity ions is known to significantly influence mineral surface morphology during crystal growth from aqueous solution, but knowledge on impurity ion-mineral interactions during dissolution under far-from equilibrium conditions remains limited. Here we show that calcite (CaCO 3) exhibits a rich array of dissolution features in the presence of Pb. During the initial stage, calcite exhibits non-classical surface features characterized as micro pyramids developed spontaneously in acidic Pb-bearing solutions. Subsequent pseudomorphic growth of cerussite (PbCO 3) was observed, where nucleation occurred entirely within a pore space created by dissolution at the calcite/substrate interface. Uneven growth rates yielded amore » cerussite shell made of lath- or dendritic-shaped crystals. The cerussite phase was separated from the calcite by pores of less than 200 nm under transmission X-ray microscopy, consistent with the interface-coupled dissolution-precipitation mechanism. These results show that impurity metal ions exert significant control over the microscale dissolution features found on mineral surfaces and provide new insights into interpreting and designing micro structures observed in naturally-occurring and synthetic carbonate minerals by dissolution. In addition, heterogeneous micro-environments created in transport limited reactions under pore spaces may lead to unusual growth forms during crystal nucleation and precipitation.« less

Conceptualizing science learning as a collective social practice: changing the social pedagogical compass for a child with visual impairment

NASA Astrophysics Data System (ADS)

Fleer, Marilyn; March, Sue

2015-09-01

The international literature on science learning in inclusive settings has a long history, but it is generally very limited in scope. Few studies have been undertaken that draw upon a cultural-historical reading of inclusive pedagogy, and even less in the area of science education. In addition, we know next to nothing about the science learning of preschool children with visual impairment using cultural-historical theory. This paper seeks to fill this gap by presenting a study of one child with Albinism who participated in a unit of early childhood science where fairy tales were used for learning about the concepts of sound and growth. This paper reports upon the social and material conditions that were created to support learning in the preschool, whilst also examining how the learning of growth and sound were supported at home. The study found three new pedagogical features for inclusion: Imagination in science; Ongoing scientific narrative; and Scientific mirroring. It was found that when a dialectical reading of home and centre practices feature, greater insights into inclusive pedagogy for science learning are afforded, and a view of science as a collective enterprise emerges. It is argued that a cultural-historical conception of inclusion demands that the social conditions, rather than the biology of the child, is foregrounded, and through this greater insights into how science learning for children with visual impairment is gained.

Calcium as a signal integrator in developing epithelial tissues.

PubMed

Brodskiy, Pavel A; Zartman, Jeremiah J

2018-05-16

Decoding how tissue properties emerge across multiple spatial and temporal scales from the integration of local signals is a grand challenge in quantitative biology. For example, the collective behavior of epithelial cells is critical for shaping developing embryos. Understanding how epithelial cells interpret a diverse range of local signals to coordinate tissue-level processes requires a systems-level understanding of development. Integration of multiple signaling pathways that specify cell signaling information requires second messengers such as calcium ions. Increasingly, specific roles have been uncovered for calcium signaling throughout development. Calcium signaling regulates many processes including division, migration, death, and differentiation. However, the pleiotropic and ubiquitous nature of calcium signaling implies that many additional functions remain to be discovered. Here we review a selection of recent studies to highlight important insights into how multiple signals are transduced by calcium transients in developing epithelial tissues. Quantitative imaging and computational modeling have provided important insights into how calcium signaling integration occurs. Reverse-engineering the conserved features of signal integration mediated by calcium signaling will enable novel approaches in regenerative medicine and synthetic control of morphogenesis.

Boron-Based Inhibitors of the NLRP3 Inflammasome.

PubMed

Baldwin, Alex G; Rivers-Auty, Jack; Daniels, Michael J D; White, Claire S; Schwalbe, Carl H; Schilling, Tom; Hammadi, Halah; Jaiyong, Panichakorn; Spencer, Nicholas G; England, Hazel; Luheshi, Nadia M; Kadirvel, Manikandan; Lawrence, Catherine B; Rothwell, Nancy J; Harte, Michael K; Bryce, Richard A; Allan, Stuart M; Eder, Claudia; Freeman, Sally; Brough, David

2017-11-16

NLRP3 is a receptor important for host responses to infection, yet is also known to contribute to devastating diseases such as Alzheimer's disease, diabetes, atherosclerosis, and others, making inhibitors for NLRP3 sought after. One of the inhibitors currently in use is 2-aminoethoxy diphenylborinate (2APB). Unfortunately, in addition to inhibiting NLRP3, 2APB also displays non-selective effects on cellular Ca 2+ homeostasis. Here, we use 2APB as a chemical scaffold to build a series of inhibitors, the NBC series, which inhibit the NLRP3 inflammasome in vitro and in vivo without affecting Ca 2+ homeostasis. The core chemical insight of this work is that the oxazaborine ring is a critical feature of the NBC series, and the main biological insight the use of NBC inhibitors led to was that NLRP3 inflammasome activation was independent of Ca 2+ . The NBC compounds represent useful tools to dissect NLRP3 function, and may lead to oxazaborine ring-containing therapeutics. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Lessons Learned From Trials Targeting Cytokine Pathways in Patients With Inflammatory Bowel Diseases

PubMed Central

Abraham, Clara; Dulai, Parambir S.; Vermeire, Séverine; Sandborn, William J.

2016-01-01

Insights into the pathogenesis of inflammatory bowel diseases (IBD) have provided important information for the development of therapeutics. Levels of interleukin 23 (IL23) and T-helper (Th) 17 cell pathway molecules are elevated in inflamed intestinal tissues of patients with IBD. Loss of function variants of the interleukin 23 receptor gene (IL23R) protect against IBD, and in animals, blocking IL23 reduces severity of colitis. These findings indicated that the IL23 and Th17 cell pathways might be promising targets for treatment of IBD. Clinical trials have investigated the effects of agents designed to target distinct levels of the IL23 and Th17 cell pathways, and the results are providing insights into IBD pathogenesis and additional strategies for modulating these pathways. Strategies to reduce levels of proinflammatory cytokines more broadly and increase anti-inflammatory mechanisms are also emerging for treatment of IBD. The results from trials targeting these immune system pathways have provided important lessons for future trials. Findings indicate the importance of improving approaches to integrate patient features and biomarkers of response with selection of therapeutics. PMID:27780712

SHADOZ (Southern Hemisphere Additional Ozonesondes): A Project Overview and New Insights on Tropical Tropospheric Ozone

NASA Technical Reports Server (NTRS)

Thompson, Anne M.; Witte, Jacquelyn C.; Oltmans, S. J.; Schmidlin, F. J.

2004-01-01

The SHADOZ (Southern Hemisphere Additional Ozonesondes) ozone sounding network was initiated in 1998 to improve the coverage of tropical in-situ ozone measurements for satellite validation, algorithm development and related process studies. Over 2000 soundings have been archived at the website, http://croc.gsfc.nasa.gov/shadoz, for 12 stations: Ascension Island; Nairobi and Malindi, Kenya; Irene, South Africa; Reunion Island; Watukosek, Java; Fiji; Tahiti; American Samoa; San Cristobal, Galapagos; Natal, Brazil; Paramaribo, Surinam. Key results from SHADOZ will be described from among the following: 1) By using ECC sondes with similar procedures, 5-10% accuracy and precision (1-sigma) of the sonde total ozone measurement is achieved; 2) Week-to-week variability in tropospheric ozone is so great that statistics are frequently not Gaussian; most stations vary up to a factor of 3 in tropospheric column over the course of a year; 3) Longitudinal variability in tropospheric ozone profiles is a consistent feature, with a 10-15 DU column-integrated difference between Atlantic and Pacific sites; this causes a "zonal wave-one" feature in total ozone; 4) The ozone record from Paramaribo, Surinam (6N, 55W) is a marked contrast to southern tropical ozone because Surinam is often north of the Intertropical Convergence Zone.

Software for Demonstration of Features of Chain Polymerization Processes

ERIC Educational Resources Information Center

Sosnowski, Stanislaw

2013-01-01

Free software for the demonstration of the features of homo- and copolymerization processes (free radical, controlled radical, and living) is described. The software is based on the Monte Carlo algorithms and offers insight into the kinetics, molecular weight distribution, and microstructure of the macromolecules formed in those processes. It also…

Identification and Quantification Soil Redoximorphic Features by Digital Image Processing

USDA-ARS?s Scientific Manuscript database

Soil redoximorphic features (SRFs) have provided scientists and land managers with insight into relative soil moisture for approximately 60 years. The overall objective of this study was to develop a new method of SRF identification and quantification from soil cores using a digital camera and imag...

Gaining insight in the behaviour of imidazolium-based ionic liquids as additives in reversed-phase liquid chromatography for the analysis of basic compounds.

PubMed

Ubeda-Torres, M T; Ortiz-Bolsico, C; García-Alvarez-Coque, M C; Ruiz-Angel, M J

2015-02-06

In reversed-phase liquid chromatography in the absence of additives, cationic basic compounds give rise to broad and asymmetrical peaks as a result of ionic interactions with residual free silanols on silica-based stationary phases. Ionic liquids (ILs), added to the mobile phase, have been suggested as alternatives to amines to block the activity of silanols. However, the dual character of ILs should be considered: both cation and anion may be adsorbed on the stationary phase, thereby creating a double asymmetrical layer positively or negatively charged, depending on the relative adsorption of both ions. In this work, a study of the performance of six imidazolium-based ILs (the chlorides and tetrafluoroborates of 1-ethyl-, 1-butyl- and 1-hexyl-3-methylimidazolium) as modifiers of the chromatographic behaviour of a group of 10 β-blockers is performed, and compared with triethylamine and dimethyloctylamine. In order to gain more insight in the behaviour of ILs in RPLC, the changes in the nature of the chromatographic system, at increasing concentration of the additives, were followed based on retention and peak shape modelling. The multiple interactions that amines and ILs experience inside the chromatographic system suggest that the suppressing potency should be measured based on the shape of chromatographic peaks and not on the changes in retention. The ILs 1-hexyl-3-methyl-imidazolium chloride and tetrafluoroborate offered the most interesting features for the separation of the basic drugs. Copyright © 2014 Elsevier B.V. All rights reserved.

Discriminative and informative features for biomolecular text mining with ensemble feature selection.

PubMed

Van Landeghem, Sofie; Abeel, Thomas; Saeys, Yvan; Van de Peer, Yves

2010-09-15

In the field of biomolecular text mining, black box behavior of machine learning systems currently limits understanding of the true nature of the predictions. However, feature selection (FS) is capable of identifying the most relevant features in any supervised learning setting, providing insight into the specific properties of the classification algorithm. This allows us to build more accurate classifiers while at the same time bridging the gap between the black box behavior and the end-user who has to interpret the results. We show that our FS methodology successfully discards a large fraction of machine-generated features, improving classification performance of state-of-the-art text mining algorithms. Furthermore, we illustrate how FS can be applied to gain understanding in the predictions of a framework for biomolecular event extraction from text. We include numerous examples of highly discriminative features that model either biological reality or common linguistic constructs. Finally, we discuss a number of insights from our FS analyses that will provide the opportunity to considerably improve upon current text mining tools. The FS algorithms and classifiers are available in Java-ML (http://java-ml.sf.net). The datasets are publicly available from the BioNLP'09 Shared Task web site (http://www-tsujii.is.s.u-tokyo.ac.jp/GENIA/SharedTask/).

Technologies Enabling Scientific Exploration of Asteroids and Moons

NASA Astrophysics Data System (ADS)

Shaw, A.; Fulford, P.; Chappell, L.

2016-12-01

Scientific exploration of moons and asteroids is enabled by several key technologies that yield topographic information, allow excavation of subsurface materials, and allow delivery of higher-mass scientific payloads to moons and asteroids. These key technologies include lidar systems, robotics, and solar-electric propulsion spacecraft buses. Many of these technologies have applications for a variety of planetary targets. Lidar systems yield high-resolution shape models of asteroids and moons. These shape models can then be combined with radio science information to yield insight into density and internal structure. Further, lidar systems allow investigation of topographic surface features, large and small, which yields information on regolith properties. Robotic arms can be used for a variety of purposes, especially to support excavation, revealing subsurface material and acquiring material from depth for either in situ analysis or sample return. Robotic arms with built-in force sensors can also be used to gauge the strength of materials as a function of depth, yielding insight into regolith physical properties. Mobility systems allow scientific exploration of multiple sites, and also yield insight into regolith physical properties due to the interaction of wheels with regolith. High-power solar electric propulsion (SEP) spacecraft bus systems allow more science instruments to be included on missions given their ability to support greater payload mass. In addition, leveraging a cost-effective commercially-built SEP spacecraft bus can significantly reduce mission cost.

How Different Insights from a Variety of Theories Might Help Ethical Decision-Making in Educational Counselling

ERIC Educational Resources Information Center

Tveit, Anne Dorthe; Sunde, Annikken Louise

2016-01-01

The purpose of this paper is to explore how different insights from a variety of theories might help ethical decision making in educational counselling and highlight the need for reflection. A framework for ethical decision making based on basic features of counselling, namely the interlocutors' practice or "acts", is proposed. There are…

Depressive symptom profiles and severity patterns in outpatients with psychotic vs nonpsychotic major depression.

PubMed

Gaudiano, Brandon A; Young, Diane; Chelminski, Iwona; Zimmerman, Mark

2008-01-01

Previous research suggests that patients with psychotic major depression (PMD) may differ from those with nonpsychotic major depression (NMD) not only in psychotic features but also in their depressive symptom presentation. The present study contrasted the rates and severity of depressive symptoms in outpatients diagnosed with PMD vs NMD. The sample consisted of 1112 patients diagnosed with major depression, of which 60 (5.3%) exhibited psychotic features. Depressive symptoms were assessed by trained diagnosticians at intake using the Structured Clinical Interview for Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition and supplemented by severity items from the Schedule for Affective Disorders and Schizophrenia. Patients with PMD were more likely to endorse the presence of weight loss, insomnia, psychomotor agitation, indecisiveness, and suicidality compared with NMD patients. Furthermore, PMD patients showed higher levels of severity on several depressive symptoms, including depressed mood, appetite loss, insomnia, psychomotor disturbances (agitation and retardation), fatigue, worthlessness, guilt, cognitive disturbances (concentration and indecisiveness), hopelessness, and suicidal ideation. The presence of psychomotor disturbance, insomnia, indecisiveness, and suicidal ideation was predictive of diagnostic status even after controlling for the effects of demographic characteristics and other symptoms. These findings are consistent with past research suggesting that PMD is characterized by a unique depressive symptom profile in addition to psychotic features and higher levels of overall depression severity. The identification of specific depressive symptoms in addition to delusions/hallucinations that can differentiate PMD vs NMD patients can aid in the early detection of the disorder. These investigations also provide insights into potential treatment targets for this high-risk population.

Genomic evolution and chemoresistance in germ-cell tumours.

PubMed

Taylor-Weiner, Amaro; Zack, Travis; O'Donnell, Elizabeth; Guerriero, Jennifer L; Bernard, Brandon; Reddy, Anita; Han, G Celine; AlDubayan, Saud; Amin-Mansour, Ali; Schumacher, Steven E; Litchfield, Kevin; Turnbull, Clare; Gabriel, Stacey; Beroukhim, Rameen; Getz, Gad; Carter, Scott L; Hirsch, Michelle S; Letai, Anthony; Sweeney, Christopher; Van Allen, Eliezer M

2016-11-30

Germ-cell tumours (GCTs) are derived from germ cells and occur most frequently in the testes. GCTs are histologically heterogeneous and distinctly curable with chemotherapy. Gains of chromosome arm 12p and aneuploidy are nearly universal in GCTs, but specific somatic genomic features driving tumour initiation, chemosensitivity and progression are incompletely characterized. Here, using clinical whole-exome and transcriptome sequencing of precursor, primary (testicular and mediastinal) and chemoresistant metastatic human GCTs, we show that the primary somatic feature of GCTs is highly recurrent chromosome arm level amplifications and reciprocal deletions (reciprocal loss of heterozygosity), variations that are significantly enriched in GCTs compared to 19 other cancer types. These tumours also acquire KRAS mutations during the development from precursor to primary disease, and primary testicular GCTs (TGCTs) are uniformly wild type for TP53. In addition, by functional measurement of apoptotic signalling (BH3 profiling) of fresh tumour and adjacent tissue, we find that primary TGCTs have high mitochondrial priming that facilitates chemotherapy-induced apoptosis. Finally, by phylogenetic analysis of serial TGCTs that emerge with chemotherapy resistance, we show how TGCTs gain additional reciprocal loss of heterozygosity and that this is associated with loss of pluripotency markers (NANOG and POU5F1) in chemoresistant teratomas or transformed carcinomas. Our results demonstrate the distinct genomic features underlying the origins of this disease and associated with the chemosensitivity phenotype, as well as the rare progression to chemoresistance. These results identify the convergence of cancer genomics, mitochondrial priming and GCT evolution, and may provide insights into chemosensitivity and resistance in other cancers.

Insight and psychopathology in never-treated schizophrenia.

PubMed

Tirupati, Srinivasan; Padmavati, Raman; Thara, Rangaswamy; McCreadie, Robin G

2007-01-01

Insight is a feature of schizophrenia related to psychopathology, which could be modified by treatment. The real relationship will be more evident in the never-treated state. This study compared insight and its relationship to psychopathology in 143 never-treated patients with chronic schizophrenia with 183 treated patients. The treated patients had not received any structured intervention for improvement of insight. The item on insight and judgment from the Positive and Negative Syndrome Scale for schizophrenia was used as a measure of insight. Never-treated patients were more ill and poorer in insight than the TT group. Sex, age, duration of illness, negative symptoms related to insight only in the TT group. Positive symptoms score correlated with insight in both the groups, but negative symptoms correlated with insight only among the treated patients. Delusions, uncooperativeness, and poor attention predicted 27% of variation in the level of insight in the never-treated, whereas age; duration of illness; and symptoms of emotional withdrawal, difficulty in abstract thinking, and uncooperativeness predicted 30.3% of variation in insight of the TT group. The observed differences between the never-treated and treated subjects were due to influence of treatment on the association between insight and psychopathology. A subgroup of patients with a treatment-resistant trait of negative symptoms associated with poor insight was hypothesized.

NCCN Guidelines® Insights Bladder Cancer, Version 2.2016 Featured Updates to the NCCN Guidelines

PubMed Central

Clark, Peter E.; Spiess, Philippe E.; Agarwal, Neeraj; Bangs, Rick; Boorjian, Stephen A.; Buyyounouski, Mark K.; Efstathiou, Jason A.; Flaig, Thomas W.; Friedlander, Terence; Greenberg, Richard E.; Guru, Khurshid A.; Hahn, Noah; Herr, Harry W.; Hoimes, Christopher; Inman, Brant A.; Kader, A. Karim; Kibel, Adam S.; Kuzel, Timothy M.; Lele, Subodh M.; Meeks, Joshua J.; Michalski, Jeff; Montgomery, Jeffrey S.; Pagliaro, Lance C.; Pal, Sumanta K.; Patterson, Anthony; Petrylak, Daniel; Plimack, Elizabeth R.; Pohar, Kamal S.; Porter, Michael P.; Sexton, Wade J.; Siefker-Radtke, Arlene O.; Sonpavde, Guru; Tward, Jonathan; Wile, Geoffrey; Dwyer, Mary A.; Smith, Courtney

2017-01-01

These NCCN Guidelines Insights discuss the major recent updates to the NCCN Guidelines for Bladder Cancer based on the review of the evidence in conjunction with the expert opinion of the panel. Recent updates include (1) refining the recommendation of intravesical bacillus Calmette-Guérin, (2) strengthening the recommendations for perioperative systemic chemotherapy, and (3) incorporating immunotherapy into second-line therapy for locally advanced or metastatic disease. These NCCN Guidelines Insights further discuss factors that affect integration of these recommendations into clinical practice. PMID:27697976

Cachexia in chronic obstructive pulmonary disease: new insights and therapeutic perspective

PubMed Central

Sanders, Karin J. C.; Kneppers, Anita E. M.; van de Bool, Coby; Langen, Ramon C. J.

2015-01-01

Abstract Cachexia and muscle wasting are well recognized as common and partly reversible features of chronic obstructive pulmonary disease (COPD), adversely affecting disease progression and prognosis. This argues for integration of weight and muscle maintenance in patient care. In this review, recent insights are presented in the diagnosis of muscle wasting in COPD, the pathophysiology of muscle wasting, and putative mechanisms involved in a disturbed energy balance as cachexia driver. We discuss the therapeutic implications of these new insights for optimizing and personalizing management of COPD‐induced cachexia. PMID:27066314

Folate biosynthesis pathway: mechanisms and insights into drug design for infectious diseases.

PubMed

Bertacine Dias, Marcio V; Santos, Jademilson C; Libreros-Zúñiga, Gerardo A; Ribeiro, João A; Chavez-Pacheco, Sair M

2018-04-01

Folate pathway is a key target for the development of new drugs against infectious diseases since the discovery of sulfa drugs and trimethoprim. The knowledge about this pathway has increased in the last years and the catalytic mechanism and structures of all enzymes of the pathway are fairly understood. In addition, differences among enzymes from prokaryotes and eukaryotes could be used for the design of specific inhibitors. In this review, we show a panorama of progress that has been achieved within the folate pathway obtained in the last years. We explored the structure and mechanism of enzymes, several genetic features, strategies, and approaches used in the design of new inhibitors that have been used as targets in pathogen chemotherapy.

Sampling the sound field in auditoria using large natural-scale array measurements.

PubMed

Witew, Ingo B; Vorländer, Michael; Xiang, Ning

2017-03-01

Suitable data for spatial wave field analyses in concert halls need to satisfy the sampling theorem and hence requires densely spaced measurement positions over extended regions. The described measurement apparatus is capable of automatically sampling the sound field in auditoria over a surface of 5.30 m × 8.00 m to any appointed resolutions. In addition to discussing design features, a case study based on measured impulse responses is presented. The experimental data allow wave field animations demonstrating how sound propagating at grazing incidence over theater seating is scattered from rows of chairs (seat-dip effect). The visualized data of reflections and scattering from an auditorium's boundaries give insights and opportunities for advanced analyses.

Data processing in neutron protein crystallography using positron-sensitive detectors

NASA Astrophysics Data System (ADS)

Schoenborn, B. P.

Neutrons provide a unique probe for localizing hydrogen atoms and for distinguishing hydrogen from deuterons. Hydrogen atoms largely determine the three dimensional structure of proteins and are responsible for many catalytic reactions. The study of hydrogen bonding and hydrogen exchange will therefore give insight into reaction mechanisms and conformational fluctuations. In addition, neutrons provide the ability to distinguish N from C and O and to allow correct orientation of groups such as histidine and glutamine. To take advantage of these unique features of neutron crystallography, one needs accurate Fourier maps depicting atomic structure to a high precision. Special attention is given to subtraction of the high background associated with hydrogen containing molecules, which produces a disproportionately large statistical error.

Cardiomyopathies in Noonan syndrome and the other RASopathies

PubMed Central

Gelb, Bruce D.; Roberts, Amy E.; Tartaglia, Marco

2015-01-01

Noonan syndrome and related disorders (Noonan syndrome with multiple lentigines, Costello syndrome, cardiofaciocutaneous syndrome, Noonan syndrome with loose anagen hair, and other related traits) are autosomal dominant traits. Mutations causing these disorders alter proteins relevant for signaling through RAS. Thus, these traits are now collectively called the RASopathies. While the RASopathies have pleiomorphic features, this review will focus on the hypertrophic cardiomyopathy observed in varying percentages of all of these traits. In addition, inherited abnormalities in one pathway gene, RAF1, cause pediatric-onset dilated cardiomyopathy. The pathogeneses for the RASopathy-associated cardiomyopathies are being elucidated, principally using animal models, leading to genotype-specific insights into how signal transduction is perturbed. Based on those findings, small molecule therapies seem possible for RASopathy-associated cardiomyopathies. PMID:26380542

Qualitative research methods: key features and insights gained from use in infection prevention research.

PubMed

Forman, Jane; Creswell, John W; Damschroder, Laura; Kowalski, Christine P; Krein, Sarah L

2008-12-01

Infection control professionals and hospital epidemiologists are accustomed to using quantitative research. Although quantitative studies are extremely important in the field of infection control and prevention, often they cannot help us explain why certain factors affect the use of infection control practices and identify the underlying mechanisms through which they do so. Qualitative research methods, which use open-ended techniques, such as interviews, to collect data and nonstatistical techniques to analyze it, provide detailed, diverse insights of individuals, useful quotes that bring a realism to applied research, and information about how different health care settings operate. Qualitative research can illuminate the processes underlying statistical correlations, inform the development of interventions, and show how interventions work to produce observed outcomes. This article describes the key features of qualitative research and the advantages that such features add to existing quantitative research approaches in the study of infection control. We address the goal of qualitative research, the nature of the research process, sampling, data collection and analysis, validity, generalizability of findings, and presentation of findings. Health services researchers are increasingly using qualitative methods to address practical problems by uncovering interacting influences in complex health care environments. Qualitative research methods, applied with expertise and rigor, can contribute important insights to infection prevention efforts.

Hybrid genome assembly and annotation of Paenibacillus pasadenensis strain R16 reveals insights on endophytic life style and antifungal activity

PubMed Central

Passera, Alessandro; Marcolungo, Luca; Brasca, Milena; Quaglino, Fabio; Cantaloni, Chiara; Delledonne, Massimo

2018-01-01

Bacteria of the Paenibacillus genus are becoming important in many fields of science, including agriculture, for their positive effects on the health of plants. However, there are little information available on this genus compared to other bacteria (such as Bacillus or Pseudomonas), especially when considering genomic information. Sequencing the genomes of plant-beneficial bacteria is a crucial step to identify the genetic elements underlying the adaptation to life inside a plant host and, in particular, which of these features determine the differences between a helpful microorganism and a pathogenic one. In this study, we have characterized the genome of Paenibacillus pasadenensis, strain R16, recently investigated for its antifungal activities and plant-associated features. An hybrid assembly approach was used integrating the very precise reads obtained by Illumina technology and long fragments acquired with Oxford Nanopore Technology (ONT) sequencing. De novo genome assembly based solely on Illumina reads generated a relatively fragmented assembly of 5.72 Mbp in 99 ungapped sequences with an N50 length of 544 Kbp; hybrid assembly, integrating Illumina and ONT reads, improved the assembly quality, generating a genome of 5.75 Mbp, organized in 6 contigs with an N50 length of 3.4 Mbp. Annotation of the latter genome identified 4987 coding sequences, of which 1610 are hypothetical proteins. Enrichment analysis identified pathways of particular interest for the endophyte biology, including the chitin-utilization pathway and the incomplete siderophore pathway which hints at siderophore parasitism. In addition the analysis led to the identification of genes for the production of terpenes, as for example farnesol, that was hypothesized as the main antifungal molecule produced by the strain. The functional analysis on the genome confirmed several plant-associated, plant-growth promotion, and biocontrol traits of strain R16, thus adding insights in the genetic bases of these complex features, and of the Paenibacillus genus in general. PMID:29351296

Paleodrainage insights into the fluvial and glacial history of the western Chukchi margin, Arctic Alaska

NASA Astrophysics Data System (ADS)

Stockmaster, B. A.; Hill, J. C.; Klotsko, S.; Driscoll, N. W.

2016-12-01

CHIRP subbottom data collected from the Chukchi shelf offshore of northwest Alaska reveal extensive paleodrainage networks that incised the margin during sea level lowstands. These features are cut into folded Cretaceous bedrock strata and likely represent multiple sea level cycles. Several large incised valleys, 10s of km wide and up to 50m deep, as well as numerous smaller, individual channels have been identified. Possible sources of fluvial input include drainage from the Hope Valley to the south, as well as several smaller rivers on the northwest Alaskan coast such as the Utukok, Kokolik, Kukpowruk, and Kuk Rivers. Correlation of sediment infill patterns provides insight to paleochannels and paleovalleys as well as outlining potential drainage networks. This new data will be used to examine sediment infill and erosion patterns to assess whether some of the valleys were formed by non-fluvial (i.e. glacial) processes. Preliminary results indicate the presence of six paleodrainage networks across the eastern Chukchi shelf, based on shape, size and infill of the paleovalleys: Incised Valley, Middle Valley, Northern Valley, Borderlands Valley, the Hanna Bank Valley and the Barrow Valley. All of the paleodrainage valleys are oriented perpendicular to the coast except for Barrow Valley, which follows the northwest coastline, and the Hanna Bank Valley, which is oriented parallel. The Barrow Valley also displays several interesting features in the subsurface. In all of the profiles across this paleovalley, the fluvial infill is overlain by high amplitude, acoustically laminated reflectors that appear to represent hemipelagic marine sediment, indicating rapid sea level rise flooded the shelf. There also appears to be 1 m erosional relief on the transgressive surface, which suggests there may have been an additional source of erosion within the Barrow Valley during sea level rise, possibly from an ice shelf or other glacial features. The presence of ice could also possibly explain the occupation of Barrow Canyon that would have diverted the Barrow Valley drainage.

The development of a decision support system with an interactive clinical user interface for estimating treatment parameters in radiation therapy in order to reduce radiation dose in head and neck patients

NASA Astrophysics Data System (ADS)

Verma, Sneha; Liu, Joseph; Deshpande, Ruchi; DeMarco, John; Liu, Brent J.

2017-03-01

The primary goal in radiation therapy is to target the tumor with the maximum possible radiation dose while limiting the radiation exposure of the surrounding healthy tissues. However, in order to achieve an optimized treatment plan, many constraints, such as gender, age, tumor type, location, etc. need to be considered. The location of the malignant tumor with respect to the vital organs is another possible important factor for treatment planning process which can be quantified as a feature making it easier to analyze its effects. Incorporation of such features into the patient's medical history could provide additional knowledge that could lead to better treatment outcomes. To show the value of features such as relative locations of tumors and surrounding organs, the data is first processed in order to calculate the features and formulate a feature matrix. Then these feature are matched with retrospective cases with similar features to provide the clinician with insight on delivered dose in similar cases from past. This process provides a range of doses that can be delivered to the patient while limiting the radiation exposure of surrounding organs based on similar retrospective cases. As the number of patients increase, there will be an increase in computations needed for feature extraction as well as an increase in the workload for the physician to find the perfect dose amount. In order to show how such algorithms can be integrated we designed and developed a system with a streamlined workflow and interface as prototype for the clinician to test and explore. Integration of the tumor location feature with the clinician's experience and training could play a vital role in designing new treatment algorithms and better outcomes. Last year, we presented how multi-institutional data into a decision support system is incorporated. This year the presentation is focused on the interface and demonstration of the working prototype of informatics system.

Star Messenger: Galileo at the Millennium

NASA Astrophysics Data System (ADS)

White, R. E.

1999-05-01

Smith College has recently established the Louise B. and Edmund J. Kahn Liberal Arts Institute to foster interdisciplinary scholarship among the faculty. In the 1999-2000 academic year, the Kahn Institute is sponsoring a project entitled "Star Messenger: Galileo at the Millennium." The project will explore the impact of the astronomical discoveries of Galileo and his contemporaries on the Renaissance world-view and also use Galileo's experience as a lens for examining scientific and cultural developments at the symbolic juncture represented by the year 2000. Seven faculty fellows and 10-12 student fellows will participate in a year-long colloquium pursuing these themes, aided by the participation of some five Visiting Fellows. The inaugural public event will be a symposium on the historical Galileo, with presentation by three noted scholars, each of whom will return to campus for a second meeting with the Kahn colloquium. Additional events will include an exhibit of prints, artifacts, and rare books related to Galileo and his time, an early music concert featuring music composed by Galileo's father, and a series of other events sponsored by diverse departments and programs, all related to the broad themes of the Galileo project. The culminating events will be the premiere of a new music theater work, which will encapsulate the insights of the colloquium about human reactions to novel insights about the world, and a symposium presenting the research results of faculty and student fellows. The symposium will feature a capstone lecture by an visionary scholar projecting the implication of historical and contemporary trends into the future.

A morphometric assessment and classification of coral reef spur and groove morphology

NASA Astrophysics Data System (ADS)

Duce, S.; Vila-Concejo, A.; Hamylton, S. M.; Webster, J. M.; Bruce, E.; Beaman, R. J.

2016-07-01

Spurs and grooves (SaGs) are a common and important feature of coral reef fore slopes worldwide. However, they are difficult to access and hence their morphodynamics and formation are poorly understood. We use remote sensing, with extensive ground truthing, to measure SaG morphometrics and environmental factors at 11,430 grooves across 17 reefs in the southern Great Barrier Reef, Australia. We revealed strong positive correlations between groove length, orientation and wave exposure with longer, more closely-spaced grooves oriented easterly reflecting the dominant swell regime. Wave exposure was found to be the most important factor controlling SaG distribution and morphology. Gradient of the upper reef slope was also an important limiting factor, with SaGs less likely to develop in steeply sloping (> 5°) areas. We used a subset of the morphometric data (11 reefs) to statistically define four classes of SaG. This classification scheme was tested on the remaining six reefs. SaGs in the four classes differ in morphology, groove substrate and coral cover. These differences provide insights into SaG formation mechanisms with implications to reef platform growth and evolution. We hypothesize SaG formation is dominated by coral growth processes at two classes and erosion processes at one class. A fourth class may represent relic features formed earlier in the Holocene transgression. The classes are comparable with SaGs elsewhere, suggesting the classification could be applied globally with the addition of new classes if necessary. While further research is required, we show remotely sensed SaG morphometrics can provide useful insights into reef platform evolution.

The Fifth NASA Symposium on VLSI Design

NASA Technical Reports Server (NTRS)

1993-01-01

The fifth annual NASA Symposium on VLSI Design had 13 sessions including Radiation Effects, Architectures, Mixed Signal, Design Techniques, Fault Testing, Synthesis, Signal Processing, and other Featured Presentations. The symposium provides insights into developments in VLSI and digital systems which can be used to increase data systems performance. The presentations share insights into next generation advances that will serve as a basis for future VLSI design.

Costs of storing colour and complex shape in visual working memory: Insights from pupil size and slow waves.

PubMed

Kursawe, Michael A; Zimmer, Hubert D

2015-06-01

We investigated the impact of perceptual processing demands on visual working memory of coloured complex random polygons during change detection. Processing load was assessed by pupil size (Exp. 1) and additionally slow wave potentials (Exp. 2). Task difficulty was manipulated by presenting different set sizes (1, 2, 4 items) and by making different features (colour, shape, or both) task-relevant. Memory performance in the colour condition was better than in the shape and both condition which did not differ. Pupil dilation and the posterior N1 increased with set size independent of type of feature. In contrast, slow waves and a posterior P2 component showed set size effects but only if shape was task-relevant. In the colour condition slow waves did not vary with set size. We suggest that pupil size and N1 indicates different states of attentional effort corresponding to the number of presented items. In contrast, slow waves reflect processes related to encoding and maintenance strategies. The observation that their potentials vary with the type of feature (simple colour versus complex shape) indicates that perceptual complexity already influences encoding and storage and not only comparison of targets with memory entries at the moment of testing. Copyright © 2015 Elsevier B.V. All rights reserved.

Integrative topological analysis of mass spectrometry data reveals molecular features with clinical relevance in esophageal squamous cell carcinoma

PubMed Central

Gao, She-Gan; Liu, Rui-Min; Zhao, Yun-Gang; Wang, Pei; Ward, Douglas G.; Wang, Guang-Chao; Guo, Xiang-Qian; Gu, Juan; Niu, Wan-Bin; Zhang, Tian; Martin, Ashley; Guo, Zhi-Peng; Feng, Xiao-Shan; Qi, Yi-Jun; Ma, Yuan-Fang

2016-01-01

Combining MS-based proteomic data with network and topological features of such network would identify more clinically relevant molecules and meaningfully expand the repertoire of proteins derived from MS analysis. The integrative topological indexes representing 95.96% information of seven individual topological measures of node proteins were calculated within a protein-protein interaction (PPI) network, built using 244 differentially expressed proteins (DEPs) identified by iTRAQ 2D-LC-MS/MS. Compared with DEPs, differentially expressed genes (DEGs) and comprehensive features (CFs), structurally dominant nodes (SDNs) based on integrative topological index distribution produced comparable classification performance in three different clinical settings using five independent gene expression data sets. The signature molecules of SDN-based classifier for distinction of early from late clinical TNM stages were enriched in biological traits of protein synthesis, intracellular localization and ribosome biogenesis, which suggests that ribosome biogenesis represents a promising therapeutic target for treating ESCC. In addition, ITGB1 expression selected exclusively by integrative topological measures correlated with clinical stages and prognosis, which was further validated with two independent cohorts of ESCC samples. Thus the integrative topological analysis of PPI networks proposed in this study provides an alternative approach to identify potential biomarkers and therapeutic targets from MS/MS data with functional insights in ESCC. PMID:26898710

Role of dystroglycan in limiting contraction-induced injury to the sarcomeric cytoskeleton of mature skeletal muscle.

PubMed

Rader, Erik P; Turk, Rolf; Willer, Tobias; Beltrán, Daniel; Inamori, Kei-Ichiro; Peterson, Taylor A; Engle, Jeffrey; Prouty, Sally; Matsumura, Kiichiro; Saito, Fumiaki; Anderson, Mary E; Campbell, Kevin P

2016-09-27

Dystroglycan (DG) is a highly expressed extracellular matrix receptor that is linked to the cytoskeleton in skeletal muscle. DG is critical for the function of skeletal muscle, and muscle with primary defects in the expression and/or function of DG throughout development has many pathological features and a severe muscular dystrophy phenotype. In addition, reduction in DG at the sarcolemma is a common feature in muscle biopsies from patients with various types of muscular dystrophy. However, the consequence of disrupting DG in mature muscle is not known. Here, we investigated muscles of transgenic mice several months after genetic knockdown of DG at maturity. In our study, an increase in susceptibility to contraction-induced injury was the first pathological feature observed after the levels of DG at the sarcolemma were reduced. The contraction-induced injury was not accompanied by increased necrosis, excitation-contraction uncoupling, or fragility of the sarcolemma. Rather, disruption of the sarcomeric cytoskeleton was evident as reduced passive tension and decreased titin immunostaining. These results reveal a role for DG in maintaining the stability of the sarcomeric cytoskeleton during contraction and provide mechanistic insight into the cause of the reduction in strength that occurs in muscular dystrophy after lengthening contractions.

Pb 2+–Calcite Interactions under Far-from-Equilibrium Conditions: Formation of Micropyramids and Pseudomorphic Growth of Cerussite

DOE PAGES

Yuan, Ke; De Andrade, Vincent; Feng, Zhange; ...

2018-01-04

The presence of impurity ions is known to significantly influence mineral surface morphology during crystal growth from aqueous solution, but knowledge on impurity ion-mineral interactions during dissolution under far-from equilibrium conditions remains limited. Here we show that calcite (CaCO 3) exhibits a rich array of dissolution features in the presence of Pb. During the initial stage, calcite exhibits non-classical surface features characterized as micro pyramids developed spontaneously in acidic Pb-bearing solutions. Subsequent pseudomorphic growth of cerussite (PbCO 3) was observed, where nucleation occurred entirely within a pore space created by dissolution at the calcite/substrate interface. Uneven growth rates yielded amore » cerussite shell made of lath- or dendritic-shaped crystals. The cerussite phase was separated from the calcite by pores of less than 200 nm under transmission X-ray microscopy, consistent with the interface-coupled dissolution-precipitation mechanism. These results show that impurity metal ions exert significant control over the microscale dissolution features found on mineral surfaces and provide new insights into interpreting and designing micro structures observed in naturally-occurring and synthetic carbonate minerals by dissolution. In addition, heterogeneous micro-environments created in transport limited reactions under pore spaces may lead to unusual growth forms during crystal nucleation and precipitation.« less

Laterality of repetitive finger movement performance and clinical features of Parkinson's disease.

PubMed

Stegemöller, Elizabeth; Zaman, Andrew; MacKinnon, Colum D; Tillman, Mark D; Hass, Chris J; Okun, Michael S

2016-10-01

Impairments in acoustically cued repetitive finger movement often emerge at rates near to and above 2Hz in persons with Parkinson's Disease (PD) in which some patients move faster (hastening) and others move slower (bradykinetic). The clinical features impacting this differential performance of repetitive finger movement remain unknown. The purpose of this study was to compare repetitive finger movement performance between the more and less affected side, and the difference in clinical ratings among performance groups. Forty-one participants diagnosed with idiopathic PD completed an acoustically cued repetitive finger movement task while "on" medication. Eighteen participants moved faster, 10 moved slower, and 13 were able to maintain the appropriate rate at rates above 2Hz. Clinical measures of laterality, disease severity, and the UPDRS were obtained. There were no significant differences between the more and less affected sides regardless of performance group. Comparison of disease severity, tremor, and rigidity among performance groups revealed no significant differences. Comparison of posture and postural instability scores revealed that the participants that demonstrated hastening had worse posture and postural instability scores. Consideration of movement rate during the clinical evaluation of repetitive finger movement may provide additional insight into varying disease features in persons with PD. Copyright © 2016 Elsevier B.V. All rights reserved.

Household expansion linked to agricultural intensification during emergence of Hawaiian archaic states

PubMed Central

Field, Julie S.; Ladefoged, Thegn N.; Kirch, Patrick V.

2011-01-01

The Leeward Kohala Field System (LKFS) covering ∼60 km2 on Hawai‘i Island is one of the world's best-studied archaeological examples of preindustrial agricultural intensification. Archaeological correlates for households over a 400-y period of intensification of the LKFS (A.D. 1400–1800) indicate that household age, number, and distribution closely match the expansion of agricultural features at both macro- and microscales. We excavated and dated residential complexes within portions of five traditional Hawaiian land units (ahupua‘a), two in the central core of the field system and three in the southern margins. Forty-eight radiocarbon dates from 43 residential features indicate an overall pattern of exponential increase in the numbers of households over time. Spatial distribution of these dates suggests that the core of the LKFS may have reached a population saturation point earlier than in the southern margins. Bayesian statistical analysis of radiocarbon dates from residential features in the core region, combined with spatial analysis of agricultural and residential construction sequences, demonstrates that the progressive subdivision of territories into smaller socioeconomic units was matched by addition of new residences, probably through a process of household fissioning. These results provide insights into the economic processes underlying the sociopolitical transformation from chiefdom to archaic state in precontact Hawai‘i. PMID:21502516

An analysis of a digital variant of the Trail Making Test using machine learning techniques.

PubMed

Dahmen, Jessamyn; Cook, Diane; Fellows, Robert; Schmitter-Edgecombe, Maureen

2017-01-01

The goal of this work is to develop a digital version of a standard cognitive assessment, the Trail Making Test (TMT), and assess its utility. This paper introduces a novel digital version of the TMT and introduces a machine learning based approach to assess its capabilities. Using digital Trail Making Test (dTMT) data collected from (N = 54) older adult participants as feature sets, we use machine learning techniques to analyze the utility of the dTMT and evaluate the insights provided by the digital features. Predicted TMT scores correlate well with clinical digital test scores (r = 0.98) and paper time to completion scores (r = 0.65). Predicted TICS exhibited a small correlation with clinically derived TICS scores (r = 0.12 Part A, r = 0.10 Part B). Predicted FAB scores exhibited a small correlation with clinically derived FAB scores (r = 0.13 Part A, r = 0.29 for Part B). Digitally derived features were also used to predict diagnosis (AUC of 0.65). Our findings indicate that the dTMT is capable of measuring the same aspects of cognition as the paper-based TMT. Furthermore, the dTMT's additional data may be able to help monitor other cognitive processes not captured by the paper-based TMT alone.

Investigation of binding features: effects on the interaction between CYP2A6 and inhibitors.

PubMed

Ai, Chunzhi; Li, Yan; Wang, Yonghua; Li, Wei; Dong, Peipei; Ge, Guangbo; Yang, Ling

2010-07-15

A computational investigation has been carried out on CYP2A6 and its naphthalene inhibitors to explore the crucial molecular features contributing to binding specificity. The molecular bioactive orientations were obtained by docking (FlexX) these compounds into the active site of the enzyme. And the density functional theory method was further used to optimize the molecular structures with the subsequent analysis of molecular lipophilic potential (MLP) and molecular electrostatic potential (MEP). The minimal MLPs, minimal MEPs, and the band gap energies (the energy difference between the highest occupied molecular orbital and lowest unoccupied molecular orbital) showed high correlations with the inhibition activities (pIC(50)s), illustrating their significant roles in driving the inhibitor to adopt an appropriate bioactive conformation oriented in the active site of CYP2A6 enzyme. The differences in MLPs, MEPs, and the orbital energies have been identified as key features in determining the binding specificity of this series of compounds to CYP2A6 and the consequent inhibitory effects. In addition, the combinational use of the docking, MLP and MEP analysis is also demonstrated as a good attempt to gain an insight into the interaction between CYP2A6 and its inhibitors. Copyright 2010 Wiley Periodicals, Inc.

Salient Key Features of Actual English Instructional Practices in Saudi Arabia

ERIC Educational Resources Information Center

Al-Seghayer, Khalid

2015-01-01

This is a comprehensive review of the salient key features of the actual English instructional practices in Saudi Arabia. The goal of this work is to gain insights into the practices and pedagogic approaches to English as a foreign language (EFL) teaching currently employed in this country. In particular, we identify the following central features…

ASTROS: A multidisciplinary automated structural design tool

NASA Technical Reports Server (NTRS)

Neill, D. J.

1989-01-01

ASTROS (Automated Structural Optimization System) is a finite-element-based multidisciplinary structural optimization procedure developed under Air Force sponsorship to perform automated preliminary structural design. The design task is the determination of the structural sizes that provide an optimal structure while satisfying numerous constraints from many disciplines. In addition to its automated design features, ASTROS provides a general transient and frequency response capability, as well as a special feature to perform a transient analysis of a vehicle subjected to a nuclear blast. The motivation for the development of a single multidisciplinary design tool is that such a tool can provide improved structural designs in less time than is currently needed. The role of such a tool is even more apparent as modern materials come into widespread use. Balancing conflicting requirements for the structure's strength and stiffness while exploiting the benefits of material anisotropy is perhaps an impossible task without assistance from an automated design tool. Finally, the use of a single tool can bring the design task into better focus among design team members, thereby improving their insight into the overall task.

Satellite Remote Sensing of Atmospheric Pollution: the Far-Reaching Impact of Burning in Southern Africa

NASA Technical Reports Server (NTRS)

Fishman, Jack; Al-Saadi, Jassim A.; Neil, Doreen O.; Creilson, John K.; Severance, Kurt; Thomason, Larry W.; Edwards, David R.

2008-01-01

When the first observations of a tropospheric trace gas were obtained in the 1980s, carbon monoxide enhancements from tropical biomass burning dominated the observed features. In 2005, an active remote-sensing system to provide detailed information on the vertical distribution of aerosols and clouds was launched, and again, one of the most imposing features observed was the presence of emissions from tropical biomass burning. This paper presents a brief overview of space-borne observations of the distribution of trace gases and aerosols and how tropical biomass burning, primarily in the Southern Hemisphere, has provided an initially surprising picture of the distribution of these species and how they have evolved from prevailing transport patterns in that hemisphere. We also show how interpretation of these observations has improved significantly as a result of the improved capability of trajectory modeling in recent years and how information from this capability has provided additional insight into previous measurements form satellites. Key words: pollution; biomass burning; aerosols; tropical trace gas emissions; Southern Hemisphere; carbon monoxide.

Understanding the direction of evolution in Burkholderia glumae through comparative genomics.

PubMed

Lee, Hyun-Hee; Park, Jungwook; Kim, Jinnyun; Park, Inmyoung; Seo, Young-Su

2016-02-01

Members of the genus Burkholderia occupy remarkably diverse niches, with genome sizes ranging from ~3.75 to 11.29 Mbp. The genome of Burkholderia glumae ranges in size from ~5.81 to 7.89 Mbp. Unlike other plant pathogenic bacteria, B. glumae can infect a wide range of monocot and dicot plants. Comparative genome analysis of B. glumae strains can provide insight into genome variation as well as differential features of whole metabolism or pathways between multiple strains of B. glumae infecting the same host. Comparative analysis of complete genomes among B. glumae BGR1, B. glumae LMG 2196, and B. glumae PG1 revealed the largest departmentalization of genes onto separate replicons in B. glumae BGR1 and considerable downsizing of the genome in B. glumae LMG 2196. In addition, the presence of large-scale evolutionary events such as rearrangement and inversion and the development of highly specialized systems were found to be related to virulence-associated features in the three B. glumae strains. This connection may explain why this bacterium broadens its host range and reinforces its interaction with hosts.

Grouping like catchments: A novel means to compare 40+ watersheds in the Northeastern U.S.

NASA Astrophysics Data System (ADS)

Shaw, S. B.; Walter, M.; Marjerison, R. D.

2008-12-01

One difficulty in understanding the effect of multi-scale patterns in watersheds comes from finding a concise way to identify and compare features across many basins. Comparing raw data (i.e. discharge time series) requires one to account for highly variable climate drivers while extracting meaningful metrics from the data series. Comparing model parameters imposes model assumptions that may obscure fundamental differences, potentially making it an exercise in comparing calibration factors. As a possible middle ground, we have found that the probability of a given basin-wide runoff response can be predicted by combining rainfall frequency with 1. a curve establishing a relationship between basin storage and base flow and 2. the baseflow flow-duration curve. In addition to providing a means to predict runoff, these curves succinctly present empirical runoff-response information, allowing ready graphical comparison of multiple watersheds. From 40+ watersheds throughout the Northeastern U.S., we demonstrate the potential to group watersheds and identify critical hydrologic features, providing particular insight into the influence of land use patterns as well as basin scale.

[Impulse control in addiction: a translational perspective].

PubMed

Schmaal, L; Broos, N; Joos, L; Pattij, T; Goudriaan, A E

2013-01-01

Impulsivity is a hallmark of addiction and predicts treatment response and relapse. Impulsivity is, however, a complex construct. Translational cross-species research is needed to give us greater insight into the neurobiology and the role of impulsivity in addiction and to help with the development of new treatment strategies for improving patients' impulse control. To review recent evidence concerning the concept of impulsivity and the role of impulsivity in addiction. The concept and neurobiology of impulsivity are reviewed from a translational perspective. The role of impulsivity in addiction and implications for treatment are discussed. Our recent translational cross-species study indicates that impulsivity is made up of several, separate independent features with partly distinct underlying neurobiological substrates. There are also indications that these features make a unique and independent contribution to separate stages of the addiction cycle. In addition, the improvement of impulse control is a promising new target area for treatments that could lead to better results. However, those involved in developing new treatment strategies will have to take into account the complexity and multidimensional character of impulsivity.

In Silico Identification of Potent Pancreatic Triacylglycerol Lipase Inhibitors from Traditional Chinese Medicine

PubMed Central

Chen, Kuan-Yu; Chang, Su-Sen; Chen, Calvin Yu-Chian

2012-01-01

Pancreatic triacylglycerol lipase (PNLIP) are primary lipases that are critical for triacylglyceride digestion in human. Since reduced metabolism of triacylglyceride might be a plausible concept for weight loss, we screened for potential PNLIP inhibitors from traditional Chinese medicine (TCM) with the aim to identify weight loss candidate compounds. TCM candidates Aurantiamide, Cnidiadin, and 2-hexadecenoic acid exhibited higher Dock Scores than the commercial drug Orlistat, and were also predicted to have inhibitory characteristics against PNLIP using constructed MLR (R2 = 0.8664) and SVM (R2 = 0.9030) models. Molecular dynamics indicated that the TCM-PNLIP complexes formed were stable. We identified that the PNLIP binding site has several residues that can serve as anchors, and a hydrophobic corridor that provides additional stability to the complex. Aurantiamide, Cnidiadin, and 2-hexadecenoic acid all have features that correspond to these binding site features, indicating their potential as candidates for PNLIP inhibitors. The information presented in this study may provide helpful insights to designing novel weight-control drugs. PMID:22970152

CRISPRscan: designing highly efficient sgRNAs for CRISPR/Cas9 targeting in vivo

PubMed Central

Moreno-Mateos, Miguel A.; Vejnar, Charles E.; Beaudoin, Jean-Denis; Fernandez, Juan P.; Mis, Emily K.; Khokha, Mustafa K.; Giraldez, Antonio J.

2015-01-01

CRISPR/Cas9 technology provides a powerful system for genome engineering. However, variable activity across different single guide RNAs (sgRNAs) remains a significant limitation. We have analyzed the molecular features that influence sgRNA stability, activity and loading into Cas9 in vivo. We observe that guanine enrichment and adenine depletion increase sgRNA stability and activity, while loading, nucleosome positioning and Cas9 off-target binding are not major determinants. We additionally identified truncated and 5′ mismatch-containing sgRNAs as efficient alternatives to canonical sgRNAs. Based on these results, we created a predictive sgRNA-scoring algorithm (CRISPRscan.org) that effectively captures the sequence features affecting Cas9/sgRNA activity in vivo. Finally, we show that targeting Cas9 to the germ line using a Cas9-nanos-3′-UTR fusion can generate maternal-zygotic mutants, increase viability and reduce somatic mutations. Together, these results provide novel insights into the determinants that influence Cas9 activity and a framework to identify highly efficient sgRNAs for genome targeting in vivo. PMID:26322839

Monogenic diabetes in children and young adults: Challenges for researcher, clinician and patient

PubMed Central

2006-01-01

Monogenic diabetes results from one or more mutations in a single gene which might hence be rare but has great impact leading to diabetes at a very young age. It has resulted in great challenges for researchers elucidating the aetiology of diabetes and related features in other organ systems, for clinicians specifying a diagnosis that leads to improved genetic counselling, predicting of clinical course and changes in treatment, and for patients to altered treatment that has lead to coming off insulin and injections with no alternative (Glucokinase mutations), insulin injections being replaced by tablets (e.g. low dose in HNFα or high dose in potassium channel defects -Kir6.2 and SUR1) or with tablets in addition to insulin (e.g. metformin in insulin resistant syndromes). Genetic testing requires guidance to test for what gene especially given limited resources. Monogenic diabetes should be considered in any diabetic patient who has features inconsistent with their current diagnosis (unspecified neonatal diabetes, type 1 or type 2 diabetes) and clinical features of a specific subtype of monogenic diabetes (neonatal diabetes, familial diabetes, mild hyperglycaemia, syndromes). Guidance is given by clinical and physiological features in patient and family and the likelihood of the proposed mutation altering clinical care. In this article, I aimed to provide insight in the genes and mutations involved in insulin synthesis, secretion, and resistance, and to provide guidance for genetic testing by showing the clinical and physiological features and tests for each specified diagnosis as well as the opportunities for treatment. PMID:17186387

A formal theory of feature binding in object perception.

PubMed

Ashby, F G; Prinzmetal, W; Ivry, R; Maddox, W T

1996-01-01

Visual objects are perceived correctly only if their features are identified and then bound together. Illusory conjunctions result when feature identification is correct but an error occurs during feature binding. A new model is proposed that assumes feature binding errors occur because of uncertainty about the location of visual features. This model accounted for data from 2 new experiments better than a model derived from A. M. Treisman and H. Schmidt's (1982) feature integration theory. The traditional method for detecting the occurrence of true illusory conjunctions is shown to be fundamentally flawed. A reexamination of 2 previous studies provided new insights into the role of attention and location information in object perception and a reinterpretation of the deficits in patients who exhibit attentional disorders.

Sleep does not facilitate insight in older adults.

PubMed

Debarnot, Ursula; Rossi, Marta; Faraguna, Ugo; Schwartz, Sophie; Sebastiani, Laura

2017-04-01

Sleep has been shown to foster the process of insight generation in young adults during problem solving activities. Aging is characterized by substantial changes in sleep architecture altering memory consolidation. Whether sleep might promote the occurrence of insight in older adults as well has not yet been tested experimentally. To address this issue, we tested healthy young and old volunteers on an insight problem solving task, involving both explicit and implicit features, before and after a night of sleep or a comparable wakefulness period. Data showed that insight emerged significantly less frequently after a night of sleep in older adults compared to young. Moreover, there was no difference in the magnitude of insight occurrence following sleep and daytime -consolidation in aged participants. We further found that acquisition of implicit knowledge in the task before sleep potentiated the gain of insight in young participants, but this effect was not observed in aged participants. Overall, present findings demonstrate that a period of sleep does not significantly promote insight in problem solving in older adults. Copyright © 2017 Elsevier Inc. All rights reserved.

Geophysics of Martian Periglacial Processes

NASA Technical Reports Server (NTRS)

Mellon, Michael T.

2004-01-01

Through the examination of small-scale geologic features potentially related to water and ice in the martian subsurface (specifically small-scale polygonal ground and young gully-like features), determine the state, distribution and recent history of subsurface water and ice on Mars. To refine existing models and develop new models of near-surface water and ice, and develop new insights about the nature of water on Mars as manifested by these geologic features. Through an improved understanding of potentially water-related geologic features, utilize these features in addressing questions about where to best search for present day water and what space craft may encounter that might facilitate or inhibit the search for water.

Accurate diagnosis of thyroid follicular lesions from nuclear morphology using supervised learning.

PubMed

Ozolek, John A; Tosun, Akif Burak; Wang, Wei; Chen, Cheng; Kolouri, Soheil; Basu, Saurav; Huang, Hu; Rohde, Gustavo K

2014-07-01

Follicular lesions of the thyroid remain significant diagnostic challenges in surgical pathology and cytology. The diagnosis often requires considerable resources and ancillary tests including immunohistochemistry, molecular studies, and expert consultation. Visual analyses of nuclear morphological features, generally speaking, have not been helpful in distinguishing this group of lesions. Here we describe a method for distinguishing between follicular lesions of the thyroid based on nuclear morphology. The method utilizes an optimal transport-based linear embedding for segmented nuclei, together with an adaptation of existing classification methods. We show the method outputs assignments (classification results) which are near perfectly correlated with the clinical diagnosis of several lesion types' lesions utilizing a database of 94 patients in total. Experimental comparisons also show the new method can significantly outperform standard numerical feature-type methods in terms of agreement with the clinical diagnosis gold standard. In addition, the new method could potentially be used to derive insights into biologically meaningful nuclear morphology differences in these lesions. Our methods could be incorporated into a tool for pathologists to aid in distinguishing between follicular lesions of the thyroid. In addition, these results could potentially provide nuclear morphological correlates of biological behavior and reduce health care costs by decreasing histotechnician and pathologist time and obviating the need for ancillary testing. Copyright © 2014 Elsevier B.V. All rights reserved.

The 830--1120 A Spectrum of a Bright Comet: First Results on Hale-Bopp

NASA Astrophysics Data System (ADS)

Stern, S. Alan; Festou, Michel C.; Slater, David C.; Parker, Joel Wm.; A'Hearn, Michael F.

1998-09-01

The EUVS planetary sounding rocket spectrograph was flown on 29 March 1997 from White Sands, New Mexico to observe comet Hale-Bopp in the bandpass from 830--1120 Angstroms. At the time of launch the comet was near perihelion, 0.92 AU from the Sun, 1.34 AU from Earth, and traveling at a heliocentric radial velocity of +0.70 km/s. EUVS obtained its primary spectra of the comet at resolution near 3 Angstroms, collecting 9340 counts over approximately 330 seconds of integration time. To our knowledge, the resulting dataset is both the most sensitive and the highest spectral resolution probe of a comet in the UV below 1200 Angstroms yet achieved. The spectrum includes significant detections which we tentatively attribute to due to 834 Angstroms 0 II, the 1026 Angstroms H I Lyman beta /O I blend, and 989 Angstroms O I; we will also discuss evidence for Argon signatures, as well as two additional, yet to be identified features. We will describe the EUVS Hale-Bopp experiment and its results, including feature brightnesses, corresponding columns, and species abundance ratios in the inner coma. In addition to its value for providing insight into comets in general, and Hale-Bopp in particular, this spectrum is serving as an excellent input for New Millennium Deep Space 1/MICAS and Rosetta/ALICE UV observation planning below 1200 Angstroms.

Getting Under Mars' Skin: The InSight Mission to the Deep Interior of Mars

NASA Astrophysics Data System (ADS)

Banerdt, W. B.; Asmar, S.; Banfield, D. J.; Christensen, U. R.; Clinton, J. F.; Dehant, V. M. A.; Folkner, W. M.; Garcia, R.; Giardini, D.; Golombek, M. P.; Grott, M.; Hudson, T.; Johnson, C. L.; Kargl, G.; Knapmeyer-Endrun, B.; Kobayashi, N.; Lognonne, P. H.; Maki, J.; Mimoun, D.; Mocquet, A.; Morgan, P.; Panning, M. P.; Pike, W. T.; Spohn, T.; Tromp, J.; Weber, R. C.; Wieczorek, M. A.; Russell, C. T.

2015-12-01

The InSight mission to Mars will launch in March of 2016, landing six months later in Elysium Planitia. In contrast to the 43 previous missions to Mars, which have thoroughly explored its surface features and chemistry, atmosphere, and searched for past or present life, InSight will focus on the deep interior of the planet. InSight will investigate the fundamental processes of terrestrial planet formation and evolution by performing the first comprehensive surface-based geophysical measurements on Mars. It will provide key information on the composition and structure of an Earth-like planet that has gone through most of the evolutionary stages of the Earth up to plate tectonics. The planet Mars can play a key role in understanding early terrestrial planet formation and evolution. Unlike the Earth, its overall structure appears to be relatively unchanged since the first few hundred million years after formation; unlike the Moon, it is large enough that the P-T conditions within the planet span an appreciable fraction of the terrestrial planet range. Thus the large-scale chemical and structural evidence preserved in Mars' interior should tell us a great deal about the processes of planetary differentiation and heat transport. InSight will undertake this investigation using the "traditional" geophysical techniques of seismology, precision tracking (for rotational dynamics), and heat flow measurement. The predominant challenge, in addition to the technical problems of the remote installation and operation of instruments on a distant and harsh planetary surface, comes from the practical limitation of working with data acquired from a single station. We will discuss how we overcome these limitations through the application of single-station seismic analysis techniques, which take advantage of some of the specific attributes of Mars, and global heat flow modeling, which allows the interpretation of a single measurement of a spatially inhomogeneous surface distribution.

Multicentre validation of a sepsis prediction algorithm using only vital sign data in the emergency department, general ward and ICU

PubMed Central

Mao, Qingqing; Jay, Melissa; Calvert, Jacob; Barton, Christopher; Shimabukuro, David; Shieh, Lisa; Chettipally, Uli; Fletcher, Grant; Kerem, Yaniv; Zhou, Yifan; Das, Ritankar

2018-01-01

Objectives We validate a machine learning-based sepsis-prediction algorithm (InSight) for the detection and prediction of three sepsis-related gold standards, using only six vital signs. We evaluate robustness to missing data, customisation to site-specific data using transfer learning and generalisability to new settings. Design A machine-learning algorithm with gradient tree boosting. Features for prediction were created from combinations of six vital sign measurements and their changes over time. Setting A mixed-ward retrospective dataset from the University of California, San Francisco (UCSF) Medical Center (San Francisco, California, USA) as the primary source, an intensive care unit dataset from the Beth Israel Deaconess Medical Center (Boston, Massachusetts, USA) as a transfer-learning source and four additional institutions’ datasets to evaluate generalisability. Participants 684 443 total encounters, with 90 353 encounters from June 2011 to March 2016 at UCSF. Interventions None. Primary and secondary outcome measures Area under the receiver operating characteristic (AUROC) curve for detection and prediction of sepsis, severe sepsis and septic shock. Results For detection of sepsis and severe sepsis, InSight achieves an AUROC curve of 0.92 (95% CI 0.90 to 0.93) and 0.87 (95% CI 0.86 to 0.88), respectively. Four hours before onset, InSight predicts septic shock with an AUROC of 0.96 (95% CI 0.94 to 0.98) and severe sepsis with an AUROC of 0.85 (95% CI 0.79 to 0.91). Conclusions InSight outperforms existing sepsis scoring systems in identifying and predicting sepsis, severe sepsis and septic shock. This is the first sepsis screening system to exceed an AUROC of 0.90 using only vital sign inputs. InSight is robust to missing data, can be customised to novel hospital data using a small fraction of site data and retains strong discrimination across all institutions. PMID:29374661

Protein sequences insight into heavy metal tolerance in Cronobacter sakazakii BAA-894 encoded by plasmid pESA3.

PubMed

Chaturvedi, Navaneet; Kajsik, Michal; Forsythe, Stephen; Pandey, Paras Nath

2015-12-01

The recently annotated genome of the bacterium Cronobacter sakazakii BAA-894 suggests that the organism has the ability to bind heavy metals. This study demonstrates heavy metal tolerance in C. sakazakii, in which proteins with the heavy metal interaction were recognized by computational and experimental study. As the result, approximately one-fourth of proteins encoded on the plasmid pESA3 are proposed to have potential interaction with heavy metals. Interaction between heavy metals and predicted proteins was further corroborated using protein crystal structures from protein data bank database and comparison of metal-binding ligands. In addition, a phylogenetic study was undertaken for the toxic heavy metals, arsenic, cadmium, lead and mercury, which generated relatedness clustering for lead, cadmium and arsenic. Laboratory studies confirmed the organism's tolerance to tellurite, copper and silver. These experimental and computational study data extend our understanding of the genes encoding for proteins of this important neonatal pathogen and provide further insights into the genotypes associated with features that can contribute to its persistence in the environment. The information will be of value for future environmental protection from heavy toxic metals.

Plasticity-Driven Self-Organization under Topological Constraints Accounts for Non-random Features of Cortical Synaptic Wiring

PubMed Central

Miner, Daniel; Triesch, Jochen

2016-01-01

Understanding the structure and dynamics of cortical connectivity is vital to understanding cortical function. Experimental data strongly suggest that local recurrent connectivity in the cortex is significantly non-random, exhibiting, for example, above-chance bidirectionality and an overrepresentation of certain triangular motifs. Additional evidence suggests a significant distance dependency to connectivity over a local scale of a few hundred microns, and particular patterns of synaptic turnover dynamics, including a heavy-tailed distribution of synaptic efficacies, a power law distribution of synaptic lifetimes, and a tendency for stronger synapses to be more stable over time. Understanding how many of these non-random features simultaneously arise would provide valuable insights into the development and function of the cortex. While previous work has modeled some of the individual features of local cortical wiring, there is no model that begins to comprehensively account for all of them. We present a spiking network model of a rodent Layer 5 cortical slice which, via the interactions of a few simple biologically motivated intrinsic, synaptic, and structural plasticity mechanisms, qualitatively reproduces these non-random effects when combined with simple topological constraints. Our model suggests that mechanisms of self-organization arising from a small number of plasticity rules provide a parsimonious explanation for numerous experimentally observed non-random features of recurrent cortical wiring. Interestingly, similar mechanisms have been shown to endow recurrent networks with powerful learning abilities, suggesting that these mechanism are central to understanding both structure and function of cortical synaptic wiring. PMID:26866369

The Geomorphology of Comet Churymov-Gerasimenko As Revealed By Rosetta/Osiris: Implicationsfor Past Collisional Evolution

NASA Astrophysics Data System (ADS)

Marchi, S.; A'Hearn, M. F.; Barbieri, C.; Barucci, M. A.; Besse, S.; Cremonese, G.; Ip, W. H.; Keller, H. U.; Koschny, D.; Kuhrt, E.; Lamy, P. L.; Marzari, F.; Massironi, M.; Pajola, M.; Rickman, H.; Rodrigo, R.; Sierks, H.; Snodgrass, C.; Thomas, N.; Vincent, J. B.

2014-12-01

In this paper we present the major geomorphological features of comet Churymov-Gerasimenko (C-G), with emphasis on those that may have formed through collisional processes. The C-G nucleus has been imaged with the Rosetta/OSIRIS camera system at varying spatial resolution. At the moment of this writing the maximum spatial resolution achieved is ~20 meter per pixel, and it will improve to reach the unprecedented centimeter-scale in November 2014. This resolution should allow us to identify and characterize pits, lineaments and blocks that could be the result of collisional evolution. Indeed, C-G has spent some 1000 years on orbits crossing the main asteroid belt, and a much longer time in the outer solar system. Collisions may have, therefore, shaped the morphology of the nucleus in various ways. Previously imaged Jupiter Family Comets (e.g., Tempel 1) show significant numbers of pits and lineaments, some of which could be due to collisions. Additional proposed formation mechanisms are related to cometary activity processes, such as volatile outgassing.In addition to small scale features, the overall shape of C-G could also provide insights into the role of collisional processes. A striking feature is that C-G's shape is that of a contact binary. Similar shapes have been observed on rocky asteroids (e.g., Itokawa) and are generally interpreted as an indication of their rubble pile nature. A possibility is that C-G underwent similar processes, and therefore it may be constituted by reaccumulated fragments ejected from a larger precursor. An alternative view is that the current shape is the result of inhomogeneous outgassing activity, which may have dug a ~1-km deep trench responsible for the apparent contact binary shape.The role of the various proposed formation mechanisms (collisional vs outgassing) for both small scale and global features will be investigated and their implications for the evolution of C-G will be discussed.

Lava Eruption and Emplacement: Using Clues from Hawaii and Iceland to Probe the Lunar Past

NASA Technical Reports Server (NTRS)

Needham, Debra Hurwitz; Hamilton, C. W.; Bleacher, J. E.; Whelley, P. L.; Young, K. E.; Scheidt, S. P.; Richardson, J. A.; Sutton, S. S.

2017-01-01

Investigating recent eruptions on Earth is crucial to improving understanding of relationships between eruption dynamics and final lava flow morphologies. In this study, we investigated eruptions in Holuhraun, Iceland, and Kilauea, Hawaii to gain insight into the lava dynamics near the source vent, the initiation of lava channels, and the origin of down-channel features. Insights are applied to Rima Bode on the lunar nearside to deduce the sequence of events that formed this lunar sinuous rille system. These insights are crucial to correctly interpreting whether the volcanic features associated with Rima Bode directly relate to eruption conditions at the vent and, thus, can help us understand those eruption dynamics, or, alternatively, whether the features formed as a result of more localized influences on lava flow dynamics. For example, if the lava channel developed early in the eruption and was linked to pulses in vent activity, its morphology can be analyzed to interpret the flux and duration of the eruption. Conversely, if the lava channel initiated late in the eruption as the result of a catastrophic breaching of lava that had previously pooled within the vent [e.g., 1], then the final channel morphology will not indicate eruption dynamics but rather local dynamics associated with that breach event. Distinguishing between these two scenarios is crucial for correctly interpreting the intensity and duration of volcanic history on the Moon.

Lava Eruption and Emplacement: Using Clues from Hawaii and Iceland to Probe the Lunar Past

NASA Technical Reports Server (NTRS)

Needham, D. H.; Hamilton, C. W.; Bleacher, J. E.; Whelley, P. L.; Young, K. E.; Scheidt, S. P.; Richardson, J. A.; Sutton, S. S.

2017-01-01

Investigating recent eruptions on Earth is crucial to improving understanding of relationships between eruption dynamics and final lava flow morphologies. In this study, we investigated eruptions in Holuhraun, Iceland, and Kilauea, Hawaii to gain insight into the lava dynamics near the source vent, the initiation of lava channels, and the origin of down-channel features. Insights are applied to Rima Bode on the lunar nearside to deduce the sequence of events that formed this lunar sinuous rille system.These insights are crucial to correctly interpreting whether the volcanic features associated with Rima Bode directly relate to eruption conditions at the vent and, thus, can help us understand those eruption dynamics, or, alternatively, whether the features formed as a result of more localized influences on lava flow dynamics. For example, if the lava channel developed early in the eruption and was linked to pulses in vent activity, its morphology can be analyzed to interpret the flux and duration of the eruption. Conversely, if the lava channel initiated late in the eruption as the result of a catastrophic breaching of lava that had previously pooled within the vent [e.g., 1], then the final channel morphology will not indicate eruption dynamics but rather local dynamics associated with that breach event. Distinguishing between these two scenarios is crucial for correctly interpreting the intensity and duration of volcanic history on the Moon.

Getting To Know You: Profiles of Children's Authors Featured in "Language Arts" 1985-90.

ERIC Educational Resources Information Center

Kiefer, Barbara, Comp.

This book is a selection of profiles of children's authors featured in the journal "Language Arts" over the years. The book's 12 individual profiles highlight some of the real people who contribute to children's book publishing, provide a sample of a few of the many genres of books available for children, and give an insight into the…

Real-time quasi-3D tomographic reconstruction

NASA Astrophysics Data System (ADS)

Buurlage, Jan-Willem; Kohr, Holger; Palenstijn, Willem Jan; Joost Batenburg, K.

2018-06-01

Developments in acquisition technology and a growing need for time-resolved experiments pose great computational challenges in tomography. In addition, access to reconstructions in real time is a highly demanded feature but has so far been out of reach. We show that by exploiting the mathematical properties of filtered backprojection-type methods, having access to real-time reconstructions of arbitrarily oriented slices becomes feasible. Furthermore, we present , software for visualization and on-demand reconstruction of slices. A user of can interactively shift and rotate slices in a GUI, while the software updates the slice in real time. For certain use cases, the possibility to study arbitrarily oriented slices in real time directly from the measured data provides sufficient visual and quantitative insight. Two such applications are discussed in this article.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Z.; Gosser, Y; Baker, P

Cutinases are responsible for hydrolysis of the protective cutin lipid polyester matrix in plants and thus have been exploited for hydrolysis of small molecule esters and polyesters. Here we explore the reactivity, stability, and structure of Aspergillus oryzae cutinase and compare it to the well-studied enzyme from Fusarium solani. Two critical differences are highlighted in the crystallographic analysis of the A. oryzae structure: (i) an additional disulfide bond and (ii) a topologically favored catalytic triad with a continuous and deep groove. These structural features of A. oryzae cutinase are proposed to result in an improved hydrolytic activity and altered substratemore » specificity profile, enhanced thermostability, and remarkable reactivity toward the degradation of the synthetic polyester polycaprolactone. The results presented here provide insight into engineering new cutinase-inspired biocatalysts with tailor-made properties.« less

Genome-scale identification of Legionella pneumophila effectors using a machine learning approach.

PubMed

Burstein, David; Zusman, Tal; Degtyar, Elena; Viner, Ram; Segal, Gil; Pupko, Tal

2009-07-01

A large number of highly pathogenic bacteria utilize secretion systems to translocate effector proteins into host cells. Using these effectors, the bacteria subvert host cell processes during infection. Legionella pneumophila translocates effectors via the Icm/Dot type-IV secretion system and to date, approximately 100 effectors have been identified by various experimental and computational techniques. Effector identification is a critical first step towards the understanding of the pathogenesis system in L. pneumophila as well as in other bacterial pathogens. Here, we formulate the task of effector identification as a classification problem: each L. pneumophila open reading frame (ORF) was classified as either effector or not. We computationally defined a set of features that best distinguish effectors from non-effectors. These features cover a wide range of characteristics including taxonomical dispersion, regulatory data, genomic organization, similarity to eukaryotic proteomes and more. Machine learning algorithms utilizing these features were then applied to classify all the ORFs within the L. pneumophila genome. Using this approach we were able to predict and experimentally validate 40 new effectors, reaching a success rate of above 90%. Increasing the number of validated effectors to around 140, we were able to gain novel insights into their characteristics. Effectors were found to have low G+C content, supporting the hypothesis that a large number of effectors originate via horizontal gene transfer, probably from their protozoan host. In addition, effectors were found to cluster in specific genomic regions. Finally, we were able to provide a novel description of the C-terminal translocation signal required for effector translocation by the Icm/Dot secretion system. To conclude, we have discovered 40 novel L. pneumophila effectors, predicted over a hundred additional highly probable effectors, and shown the applicability of machine learning algorithms for the identification and characterization of bacterial pathogenesis determinants.

New insights into the geodiversity of the southeast Indian Ocean seafloor revealed by Malaysia Airlines flight MH370 search data

NASA Astrophysics Data System (ADS)

Picard, K.; Brooke, B. B.; Harris, P. T.; Siwabessy, J. P. W.; Coffin, M. F.; Tran, M.; Spinoccia, M.; Weales, J.; Macmillan-Lawler, M.; Sullivan, J.

2017-12-01

A large multibeam echo sounder (MBES) dataset (710, 000 km2, inclusive of transit data) was acquired in the SE Indian Ocean to assist the search for Malaysia Airlines Flight 370 (MH370). Here, we present the results of a geomorphic analysis of this new data and compare with the Global Seafloor Geomorphic Features Map (GSFM) that is based on coarser resolution satellite-derived bathymetry data. The analyses show that abyssal plains and basins are significantly more rugged than their representation in the GSFM, with a 20% increase in the extent of hills and mountains. The new model also reveals four times more seamounts than presented in the GSFM, suggesting a greater number of these features than previously estimated for the broader region and indeed globally. This is important considering the potential ecological significance of these high-relief structures. Analyses of the new data also enabled knolls, fans, valleys, canyons, troughs and holes to be identified, doubling the number of discrete features mapped and revealing the true geodiversity of the deep ocean in this area. This high-resolution mapping of the seafloor also provides new insights into the geological evolution of the region, both in terms of structural, tectonic, and sedimentary processes. For example, sub-parallel ridges extend over approximately 20% of the area mapped and their form and alignment provide valuable insight into Southeast Indian Ridge seafloor spreading processes. Rifting is recorded along the Broken Ridge - Diamantina Escarpment, with rift blocks and well-bedded sedimentary bedrock exposures discernible down to 2,400 m water depth. Ocean floor sedimentary processes are represented in sediment mass transport features, especially along and north of Broken Ridge, and pockmarks (the finest-scale features mapped) south of Diamantina Trench. The new MBES data highlight the complexity of the search area and serve to demonstrate how little we know about the 85-90% of the ocean floor that has not been mapped with this technology. The availability of high-resolution and accurate maps of the ocean floor can clearly provide new insights into the Earth's geological evolution, modern ocean floor processes, and the location of sites that are likely to have relatively high biodiversity.

Correlates of insight into different symptom dimensions in obsessive-compulsive disorder.

PubMed

Fontenelle, Jùlia M; Harrison, Ben J; Santana, Lívia; Conceição do Rosário, Maria; Versiani, Marcio; Fontenelle, Leonardo F

2013-02-01

In this study, we evaluated insight into different obsessive-compulsive disorder (OCD) symptom dimensions and their impact on clinical and sociodemographic features of patients with OCD. Sixty OCD patients were assessed with the Brown Assessment of Beliefs Scale (BABS), the Dimensional Yale-Brown Obsessive-Compulsive Scale-Short Version, the Beck Depression Inventory, and the Sheehan Disability Scale. Two methods of using BABS were employed: 1) a traditional approach, which considers a composite of the insight into existing OCD symptoms, and 2) an alternative approach, which includes assessments of insight into each OCD symptom dimension separately. Composite BABS scores correlated with global severity of OCD and depressive symptoms, and degree of interference on social life/leisure activities and family life/home responsibilities. Dimension-specific correlations between severity of symptoms and insight ranged from very high (P = .87, for hoarding) to moderate (P = .61, for miscellaneous symptoms). Greater severity of depression and concomitant generalized anxiety disorder were independently associated with lower levels of insight into aggressive/checking symptoms. While earlier-onset OCD was associated with lower insight into sexual/religious and symmetry symptoms, later-onset OCD displayed lower insight into hoarding. Assessing insight into dimension-specific OCD symptoms may challenge the existence of clear-cut OCD with fair or poor insight.

The yeast Golgi apparatus: insights and mysteries

PubMed Central

Papanikou, Effrosyni; Glick, Benjamin S.

2009-01-01

The Golgi apparatus is known to modify and sort newly synthesized secretory proteins. However, fundamental mysteries remain about the structure, operation, and dynamics of this organelle. Important insights have emerged from studying the Golgi in yeasts. For example, yeasts have provided direct evidence for Golgi cisternal maturation, a mechanism that is likely to be broadly conserved. Here, we highlight features of the yeast Golgi as well as challenges that lie ahead. PMID:19879270

Strategic Insights. Volume 10, Issue 3, Winter 2011

DTIC Science & Technology

2011-01-01

The cover on this edition of Strategic Insights features the NATO sigil overlaid with Leonardo da Vinci’s Vitruvian Man. The original Vitruvian...Man was designed by the Roman architect Vitruvius in an attempt to define artistic proportions for the human body. Da Vinci made adjustments to...Vitruvius’s proportions, making them more accurate. Specifically, da Vinci realized that the circle and square that outline the limits of the man’s limbs

Insights into multimodal imaging classification of ADHD

PubMed Central

Colby, John B.; Rudie, Jeffrey D.; Brown, Jesse A.; Douglas, Pamela K.; Cohen, Mark S.; Shehzad, Zarrar

2012-01-01

Attention deficit hyperactivity disorder (ADHD) currently is diagnosed in children by clinicians via subjective ADHD-specific behavioral instruments and by reports from the parents and teachers. Considering its high prevalence and large economic and societal costs, a quantitative tool that aids in diagnosis by characterizing underlying neurobiology would be extremely valuable. This provided motivation for the ADHD-200 machine learning (ML) competition, a multisite collaborative effort to investigate imaging classifiers for ADHD. Here we present our ML approach, which used structural and functional magnetic resonance imaging data, combined with demographic information, to predict diagnostic status of individuals with ADHD from typically developing (TD) children across eight different research sites. Structural features included quantitative metrics from 113 cortical and non-cortical regions. Functional features included Pearson correlation functional connectivity matrices, nodal and global graph theoretical measures, nodal power spectra, voxelwise global connectivity, and voxelwise regional homogeneity. We performed feature ranking for each site and modality using the multiple support vector machine recursive feature elimination (SVM-RFE) algorithm, and feature subset selection by optimizing the expected generalization performance of a radial basis function kernel SVM (RBF-SVM) trained across a range of the top features. Site-specific RBF-SVMs using these optimal feature sets from each imaging modality were used to predict the class labels of an independent hold-out test set. A voting approach was used to combine these multiple predictions and assign final class labels. With this methodology we were able to predict diagnosis of ADHD with 55% accuracy (versus a 39% chance level in this sample), 33% sensitivity, and 80% specificity. This approach also allowed us to evaluate predictive structural and functional features giving insight into abnormal brain circuitry in ADHD. PMID:22912605

Dystonia.

PubMed

Morgante, Francesca; Klein, Christine

2013-10-01

The purpose of this review is to provide an update on the classification, phenomenology, pathophysiology, and treatment of dystonia. A revised definition based on the main phenomenologic features of dystonia has recently been developed in an expert consensus approach. Classification is based on two main axes: clinical features and etiology. Currently, genes have been reported for 14 types of monogenic isolated and combined dystonia. Isolated dystonia (with dystonic tremor) can be caused by mutations in TOR1A (DYT1), TUBB4 (DYT4), THAP1 (DYT6), PRKRA (DYT16), CIZ1 (DYT23), ANO3 (DYT24), and GNAL (DYT25). Combined dystonias (with parkinsonism or myoclonus) are further subdivided into persistent (GCHI [DYT5], SGCE [DYT11], and ATP1A3 [DYT12], with TAF1 most likely but not yet proven to be linked to DYT3) and paroxysmal (PNKD [DYT8], PRRT2 [DYT10], and SLC2A1 [DYT18]). Recent insights from neurophysiologic studies identified functional abnormalities in two networks in dystonia: the basal ganglia-sensorimotor network and, more recently, the cerebellothalamocortical pathway. Besides the well-known lack of inhibition at different CNS levels, dystonia is specifically characterized by maladaptive plasticity in the sensorimotor cortex and loss of cortical surround inhibition. The exact role (modulatory or compensatory) of the cerebellar-cortical pathways still has to be further elucidated. In addition to botulinum toxin for focal forms, deep brain stimulation of the globus pallidus internus is increasingly recognized as an effective treatment for generalized and segmental dystonia. The revised classification and identification of new genes for different forms of dystonia, including adult-onset segmental dystonia, enable an improved diagnostic approach. Recent pathophysiologic insights have fundamentally contributed to a better understanding of the disease mechanisms and impact on treatment, such as functional neurosurgery and nonpharmacologic treatment options.

Effects of antipsychotic drugs on insight in schizophrenia.

PubMed

Bianchini, Oriana; Porcelli, Stefano; Nespeca, Claudia; Cannavò, Dario; Trappoli, Angela; Aguglia, Eugenio; De Ronchi, Diana; Serretti, Alessandro

2014-08-15

Lack of insight is predominant in schizophrenia though the causes are still unclear. The present study was carried on to investigate the effect of three Second Generation Antipsychotics (SGAs) and Haloperidol on insight and the associations among different clusters of symptoms and insight. Fifty-five patients have been recruited at the moment of pharmacological switch needed for psychotic exacerbation, from other antipsychotic drugs to Olanzapine, Aripiprazole, Ziprasidone and Haloperidol. Patients have been followed for 6 months and evaluated at baseline, after 3 months and after 6 months. Regarding the insight improvement, all SGAs resulted more effective than Haloperidol, while no difference was detected among different SGAs. Concerning psychopathology, all SGAs showed a better efficacy than Haloperidol, positive symptoms apart. All SGAs showed a similar efficacy on all domains, except for negative symptoms which resulted less responsive to ziprasidone and haloperidol. An association between improvement of insight and psychopathology was detected. Furthermore, insight appears to be related to psychopathology severity, particularly to negative symptoms. However, the observed different effectiveness of Ziprasidone on negative symptoms and insight suggests that these psychopathological features may be not strictly related and, thus, they may be sustained by different psychopathological processes. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

[Insight in schizophrenia: relationship to family history, and positive and negative symptoms].

PubMed

Danki, Demet; Dilbaz, Nesrin; Okay, Ihsan Tuncer; Telci, Sükran

2007-01-01

To determine the level of insight among patients with schizophrenia and to compare sociodemographic and clinical features. The study included 66 patients with schizophrenia based on DSM-IV criteria. A semi-structured sociodemographic instrument, the Positive and Negative Syndrome Scale (PANSS), and the Schedule for Assessing the Three Components of Insight (SATCI) were used for the study. Family history was significantly related to low-level insight in schizophrenic patients. Positive symptom scores in patients with a family history of schizophrenia were significantly higher than in patients without such a family history. Positive and general psychopathological symptoms were inversely related to level of insight in patients with schizophrenia. There was no significant relationship between the negative symptoms scores and level of insight. Family history of schizophrenia in schizophrenic patients was significantly related to low-level insight. Insight in the schizophrenic patients was affected by biological, psychological, and psychosociological factors. Family history of schizophrenia was one of these factors, which may affect the level of insight in numerous ways. Studies of patient family position and its relationship to insight have generally explored the effects of family situation on schizophrenia and insight, but not family history and its relationship to insight. In this study positive symptom severity was higher in patients with a family history of schizophrenia than in those without such a history. There was a positive relationship between low-level insight and both high positive and general psychopathology symptom levels in patients with schizophrenia.

The effects of aging on insight into illness in schizophrenia: a review†

PubMed Central

Gerretsen, Philip; Plitman, Eric; Rajji, Tarek K.; Graff-Guerrero, Ariel

2015-01-01

Objectives Impaired insight into illness is a prevalent feature of schizophrenia, which negatively influences treatment adherence and clinical outcomes. Little is known about the effects of aging on insight impairment. We aimed to review the available research literature on the effects of aging on insight into illness in schizophrenia, in relation to positive, negative, and cognitive symptoms. Ultimately, we propose a trajectory of insight in schizophrenia across the lifespan. Method A systematic Medline® literature search was conducted, searching for English language studies describing the relationship of insight into illness in schizophrenia with aging. Results We identified 62 studies. Insight impairment is associated with illness severity, premorbid intellectual function (i.e. IQ), executive function, and memory. Insight impairment improves modestly during midlife, worsening again in late life. It tends to fluctuate with each episode of psychosis, likely in relation to worsening positive symptoms that improve with antipsychotic treatment. The relationship between insight impairment and cognitive dysfunction appears to attenuate with age, while the relationship with lower premorbid intellectual function is preserved. The association between impaired insight and negative symptoms is unclear. Conclusions The available literature suggests that the course of insight impairment follows a U-shaped curve, where insight impairment is severe during the first episode of psychosis, modestly improves over midlife, and declines again in late life. Future studies are required to investigate the trajectory of insight into illness and its core domains across the lifespan from prodromal phase to late life. PMID:25055980

Insight in schizophrenia: from conceptualization to neuroscience.

PubMed

Ouzir, Mounir; Azorin, Jean Michel; Adida, Marc; Boussaoud, Driss; Battas, Omar

2012-04-01

Lack of insight into illness is a prevalent and distinguishing feature of schizophrenia, which has a complex history and has been given a variety of definitions. Currently, insight is measured and treated as a multidimensional phenomenon, because it is believed to result from psychological, neuropsychological and organic factors. Thus, schizophrenia patients may display dramatic disorders including demoralization, depression and a higher risk of suicide, all of which are directly or indirectly related to a lack of insight into their illness, and make the treatment difficult. To improve the treatment of people with schizophrenia, it is thus crucial to advance research on insight into their illness. Insight is studied in a variety of ways. Studies may focus on the relationship between insight and psychopathology, may view behavioral outcomes or look discretely at the cognitive dysfunction versus anatomy level of insight. All have merit but they are dispersed across a wide body of literature and rarely are the findings integrated and synthesized in a meaningful way. The aim of this study was to synthesize findings across the large body of literature dealing with insight, to highlight its multidimensional nature, measurement, neuropsychology and social impact in schizophrenia. The extensive literature on the cognitive consequences of lack of insight and the contribution of neuroimaging techniques to elucidating neurological etiology of insight deficits, is also reviewed. © 2012 The Authors. Psychiatry and Clinical Neurosciences © 2012 Japanese Society of Psychiatry and Neurology.

Monochromatic Measurements of the JPSS-1 VIIRS Polarization Sensitivity

NASA Technical Reports Server (NTRS)

McIntire, Jeff; Moyer, David; Brown, Steven W.; Lykke, Keith R.; Waluschka, Eugene; Oudrari, Hassan; Xiong, Xiaoxiong

2016-01-01

Polarization sensitivity is a critical property that must be characterized for spaceborne remote sensing instruments designed to measure reflected solar radiation. Broadband testing of the first Joint Polar-orbiting Satellite System (JPSS-1) Visible Infrared Imaging Radiometer Suite (VIIRS) showed unexpectedly large polarization sensitivities for the bluest bands on VIIRS (centered between 400 and 600 nm). Subsequent ray trace modeling indicated that large diattenuation on the edges of the bandpass for these spectral bands was the driver behind these large sensitivities. Additional testing using the National Institute of Standards and Technologies Traveling Spectral Irradiance and Radiance Responsivity Calibrations Using Uniform Sources was added to the test program to verify and enhance the model. The testing was limited in scope to two spectral bands at two scan angles; nonetheless, this additional testing provided valuable insight into the polarization sensitivity. Analysis has shown that the derived diattenuation agreed with the broadband measurements to within an absolute difference of about0.4 and that the ray trace model reproduced the general features of the measured data. Additionally, by deriving the spectral responsivity, the linear diattenuation is shown to be explicitly dependent on the changes in bandwidth with polarization state.

Nebular Phase Observations of the Type Ia Supernova 2014J in the Near Infrared

NASA Astrophysics Data System (ADS)

Diamond, Tiara

2018-01-01

Late-time spectra of SNe Ia show numerous strong emission features of iron and cobalt throughout the near infrared region. As the spectrum ages, the cobalt features fade as is expected from the decay of 56Co to 56Fe. The strong 1.6440 μm [Fe II] feature is sensitive to the central density of the white dwarf just prior to the runaway because of electron capture in the early stages of burning, hence the line profile width and evolution can be used to probe possible progenitor scenarios. The line profile is dependent on the extent of mixing during any deflagration burning in addition to asymmetries in the distribution of burning products or an off-center ignition. We present observations of SN 2014J from 300–500 days post-explosion. The data are consistent with spherical models of a MCh explosion with a deflagration-to-detonation transition, central density of 0.7×109 g/cm3, and limited mixing. An asymmetry in the line profile of the last spectrum could indicate an off-center ignition or burning products that are not centered on the kinetic center of the explosion. These and other late-time spectroscopic observations in the infrared of a significant sample of SNe Ia will provide insight into the natural variety of these objects, improving our understanding of the underlying physical processes and their usability in cosmology.

Martian Impact Craters as Revealed by MGS and Odyssey

NASA Technical Reports Server (NTRS)

Barlow, N. G.

2005-01-01

A variety of ejecta and interior morphologies were revealed for martian impact craters by Viking imagery. Numerous studies have classified these ejecta and interior morphologies and looked at how these morphologies correlate with crater diameter, latitude, terrain, and elevation [1, 2, 3, 4]. Many of these features, particularly the layered (fluidized) ejecta morphologies and central pits, have been proposed to result when the crater formed in target material containing high concentrations of volatiles. The Catalog of Large Martian Impact Craters was originally derived from the Viking 1:2,000,000 photomosaics and contains information on 42,283 impact craters 5-km diameter distributed across the entire martian surface. The information in this Catalog has been used to study the distributions of craters displaying specific ejecta and interior morphologies in an attempt to understand the environmental conditions which give rise to these features and to estimate the areal and vertical extents of subsurface volatile reservoirs [4, 5]. The Catalog is currently undergoing revision utilizing Mars Global Surveyor (MGS) and Mars Odyssey data [6]. The higher resolution multispectral imagery is resulting in numerous revisions to the original classifications and the addition of new elemental, thermophysical, and topographic data is allowing new insights into the environmental conditions under which these features form. A few of the new results from analysis of data in the revised Catalog are discussed below.

An Analysis of a Digital Variant of the Trail Making Test Using Machine Learning Techniques

PubMed Central

Dahmen, Jessamyn; Cook, Diane; Fellows, Robert; Schmitter-Edgecombe, Maureen

2017-01-01

BACKGROUND The goal of this work is to develop a digital version of a standard cognitive assessment, the Trail Making Test (TMT), and assess its utility. OBJECTIVE This paper introduces a novel digital version of the TMT and introduces a machine learning based approach to assess its capabilities. METHODS Using digital Trail Making Test (dTMT) data collected from (N=54) older adult participants as feature sets, we use machine learning techniques to analyze the utility of the dTMT and evaluate the insights provided by the digital features. RESULTS Predicted TMT scores correlate well with clinical digital test scores (r=0.98) and paper time to completion scores (r=0.65). Predicted TICS exhibited a small correlation with clinically-derived TICS scores (r=0.12 Part A, r=0.10 Part B). Predicted FAB scores exhibited a small correlation with clinically-derived FAB scores (r=0.13 Part A, r=0.29 for Part B). Digitally-derived features were also used to predict diagnosis (AUC of 0.65). CONCLUSION Our findings indicate that the dTMT is capable of measuring the same aspects of cognition as the paper-based TMT. Furthermore, the dTMT’s additional data may be able to help monitor other cognitive processes not captured by the paper-based TMT alone. PMID:27886019

Neural mechanisms of rhythm perception: current findings and future perspectives.

PubMed

Grahn, Jessica A

2012-10-01

Perception of temporal patterns is fundamental to normal hearing, speech, motor control, and music. Certain types of pattern understanding are unique to humans, such as musical rhythm. Although human responses to musical rhythm are universal, there is much we do not understand about how rhythm is processed in the brain. Here, I consider findings from research into basic timing mechanisms and models through to the neuroscience of rhythm and meter. A network of neural areas, including motor regions, is regularly implicated in basic timing as well as processing of musical rhythm. However, fractionating the specific roles of individual areas in this network has remained a challenge. Distinctions in activity patterns appear between "automatic" and "cognitively controlled" timing processes, but the perception of musical rhythm requires features of both automatic and controlled processes. In addition, many experimental manipulations rely on participants directing their attention toward or away from certain stimulus features, and measuring corresponding differences in neural activity. Many temporal features, however, are implicitly processed whether attended to or not, making it difficult to create controlled baseline conditions for experimental comparisons. The variety of stimuli, paradigms, and definitions can further complicate comparisons across domains or methodologies. Despite these challenges, the high level of interest and multitude of methodological approaches from different cognitive domains (including music, language, and motor learning) have yielded new insights and hold promise for future progress. Copyright © 2012 Cognitive Science Society, Inc.

Insight and suicidality in first-episode psychosis: understanding the influence of suicidal history on insight dimensions at first presentation.

PubMed

López-Moríñigo, Javier D; Wiffen, Benjamin; O'Connor, Jennifer; Dutta, Rina; Di Forti, Marta; Murray, Robin M; David, Anthony S

2014-05-01

Lack of insight is a cardinal feature of psychosis with crucial implications for outcome. Concerns have been raised regarding a link between insight and suicidality. This study aimed to test the relationship between suicidal behaviour preceding first-episode psychosis (FEP) and insight dimensions at treatment onset. A total of 112 FEP inpatients were recruited. Suicidal events prior to admission were recorded. Insight was assessed multidimensionally with the Schedule for the Assessment of Insight - Expanded version shortly after admission. Suicidal and non-suicidal patients were compared regarding scores on 'total insight' and three insight domains: 'awareness of mental illness', 'relabeling of psychotic experiences as abnormal' and 'compliance'. This analysis was also adjusted for a set of sociodemographic, clinical, neurocognitive and psychopathological variables. Bivariate analyses demonstrated a direct association between previous suicidality and all insight domains. However, these associations did not survive multivariable regression models, which demonstrated gender (female), shorter duration of untreated psychosis (DUP) and psychopathological symptoms - depression and disorganization - to mediate the influence of suicidal history on insight, and therefore to underlie the latter. Insight dimensions in FEP patients are influenced by having suicidal antecedents through some mediating variables such as gender, DUP and depression. Further prospective studies are needed to clarify the potential implications of these findings on the management of insight in FEP. As suicidal history is associated with greater levels of both depression and insight at first presentation, these three variables might be useful in predicting further suicidal events. © 2013 Wiley Publishing Asia Pty Ltd.

The Development of New Composite Metrics for the Comprehensive Analytic and Visual Assessment of Hypoglycemia Using the Hypo-Triad.

PubMed

Thomas, Andreas; Shin, John; Jiang, Boyi; McMahon, Chantal; Kolassa, Ralf; Vigersky, Robert A

2018-01-01

Quantifying hypoglycemia has traditionally been limited to using the frequency of hypoglycemic events during a given time interval using data from blood glucose (BG) testing. However, continuous glucose monitoring (CGM) captures three parameters-a Hypo-Triad-unavailable with BG monitoring that can be used to better characterize hypoglycemia: area under the curve (AUC), time (duration of hypoglycemia), and frequency of daily episodes below a specified threshold. We developed two new analytic metrics to enhance the traditional Hypo-Triad of CGM-derived data to more effectively capture the intensity of hypoglycemia (IntHypo) and overall hypoglycemic environment called the "hypoglycemia risk volume" (HypoRV). We reanalyzed the CGM data from the ASPIRE In-Home study, a randomized, controlled trial of a sensor-integrated pump system with a low glucose threshold suspend feature (SIP+TS), using these new metrics and compared them to standard metrics of hypoglycemia. IntHypo and HypoRV provide additional insights into the benefit of a SIP+TS system on glycemic exposure when compared to the standard reporting methods. In addition, the visual display of these parameters provides a unique and intuitive way to understand the impact of a diabetes intervention on a cohort of subjects as well as on individual patients. The IntHypo and HypoRV are new and enhanced ways of analyzing CGM-derived data in diabetes intervention studies which could lead to new insights in diabetes management. They require validation using existing, ongoing, or planned studies to determine whether they are superior to existing metrics.

OBSESSIVE–COMPULSIVE DISORDER: A REVIEW OF THE DIAGNOSTIC CRITERIA AND POSSIBLE SUBTYPES AND DIMENSIONAL SPECIFIERS FOR DSM-V

PubMed Central

Leckman, James F.; Denys, Damiaan; Simpson, H. Blair; Mataix-Cols, David; Hollander, Eric; Saxena, Sanjaya; Miguel, Euripedes C.; Rauch, Scott L.; Goodman, Wayne K.; Phillips, Katharine A.; Stein, Dan J.

2014-01-01

Background Since the publication of the DSM-IV in 1994, research on obsessive–compulsive disorder (OCD) has continued to expand. It is timely to reconsider the nosology of this disorder, assessing whether changes to diagnostic criteria as well as subtypes and specifiers may improve diagnostic validity and clinical utility. Methods The existing criteria were evaluated. Key issues were identified. Electronic databases of PubMed, ScienceDirect, and PsycINFO were searched for relevant studies. Results This review presents a number of options and preliminary recommendations to be considered for DSM-V. These include: (1) clarifying and simplifying the definition of obsessions and compulsions(criterion A); (2) possibly deleting the requirement that people recognize that their obsessions or compulsions are excessive or unreasonable (criterion B); (3) rethinking the clinical significance criterion (criterion C) and, in the interim, possibly adjusting what is considered “time-consuming” for OCD; (4) listing additional disorders to help with the differential diagnosis (criterion D); (5) rethinking the medical exclusion criterion (criterion E) and clarifying what is meant by a “general medical condition”; (6) revising the specifiers (i.e., clarifying that OCD can involve a range of insight, in addition to “poor insight,” and adding “tic-related OCD”); and (7) highlighting in the DSM-V text important clinical features of OCD that are not currently mentioned in the criteria (e.g., the major symptom dimensions). Conclusions A number of changes to the existing diagnostic criteria for OCD are proposed. These proposed criteria may change as the DSM-V process progresses. PMID:20217853

Obsessive-compulsive disorder: a review of the diagnostic criteria and possible subtypes and dimensional specifiers for DSM-V.

PubMed

Leckman, James F; Denys, Damiaan; Simpson, H Blair; Mataix-Cols, David; Hollander, Eric; Saxena, Sanjaya; Miguel, Euripedes C; Rauch, Scott L; Goodman, Wayne K; Phillips, Katharine A; Stein, Dan J

2010-06-01

Since the publication of the DSM-IV in 1994, research on obsessive-compulsive disorder (OCD) has continued to expand. It is timely to reconsider the nosology of this disorder, assessing whether changes to diagnostic criteria as well as subtypes and specifiers may improve diagnostic validity and clinical utility. The existing criteria were evaluated. Key issues were identified. Electronic databases of PubMed, ScienceDirect, and PsycINFO were searched for relevant studies. This review presents a number of options and preliminary recommendations to be considered for DSM-V. These include: (1) clarifying and simplifying the definition of obsessions and compulsions (criterion A); (2) possibly deleting the requirement that people recognize that their obsessions or compulsions are excessive or unreasonable (criterion B); (3) rethinking the clinical significance criterion (criterion C) and, in the interim, possibly adjusting what is considered "time-consuming" for OCD; (4) listing additional disorders to help with the differential diagnosis (criterion D); (5) rethinking the medical exclusion criterion (criterion E) and clarifying what is meant by a "general medical condition"; (6) revising the specifiers (i.e., clarifying that OCD can involve a range of insight, in addition to "poor insight," and adding "tic-related OCD"); and (7) highlighting in the DSM-V text important clinical features of OCD that are not currently mentioned in the criteria (e.g., the major symptom dimensions). A number of changes to the existing diagnostic criteria for OCD are proposed. These proposed criteria may change as the DSM-V process progresses. (c) 2010 Wiley-Liss, Inc.

Decision theory for computing variable and value ordering decisions for scheduling problems

NASA Technical Reports Server (NTRS)

Linden, Theodore A.

1993-01-01

Heuristics that guide search are critical when solving large planning and scheduling problems, but most variable and value ordering heuristics are sensitive to only one feature of the search state. One wants to combine evidence from all features of the search state into a subjective probability that a value choice is best, but there has been no solid semantics for merging evidence when it is conceived in these terms. Instead, variable and value ordering decisions should be viewed as problems in decision theory. This led to two key insights: (1) The fundamental concept that allows heuristic evidence to be merged is the net incremental utility that will be achieved by assigning a value to a variable. Probability distributions about net incremental utility can merge evidence from the utility function, binary constraints, resource constraints, and other problem features. The subjective probability that a value is the best choice is then derived from probability distributions about net incremental utility. (2) The methods used for rumor control in Bayesian Networks are the primary way to prevent cycling in the computation of probable net incremental utility. These insights lead to semantically justifiable ways to compute heuristic variable and value ordering decisions that merge evidence from all available features of the search state.

A mass action model of a Fibroblast Growth Factor signaling pathway and its simplification.

PubMed

Gaffney, E A; Heath, J K; Kwiatkowska, M Z

2008-11-01

We consider a kinetic law of mass action model for Fibroblast Growth Factor (FGF) signaling, focusing on the induction of the RAS-MAP kinase pathway via GRB2 binding. Our biologically simple model suffers a combinatorial explosion in the number of differential equations required to simulate the system. In addition to numerically solving the full model, we show that it can be accurately simplified. This requires combining matched asymptotics, the quasi-steady state hypothesis, and the fact subsets of the equations decouple asymptotically. Both the full and simplified models reproduce the qualitative dynamics observed experimentally and in previous stochastic models. The simplified model also elucidates both the qualitative features of GRB2 binding and the complex relationship between SHP2 levels, the rate SHP2 induces dephosphorylation and levels of bound GRB2. In addition to providing insight into the important and redundant features of FGF signaling, such work further highlights the usefulness of numerous simplification techniques in the study of mass action models of signal transduction, as also illustrated recently by Borisov and co-workers (Borisov et al. in Biophys. J. 89, 951-966, 2005, Biosystems 83, 152-166, 2006; Kiyatkin et al. in J. Biol. Chem. 281, 19925-19938, 2006). These developments will facilitate the construction of tractable models of FGF signaling, incorporating further biological realism, such as spatial effects or realistic binding stoichiometries, despite a more severe combinatorial explosion associated with the latter.

Routing and Scheduling Algorithms for WirelessHART Networks: A Survey

PubMed Central

Nobre, Marcelo; Silva, Ivanovitch; Guedes, Luiz Affonso

2015-01-01

Wireless communication is a trend nowadays for the industrial environment. A number of different technologies have emerged as solutions satisfying strict industrial requirements (e.g., WirelessHART, ISA100.11a, WIA-PA). As the industrial environment presents a vast range of applications, adopting an adequate solution for each case is vital to obtain good performance of the system. In this context, the routing and scheduling schemes associated with these technologies have a direct impact on important features, like latency and energy consumption. This situation has led to the development of a vast number of routing and scheduling schemes. In the present paper, we focus on the WirelessHART technology, emphasizing its most important routing and scheduling aspects in order to guide both end users and the developers of new algorithms. Furthermore, we provide a detailed literature review of the newest routing and scheduling techniques for WirelessHART, discussing each of their features. These routing algorithms have been evaluated in terms of their objectives, metrics, the usage of the WirelessHART structures and validation method. In addition, the scheduling algorithms were also evaluated by metrics, validation, objectives and, in addition, by multiple superframe support, as well as by the redundancy method used. Moreover, this paper briefly presents some insights into the main WirelessHART simulation modules available, in order to provide viable test platforms for the routing and scheduling algorithms. Finally, some open issues in WirelessHART routing and scheduling algorithms are discussed. PMID:25919371

Mathematical models of ABE fermentation: review and analysis.

PubMed

Mayank, Rahul; Ranjan, Amrita; Moholkar, Vijayanand S

2013-12-01

Among different liquid biofuels that have emerged in the recent past, biobutanol produced via fermentation processes is of special interest due to very similar properties to that of gasoline. For an effective design, scale-up, and optimization of the acetone-butanol-ethanol (ABE) fermentation process, it is necessary to have insight into the micro- and macro-mechanisms of the process. The mathematical models for ABE fermentation are efficient tools for this purpose, which have evolved from simple stoichiometric fermentation equations in the 1980s to the recent sophisticated and elaborate kinetic models based on metabolic pathways. In this article, we have reviewed the literature published in the area of mathematical modeling of the ABE fermentation. We have tried to present an analysis of these models in terms of their potency in describing the overall physiology of the process, design features, mode of operation along with comparison and validation with experimental results. In addition, we have also highlighted important facets of these models such as metabolic pathways, basic kinetics of different metabolites, biomass growth, inhibition modeling and other additional features such as cell retention and immobilized cultures. Our review also covers the mathematical modeling of the downstream processing of ABE fermentation, i.e. recovery and purification of solvents through flash distillation, liquid-liquid extraction, and pervaporation. We believe that this review will be a useful source of information and analysis on mathematical models for ABE fermentation for both the appropriate scientific and engineering communities.

Headaches caused by decreased intracranial pressure: diagnosis and management.

PubMed

Mokri, Bahram

2003-06-01

More patients with spontaneous intracranial hypotension are now being diagnosed, and it is realized that most cases result from spontaneous cerebrospinal fluid leaks. A broader clinical and imaging spectrum of the disorder is recognized. This paper reviews new insights into the variability of clinical manifestations, imaging features, etiological factors, anatomy of leaks, and implications of these in patient management. Spontaneous intracranial hypotension should not be equated with post-lumbar puncture headaches. In a substantial minority of patients, headaches are not orthostatic and may mimic other types of headache. Additional diverse neurological manifestations may dominate the clinical picture and patients may occasionally have no headache at all. Reports on unusual presentations of the disorder continue to appear in the literature. Furthermore, additional imaging features of cerebrospinal fluid leaks are recognized. High-flow and slow-flow leaks may present diagnostic challenges, and require modification of diagnostic studies aimed at locating the site of the leak. Stigmata of connective tissue abnormality, especially abnormalities of fibrillin and elastin, are seen in a notable minority of patients, pointing to weakness of the dural sac as one of the etiological factors. After treatment of spontaneous intracranial hypotension, surgically or by epidural blood patch, a rebound and self-limiting intracranial hypertension may sometimes develop. In the past decade, interest in spontaneous intracranial hypotension has been rekindled, with a substantial growth of knowledge on various aspects of the disorder. We are in the learning phase, and new information will probably appear in the future, with notable diagnostic and therapeutic implications.

Masks in Imaging Flow Cytometry

PubMed Central

Dominical, Venina; Samsel, Leigh; McCoy, J. Philip

2016-01-01

Data analysis in imaging flow cytometry incorporates elements of flow cytometry together with other aspects of morphological analysis of images. A crucial early step in this analysis is the creation of a mask to distinguish the portion of the image upon which further examination of specified features can be performed. Default masks are provided by the manufacturer of the imaging flow cytometer but additional custom masks can be created by the individual user for specific applications. Flawed or inaccurate masks can have a substantial negative impact on the overall analysis of a sample, thus great care must be taken to ensure the accuracy of masks. Here we discuss various types of masks and cite examples of their use. Furthermore we provide our insight for how to approach selecting and assessing the optimal mask for a specific analysis. PMID:27461256

Down to the last drop.

PubMed

1996-11-01

The November 1996 issue of the UN Educational Scientific and Cultural Organization Source journal covers issues concerning governance, bioethics, environment, and education. In addition to its regular letter to the editor, insights, page and screen, and people were presented wherein it paid tribute to the organizer of Black Art Festival, Mr. Leopold Sedar Senghor. Specifically, in the Governance section, it reports the unusual gathering of politicians and political activists to examine the viability of democracy in Latin America. In Bioethics, it tackles the tough decisions arising with new reproductive technologies while the Environment section presents the agenda for the 21st century to save planet Earth. The Education section reports the outcome of the International Conference on Education held in Geneva, which restores teachers to their rightful places in Education. The global water crisis is the main feature of this paper.

Invited Article: Relation between electric and magnetic field structures and their proton-beam images

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kugland, N. L.; Ryutov, D. D.; Plechaty, C.

2012-10-15

Proton imaging is commonly used to reveal the electric and magnetic fields that are found in high energy density plasmas. Presented here is an analysis of this technique that is directed towards developing additional insight into the underlying physics. This approach considers: formation of images in the limits of weak and strong intensity variations; caustic formation and structure; image inversion to obtain line-integrated field characteristics; direct relations between images and electric or magnetic field structures in a plasma; imaging of sharp features such as Debye sheaths and shocks. Limitations on spatial and temporal resolution are assessed, and similarities with opticalmore » shadowgraphy are noted. Synthetic proton images are presented to illustrate the analysis. These results will be useful for quantitatively analyzing experimental proton imaging data and verifying numerical codes.« less

Dysregulation of renal aquaporins and epithelial sodium channel in lithium-induced nephrogenic diabetes insipidus.

PubMed

Nielsen, Jakob; Kwon, Tae-Hwan; Christensen, Birgitte Mønster; Frøkiaer, Jørgen; Nielsen, Søren

2008-05-01

Lithium is used commonly to treat bipolar mood disorders. In addition to its primary therapeutic effects in the central nervous system lithium has a number of side effects in the kidney. The side effects include nephrogenic diabetes insipidus with polyuria, mild sodium wasting, and changes in acid/base balance. These functional changes are associated with marked structural changes in collecting duct cell composition and morphology, likely contributing to the functional changes. Over the past few years, investigations of lithium-induced renal changes have provided novel insight into the molecular mechanisms that are responsible for the disturbances in water, sodium, and acid/base metabolism. This includes dysregulation of renal aquaporins, epithelial sodium channel, and acid/base transporters. This review focuses on these issues with the aim to present this in context with clinically relevant features.

A Bayesian Multinomial Probit MODEL FOR THE ANALYSIS OF PANEL CHOICE DATA.

PubMed

Fong, Duncan K H; Kim, Sunghoon; Chen, Zhe; DeSarbo, Wayne S

2016-03-01

A new Bayesian multinomial probit model is proposed for the analysis of panel choice data. Using a parameter expansion technique, we are able to devise a Markov Chain Monte Carlo algorithm to compute our Bayesian estimates efficiently. We also show that the proposed procedure enables the estimation of individual level coefficients for the single-period multinomial probit model even when the available prior information is vague. We apply our new procedure to consumer purchase data and reanalyze a well-known scanner panel dataset that reveals new substantive insights. In addition, we delineate a number of advantageous features of our proposed procedure over several benchmark models. Finally, through a simulation analysis employing a fractional factorial design, we demonstrate that the results from our proposed model are quite robust with respect to differing factors across various conditions.

rpiCOOL: A tool for In Silico RNA-protein interaction detection using random forest.

PubMed

Akbaripour-Elahabad, Mohammad; Zahiri, Javad; Rafeh, Reza; Eslami, Morteza; Azari, Mahboobeh

2016-08-07

Understanding the principle of RNA-protein interactions (RPIs) is of critical importance to provide insights into post-transcriptional gene regulation and is useful to guide studies about many complex diseases. The limitations and difficulties associated with experimental determination of RPIs, call an urgent need to computational methods for RPI prediction. In this paper, we proposed a machine learning method to detect RNA-protein interactions based on sequence information. We used motif information and repetitive patterns, which have been extracted from experimentally validated RNA-protein interactions, in combination with sequence composition as descriptors to build a model to RPI prediction via a random forest classifier. About 20% of the "sequence motifs" and "nucleotide composition" features have been selected as the informative features with the feature selection methods. These results suggest that these two feature types contribute effectively in RPI detection. Results of 10-fold cross-validation experiments on three non-redundant benchmark datasets show a better performance of the proposed method in comparison with the current state-of-the-art methods in terms of various performance measures. In addition, the results revealed that the accuracy of the RPI prediction methods could vary considerably across different organisms. We have implemented the proposed method, namely rpiCOOL, as a stand-alone tool with a user friendly graphical user interface (GUI) that enables the researchers to predict RNA-protein interaction. The rpiCOOL is freely available at http://biocool.ir/rpicool.html for non-commercial uses. Copyright © 2016 Elsevier Ltd. All rights reserved.

Petrosal anatomy and inner ear structures of the Late Jurassic Henkelotherium (Mammalia, Cladotheria, Dryolestoidea): insight into the early evolution of the ear region in cladotherian mammals

PubMed Central

Ruf, Irina; Luo, Zhe-Xi; Wible, John R; Martin, Thomas

2009-01-01

The petrosal anatomy and inner ear structure of Jurassic cladotherian mammals represent the ancestral morphological conditions (groundplan) from which modern therian mammals (marsupials and placentals) have evolved. We present the reconstruction of the petrosal and inner ear features of the Late Jurassic dryolestoid mammal Henkelotherium guimarotae from high-resolution computed tomography and three-dimensional imaging analysis. This study of Henkelotherium revealed a combination of derived and primitive features, including: cladotherian apomorphies, such as the promontorial sulcus for the internal carotid artery and reduced lateral trough; trechnotherian characters, such as an enclosed cochlear canaliculus for the perilymphatic duct, post-promontorial tympanic sinus and caudal tympanic process; in addition to plesiomorphic mammalian features, such as the cavum supracochleare and prootic canal. The inner ear of Henkelotherium shows a division between the utricle and saccule, a cochlear canal coiled through at least 270°, a distinctive primary bony lamina for the basilar membrane, and a secondary bony lamina. The development of the primary and secondary bony laminae in the cochlear canal is suggested here to be correlated with the concurrent coiling of the bony canal and membranous duct of the inner ear cochlea, apomorphies of the more inclusive cladotherian clade that also represent the ancestral morphotype of modern therian mammals. Because these features are crucial for high-frequency hearing in extant therian mammals, their early appearance in Late Jurassic cladotherians suggests a more ancient origination for high-frequency hearing in mammalian history than previously thought. PMID:19438763

Positron Annihilation Spectroscopy and Small Angle Neutron Scattering Characterization of Nanostructural Features in Irradiated Fe-Cu-Mn Alloys

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wirth, B D; Asoka-Kumar, P; Howell, R H

2001-01-01

Radiation embrittlement of nuclear reactor pressure vessel steels results from a high number density of nanometer sized Cu-Mn-Ni rich precipitates (CRPs) and sub-nanometer matrix features, thought to be vacancy-solute cluster complexes (VSC). However, questions exist regarding both the composition of the precipitates and the defect character and composition of the matrix features. We present results of positron annihilation spectroscopy (PAS) and small angle neutron scattering (SANS) characterization of irradiated and thermally aged Fe-Cu and Fe-Cu-Mn alloys. These complementary techniques provide insight into the composition and character of both types of nanoscale features. The SANS measurements indicate populations of CRPs andmore » VSCs in both alloys. The CRPs are coarser in the Fe-Cu alloy and the number densities of CRP and VSC increase with the addition of Mn. The PAS involved measuring both the positron lifetimes and the Doppler broadened annihilation spectra in the high momentum region to provide elemental sensitivity at the annihilation site. The spectra in Fe-Cu-Mn specimens thermally aged to peak hardness at 450 C and irradiated at 288 C are nearly identical to elemental Cu. Positron lifetime and spectrum measurements in Fe-Cu specimens irradiated at 288 C clearly show the existence of long lifetime ({approx}500 ps) open volume defects, which also contain Cu. Thus the SANS and PAS provide a self-consistent picture of nanostructures composed of CRPs and VSCs and tend to discount high Fe concentrations in the CRPs.« less

Self-Efficacy and Functional Status in Schizophrenia: Relationship to Insight, Cognition and Negative Symptoms

PubMed Central

Kurtz, Matthew M.; Olfson, Rachel; Rose, Jennifer

2016-01-01

Self-efficacy, defined as the confidence one has in the ability to perform a behavior or specific task, has been introduced as a crucial motivational factor for successfully carrying out social and everyday living skills (Bandura, 1977, 1997). Few studies have assessed its role in functioning in schizophrenia. The current study was designed to investigate whether degree of illness insight determined whether self-efficacy was a mediator of the relationship between two key illness features, negative symptoms and cognition, and functional skills. Sixty-nine individuals with schizophrenia were administered measures of self-efficacy, cognition, symptoms, insight and performance-based measure of everyday living and social skill. Results revealed that self-efficacy was only linked to measures of functional skills when illness insight was intact. There was evidence of moderation of confounding effects such that when self-efficacy was controlled, the relationship between negative symptoms and measures of everyday life skills became non-significant, but only when illness insight was intact. These findings emphasize the importance of including illness insight in models of the role of self-efficacy in functioning in schizophrenia. PMID:23375941

An Admittance Survey of Large Volcanoes on Venus: Implications for Volcano Growth

NASA Technical Reports Server (NTRS)

Brian, A. W.; Smrekar, S. E.; Stofan, E. R.

2004-01-01

Estimates of the thickness of the venusian crust and elastic lithosphere are important in determining the rheological and thermal properties of Venus. These estimates offer insights into what conditions are needed for certain features, such as large volcanoes and coronae, to form. Lithospheric properties for much of the large volcano population on Venus are not well known. Previous studies of elastic thickness (Te) have concentrated on individual or small groups of edifices, or have used volcano models and fixed values of Te to match with observations of volcano morphologies. In addition, previous studies use different methods to estimate lithospheric parameters meaning it is difficult to compare their results. Following recent global studies of the admittance signatures exhibited by the venusian corona population, we performed a similar survey into large volcanoes in an effort to determine the range of lithospheric parameters shown by these features. This survey of the entire large volcano population used the same method throughout so that all estimates could be directly compared. By analysing a large number of edifices and comparing our results to observations of their morphology and models of volcano formation, we can help determine the controlling parameters that govern volcano growth on Venus.

Model of community emergence in weighted social networks

NASA Astrophysics Data System (ADS)

Kumpula, J. M.; Onnela, J.-P.; Saramäki, J.; Kertész, J.; Kaski, K.

2009-04-01

Over the years network theory has proven to be rapidly expanding methodology to investigate various complex systems and it has turned out to give quite unparalleled insight to their structure, function, and response through data analysis, modeling, and simulation. For social systems in particular the network approach has empirically revealed a modular structure due to interplay between the network topology and link weights between network nodes or individuals. This inspired us to develop a simple network model that could catch some salient features of mesoscopic community and macroscopic topology formation during network evolution. Our model is based on two fundamental mechanisms of network sociology for individuals to find new friends, namely cyclic closure and focal closure, which are mimicked by local search-link-reinforcement and random global attachment mechanisms, respectively. In addition we included to the model a node deletion mechanism by removing all its links simultaneously, which corresponds for an individual to depart from the network. Here we describe in detail the implementation of our model algorithm, which was found to be computationally efficient and produce many empirically observed features of large-scale social networks. Thus this model opens a new perspective for studying such collective social phenomena as spreading, structure formation, and evolutionary processes.

Sequence fingerprints distinguish erroneous from correct predictions of intrinsically disordered protein regions.

PubMed

Saravanan, Konda Mani; Dunker, A Keith; Krishnaswamy, Sankaran

2017-12-27

More than 60 prediction methods for intrinsically disordered proteins (IDPs) have been developed over the years, many of which are accessible on the World Wide Web. Nearly, all of these predictors give balanced accuracies in the ~65%-~80% range. Since predictors are not perfect, further studies are required to uncover the role of amino acid residues in native IDP as compared to predicted IDP regions. In the present work, we make use of sequences of 100% predicted IDP regions, false positive disorder predictions, and experimentally determined IDP regions to distinguish the characteristics of native versus predicted IDP regions. A higher occurrence of asparagine is observed in sequences of native IDP regions but not in sequences of false positive predictions of IDP regions. The occurrences of certain combinations of amino acids at the pentapeptide level provide a distinguishing feature in the IDPs with respect to globular proteins. The distinguishing features presented in this paper provide insights into the sequence fingerprints of amino acid residues in experimentally determined as compared to predicted IDP regions. These observations and additional work along these lines should enable the development of improvements in the accuracy of disorder prediction algorithm.

What controls diffuse fractures in platform carbonates? Insights from Provence (France) and Apulia (Italy)

NASA Astrophysics Data System (ADS)

Lavenu, Arthur P. C.; Lamarche, Juliette

2018-03-01

Fractures are widespread in rocks and regional opening-mode arrays are commonly ascribed to major tectonic events. However, fractures occur in otherwise undeformed rocks. Some of these are early-developed features independent of tectonics and forming a background network at regional scale. To overcome this lack of understanding, two hydrocarbon reservoir analogues from platform carbonates have been targeted: the Provence (SE France), and the Apulian platform (SE Italy). In both areas, an early fracturing stage has been observed, made of high-angle-to-bedding opening-mode fractures, and bed-parallel stylolites. These features developed synchronously during the first burial stages and prior to major tectonic events. The fracture sets are not genetically related to the present-day layering. Contrarily, fractures developed in a brittle media where facies transitions were not sharp and did not act as mechanical discontinuities. Carbonate facies distribution and early diagenetic imprint constrained the mechanical stratigraphy when fractures occurred. In addition, we observed that fractures related to late tectonic inversion were partly inhibited. Indeed, rock mechanical properties change through time. Characterizing the temporal evolution of carbonate rocks has revealed that diagenesis and sedimentary facies are the prime actors for brittleness and mechanical layering in carbonates.

Mechanical characterization of structurally porous biomaterials built via additive manufacturing: experiments, predictive models, and design maps for load-bearing bone replacement implants.

PubMed

Melancon, D; Bagheri, Z S; Johnston, R B; Liu, L; Tanzer, M; Pasini, D

2017-11-01

Porous biomaterials can be additively manufactured with micro-architecture tailored to satisfy the stringent mechano-biological requirements imposed by bone replacement implants. In a previous investigation, we introduced structurally porous biomaterials, featuring strength five times stronger than commercially available porous materials, and confirmed their bone ingrowth capability in an in vivo canine model. While encouraging, the manufactured biomaterials showed geometric mismatches between their internal porous architecture and that of its as-designed counterpart, as well as discrepancies between predicted and tested mechanical properties, issues not fully elucidated. In this work, we propose a systematic approach integrating computed tomography, mechanical testing, and statistical analysis of geometric imperfections to generate statistical based numerical models of high-strength additively manufactured porous biomaterials. The method is used to develop morphology and mechanical maps that illustrate the role played by pore size, porosity, strut thickness, and topology on the relations governing their elastic modulus and compressive yield strength. Overall, there are mismatches between the mechanical properties of ideal-geometry models and as-manufactured porous biomaterials with average errors of 49% and 41% respectively for compressive elastic modulus and yield strength. The proposed methodology gives more accurate predictions for the compressive stiffness and the compressive strength properties with a reduction of the average error to 11% and 7.6%. The implications of the results and the methodology here introduced are discussed in the relevant biomechanical and clinical context, with insight that highlights promises and limitations of additively manufactured porous biomaterials for load-bearing bone replacement implants. In this work, we perform mechanical characterization of load-bearing porous biomaterials for bone replacement over their entire design space. Results capture the shift in geometry and mechanical properties between as-designed and as-manufactured biomaterials induced by additive manufacturing. Characterization of this shift is crucial to ensure appropriate manufacturing of bone replacement implants that enable biological fixation through bone ingrowth as well as mechanical property harmonization with the native bone tissue. In addition, we propose a method to include manufacturing imperfections in the numerical models that can reduce the discrepancy between predicted and tested properties. The results give insight into the use of structurally porous biomaterials for the design and additive fabrication of load-bearing implants for bone replacement. Copyright © 2017 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Insights into Tropical Tropospheric Ozone from Satellite and Sonde Data

NASA Technical Reports Server (NTRS)

Thompson, Anne M.

2003-01-01

The first climatological overview of total, stratospheric and tropospheric ozone in the southern hemisphere tropical and subtropics is based on ozone sounding data from 10 sites comprising the Southern Hemisphere Additional OZonesondes (SHADOZ) network. Observations were made over: Ascension Island; Nairobi, Kenya; Irene, South Africa; Reunion Island; Watukosek, Java; Fiji; Tahiti; American Samoa; San Cristobal, Galapagos; Natal, Brazil. The data reside at: http://code916.gsfc.nasa.gov/Data_services/shadoz. SHADOZ ozone time-series and profiles give a perspective on tropical total, stratospheric and tropospheric ozone. Prominent features are highly variable tropospheric ozone and a zonal wave-one pattern in total (and tropospheric) column ozone. Dynamical and chemical influences appear to be of comparable magnitude though model studies are needed to quantify this. In addition to leading the SHADOZ network, we have been producing near-real tropical tropospheric ozone ('TTO') data from the Total Ozone Mapping Spectrometer (TOMS) since 1997 with Prof. Hudson and students at the University of Maryland: http://metosrv2.umd.edu/tropo. Further perspective on the complexity of tropospheric ozone variability is shown using satellite observations.

SLiMSearch 2.0: biological context for short linear motifs in proteins

PubMed Central

Davey, Norman E.; Haslam, Niall J.; Shields, Denis C.

2011-01-01

Short, linear motifs (SLiMs) play a critical role in many biological processes. The SLiMSearch 2.0 (Short, Linear Motif Search) web server allows researchers to identify occurrences of a user-defined SLiM in a proteome, using conservation and protein disorder context statistics to rank occurrences. User-friendly output and visualizations of motif context allow the user to quickly gain insight into the validity of a putatively functional motif occurrence. For each motif occurrence, overlapping UniProt features and annotated SLiMs are displayed. Visualization also includes annotated multiple sequence alignments surrounding each occurrence, showing conservation and protein disorder statistics in addition to known and predicted SLiMs, protein domains and known post-translational modifications. In addition, enrichment of Gene Ontology terms and protein interaction partners are provided as indicators of possible motif function. All web server results are available for download. Users can search motifs against the human proteome or a subset thereof defined by Uniprot accession numbers or GO term. The SLiMSearch server is available at: http://bioware.ucd.ie/slimsearch2.html. PMID:21622654

Genetic and Biochemical Map for the Biosynthesis of Occidiofungin, an Antifungal Produced by Burkholderia contaminans Strain MS14 ▿†

PubMed Central

Gu, Ganyu; Smith, Leif; Liu, Aixin; Lu, Shi-En

2011-01-01

A striking feature of Burkholderia contaminans strain MS14 is the production of a glycolipopeptide named occidiofungin. Occidiofungin has a broad range of antifungal activities against plant and animal pathogens. In this study, a complete covalent structure characterization and identification of the whole genomic DNA region for the occidiofungin gene (ocf) cluster are described. Discovery of the presence of 2,4-diaminobutyric acid and 3-chloro-β-hydroxytyrosine and elucidation of the structure of a novel C18 fatty amino acid residue have been achieved. In addition, seven additional putative open reading frames (the genes from ocfI to ocfN [ocfI-N] and ORF16) were identified. Transcription of all the putative genes ocfI-N identified in the region except ORF16 was regulated by both ambR1 and ambR2. Elucidation of the structure and the ocf gene cluster provides insight into the biosynthesis of occidiofungin and promotes future aims at understanding the biosynthetic machinery. This work provides new avenues for optimizing the production and synthesis of structural analogs of occidiofungin. PMID:21742901

Insight and white matter fractional anisotropy in first-episode schizophrenia.

PubMed

Asmal, Laila; du Plessis, Stefan; Vink, Matthijs; Fouche, Jean-Paul; Chiliza, Bonginkosi; Emsley, Robin

2017-05-01

Impaired insight is a hallmark feature of schizophrenia. Structural studies implicate predominantly prefrontal, cingulate, cuneus/precuneus, and inferior temporal brain regions. The cortical midline structures (CMS) are also implicated in functional studies primarily through self-reflective processing tasks. However, few studies have explored the relationship between white matter tracts and insight in schizophrenia, and none in first-episode schizophrenia (FES). Here, we examined for fractional anisotropy (FA) differences in 89 minimally treated FES patients and 98 matched controls, and identified those FA differences associated with impaired clinical insight in patients. We found widespread FA reduction in FES patients compared to controls. Poorer insight in patients was predicted by lower FA values in a number of white matter tracts with a predilection for tracts associated with cortical midline structures (fronto-occipital, cingulate, cingulate hippocampus, uncinate, anterior corona radiata), and more severe depressive symptoms. The association between FA abnormalities and insight was most robust for the awareness of symptoms and illness awareness domains. Our study implicates a network of tracts involved in impaired insight in schizophrenia with a predilection for the CMS. This study is a first step in delineating the white matter tracts involved in insight impairment in schizophrenia prior to chronicity. Copyright © 2016. Published by Elsevier B.V.

A study of poor insight in social anxiety disorder.

PubMed

Vigne, Paula; de Menezes, Gabriela B; Harrison, Ben J; Fontenelle, Leonardo F

2014-11-30

We investigated levels of insight among patients with Social Anxiety Disorder (SAD) as compared to patients with Obsessive-Compulsive Disorder (OCD) and evaluated whether levels of insight in SAD were related to specific sociodemographic and/or clinical features. Thirty-seven SAD patients and 51 OCD patients attending a tertiary obsessive-compulsive and anxiety disorders clinic were assessed with a sociodemographic and clinical questionnaire, a structured diagnostic interview, the Brown Assessment of Beliefs Scale (BABS), the Social Phobia Inventory (SPIN), the Beck Depression Inventory (BDI), the Sheehan Disability Scale (SDS), and the Treatment Adherence Survey-patient version (TAS-P). According to the BABS, SAD patients exhibited insight levels that were as low as those exhibited by OCD patients, with up to 29.7% of them being described as "poor insight" SAD. Although poor insight SAD patients were more frequently married, less depressed and displayed a statistical trend towards greater rates of early drop-out from cognitive-behavioral therapy, their insight levels were not associated with other variables of interest, including sex, age, employment, age at onset, duration of illness, associated psychiatric disorders, SPIN and SDS scores. Patients with poor insight SAD might perceive their symptoms as being less distressful and thus report fewer depressive symptoms and high rates of treatment non-adherence. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

The general/specific breakdown of semantic memory and the nature of superordinate knowledge: insights from superordinate and basic-level feature norms.

PubMed

Marques, J Frederico

2007-12-01

The deterioration of semantic memory usually proceeds from more specific to more general superordinate categories, although rarer cases of superordinate knowledge impairment have also been reported. The nature of superordinate knowledge and the explanation of these two semantic impairments were evaluated from the analysis of superordinate and basic-level feature norms. The results show that, in comparison to basic-level concepts, superordinate concepts are not generally less informative and have similar feature distinctiveness and proportion of individual sensory features, but their features are less shared by their members. Results are in accord with explanations based on feature connection weights and/or concept confusability for the superordinate advantage cases. Results especially support an explanation for superordinate impairments in terms of higher semantic control requirements as related to features being less shared between concept members. Implications for patients with semantic impairments are also discussed.

Defining greed.

PubMed

Seuntjens, Terri G; Zeelenberg, Marcel; Breugelmans, Seger M; van de Ven, Niels

2015-08-01

Although greed is both hailed as the motor of economic growth and blamed as the cause of economic crises, very little is known about its psychological underpinnings. Five studies explored lay conceptualizations of greed among U.S. and Dutch participants using a prototype analysis. Study 1 identified features related to greed. Study 2 determined the importance of these features; the most important features were classified as central (e.g., self-interested, never satisfied), whereas less important features were classified as peripheral (e.g., ambition, addiction). Subsequently, we found that, compared to peripheral features, participants recalled central features better (Study 3), faster (Study 4), and these central features were more present in real-life episodes of greed (Study 5). These findings provide a better understanding of the elements that make up the experience of greed and provide insights into how greed can be manipulated and measured in future research. © 2014 The British Psychological Society.

From Shell Midden to Midden-Mound: The Geoarchaeology of Mound Key, an Anthropogenic Island in Southwest Florida, USA

PubMed Central

Cherkinsky, Alexander; Roberts Thompson, Amanda D.; Walker, Karen J.; Newsom, Lee A.; Savarese, Michael

2016-01-01

Mound Key was once the capital of the Calusa Kingdom, a large Pre-Hispanic polity that controlled much of southern Florida. Mound Key, like other archaeological sites along the southwest Gulf Coast, is a large expanse of shell and other anthropogenic sediments. The challenges that these sites pose are largely due to the size and areal extent of the deposits, some of which begin up to a meter below and exceed nine meters above modern sea levels. Additionally, the complex depositional sequences at these sites present difficulties in determining their chronology. Here, we examine the development of Mound Key as an anthropogenic island through systematic coring of the deposits, excavations, and intensive radiocarbon dating. The resulting data, which include the reversals of radiocarbon dates from cores and dates from mound-top features, lend insight into the temporality of site formation. We use these insights to discuss the nature and scale of human activities that worked to form this large island in the context of its dynamic, environmental setting. We present the case that deposits within Mound Key’s central area accumulated through complex processes that represent a diversity of human action including midden accumulation and the redeposition of older sediments as mound fill. PMID:27123928

Trehalose Analogues: Latest Insights in Properties and Biocatalytic Production

PubMed Central

Walmagh, Maarten; Zhao, Renfei; Desmet, Tom

2015-01-01

Trehalose (α-d-glucopyranosyl α-d-glucopyranoside) is a non-reducing sugar with unique stabilizing properties due to its symmetrical, low energy structure consisting of two 1,1-anomerically bound glucose moieties. Many applications of this beneficial sugar have been reported in the novel food (nutricals), medical, pharmaceutical and cosmetic industries. Trehalose analogues, like lactotrehalose (α-d-glucopyranosyl α-d-galactopyranoside) or galactotrehalose (α-d-galactopyranosyl α-d-galactopyranoside), offer similar benefits as trehalose, but show additional features such as prebiotic or low-calorie sweetener due to their resistance against hydrolysis during digestion. Unfortunately, large-scale chemical production processes for trehalose analogues are not readily available at the moment due to the lack of efficient synthesis methods. Most of the procedures reported in literature suffer from low yields, elevated costs and are far from environmentally friendly. “Greener” alternatives found in the biocatalysis field, including galactosidases, trehalose phosphorylases and TreT-type trehalose synthases are suggested as primary candidates for trehalose analogue production instead. Significant progress has been made in the last decade to turn these into highly efficient biocatalysts and to broaden the variety of useful donor and acceptor sugars. In this review, we aim to provide an overview of the latest insights and future perspectives in trehalose analogue chemistry, applications and production pathways with emphasis on biocatalysis. PMID:26084050

Developmental emergence of different forms of neuromodulation in Aplysia sensory neurons.

PubMed

Marcus, E A; Carew, T J

1998-04-14

The capacity for neuromodulation and biophysical plasticity is a defining feature of most mature neuronal cell types. In several cases, modulation at the level of the individual neuron has been causally linked to changes in the functional output of a neuronal circuit and subsequent adaptive changes in the organism's behavioral responses. Understanding how such capacity for neuromodulation develops therefore may provide insights into the mechanisms both of neuronal development and learning and memory. We have examined the development of multiple forms of neuromodulation triggered by a common neurotransmitter, serotonin, in the pleural sensory neurons of Aplysia californica. We have found that multiple signaling cascades within a single neuron develop sequentially, with some being expressed only very late in development. In addition, our data suggest a model in which, within a single neuromodulatory pathway, the elements of the signaling cascade are developmentally expressed in a "retrograde" manner with the ionic channel that is modulated appearing early in development, functional elements in the second messenger cascade appearing later, and finally, coupling of the second messenger cascade to the serotonin receptor appearing quite late. These studies provide the characterization of the development of neuromodulation at the level of an identified cell type and offer insights into the potential roles of neuromodulatory processes in development and adult plasticity.

Genetic Causes of Microcephaly and Lessons for Neuronal Development

PubMed Central

Gilmore, Edward C.; Walsh, Christopher A.

2012-01-01

The study of human developmental microcephaly is providing important insights into brain development. It has become clear that developmental microcephalies are associated with abnormalities in cellular production, and that the pathophysiology of microcephaly provides remarkable insights into how the brain generates the proper number of neurons that determine brain size. Most of the genetic causes of ‘primary’ developmental microcephaly (i.e., not associated with other syndromic features) are associated with centrosomal abnormalities. In addition to other functions, centrosomal proteins control the mitotic spindle, which is essential for normal cell proliferation during mitosis. However, the brain is often uniquely affected when microcephaly genes are mutated implying special centrosomal related functions in neuronal production. Although models explaining how this could occur have some compelling data, they are not without controversy. Interestingly, some of the microcephaly genes show evidence that they were targets of evolutionary selection in primates and human ancestors, suggesting potential evolutionary roles in controlling neuronal number and brain volume across species. Mutations in DNA repair pathway genes also lead to microcephaly. Double stranded DNA breaks appear to be a prominent type of damage that needs to be repaired during brain development, yet why defects in DNA repair affect the brain preferentially and if DNA repair relates to centrosome function, are not clearly understood. PMID:24014418

A manual-based individual therapy to improve metacognition in schizophrenia: protocol of a multi-center RCT

PubMed Central

2014-01-01

Background Metacognitive dysfunction has been widely recognized as a feature of schizophrenia. As it is linked with deficits in several aspects of daily life functioning, improvement of metacognition may lead to improvement in functioning. Individual psychotherapy might be a useful form of treatment to improve metacognition in patients with schizophrenia; multiple case reports and a pilot study show promising results. The present study aims to measure the effectiveness of an individual, manual-based therapy (Metacognitive Reflection and Insight Therapy, MERIT) in improving metacognition in patients with schizophrenia. We also want to examine if improvement in metacognitive abilities is correlated with improvements in aspects of daily life functioning namely social functioning, experience of symptoms, quality of life, depression, work readiness, insight and experience of stigma. Methods/Design MERIT is currently evaluated in a multicenter randomized controlled trial. Thirteen therapists in six mental health institutions in the Netherlands participate in this study. Patients are randomly assigned to either MERIT or the control condition: treatment as usual (TAU). Discussion If proven effective, MERIT can be a useful addition to the care for schizophrenia patients. The design brings along some methodological difficulties, these issues are addressed in the discussion of this paper. Trial registration Current Controlled Trials: ISRCTN16659871. PMID:24490942

The spectroscopic chemical and photophysical properties of Martian soils and their analogs

NASA Technical Reports Server (NTRS)

Coyne, Lelia M.

1987-01-01

The program of research outlined should advance significantly the understanding of the spectral signal of montmorillonites in general and the variations produced in it by structural and surface ferric and ferrous iron and interlayer water as a function of several environmental conditions that are different between Earth and Mars. In addition, an extensive data base was collected providing spectral characterization of several features (iron, both surface and structural, OH-groups, both structural and from adsorbed water and O(-) centers) that are known, or thought to be, influential in directing the surface activity of these important materials. With this data base with which to assess the results of the Viking labeled release simulation studies, it should be possible to gain important insights into the mechanisms of surface reactivity for this important chemical reaction. The results to be gained from these studies will provide a significant body of ground base truth from which to assess: the presence of smectite clays on Mars; the mineralogical form in which the Martian iron is bound; establish upper limits on the present surface water content of Martian soils; perhaps provide insights on the Martian surface radiation history; and to make strong predictions about the nature of surface chemistry on Mars, if iron-bearing clays are a significant component of the surface mineralogical assemblage.

Testing Map Features Designed to Convey the Uncertainty of Cancer Risk: Insights Gained From Assessing Judgments of Information Adequacy and Communication Goals

PubMed Central

Severtson, Dolores J.

2015-01-01

Barriers to communicating the uncertainty of environmental health risks include preferences for certain information and low numeracy. Map features designed to communicate the magnitude and uncertainty of estimated cancer risk from air pollution were tested among 826 participants to assess how map features influenced judgments of adequacy and the intended communication goals. An uncertain versus certain visual feature was judged as less adequate but met both communication goals and addressed numeracy barriers. Expressing relative risk using words communicated uncertainty and addressed numeracy barriers but was judged as highly inadequate. Risk communication and visual cognition concepts were applied to explain findings. PMID:26412960

Testing Map Features Designed to Convey the Uncertainty of Cancer Risk: Insights Gained From Assessing Judgments of Information Adequacy and Communication Goals.

PubMed

Severtson, Dolores J

2015-02-01

Barriers to communicating the uncertainty of environmental health risks include preferences for certain information and low numeracy. Map features designed to communicate the magnitude and uncertainty of estimated cancer risk from air pollution were tested among 826 participants to assess how map features influenced judgments of adequacy and the intended communication goals. An uncertain versus certain visual feature was judged as less adequate but met both communication goals and addressed numeracy barriers. Expressing relative risk using words communicated uncertainty and addressed numeracy barriers but was judged as highly inadequate. Risk communication and visual cognition concepts were applied to explain findings.

Comparative Riftology: Insights into the Evolution of Passive Continental Margins and Continental Rifts from the Failed Midcontinent Rift (MCR)

NASA Astrophysics Data System (ADS)

Elling, R. P.; Stein, C. A.; Stein, S.; Kley, J.; Keller, G. R.; Wysession, M. E.

2017-12-01

Continental rifts evolve to seafloor spreading and are preserved in passive margins, or fail and remain as fossil features in continents. Rifts at different stages give insight into these evolutionary paths. Of particular interest is the evolution of volcanic passive margins, which are characterized by seaward dipping reflectors, volcanic rocks yielding magnetic anomalies landward of the oldest spreading anomalies, and are underlain by high-velocity lower crustal bodies. How and when these features form remains unclear. Insights are given by the Midcontinent Rift (MCR), which began to form during the 1.1 Ga rifting of Amazonia from Laurentia, but failed when seafloor spreading was established elsewhere. MCR volcanics are much thicker than other continental flood basalts, due to deposition in a narrow rift rather than a broad region, giving a rift's geometry but a LIP's magma volume. The MCR provides a snapshot of the deposition of a thick and highly magnetized volcanic section during rifting. Surface exposures and reflection seismic data near Lake Superior show a rift basin filled by inward-dipping flood basalt layers. Had the rift evolved to seafloor spreading, the basin would have split into two sets of volcanics with opposite-facing SDRs, each with a magnetic anomaly. Because the rift formed as a series of alternating half-grabens, structural asymmetries between conjugate margins would have naturally occurred had it gone to completion. Hence the MCR implies that many passive margin features form prior to seafloor spreading. Massive inversion of the MCR long after it failed has provided a much clearer picture of its structure compared to failed rifts with lesser degrees of inversion. Seismic imaging as well as gravity and magnetic modeling provide important insight into the effects of inversion on failed rifts. The MCR provides an end member for the evolution of actively extending rifts, characterized by upwelling mantle and negative gravity anomalies, to failed and inverted rifts without upwelling mantle and positive gravity anomalies.

Excited state absorption spectra of dissolved and aggregated distyrylbenzene: A TD-DFT state and vibronic analysis

NASA Astrophysics Data System (ADS)

Oliveira, Eliezer Fernando; Shi, Junqing; Lavarda, Francisco Carlos; Lüer, Larry; Milián-Medina, Begoña; Gierschner, Johannes

2017-07-01

A time-dependent density functional theory study is performed to reveal the excited state absorption (ESA) features of distyrylbenzene (DSB), a prototype π-conjugated organic oligomer. Starting with a didactic insight to ESA based on simple molecular orbital and configuration considerations, the performance of various density functional theory functionals is tested to reveal the full vibronic ESA features of DSB at short and long probe delay times.

Immanuel Kant's mind and the brain's resting state.

PubMed

Northoff, Georg

2012-07-01

The early philosopher Immanuel Kant suggested that the mind’s intrinsic features are intimately linked to the extrinsic stimuli of the environment it processes. Currently, the field faces an analogous problem with regard to the brain. Kant’s ideas may provide novel insights into how the brain’s intrinsic features must be so that they can be linked to the neural processing of extrinsic stimuli to enable the latter’s association with consciousness and self.

NASA Space Engineering Research Center Symposium on VLSI Design

NASA Technical Reports Server (NTRS)

Maki, Gary K.

1990-01-01

The NASA Space Engineering Research Center (SERC) is proud to offer, at its second symposium on VLSI design, presentations by an outstanding set of individuals from national laboratories and the electronics industry. These featured speakers share insights into next generation advances that will serve as a basis for future VLSI design. Questions of reliability in the space environment along with new directions in CAD and design are addressed by the featured speakers.

Segmentation of photospheric magnetic elements corresponding to coronal features to understand the EUV and UV irradiance variability

NASA Astrophysics Data System (ADS)

Zender, J. J.; Kariyappa, R.; Giono, G.; Bergmann, M.; Delouille, V.; Damé, L.; Hochedez, J.-F.; Kumara, S. T.

2017-09-01

Context. The magnetic field plays a dominant role in the solar irradiance variability. Determining the contribution of various magnetic features to this variability is important in the context of heliospheric studies and Sun-Earth connection. Aims: We studied the solar irradiance variability and its association with the underlying magnetic field for a period of five years (January 2011-January 2016). We used observations from the Large Yield Radiometer (LYRA), the Sun Watcher with Active Pixel System detector and Image Processing (SWAP) on board PROBA2, the Atmospheric Imaging Assembly (AIA), and the Helioseismic and Magnetic Imager (HMI) on board the Solar Dynamics Observatory (SDO). Methods: The Spatial Possibilistic Clustering Algorithm (SPoCA) is applied to the extreme ultraviolet (EUV) observations obtained from the AIA to segregate coronal features by creating segmentation maps of active regions (ARs), coronal holes (CHs) and the quiet sun (QS). Further, these maps are applied to the full-disk SWAP intensity images and the full-disk (FD) HMI line-of-sight (LOS) magnetograms to isolate the SWAP coronal features and photospheric magnetic counterparts, respectively. We then computed full-disk and feature-wise averages of EUV intensity and line of sight (LOS) magnetic flux density over ARs/CHs/QS/FD. The variability in these quantities is compared with that of LYRA irradiance values. Results: Variations in the quantities resulting from the segmentation, namely the integrated intensity and the total magnetic flux density of ARs/CHs/QS/FD regions, are compared with the LYRA irradiance variations. We find that the EUV intensity over ARs/CHs/QS/FD is well correlated with the underlying magnetic field. In addition, variations in the full-disk integrated intensity and magnetic flux density values are correlated with the LYRA irradiance variations. Conclusions: Using the segmented coronal features observed in the EUV wavelengths as proxies to isolate the underlying magnetic structures is demonstrated in this study. Sophisticated feature identification and segmentation tools are important in providing more insights into the role of various magnetic features in both the short- and long-term changes in the solar irradiance. The movie associated to Fig. 2 is available at http://www.aanda.org

Multicentre validation of a sepsis prediction algorithm using only vital sign data in the emergency department, general ward and ICU.

PubMed

Mao, Qingqing; Jay, Melissa; Hoffman, Jana L; Calvert, Jacob; Barton, Christopher; Shimabukuro, David; Shieh, Lisa; Chettipally, Uli; Fletcher, Grant; Kerem, Yaniv; Zhou, Yifan; Das, Ritankar

2018-01-26

We validate a machine learning-based sepsis-prediction algorithm ( InSight ) for the detection and prediction of three sepsis-related gold standards, using only six vital signs. We evaluate robustness to missing data, customisation to site-specific data using transfer learning and generalisability to new settings. A machine-learning algorithm with gradient tree boosting. Features for prediction were created from combinations of six vital sign measurements and their changes over time. A mixed-ward retrospective dataset from the University of California, San Francisco (UCSF) Medical Center (San Francisco, California, USA) as the primary source, an intensive care unit dataset from the Beth Israel Deaconess Medical Center (Boston, Massachusetts, USA) as a transfer-learning source and four additional institutions' datasets to evaluate generalisability. 684 443 total encounters, with 90 353 encounters from June 2011 to March 2016 at UCSF. None. Area under the receiver operating characteristic (AUROC) curve for detection and prediction of sepsis, severe sepsis and septic shock. For detection of sepsis and severe sepsis, InSight achieves an AUROC curve of 0.92 (95% CI 0.90 to 0.93) and 0.87 (95% CI 0.86 to 0.88), respectively. Four hours before onset, InSight predicts septic shock with an AUROC of 0.96 (95% CI 0.94 to 0.98) and severe sepsis with an AUROC of 0.85 (95% CI 0.79 to 0.91). InSight outperforms existing sepsis scoring systems in identifying and predicting sepsis, severe sepsis and septic shock. This is the first sepsis screening system to exceed an AUROC of 0.90 using only vital sign inputs. InSight is robust to missing data, can be customised to novel hospital data using a small fraction of site data and retains strong discrimination across all institutions. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Accuracy Maximization Analysis for Sensory-Perceptual Tasks: Computational Improvements, Filter Robustness, and Coding Advantages for Scaled Additive Noise

PubMed Central

Burge, Johannes

2017-01-01

Accuracy Maximization Analysis (AMA) is a recently developed Bayesian ideal observer method for task-specific dimensionality reduction. Given a training set of proximal stimuli (e.g. retinal images), a response noise model, and a cost function, AMA returns the filters (i.e. receptive fields) that extract the most useful stimulus features for estimating a user-specified latent variable from those stimuli. Here, we first contribute two technical advances that significantly reduce AMA’s compute time: we derive gradients of cost functions for which two popular estimators are appropriate, and we implement a stochastic gradient descent (AMA-SGD) routine for filter learning. Next, we show how the method can be used to simultaneously probe the impact on neural encoding of natural stimulus variability, the prior over the latent variable, noise power, and the choice of cost function. Then, we examine the geometry of AMA’s unique combination of properties that distinguish it from better-known statistical methods. Using binocular disparity estimation as a concrete test case, we develop insights that have general implications for understanding neural encoding and decoding in a broad class of fundamental sensory-perceptual tasks connected to the energy model. Specifically, we find that non-orthogonal (partially redundant) filters with scaled additive noise tend to outperform orthogonal filters with constant additive noise; non-orthogonal filters and scaled additive noise can interact to sculpt noise-induced stimulus encoding uncertainty to match task-irrelevant stimulus variability. Thus, we show that some properties of neural response thought to be biophysical nuisances can confer coding advantages to neural systems. Finally, we speculate that, if repurposed for the problem of neural systems identification, AMA may be able to overcome a fundamental limitation of standard subunit model estimation. As natural stimuli become more widely used in the study of psychophysical and neurophysiological performance, we expect that task-specific methods for feature learning like AMA will become increasingly important. PMID:28178266

Phylogeny of Fish-Infecting Calyptospora species (Apicomplexa: Eimeriorina)

EPA Science Inventory

There are numerous species of apicomplexans that infect poikilothermic vertebrates such as fishes, and possess unique morphological features that provide insight into the evolution of this important phylum of parasites. Here the relationship of the fish-infecting Calyptospora spe...

The Importance of Lake Overflow Floods for Early Martian Landscape Evolution: Insights From Licus Vallis

NASA Technical Reports Server (NTRS)

Goudge, T. A.; Fassett, C. I.

2017-01-01

Open-basin lake outlet valleys are incised when water breaches the basin-confining topography and overflows. Outlet valleys record this flooding event and provide insight into how the lake and surrounding terrain evolved over time. Here we present a study of the paleolake outlet Licus Vallis, a >350 km long, >2 km wide, >100 m deep valley that heads at the outlet breach of an approx.30 km diameter impact crater. Multiple geomorphic features of this valley system suggest it records a more complex evolution than formation from a single lake overflow flood. This provides unique insight into the paleohydrology of lakes on early Mars, as we can make inferences beyond the most recent phase of activity..

Insights from the supplementary motor area syndrome in balancing movement initiation and inhibition

PubMed Central

Potgieser, A. R. E.; de Jong, B. M.; Wagemakers, M.; Hoving, E. W.; Groen, R. J. M.

2014-01-01

The supplementary motor area (SMA) syndrome is a characteristic neurosurgical syndrome that can occur after unilateral resection of the SMA. Clinical symptoms may vary from none to a global akinesia, predominantly on the contralateral side, with preserved muscle strength and mutism. A remarkable feature is that these symptoms completely resolve within weeks to months, leaving only a disturbance in alternating bimanual movements. In this review we give an overview of the old and new insights from the SMA syndrome and extrapolate these findings to seemingly unrelated diseases and symptoms such as Parkinson’s disease (PD) and tics. Furthermore, we integrate findings from lesion, stimulation and functional imaging studies to provide insight in the motor function of the SMA. PMID:25506324

The Geology of Inferno Chasm, Idaho: a Terrestrial Analog for Lunar Rilles?

NASA Technical Reports Server (NTRS)

Garry, William B.; Hughes, Scott S.; Kobs Nawotniak, Shannon E.; Neish, Catherine D.; Haberle, Christopher W.; Heldmann, Jennifer L.; Lim, Darlene S. S.

2014-01-01

Lunar sinuous rilles are thought to have formed by thermal erosion, mechanical erosion, construction, or a combination of these processes via emplacement by lava tubes or lava channels. The investigation of Hadley Rille by Apollo 15 provided the first field observations of a rille, but remote sensing observations remain our primary method for studying these features. Terrestrial volcanic features with similar morphologies to lunar rilles can provide insight into their formation on the Moon.

Body condition of the deep water demersal resources at two adjacent oligotrophic areas of the western Mediterranean and the influence of the environmental features

NASA Astrophysics Data System (ADS)

Rueda, L.; Moranta, J.; Abelló, P.; Balbín, R.; Barberá, C.; Fernández de Puelles, M. L.; Olivar, M. P.; Ordines, F.; Ramón, M.; Torres, A. P.; Valls, M.; Massutí, E.

2014-10-01

Body condition indices not only are often used as reliable indicators of the nutritional status of individuals but also can they be utilized to provide insights regarding food availability and habitat quality. The aim of this study was to evaluate the connection between the body condition of the demersal species and the environmental features in the water column (i.e. the hydrographic conditions and the potential trophic resources) in two proximate areas, the north and south regions of the Balearic Islands (western Mediterranean), viz., the Balearic sub-basin (BsB) and the Algerian sub-basin (AsB), respectively, with different geomorphological and hydrodynamic features. Body condition indices were calculated for individuals of 21 demersal species including 11 teleosts, 4 elasmobranchs, 3 cephalopods and 3 crustaceans, which represented > 70-77% of the deep water resources, captured by bottom trawling. The morphometric indices, viz., Relative Condition Index (Kn) and Standardised Residuals (SR) from the length-weight relationship, were used. The results for each one of the 21 species indicated a significantly better condition in terms of Kn and SR in the BsB, for 7 and 9 species, respectively. In addition, a general model, including the 21 species together, showed better body condition in the BsB, and during the summer. The spatial and temporal differences in the body condition are discussed in the context of the environmental variables characterising both the study areas, which showed significant variations, for some of the hydrographic features (chlorophyll a, dissolved oxygen, salinity, potential density and temperature), as well as for some of the potential trophic resources (mesopelagic and epibenthic fauna). These findings suggest an environmental effect on the body condition of the deep-water resources in the Balearic Islands, one of the most oligotrophic areas of the western Mediterranean, and reveal more suitable environmental conditions for these species on the northern insular margin, off the Archipelago. In addition to these ecological connections, the results also hold interest for the management and conservation of the habitats essential for the sustainability of fisheries.

Improving deep convolutional neural networks with mixed maxout units.

PubMed

Zhao, Hui-Zhen; Liu, Fu-Xian; Li, Long-Yue

2017-01-01

Motivated by insights from the maxout-units-based deep Convolutional Neural Network (CNN) that "non-maximal features are unable to deliver" and "feature mapping subspace pooling is insufficient," we present a novel mixed variant of the recently introduced maxout unit called a mixout unit. Specifically, we do so by calculating the exponential probabilities of feature mappings gained by applying different convolutional transformations over the same input and then calculating the expected values according to their exponential probabilities. Moreover, we introduce the Bernoulli distribution to balance the maximum values with the expected values of the feature mappings subspace. Finally, we design a simple model to verify the pooling ability of mixout units and a Mixout-units-based Network-in-Network (NiN) model to analyze the feature learning ability of the mixout models. We argue that our proposed units improve the pooling ability and that mixout models can achieve better feature learning and classification performance.

Late electrophysiological modulations of feature-based attention to object shapes.

PubMed

Stojanoski, Bobby Boge; Niemeier, Matthias

2014-03-01

Feature-based attention has been shown to aid object perception. Our previous ERP effects revealed temporally late feature-based modulation in response to objects relative to motion. The aim of the current study was to confirm the timing of feature-based influences on object perception while cueing within the feature dimension of shape. Participants were told to expect either "pillow" or "flower" objects embedded among random white and black lines. Participants more accurately reported the object's main color for valid compared to invalid shapes. ERPs revealed modulation from 252-502 ms, from occipital to frontal electrodes. Our results are consistent with previous findings examining the time course for processing similar stimuli (illusory contours). Our results provide novel insights into how attending to features of higher complexity aids object perception presumably via feed-forward and feedback mechanisms along the visual hierarchy. Copyright © 2014 Society for Psychophysiological Research.

Value-Driven Attentional Capture is Modulated by Spatial Context

PubMed Central

Anderson, Brian A.

2014-01-01

When stimuli are associated with reward outcome, their visual features acquire high attentional priority such that stimuli possessing those features involuntarily capture attention. Whether a particular feature is predictive of reward, however, will vary with a number of contextual factors. One such factor is spatial location: for example, red berries are likely to be found in low-lying bushes, whereas yellow bananas are likely to be found on treetops. In the present study, I explore whether the attentional priority afforded to reward-associated features is modulated by such location-based contingencies. The results demonstrate that when a stimulus feature is associated with a reward outcome in one spatial location but not another, attentional capture by that feature is selective to when it appears in the rewarded location. This finding provides insight into how reward learning effectively modulates attention in an environment with complex stimulus–reward contingencies, thereby supporting efficient foraging. PMID:26069450

Elucidating high-dimensional cancer hallmark annotation via enriched ontology.

PubMed

Yan, Shankai; Wong, Ka-Chun

2017-09-01

Cancer hallmark annotation is a promising technique that could discover novel knowledge about cancer from the biomedical literature. The automated annotation of cancer hallmarks could reveal relevant cancer transformation processes in the literature or extract the articles that correspond to the cancer hallmark of interest. It acts as a complementary approach that can retrieve knowledge from massive text information, advancing numerous focused studies in cancer research. Nonetheless, the high-dimensional nature of cancer hallmark annotation imposes a unique challenge. To address the curse of dimensionality, we compared multiple cancer hallmark annotation methods on 1580 PubMed abstracts. Based on the insights, a novel approach, UDT-RF, which makes use of ontological features is proposed. It expands the feature space via the Medical Subject Headings (MeSH) ontology graph and utilizes novel feature selections for elucidating the high-dimensional cancer hallmark annotation space. To demonstrate its effectiveness, state-of-the-art methods are compared and evaluated by a multitude of performance metrics, revealing the full performance spectrum on the full set of cancer hallmarks. Several case studies are conducted, demonstrating how the proposed approach could reveal novel insights into cancers. https://github.com/cskyan/chmannot. Copyright © 2017 Elsevier Inc. All rights reserved.

How time delay and network design shape response patterns in biochemical negative feedback systems.

PubMed

Börsch, Anastasiya; Schaber, Jörg

2016-08-24

Negative feedback in combination with time delay can bring about both sustained oscillations and adaptive behaviour in cellular networks. Here, we study which design features of systems with delayed negative feedback shape characteristic response patterns with special emphasis on the role of time delay. To this end, we analyse generic two-dimensional delay differential equations describing the dynamics of biochemical signal-response networks. We investigate the influence of several design features on the stability of the model equilibrium, i.e., presence of auto-inhibition and/or mass conservation and the kind and/or strength of the delayed negative feedback. We show that auto-inhibition and mass conservation have a stabilizing effect, whereas increasing abruptness and decreasing feedback threshold have a de-stabilizing effect on the model equilibrium. Moreover, applying our theoretical analysis to the mammalian p53 system we show that an auto-inhibitory feedback can decouple period and amplitude of an oscillatory response, whereas the delayed feedback can not. Our theoretical framework provides insight into how time delay and design features of biochemical networks act together to elicit specific characteristic response patterns. Such insight is useful for constructing synthetic networks and controlling their behaviour in response to external stimulation.

The Reconstruction Toolkit (RTK), an open-source cone-beam CT reconstruction toolkit based on the Insight Toolkit (ITK)

NASA Astrophysics Data System (ADS)

Rit, S.; Vila Oliva, M.; Brousmiche, S.; Labarbe, R.; Sarrut, D.; Sharp, G. C.

2014-03-01

We propose the Reconstruction Toolkit (RTK, http://www.openrtk.org), an open-source toolkit for fast cone-beam CT reconstruction, based on the Insight Toolkit (ITK) and using GPU code extracted from Plastimatch. RTK is developed by an open consortium (see affiliations) under the non-contaminating Apache 2.0 license. The quality of the platform is daily checked with regression tests in partnership with Kitware, the company supporting ITK. Several features are already available: Elekta, Varian and IBA inputs, multi-threaded Feldkamp-David-Kress reconstruction on CPU and GPU, Parker short scan weighting, multi-threaded CPU and GPU forward projectors, etc. Each feature is either accessible through command line tools or C++ classes that can be included in independent software. A MIDAS community has been opened to share CatPhan datasets of several vendors (Elekta, Varian and IBA). RTK will be used in the upcoming cone-beam CT scanner developed by IBA for proton therapy rooms. Many features are under development: new input format support, iterative reconstruction, hybrid Monte Carlo / deterministic CBCT simulation, etc. RTK has been built to freely share tomographic reconstruction developments between researchers and is open for new contributions.

Causes of death after fluid bolus resuscitation: new insights from FEAST.

PubMed

Myburgh, John; Finfer, Simon

2013-03-14

The Fluid Expansion as Supportive Therapy (FEAST study) was an extremely well conducted study that gave unexpected results. The investigators had reported that febrile children with impaired perfusion treated in low-income countries without access to intensive care are more likely to die if they receive bolus resuscitation with albumin or saline compared with no bolus resuscitation at all. In a secondary analysis of the trial, published in BMC Medicine, the authors found that increased mortality was evident in patients who presented with clinical features of severe shock in isolation or in conjunction with features of respiratory or neurological failure. The cause of excess deaths was primarily refractory shock and not fluid overload. These features are consistent with a potential cardiotoxic or ischemia-reperfusion injury following resuscitation with boluses of intravenous fluid. Although these effects may have been amplified by the absence of invasive monitoring, mechanical ventilation or vasopressors, the results provide compelling insights into the effects of intravenous fluid resuscitation and potential adverse effects that extend beyond the initial resuscitation period. These data add to the increasing body of literature about the safety and efficacy of intravenous resuscitation fluids, which may be applicable to management of other populations of critically ill patients.

Extraction of Features from High-resolution 3D LiDaR Point-cloud Data

NASA Astrophysics Data System (ADS)

Keller, P.; Kreylos, O.; Hamann, B.; Kellogg, L. H.; Cowgill, E. S.; Yikilmaz, M. B.; Hering-Bertram, M.; Hagen, H.

2008-12-01

Airborne and tripod-based LiDaR scans are capable of producing new insight into geologic features by providing high-quality 3D measurements of the landscape. High-resolution LiDaR is a promising method for studying slip on faults, erosion, and other landscape-altering processes. LiDaR scans can produce up to several billion individual point returns associated with the reflection of a laser from natural and engineered surfaces; these point clouds are typically used to derive a high-resolution digital elevation model (DEM). Currently, there exist only few methods that can support the analysis of the data at full resolution and in the natural 3D perspective in which it was collected by working directly with the points. We are developing new algorithms for extracting features from LiDaR scans, and present method for determining the local curvature of a LiDaR data set, working directly with the individual point returns of a scan. Computing the curvature enables us to rapidly and automatically identify key features such as ridge-lines, stream beds, and edges of terraces. We fit polynomial surface patches via a moving least squares (MLS) approach to local point neighborhoods, determining curvature values for each point. The size of the local point neighborhood is defined by a user. Since both terrestrial and airborne LiDaR scans suffer from high noise, we apply additional pre- and post-processing smoothing steps to eliminate unwanted features. LiDaR data also captures objects like buildings and trees complicating greatly the task of extracting reliable curvature values. Hence, we use a stochastic approach to determine whether a point can be reliably used to estimate curvature or not. Additionally, we have developed a graph-based approach to establish connectivities among points that correspond to regions of high curvature. The result is an explicit description of ridge-lines, for example. We have applied our method to the raw point cloud data collected as part of the GeoEarthScope B-4 project on a section of the San Andreas Fault (Segment SA09). This section provides an excellent test site for our method as it exposes the fault clearly, contains few extraneous structures, and exhibits multiple dry stream-beds that have been off-set by motion on the fault.

Structural studies of G protein-coupled receptors.

PubMed

Lu, Mengjie; Wu, Beili

2016-11-01

G protein-coupled receptors (GPCRs) comprise the largest membrane protein family. These receptors sense a variety of signaling molecules, activate multiple intracellular signal pathways, and act as the targets of over 40% of marketed drugs. Recent progress on GPCR structural studies provides invaluable insights into the structure-function relationship of the GPCR superfamily, deepening our understanding about the molecular mechanisms of GPCR signal transduction. Here, we review recent breakthroughs on GPCR structure determination and the structural features of GPCRs, and take the structures of chemokine receptor CCR5 and purinergic receptors P2Y 1 R and P2Y 12 R as examples to discuss the importance of GPCR structures on functional studies and drug discovery. In addition, we discuss the prospect of GPCR structure-based drug discovery. © 2016 IUBMB Life, 68(11):894-903, 2016. © 2016 International Union of Biochemistry and Molecular Biology.

Ultrafast spectral dynamics of dual-color-soliton intracavity collision in a mode-locked fiber laser

NASA Astrophysics Data System (ADS)

Wei, Yuan; Li, Bowen; Wei, Xiaoming; Yu, Ying; Wong, Kenneth K. Y.

2018-02-01

The single-shot spectral dynamics of dual-color-soliton collisions inside a mode-locked laser is experimentally and numerically investigated. By using the all-optically dispersive Fourier transform, we spectrally unveil the collision-induced soliton self-reshaping process, which features dynamic spectral fringes over the soliton main lobe, and the rebuilding of Kelly sidebands with wavelength drifting. Meanwhile, the numerical simulations validate the experimental observation and provide additional insights into the physical mechanism of the collision-induced spectral dynamics from the temporal domain perspective. It is verified that the dynamic interference between the soliton and the dispersive waves is responsible for the observed collision-induced spectral evolution. These dynamic phenomena not only demonstrate the role of dispersive waves in the sophisticated soliton interaction inside the laser cavity, but also facilitate a deeper understanding of the soliton's inherent stability.

Cannabidiol, a Non-Psychoactive Cannabinoid Compound, Inhibits Proliferation and Invasion in U87-MG and T98G Glioma Cells through a Multitarget Effect

PubMed Central

Solinas, Marta; Massi, Paola; Cinquina, Valentina; Valenti, Marta; Bolognini, Daniele; Gariboldi, Marzia; Monti, Elena; Rubino, Tiziana; Parolaro, Daniela

2013-01-01

In the present study, we found that CBD inhibited U87-MG and T98G cell proliferation and invasiveness in vitro and caused a decrease in the expression of a set of proteins specifically involved in growth, invasion and angiogenesis. In addition, CBD treatment caused a dose-related down-regulation of ERK and Akt prosurvival signaling pathways in U87-MG and T98G cells and decreased hypoxia inducible factor HIF-1α expression in U87-MG cells. Taken together, these results provide new insights into the antitumor action of CBD, showing that this cannabinoid affects multiple tumoral features and molecular pathways. As CBD is a non-psychoactive phytocannabinoid that appears to be devoid of side effects, our results support its exploitation as an effective anti-cancer drug in the management of gliomas. PMID:24204703

Quantum scar and breakdown of universality in graphene: A theoretical insight

NASA Astrophysics Data System (ADS)

Iyakutti, Kombiah; Rajeswarapalanichamy, Ratnavelu; Surya, Velappa Jayaraman; Kawazoe, Yoshiyuki

2017-12-01

Graphene has brought forward a lot of new physics. One of them is the emergence of massless Dirac fermions in addition to the electrons and these features are new to physics. In this theoretical study, the signatures for quantum scar and the breakdown of universality in graphene are investigated with reference to the presence of these two types of fermions. Taking the graphene quantum dot (QD) potential as the confining potential, the radial part of Dirac equations are solved numerically. Concentrations of the two component eigen-wavefunctions about classical periodic orbits emerge as the signatures for the quantum scar. The sudden variations, in the ratio of the radial wave-functions (large and small components), R(g/f), with mass ratio κ are the signatures for breakdown of universality in graphene. The breakdown of universality occurs for the states k = -1 and k = 1, and the state k = -1 is more susceptible to the breakdown of universality.

Transition Characteristic Analysis of Traffic Evolution Process for Urban Traffic Network

PubMed Central

Chen, Hong; Li, Yang

2014-01-01

The characterization of the dynamics of traffic states remains fundamental to seeking for the solutions of diverse traffic problems. To gain more insights into traffic dynamics in the temporal domain, this paper explored temporal characteristics and distinct regularity in the traffic evolution process of urban traffic network. We defined traffic state pattern through clustering multidimensional traffic time series using self-organizing maps and construct a pattern transition network model that is appropriate for representing and analyzing the evolution progress. The methodology is illustrated by an application to data flow rate of multiple road sections from Network of Shenzhen's Nanshan District, China. Analysis and numerical results demonstrated that the methodology permits extracting many useful traffic transition characteristics including stability, preference, activity, and attractiveness. In addition, more information about the relationships between these characteristics was extracted, which should be helpful in understanding the complex behavior of the temporal evolution features of traffic patterns. PMID:24982969

Pathomechanisms in Lysosomal Storage Disorders

PubMed Central

Walkley, Steven U.; Vanier, Marie T.

2015-01-01

Lysosomal diseases are inherited metabolic disorders caused by defects in a wide spectrum of lysosomal and a few non-lysosomal proteins. In most cases a single type of primary storage material is identified, which has been used to name and classify the disorders: hence the terms sphingolipidoses, gangliosidoses, mucopolysaccharidoses, glycoproteinoses, and so forth. In addition to this primary storage, however, a host of secondary storage products can also be identified, more often than not having no direct link to the primary protein defect. Lipids - glycosphingolipids and phospholipids, as well as cholesterol - are the most ubiquitous and best studied of these secondary storage materials. While in the past typically considered nonspecific and nonconsequential features of these diseases, newer studies suggest direct links between secondary storage and disease pathogenesis and support the view that understanding all aspects of this sequestration process will provide important insights into the cell biology and treatment of lysosomal disease. PMID:19111580

>From individual choice to group decision-making

NASA Astrophysics Data System (ADS)

Galam, Serge; Zucker, Jean-Daniel

2000-12-01

Some universal features are independent of both the social nature of the individuals making the decision and the nature of the decision itself. On this basis a simple magnet like model is built. Pair interactions are introduced to measure the degree of exchange among individuals while discussing. An external uniform field is included to account for a possible pressure from outside. Individual biases with respect to the issue at stake are also included using local random fields. A unique postulate of minimum conflict is assumed. The model is then solved with emphasis on its psycho-sociological implications. Counter-intuitive results are obtained. At this stage no new physical technicality is involved. Instead the full psycho-sociological implications of the model are drawn. Few cases are then detailed to enlight them. In addition, several numerical experiments based on our model are shown to give both an insight on the dynamics of the model and suggest further research directions.

Teaching and assessing professionalism in medicine.

PubMed

Duff, Patrick

2004-12-01

Professionalism is the single most important of the clinical competencies. Lack of professional behavior, in turn, is the single most common cause for disciplinary action against third and fourth-year medical students, residents, fellows, and clinical practitioners. Desirable professional attributes include humility, honesty, responsibility, reliability, and accountability. The ability to preserve an appropriate balance between patient care responsibilities and personal commitments also is an important feature of professional behavior. Altruism, respectfulness, loyalty, compassion, sensitivity, and tactfulness are other desirable professional attributes. In addition, professionalism requires a heightened sense of intellectual curiosity, insight into personal strengths and weaknesses, maturity, and commitment to clinical excellence and self-directed learning. Professionalism can be taught and assessed through lectures, small-group seminars, role-playing exercises, directed reading, and one-on-one observation and counseling. However, the most effective way of teaching professionalism is for instructors to model appropriate behavior and to impose a consistent policy of zero tolerance for unprofessional behavior.

Cytoscape tools for the web age: D3.js and Cytoscape.js exporters

PubMed Central

Ono, Keiichiro; Demchak, Barry; Ideker, Trey

2014-01-01

In this paper we present new data export modules for Cytoscape 3 that can generate network files for Cytoscape.js and D3.js. Cytoscape.js exporter is implemented as a core feature of Cytoscape 3, and D3.js exporter is available as a Cytoscape 3 app. These modules enable users to seamlessly export network and table data sets generated in Cytoscape to popular JavaScript library readable formats. In addition, we implemented template web applications for browser-based interactive network visualization that can be used as basis for complex data visualization applications for bioinformatics research. Example web applications created with these tools demonstrate how Cytoscape works in modern data visualization workflows built with traditional desktop tools and emerging web-based technologies. This interactivity enables researchers more flexibility than with static images, thereby greatly improving the quality of insights researchers can gain from them. PMID:25520778

The importance of stress percolation patterns in rocks and other polycrystalline materials.

PubMed

Burnley, P C

2013-01-01

A new framework for thinking about the deformation behavior of rocks and other heterogeneous polycrystalline materials is proposed, based on understanding the patterns of stress transmission through these materials. Here, using finite element models, I show that stress percolates through polycrystalline materials that have heterogeneous elastic and plastic properties of the same order as those found in rocks. The pattern of stress percolation is related to the degree of heterogeneity in and statistical distribution of the elastic and plastic properties of the constituent grains in the aggregate. The development of these stress patterns leads directly to shear localization, and their existence provides insight into the formation of rhythmic features such as compositional banding and foliation in rocks that are reacting or dissolving while being deformed. In addition, this framework provides a foundation for understanding and predicting the macroscopic rheology of polycrystalline materials based on single-crystal elastic and plastic mechanical properties.

The importance of stress percolation patterns in rocks and other polycrystalline materials

PubMed Central

Burnley, P.C.

2013-01-01

A new framework for thinking about the deformation behavior of rocks and other heterogeneous polycrystalline materials is proposed, based on understanding the patterns of stress transmission through these materials. Here, using finite element models, I show that stress percolates through polycrystalline materials that have heterogeneous elastic and plastic properties of the same order as those found in rocks. The pattern of stress percolation is related to the degree of heterogeneity in and statistical distribution of the elastic and plastic properties of the constituent grains in the aggregate. The development of these stress patterns leads directly to shear localization, and their existence provides insight into the formation of rhythmic features such as compositional banding and foliation in rocks that are reacting or dissolving while being deformed. In addition, this framework provides a foundation for understanding and predicting the macroscopic rheology of polycrystalline materials based on single-crystal elastic and plastic mechanical properties. PMID:23823992

Osteoarthritis and osteoporosis: what is the overlap?

PubMed

Bultink, Irene E M; Lems, Willem F

2013-05-01

Osteoarthritis (OA) and osteoporosis (OP) are highly prevalent health problems, associated with considerable morbidity. In the past, attention was focused on a supposed inverse relationship between OA and OP, since both disorders usually affect the elderly, but were regarded to rarely coexist in a single person. However, recent studies have revealed several factors which contribute to the pathogenesis of both disorders. These insights might contribute to the development of shared new treatment options in the near future. Increased subchondral bone loss is a characteristic feature of OP and the early stage of OA, and this finding is the rationale for studies on the effect of anti-osteoporotic drugs in OA. In addition, inflammation and unfavourable body composition have been recognized as contributing factors for both disorders. Underweight is a risk factor for OP, while obesity stimulates the development of OA, by mechanical overloading of weight-bearing joints but also by supposed unfavourable effects of adipokines.

Cytoscape tools for the web age: D3.js and Cytoscape.js exporters.

PubMed

Ono, Keiichiro; Demchak, Barry; Ideker, Trey

2014-01-01

In this paper we present new data export modules for Cytoscape 3 that can generate network files for Cytoscape.js and D3.js. Cytoscape.js exporter is implemented as a core feature of Cytoscape 3, and D3.js exporter is available as a Cytoscape 3 app. These modules enable users to seamlessly export network and table data sets generated in Cytoscape to popular JavaScript library readable formats. In addition, we implemented template web applications for browser-based interactive network visualization that can be used as basis for complex data visualization applications for bioinformatics research. Example web applications created with these tools demonstrate how Cytoscape works in modern data visualization workflows built with traditional desktop tools and emerging web-based technologies. This interactivity enables researchers more flexibility than with static images, thereby greatly improving the quality of insights researchers can gain from them.

Sex differences in prenatal epigenetic programming of stress pathways.

PubMed

Bale, Tracy L

2011-07-01

Maternal stress experience is associated with neurodevelopmental disorders including schizophrenia and autism. Recent studies have examined mechanisms by which changes in the maternal milieu may be transmitted to the developing embryo and potentially translated into programming of the epigenome. Animal models of prenatal stress have identified important sex- and temporal-specific effects on offspring stress responsivity. As dysregulation of stress pathways is a common feature in most neuropsychiatric diseases, molecular and epigenetic analyses at the maternal-embryo interface, especially in the placenta, may provide unique insight into identifying much-needed predictive biomarkers. In addition, as most neurodevelopmental disorders present with a sex bias, examination of sex differences in the inheritance of phenotypic outcomes may pinpoint gene targets and specific windows of vulnerability in neurodevelopment, which have been disrupted. This review discusses the association and possible contributing mechanisms of prenatal stress in programming offspring stress pathway dysregulation and the importance of sex.

Coarse-grained mechanics of viral shells

NASA Astrophysics Data System (ADS)

Klug, William S.; Gibbons, Melissa M.

2008-03-01

We present an approach for creating three-dimensional finite element models of viral capsids from atomic-level structural data (X-ray or cryo-EM). The models capture heterogeneous geometric features and are used in conjunction with three-dimensional nonlinear continuum elasticity to simulate nanoindentation experiments as performed using atomic force microscopy. The method is extremely flexible; able to capture varying levels of detail in the three-dimensional structure. Nanoindentation simulations are presented for several viruses: Hepatitis B, CCMV, HK97, and φ29. In addition to purely continuum elastic models a multiscale technique is developed that combines finite-element kinematics with MD energetics such that large-scale deformations are facilitated by a reduction in degrees of freedom. Simulations of these capsid deformation experiments provide a testing ground for the techniques, as well as insight into the strength-determining mechanisms of capsid deformation. These methods can be extended as a framework for modeling other proteins and macromolecular structures in cell biology.

Social Function in Multiple X and Y Chromosome Disorders: XXY, XYY, XXYY, XXXY

PubMed Central

Visootsak, Jeannie; Graham, John M.

2014-01-01

Klinefelter syndrome (47,XXY) was initially described in the context of its endocrinologic and physical features; however, subsequent studies have revealed specific impairments in verbal skills and social functioning. Males with sex chromosomal aneuploidies are known to have variability in their developmental profile with the majority presenting with expressive language deficits. As a consequence of language delays, they have an increased likelihood of language-based learning disabilities and social-emotional problems that may persist through adulthood. Studies on males with 47,XXY have revealed unique behavioral and social profiles with possible vulnerability to autistic traits. The prevalence of males with more than one extra sex chromosome (e.g., 48,XXYY and 48,XXXY) and an additional Y (e.g., 47,XYY) is less common, but it is important to understand their social functioning as it provides insight into treatment implications. PMID:20014367

Querying and Extracting Timeline Information from Road Traffic Sensor Data

PubMed Central

Imawan, Ardi; Indikawati, Fitri Indra; Kwon, Joonho; Rao, Praveen

2016-01-01

The escalation of traffic congestion in urban cities has urged many countries to use intelligent transportation system (ITS) centers to collect historical traffic sensor data from multiple heterogeneous sources. By analyzing historical traffic data, we can obtain valuable insights into traffic behavior. Many existing applications have been proposed with limited analysis results because of the inability to cope with several types of analytical queries. In this paper, we propose the QET (querying and extracting timeline information) system—a novel analytical query processing method based on a timeline model for road traffic sensor data. To address query performance, we build a TQ-index (timeline query-index) that exploits spatio-temporal features of timeline modeling. We also propose an intuitive timeline visualization method to display congestion events obtained from specified query parameters. In addition, we demonstrate the benefit of our system through a performance evaluation using a Busan ITS dataset and a Seattle freeway dataset. PMID:27563900

The effect of spaceflight and microgravity on the human brain.

PubMed

Van Ombergen, Angelique; Demertzi, Athena; Tomilovskaya, Elena; Jeurissen, Ben; Sijbers, Jan; Kozlovskaya, Inessa B; Parizel, Paul M; Van de Heyning, Paul H; Sunaert, Stefan; Laureys, Steven; Wuyts, Floris L

2017-10-01

Microgravity, confinement, isolation, and immobilization are just some of the features astronauts have to cope with during space missions. Consequently, long-duration space travel can have detrimental effects on human physiology. Although research has focused on the cardiovascular and musculoskeletal system in particular, the exact impact of spaceflight on the human central nervous system remains to be determined. Previous studies have reported psychological problems, cephalic fluid shifts, neurovestibular problems, and cognitive alterations, but there is paucity in the knowledge of the underlying neural substrates. Previous space analogue studies and preliminary spaceflight studies have shown an involvement of the cerebellum, cortical sensorimotor, and somatosensory areas and the vestibular pathways. Extending this knowledge is crucial, especially in view of long-duration interplanetary missions (e.g., Mars missions) and space tourism. In addition, the acquired insight could be relevant for vestibular patients, patients with neurodegenerative disorders, as well as the elderly population, coping with multisensory deficit syndromes, immobilization, and inactivity.

Beyond 'Doing Gender': Incorporating Race, Class, Place, and Life Transitions into Feminist Drug Research.

PubMed

Miller, Jody; Carbone-Lopez, Kristin

2015-05-01

This essay draws from our research with US rural women methamphetamine users in 2009 to offer strategies for "revisioning" the drug use(r) field to better understand the impact of gender on drug use and drug market participation. We highlight the insights and limitations of a popular strategy in feminist research that conceptualizes gender as performance- commonly referred to as "doing gender"-using illustrations from our research. We encourage scholars to move beyond a primarily normative orientation in studying gender, and investigate gendered organizational features of social life including their intersections with other aspects of social inequality such as those of race, class, and place. In addition, we suggest that feminist scholars can integrate gender in a rigorous way into theoretical perspectives that are typically inattentive to its import, as a means of challenging, enriching, and refining research on drug use, drug users, and drug market participation.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Boyack, B.E.; Steiner, J.L.; Harmony, S.C.

The PIUS Advanced Reactor is a 640-MW(e) pressurized-water reactor developed by Asea Brown Boveri. A unique feature of the PIUS concept is the absence of mechanical control and shutdown rods. Reactivity normally is controlled by the boron concentration in the coolant and the temperature of the moderator coolant. Analyses of five initiating events have been completed on the basis of calculations performed with the system neutronic and thermal-hydraulic analysis code TRAC-PF1/MOD2. The initiating events analyzed are (1) reactor scram, (2) loss of off-site power (3) main steam-line break, (4) small-break loss of coolant, and (5) large-break loss of coolant. Inmore » addition to the baseline calculation for each sequence, sensitivity studies were performed to explore the response of the PIUS reactor to severe off-normal conditions having a very low probability of occurrence. The sensitivity studies provide insights into the robustness of the design.« less

ScMO(BO3) (M = Ca and Cd): new Sc-based oxyborates featuring interesting edge-sharing sandwich-like chains and UV cut-off edges.

PubMed

Ma, Ruru; Xu, Dongdong; Yang, Yun; Su, Xin; Lei, Binghua; Yang, Zhihua; Pan, Shilie

2017-11-07

Two new isostructural rare-earth oxyborates ScMO(BO 3 ) (M = Ca and Cd) with a three-dimensional (3D) cationic framework and parallel arranged [BO 3 ] triangles have been synthesized by the flux method. In the 3D cationic framework, an interesting sandwich-like basic building unit (BBU) is constructed by two [Ca(1)O 4 ] 6- chains and two [Sc(1)O 4 ] 5- chains. ScMO(BO 3 ) melt incongruently, which shows that title compounds can be grown by the flux method. The UV cut-off edges for ScCaO(BO 3 ) and ScCdO(BO 3 ) are 230 and 249 nm, respectively. In addition, the first-principles calculations are performed to gain further insights into the relationship between the microscopic electronic structures and associated optical properties.

Chang'e-2 spacecraft observations of asteroid 4179 Toutatis

NASA Astrophysics Data System (ADS)

Ji, Jianghui; Jiang, Yun; Zhao, Yuhui; Wang, Su; Yu, Liangliang

2016-01-01

On 13 December 2012, Chang'e-2 completed a successful flyby of the near-Earth asteroid 4179 Toutatis at a closest distance of 770 meters from the asteroid's surface. The observations show that Toutatis has an irregular surface and its shape resembles a ginger-root of a smaller lobe (head) and a larger lobe (body). Such bilobate shape is indicative of a contact binary origin for Toutatis. In addition, the high-resolution images better than 3 meters provide a number of new discoveries about this asteroid, such as an 800-meter depression at the end of the large lobe, a sharply perpendicular silhouette near the neck region, boulders, indicating that Toutatis is probably a rubble-pile asteroid. Chang'e-2 observations have significantly revealed new insights into the geological features and the formation and evolution of this asteroid. In final, we brief the future Chinese asteroid mission concept.

Bardet-Biedl syndrome: Mapping of a new locus to chromosome 3 and fine-mapping of the chromosome 16 linked locus

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kwitek-Black, A.E.; Rokhlina, T.; Nishimura, D.Y.

Bardet-Biedl syndrome (BBS) is a heterogeneous autosomal recessive disorder characterized by mental retardation, post-axial polydactyly, obesity, retinitis pigmentosa, and hypogonadism. Other features of this disease include renal and cardiovascular abnormalities and an increased incidence of hypertension and diabetes mellitus. The molecular etiology for BBS is not known. We previously linked BBS to chromosome 16q13 in a large inbred Bedouin family, and excluded this locus in a second large inbred Bedouin family. We now report linkage of this second family to markers on chromosome 3q, proving non-allelic, genetic heterogeneity in the Bedouin population. A third large inbred Bedouin family was excludedmore » from the 3q and 16q BBS loci. In addition to the identification of a new BBS locus on chromosome 3, we have identified and utilized additional short tandem repeat polymorphisms (STRPs) in the 16q BBS region to narrow the candidate interval to 3 cM. Additional recombinant individuals will allow further refinement of the interval. Identification of genes causing BBS has the potential to provide insight into diverse genetic traits and disease processes including obesity, hypertension, diabetes, retinal degeneration, and abnormal limb, renal and cardiac development.« less

Avian Egg and Egg Coat.

PubMed

Okumura, Hiroki

2017-01-01

An ovulated egg of vertebrates is surrounded by unique extracellular matrix, the egg coat or zona pellucida, playing important roles in fertilization and early development. The vertebrate egg coat is composed of two to six zona pellucida (ZP) glycoproteins that are characterized by the evolutionarily conserved ZP-domain module and classified into six subfamilies based on phylogenetic analyses. Interestingly, investigations of biochemical and functional features of the ZP glycoproteins show that the roles of each ZP-glycoprotein family member in the egg-coat formation and the egg-sperm interactions seemingly vary across vertebrates. This might be one reason why comprehensive understandings of the molecular basis of either architecture or physiological functions of egg coat still remain elusive despite more than 3 decades of intensive investigations. In this chapter, an overview of avian egg focusing on the oogenesis are provided in the first section, and unique features of avian egg coat, i.e., perivitelline layer, including the morphology, biogenesis pathway, and physiological functions are discussed mainly on chicken and quail in terms of the characteristics of ZP glycoproteins in the following sections. In addition, these features of avian egg coat are compared to mammalian zona pellucida, from the viewpoint that the structural and functional varieties of ZP glycoproteins might be associated with the evolutionary adaptation to their reproductive strategies. By comparing the egg coat of birds and mammals whose reproductive strategies are largely different, new insights into the molecular mechanisms of vertebrate egg-sperm interactions might be provided.

Functional nucleic acid-based hydrogels for bioanalytical and biomedical applications

PubMed Central

Mo, Liuting; Lu, Chun-Hua; Fu, Ting

2016-01-01

Hydrogels are crosslinked hydrophilic polymers that can absorb a large amount of water. By their hydrophilic, biocompatible and highly tunable nature, hydrogels can be tailored for applications in bioanalysis and biomedicine. Of particular interest are DNA-based hydrogels owing to the unique features of nucleic acids. Since the discovery of DNA double helical structure, interest in DNA has expanded beyond its genetic role to applications in nanotechnology and materials science. In particular, DNA-based hydrogels present such remarkable features as stability, flexibility, precise programmability, stimuli-responsive DNA conformations, facile synthesis and modification. Moreover, functional nucleic acids (FNAs) have allowed the construction of hydrogels based on aptamers, DNAzymes, i-motif nanostructures, siRNAs and CpG oligodeoxynucleotides to provide additional molecular recognition, catalytic activities and therapeutic potential, making them key players in biological analysis and biomedical applications. To date, a variety of applications have been demonstrated with FNA-based hydrogels, including biosensing, environmental analysis, controlled drug release, cell adhesion and targeted cancer therapy. In this review, we focus on advances in the development of FNA-based hydrogels, which have fully incorporated both the unique features of FNAs and DNA-based hydrogels. We first introduce different strategies for constructing DNA-based hydrogels. Subsequently, various types of FNAs and the most recent developments of FNA-based hydrogels for bioanalytical and biomedical applications are described with some selected examples. Finally, the review provides an insight into the remaining challenges and future perspectives of FNA-based hydrogels. PMID:26758955

Outcome of first-episode schizophrenia in India: longitudinal study of effect of insight and psychopathology.

PubMed

Saravanan, Balasubramanian; Jacob, K S; Johnson, Shanthi; Prince, Martin; Bhugra, Dinesh; David, Anthony S

2010-06-01

Transcultural studies have found lack of insight to be an almost invariable feature of acute and chronic schizophrenia, but its influence on prognosis is unclear. To investigate the relationship between insight, psychopathology and outcome of first-episode schizophrenia in Vellore, India. Patients with a DSM-IV diagnosis of schizophrenia (n = 131) were assessed prospectively at baseline and at 6-month and 12-month follow-up. Demographic and clinical measures included insight, psychopathology, duration of untreated psychosis (DUP) and social functioning. Linear and logistic regression was used to measure predictors of outcome. Follow-up data were available for 115 patients at 1 year. All achieved remission, half of them with and half without residual symptoms. Changes in psychopathology and insight during the first 6 months and DUP strongly predicted outcome (relapse or functional impairment), controlling for baseline measures. Outcome of schizophrenia in this setting is driven by early symptomatic improvement and is relatively favourable, in line with other studies from low- and middle-income countries. Early improvement in insight might be a useful clinical guide to future outcome. Reduction of DUP should be a target for intervention.

Current controversies in the relationships between autism and epilepsy.

PubMed

Besag, Frank M C

2015-06-01

The controversies that have arisen in endeavoring to establish the nature of the relationships between autism and epilepsy might be summarized in a few simple questions, most of which do not yet have clear, complete answers. Does epilepsy cause autism? Does autism cause epilepsy? Are there underlying brain mechanisms that predispose to both conditions? What is the role of genetics in this regard? What is the importance of prenatal, perinatal, and postnatal environmental factors? Do any of the proposed relationships between autism and epilepsy provide insight into useful management or treatment? Is the prognosis of either autism or epilepsy different when the other condition is also present? What is the role of additional comorbidities, such as intellectual impairment or attention deficit hyperactivity disorder, in the relationship between the two conditions and in influencing treatment choices? From the evidence currently available, it would appear that epilepsy can rarely be the cause of autistic features but is not the cause of autism in most cases. There is currently no credible mechanism for suggesting that autism might cause epilepsy. There is strong evidence for an underlying predisposition for both conditions, particularly arising from genetic investigations. However, many issues remain unresolved. Considering the amount of research that has been published in this area, it is surprising that so few definitive answers have been established. The papers in this issue's special section provide additional insights into the relationships between autism and epilepsy; while they do not provide answers to all the questions, they represent considerable progress in this area and, at the very least, give some strong indication of what research might, in the future, provide such answers. Copyright © 2015. Published by Elsevier Inc.

Comparing Mycobacterium tuberculosis genomes using genome topology networks.

PubMed

Jiang, Jianping; Gu, Jianlei; Zhang, Liang; Zhang, Chenyi; Deng, Xiao; Dou, Tonghai; Zhao, Guoping; Zhou, Yan

2015-02-14

Over the last decade, emerging research methods, such as comparative genomic analysis and phylogenetic study, have yielded new insights into genotypes and phenotypes of closely related bacterial strains. Several findings have revealed that genomic structural variations (SVs), including gene gain/loss, gene duplication and genome rearrangement, can lead to different phenotypes among strains, and an investigation of genes affected by SVs may extend our knowledge of the relationships between SVs and phenotypes in microbes, especially in pathogenic bacteria. In this work, we introduce a 'Genome Topology Network' (GTN) method based on gene homology and gene locations to analyze genomic SVs and perform phylogenetic analysis. Furthermore, the concept of 'unfixed ortholog' has been proposed, whose members are affected by SVs in genome topology among close species. To improve the precision of 'unfixed ortholog' recognition, a strategy to detect annotation differences and complete gene annotation was applied. To assess the GTN method, a set of thirteen complete M. tuberculosis genomes was analyzed as a case study. GTNs with two different gene homology-assigning methods were built, the Clusters of Orthologous Groups (COG) method and the orthoMCL clustering method, and two phylogenetic trees were constructed accordingly, which may provide additional insights into whole genome-based phylogenetic analysis. We obtained 24 unfixable COG groups, of which most members were related to immunogenicity and drug resistance, such as PPE-repeat proteins (COG5651) and transcriptional regulator TetR gene family members (COG1309). The GTN method has been implemented in PERL and released on our website. The tool can be downloaded from http://homepage.fudan.edu.cn/zhouyan/gtn/ , and allows re-annotating the 'lost' genes among closely related genomes, analyzing genes affected by SVs, and performing phylogenetic analysis. With this tool, many immunogenic-related and drug resistance-related genes were found to be affected by SVs in M. tuberculosis genomes. We believe that the GTN method will be suitable for the exploration of genomic SVs in connection with biological features of bacterial strains, and that GTN-based phylogenetic analysis will provide additional insights into whole genome-based phylogenetic analysis.

The Functional Anatomy of the Carpometacarpal Complex in Anthropoids and Its Implications for the Evolution of the Hominoid Hand.

PubMed

Selby, Michael S; Simpson, Scott W; Lovejoy, C Owen

2016-05-01

Previously, we described several features of the carpometacarpal joints in extant large-bodied apes that are likely adaptations to the functional demands of vertical climbing and suspension. We observed that all hominids, including modern humans and the 4.4-million-year-old hominid Ardipithecus ramidus, lacked these features. Here, we assess the uniqueness of these features in a large sample of monkey, ape, and human hands. These new data provide additional insights into the functional adaptations and evolution of the anthropoid hand. Our survey highlights a series of anatomical adaptations that restrict motion between the second and third metacarpals (MC2 and MC3) and their associated carpals in extant apes, achieved via joint reorganization and novel energy dissipation mechanisms. Their hamate-MC4 and -MC5 joint surface morphologies suggest limited mobility, at least in Pan. Gibbons and spider monkeys have several characters (angled MC3, complex capitate-MC3 joint topography, variably present capitate-MC3 ligaments) that suggest functional convergence in response to suspensory locomotion. Baboons have carpometacarpal morphology suggesting flexion/extension at these joints beyond that observed in most other Old World monkeys, probably as an energy dissipating mechanism minimizing collision forces during terrestrial locomotion. All hominids lack these specializations of the extant great apes, suggesting that vertical climbing was never a central feature of our ancestral locomotor repertoire. Furthermore, the reinforced carpometacarpus of vertically climbing African apes was likely appropriated for knuckle-walking in concert with other novel potential energy dissipating mechanisms. The most parsimonious explanation of the structural similarity of these carpometacarpal specializations in great apes is that they evolved independently. © 2016 Wiley Periodicals, Inc.

Corresponding-states behavior of SPC/E-based modified (bent and hybrid) water models

NASA Astrophysics Data System (ADS)

Weiss, Volker C.

2017-02-01

The remarkable and sometimes anomalous properties of water can be traced back at the molecular level to the tetrahedral coordination of molecules due to the ability of a water molecule to form four hydrogen bonds to its neighbors; this feature allows for the formation of a network that greatly influences the thermodynamic behavior. Computer simulations are becoming increasingly important for our understanding of water. Molecular models of water, such as SPC/E, are needed for this purpose, and they have proved to capture many important features of real water. Modifications of the SPC/E model have been proposed, some changing the H-O-H angle (bent models) and others increasing the importance of dispersion interactions (hybrid models), to study the structural features that set water apart from other polar fluids and from simple fluids such as argon. Here, we focus on the properties at liquid-vapor equilibrium and study the coexistence curve, the interfacial tension, and the vapor pressure in a corresponding-states approach. In particular, we calculate Guggenheim's ratio for the reduced apparent enthalpy of vaporization and Guldberg's ratio for the reduced normal boiling point. This analysis offers additional insight from a more macroscopic, thermodynamic perspective and augments that which has already been learned at the molecular level from simulations. In the hybrid models, the relative importance of dispersion interactions is increased, which turns the modified water into a Lennard-Jones-like fluid. Consequently, in a corresponding-states framework, the typical behavior of simple fluids, such as argon, is seen to be approached asymptotically. For the bent models, decreasing the bond angle turns the model essentially into a polar diatomic fluid in which the particles form linear molecular arrangements; as a consequence, characteristic features of the corresponding-states behavior of hydrogen halides emerge.

Machine Learning Meta-analysis of Large Metagenomic Datasets: Tools and Biological Insights.

PubMed

Pasolli, Edoardo; Truong, Duy Tin; Malik, Faizan; Waldron, Levi; Segata, Nicola

2016-07-01

Shotgun metagenomic analysis of the human associated microbiome provides a rich set of microbial features for prediction and biomarker discovery in the context of human diseases and health conditions. However, the use of such high-resolution microbial features presents new challenges, and validated computational tools for learning tasks are lacking. Moreover, classification rules have scarcely been validated in independent studies, posing questions about the generality and generalization of disease-predictive models across cohorts. In this paper, we comprehensively assess approaches to metagenomics-based prediction tasks and for quantitative assessment of the strength of potential microbiome-phenotype associations. We develop a computational framework for prediction tasks using quantitative microbiome profiles, including species-level relative abundances and presence of strain-specific markers. A comprehensive meta-analysis, with particular emphasis on generalization across cohorts, was performed in a collection of 2424 publicly available metagenomic samples from eight large-scale studies. Cross-validation revealed good disease-prediction capabilities, which were in general improved by feature selection and use of strain-specific markers instead of species-level taxonomic abundance. In cross-study analysis, models transferred between studies were in some cases less accurate than models tested by within-study cross-validation. Interestingly, the addition of healthy (control) samples from other studies to training sets improved disease prediction capabilities. Some microbial species (most notably Streptococcus anginosus) seem to characterize general dysbiotic states of the microbiome rather than connections with a specific disease. Our results in modelling features of the "healthy" microbiome can be considered a first step toward defining general microbial dysbiosis. The software framework, microbiome profiles, and metadata for thousands of samples are publicly available at http://segatalab.cibio.unitn.it/tools/metaml.

The Influence of Runoff and Surface Hydrology on Titan's Weather and Climate

NASA Astrophysics Data System (ADS)

Faulk, S.; Lora, J. M.; Mitchell, J.; Moon, S.

2017-12-01

Titan's surface liquid distribution has been shown by general circulation models (GCMs) to greatly influence the hydrological cycle, producing characteristic weather and seasonal climate patterns. Simulations from the Titan Atmospheric Model (TAM) with imposed polar methane "wetlands" reservoirs realistically produce observed cloud features and temperature profiles of Titan's atmosphere, whereas "aquaplanet" simulations with a global methane ocean are not as successful. In addition, wetlands simulations, unlike aquaplanet simulations, demonstrate strong correlations between extreme rainfall behavior and observed geomorphic features, indicating the influential role of precipitation in shaping Titan's surface. The wetlands configuration is, in part, motivated by Titan's large-scale topography featuring low-latitude highlands and high-latitude lowlands, with the implication being that methane may concentrate in the high-latitude lowlands by way of runoff and subsurface flow of a global or regional methane table. However, the extent to which topography controls the surface liquid distribution and thus impacts the global hydrological cycle by driving surface and subsurface flow is unclear. Here we present TAM simulations wherein the imposed wetlands reservoirs are replaced by a surface runoff scheme that allows surface liquid to self-consistently redistribute under the influence of topography. We discuss the impact of surface runoff on the surface liquid distribution over seasonal timescales and compare the resulting hydrological cycle to observed cloud and surface features, as well as to the hydrological cycles of the TAM wetlands and aquaplanet simulations. While still idealized, this more realistic representation of Titan's hydrology provides new insight into the complex interaction between Titan's atmosphere and surface, demonstrates the influence of surface runoff on Titan's global climate, and lays the groundwork for further surface hydrology developments in Titan GCMs, including infiltration and subsurface flow.

The impact of runoff and surface hydrology on Titan's climate

NASA Astrophysics Data System (ADS)

Faulk, Sean; Lora, Juan; Mitchell, Jonathan

2017-10-01

Titan’s surface liquid distribution has been shown by general circulation models (GCMs) to greatly influence the hydrological cycle. Simulations from the Titan Atmospheric Model (TAM) with imposed polar methane “wetlands” reservoirs realistically produce many observed features of Titan’s atmosphere, whereas “aquaplanet” simulations with a global methane ocean are not as successful. In addition, wetlands simulations, unlike aquaplanet simulations, demonstrate strong correlations between extreme rainfall behavior and observed geomorphic features, indicating the influential role of precipitation in shaping Titan’s surface. The wetlands configuration is, in part, motivated by Titan’s large-scale topography featuring low-latitude highlands and high-latitude lowlands, with the implication being that methane may concentrate in the high-latitude lowlands by way of runoff and subsurface flow. However, the extent to which topography controls the surface liquid distribution and thus impacts the global hydrological cycle by driving surface and subsurface flow is unclear. Here we present TAM simulations wherein the imposed wetlands reservoirs are replaced by a surface runoff scheme that allows surface liquid to self-consistently redistribute under the influence of topography. To isolate the singular impact of surface runoff on Titan’s climatology, we run simulations without parameterizations of subsurface flow and topography-atmosphere interactions. We discuss the impact of surface runoff on the surface liquid distribution over seasonal timescales and compare the resulting hydrological cycle to observed cloud and surface features, as well as to the hydrological cycles of the TAM wetlands and aquaplanet simulations. While still idealized, this more realistic representation of Titan’s hydrology provides new insight into the complex interaction between Titan’s atmosphere and surface, demonstrates the influence of surface runoff on Titan’s global climate, and lays the groundwork for further surface hydrology developments in Titan GCMs.

The molecular basis of breast cancer pathological phenotypes.

PubMed

Heng, Yujing J; Lester, Susan C; Tse, Gary Mk; Factor, Rachel E; Allison, Kimberly H; Collins, Laura C; Chen, Yunn-Yi; Jensen, Kristin C; Johnson, Nicole B; Jeong, Jong Cheol; Punjabi, Rahi; Shin, Sandra J; Singh, Kamaljeet; Krings, Gregor; Eberhard, David A; Tan, Puay Hoon; Korski, Konstanty; Waldman, Frederic M; Gutman, David A; Sanders, Melinda; Reis-Filho, Jorge S; Flanagan, Sydney R; Gendoo, Deena Ma; Chen, Gregory M; Haibe-Kains, Benjamin; Ciriello, Giovanni; Hoadley, Katherine A; Perou, Charles M; Beck, Andrew H

2017-02-01

The histopathological evaluation of morphological features in breast tumours provides prognostic information to guide therapy. Adjunct molecular analyses provide further diagnostic, prognostic and predictive information. However, there is limited knowledge of the molecular basis of morphological phenotypes in invasive breast cancer. This study integrated genomic, transcriptomic and protein data to provide a comprehensive molecular profiling of morphological features in breast cancer. Fifteen pathologists assessed 850 invasive breast cancer cases from The Cancer Genome Atlas (TCGA). Morphological features were significantly associated with genomic alteration, DNA methylation subtype, PAM50 and microRNA subtypes, proliferation scores, gene expression and/or reverse-phase protein assay subtype. Marked nuclear pleomorphism, necrosis, inflammation and a high mitotic count were associated with the basal-like subtype, and had a similar molecular basis. Omics-based signatures were constructed to predict morphological features. The association of morphology transcriptome signatures with overall survival in oestrogen receptor (ER)-positive and ER-negative breast cancer was first assessed by use of the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) dataset; signatures that remained prognostic in the METABRIC multivariate analysis were further evaluated in five additional datasets. The transcriptomic signature of poorly differentiated epithelial tubules was prognostic in ER-positive breast cancer. No signature was prognostic in ER-negative breast cancer. This study provided new insights into the molecular basis of breast cancer morphological phenotypes. The integration of morphological with molecular data has the potential to refine breast cancer classification, predict response to therapy, enhance our understanding of breast cancer biology, and improve clinical management. This work is publicly accessible at www.dx.ai/tcga_breast. Copyright © 2016 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd. Copyright © 2016 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

Quantification of Lignin and Its Structural Features in Plant Biomass Using 13C Lignin as Internal Standard for Pyrolysis-GC-SIM-MS.

PubMed

van Erven, Gijs; de Visser, Ries; Merkx, Donny W H; Strolenberg, Willem; de Gijsel, Peter; Gruppen, Harry; Kabel, Mirjam A

2017-10-17

Understanding the mechanisms underlying plant biomass recalcitrance at the molecular level can only be achieved by accurate analyses of both the content and structural features of the molecules involved. Current quantification of lignin is, however, majorly based on unspecific gravimetric analysis after sulfuric acid hydrolysis. Hence, our research aimed at specific lignin quantification with concurrent characterization of its structural features. Hereto, for the first time, a polymeric 13 C lignin was used as internal standard (IS) for lignin quantification via analytical pyrolysis coupled to gas chromatography with mass-spectrometric detection in selected ion monitoring mode (py-GC-SIM-MS). In addition, relative response factors (RRFs) for the various pyrolysis products obtained were determined and applied. First, 12 C and 13 C lignin were isolated from nonlabeled and uniformly 13 C labeled wheat straw, respectively, and characterized by heteronuclear single quantum coherence (HSQC), nuclear magnetic resonance (NMR), and py-GC/MS. The two lignin isolates were found to have identical structures. Second, 13 C-IS based lignin quantification by py-GC-SIM-MS was validated in reconstituted biomass model systems with known contents of the 12 C lignin analogue and was shown to be extremely accurate (>99.9%, R 2 > 0.999) and precise (RSD < 1.5%). Third, 13 C-IS based lignin quantification was applied to four common poaceous biomass sources (wheat straw, barley straw, corn stover, and sugar cane bagasse), and lignin contents were in good agreement with the total gravimetrically determined lignin contents. Our robust method proves to be a promising alternative for the high-throughput quantification of lignin in milled biomass samples directly and simultaneously provides a direct insight into the structural features of lignin.

Quantification of Lignin and Its Structural Features in Plant Biomass Using 13C Lignin as Internal Standard for Pyrolysis-GC-SIM-MS

PubMed Central

2017-01-01

Understanding the mechanisms underlying plant biomass recalcitrance at the molecular level can only be achieved by accurate analyses of both the content and structural features of the molecules involved. Current quantification of lignin is, however, majorly based on unspecific gravimetric analysis after sulfuric acid hydrolysis. Hence, our research aimed at specific lignin quantification with concurrent characterization of its structural features. Hereto, for the first time, a polymeric 13C lignin was used as internal standard (IS) for lignin quantification via analytical pyrolysis coupled to gas chromatography with mass-spectrometric detection in selected ion monitoring mode (py-GC-SIM-MS). In addition, relative response factors (RRFs) for the various pyrolysis products obtained were determined and applied. First, 12C and 13C lignin were isolated from nonlabeled and uniformly 13C labeled wheat straw, respectively, and characterized by heteronuclear single quantum coherence (HSQC), nuclear magnetic resonance (NMR), and py-GC/MS. The two lignin isolates were found to have identical structures. Second, 13C-IS based lignin quantification by py-GC-SIM-MS was validated in reconstituted biomass model systems with known contents of the 12C lignin analogue and was shown to be extremely accurate (>99.9%, R2 > 0.999) and precise (RSD < 1.5%). Third, 13C-IS based lignin quantification was applied to four common poaceous biomass sources (wheat straw, barley straw, corn stover, and sugar cane bagasse), and lignin contents were in good agreement with the total gravimetrically determined lignin contents. Our robust method proves to be a promising alternative for the high-throughput quantification of lignin in milled biomass samples directly and simultaneously provides a direct insight into the structural features of lignin. PMID:28926698

Deep X-ray Observations of an Ongoing Merger and 400 Myr of AGN Activity in Cygnus A

NASA Astrophysics Data System (ADS)

Wise, Michael W.; De Vries, Martijn; Nulsen, Paul; Snios, Bradford; Birkinshaw, Mark; Worrall, Diana; Duffy, Ryan; Halbesma, Timo; Donnert, Julius; Hardcastle, Martin

2017-08-01

We present a detailed spatial and spectral analysis of the large-scale X-ray emission associated with the merging cluster of galaxies containing the powerful Cygnus A radio galaxy. Using a new 1 Msec exposure from the ongoing Chandra XVP project, we have mapped the large-scale structure, temperature and abundance of the ICM in a 1 Mpc x 1 Mpc region surrounding Cygnus A. This new, deep exposure resolves unprecedented detail in the jets, lobes, and cocoon shock associated with Cygnus A, and provides new insights into the emission mechanisms that produce these features as well as implications for the ongoing activity of the central AGN. On larger scales, these new data reveal complex and dramatic temperature, pressure, entropy and metallicity structure in the ICM surrounding Cygnus A. We confirm the presence of large-scale X-ray emission associated with the two merging cluster components seen previously in lower resolution data. The temperature structure on the scale of the merger exhibits an asymmetric enhancement to the NW consistent with projected hotter gas from the merger shock. Using the derived density and temperature profiles in the two merging sub-cluster components as inputs, we have constructed a grid of hydro-dynamical simulations to constrain the geometry of the merger system. These models imply a pre-merger system with a 1:1 mass ratio at the virial radius with an inclination toward the line of sight of 35-45 deg. In addition to the merger-induced temperature asymmetry, we find evidence for additional surface brightness and temperature features indicative of previous outburst activity in Cygnus A over the past 400 Myr. Based on the location and strength of these features, we derive the energy associated with these previous outbursts and place constraints on the growth of the black hole in Cygnus A over that timescale.

On the Design of an Efficient Cardiac Health Monitoring System Through Combined Analysis of ECG and SCG Signals.

PubMed

Sahoo, Prasan Kumar; Thakkar, Hiren Kumar; Lin, Wen-Yen; Chang, Po-Cheng; Lee, Ming-Yih

2018-01-28

Cardiovascular disease (CVD) is a major public concern and socioeconomic problem across the globe. The popular high-end cardiac health monitoring systems such as magnetic resonance imaging (MRI), computerized tomography scan (CT scan), and echocardiography (Echo) are highly expensive and do not support long-term continuous monitoring of patients without disrupting their activities of daily living (ADL). In this paper, the continuous and non-invasive cardiac health monitoring using unobtrusive sensors is explored aiming to provide a feasible and low-cost alternative to foresee possible cardiac anomalies in an early stage. It is learned that cardiac health monitoring based on sole usage of electrocardiogram (ECG) signals may not provide powerful insights as ECG provides shallow information on various cardiac activities in the form of electrical impulses only. Hence, a novel low-cost, non-invasive seismocardiogram (SCG) signal along with ECG signals are jointly investigated for the robust cardiac health monitoring. For this purpose, the in-laboratory data collection model is designed for simultaneous acquisition of ECG and SCG signals followed by mechanisms for the automatic delineation of relevant feature points in acquired ECG and SCG signals. In addition, separate feature points based novel approach is adopted to distinguish between normal and abnormal morphology in each ECG and SCG cardiac cycle. Finally, a combined analysis of ECG and SCG is carried out by designing a Naïve Bayes conditional probability model. Experiments on Institutional Review Board (IRB) approved licensed ECG/SCG signals acquired from real subjects containing 12,000 cardiac cycles show that the proposed feature point delineation mechanisms and abnormal morphology detection methods consistently perform well and give promising results. In addition, experimental results show that the combined analysis of ECG and SCG signals provide more reliable cardiac health monitoring compared to the standalone use of ECG and SCG.

On the Design of an Efficient Cardiac Health Monitoring System Through Combined Analysis of ECG and SCG Signals

PubMed Central

Lin, Wen-Yen; Chang, Po-Cheng

2018-01-01

Cardiovascular disease (CVD) is a major public concern and socioeconomic problem across the globe. The popular high-end cardiac health monitoring systems such as magnetic resonance imaging (MRI), computerized tomography scan (CT scan), and echocardiography (Echo) are highly expensive and do not support long-term continuous monitoring of patients without disrupting their activities of daily living (ADL). In this paper, the continuous and non-invasive cardiac health monitoring using unobtrusive sensors is explored aiming to provide a feasible and low-cost alternative to foresee possible cardiac anomalies in an early stage. It is learned that cardiac health monitoring based on sole usage of electrocardiogram (ECG) signals may not provide powerful insights as ECG provides shallow information on various cardiac activities in the form of electrical impulses only. Hence, a novel low-cost, non-invasive seismocardiogram (SCG) signal along with ECG signals are jointly investigated for the robust cardiac health monitoring. For this purpose, the in-laboratory data collection model is designed for simultaneous acquisition of ECG and SCG signals followed by mechanisms for the automatic delineation of relevant feature points in acquired ECG and SCG signals. In addition, separate feature points based novel approach is adopted to distinguish between normal and abnormal morphology in each ECG and SCG cardiac cycle. Finally, a combined analysis of ECG and SCG is carried out by designing a Naïve Bayes conditional probability model. Experiments on Institutional Review Board (IRB) approved licensed ECG/SCG signals acquired from real subjects containing 12,000 cardiac cycles show that the proposed feature point delineation mechanisms and abnormal morphology detection methods consistently perform well and give promising results. In addition, experimental results show that the combined analysis of ECG and SCG signals provide more reliable cardiac health monitoring compared to the standalone use of ECG and SCG. PMID:29382098

Data processing, multi-omic pathway mapping, and metabolite activity analysis using XCMS Online

PubMed Central

Forsberg, Erica M; Huan, Tao; Rinehart, Duane; Benton, H Paul; Warth, Benedikt; Hilmers, Brian; Siuzdak, Gary

2018-01-01

Systems biology is the study of complex living organisms, and as such, analysis on a systems-wide scale involves the collection of information-dense data sets that are representative of an entire phenotype. To uncover dynamic biological mechanisms, bioinformatics tools have become essential to facilitating data interpretation in large-scale analyses. Global metabolomics is one such method for performing systems biology, as metabolites represent the downstream functional products of ongoing biological processes. We have developed XCMS Online, a platform that enables online metabolomics data processing and interpretation. A systems biology workflow recently implemented within XCMS Online enables rapid metabolic pathway mapping using raw metabolomics data for investigating dysregulated metabolic processes. In addition, this platform supports integration of multi-omic (such as genomic and proteomic) data to garner further systems-wide mechanistic insight. Here, we provide an in-depth procedure showing how to effectively navigate and use the systems biology workflow within XCMS Online without a priori knowledge of the platform, including uploading liquid chromatography (LCLC)–mass spectrometry (MS) data from metabolite-extracted biological samples, defining the job parameters to identify features, correcting for retention time deviations, conducting statistical analysis of features between sample classes and performing predictive metabolic pathway analysis. Additional multi-omics data can be uploaded and overlaid with previously identified pathways to enhance systems-wide analysis of the observed dysregulations. We also describe unique visualization tools to assist in elucidation of statistically significant dysregulated metabolic pathways. Parameter input takes 5–10 min, depending on user experience; data processing typically takes 1–3 h, and data analysis takes ~30 min. PMID:29494574

Robust electroencephalogram phase estimation with applications in brain-computer interface systems.

PubMed

Seraj, Esmaeil; Sameni, Reza

2017-03-01

In this study, a robust method is developed for frequency-specific electroencephalogram (EEG) phase extraction using the analytic representation of the EEG. Based on recent theoretical findings in this area, it is shown that some of the phase variations-previously associated to the brain response-are systematic side-effects of the methods used for EEG phase calculation, especially during low analytical amplitude segments of the EEG. With this insight, the proposed method generates randomized ensembles of the EEG phase using minor perturbations in the zero-pole loci of narrow-band filters, followed by phase estimation using the signal's analytical form and ensemble averaging over the randomized ensembles to obtain a robust EEG phase and frequency. This Monte Carlo estimation method is shown to be very robust to noise and minor changes of the filter parameters and reduces the effect of fake EEG phase jumps, which do not have a cerebral origin. As proof of concept, the proposed method is used for extracting EEG phase features for a brain computer interface (BCI) application. The results show significant improvement in classification rates using rather simple phase-related features and a standard K-nearest neighbors and random forest classifiers, over a standard BCI dataset. The average performance was improved between 4-7% (in absence of additive noise) and 8-12% (in presence of additive noise). The significance of these improvements was statistically confirmed by a paired sample t-test, with 0.01 and 0.03 p-values, respectively. The proposed method for EEG phase calculation is very generic and may be applied to other EEG phase-based studies.

Canonical Correlation Analysis for Feature-Based Fusion of Biomedical Imaging Modalities and Its Application to Detection of Associative Networks in Schizophrenia.

PubMed

Correa, Nicolle M; Li, Yi-Ou; Adalı, Tülay; Calhoun, Vince D

2008-12-01

Typically data acquired through imaging techniques such as functional magnetic resonance imaging (fMRI), structural MRI (sMRI), and electroencephalography (EEG) are analyzed separately. However, fusing information from such complementary modalities promises to provide additional insight into connectivity across brain networks and changes due to disease. We propose a data fusion scheme at the feature level using canonical correlation analysis (CCA) to determine inter-subject covariations across modalities. As we show both with simulation results and application to real data, multimodal CCA (mCCA) proves to be a flexible and powerful method for discovering associations among various data types. We demonstrate the versatility of the method with application to two datasets, an fMRI and EEG, and an fMRI and sMRI dataset, both collected from patients diagnosed with schizophrenia and healthy controls. CCA results for fMRI and EEG data collected for an auditory oddball task reveal associations of the temporal and motor areas with the N2 and P3 peaks. For the application to fMRI and sMRI data collected for an auditory sensorimotor task, CCA results show an interesting joint relationship between fMRI and gray matter, with patients with schizophrenia showing more functional activity in motor areas and less activity in temporal areas associated with less gray matter as compared to healthy controls. Additionally, we compare our scheme with an independent component analysis based fusion method, joint-ICA that has proven useful for such a study and note that the two methods provide complementary perspectives on data fusion.

Clinical and neuropsychological correlates of insight in schizophrenia and bipolar I disorder: does diagnosis matter?

PubMed

Varga, Monica; Magnusson, Andres; Flekkøy, Kjell; David, Anthony S; Opjordsmoen, Stein

2007-01-01

Lack of insight is a well-recognized feature of schizophrenia and is associated with symptom severity and cognitive impairments. However, the diagnostic specificity of insight variables and their correlates is not known. To assess this specificity, we compared awareness of illness and neuropsychological function between patients with chronic schizophrenia and bipolar I disorder. We assessed insight, level of psychopathology, and cognitive performance on a neuropsychological test battery in 37 patients with Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition bipolar I disorder, 32 patients with schizophrenia, and 31 healthy subjects for comparison. There was no significant difference between the 2 diagnostic groups on general illness awareness. However, patients with bipolar disorder had better awareness of their symptoms and their pathologic nature compared to patients with schizophrenia. Similar patterns of association emerged between insight and clinical variables. General unawareness was associated with clinical severity, especially of the affective type, and working memory deficits (Wechsler Adult Intelligence Scale digit span) in both diagnostic groups. The contribution of other cognitive deficits to insight differed across the groups. Misattribution differed from the other aspects of insight in its relative independence of clinical and neurocognitive correlates. Both patient groups were neurocognitively impaired, with the schizophrenia group performing significantly worse on conceptual ability, verbal learning, visuospatial processing, and motor speed. The results suggest that differences in general insight in major mental disorders may be explained by symptom severity and working memory function rather than the specific diagnosis. Subcomponents of insight are influenced by different factors emphasizing the need to consider insight as multidimensional.

Windblown Features on Venus and Geological Mapping

NASA Technical Reports Server (NTRS)

Greeley, Ronald

1999-01-01

The objectives of this study were to: 1) develop a global data base of aeolian features by searching Magellan coverage for possible time-variable wind streaks, 2) analyze the data base to characterize aeolian features and processes on Venus, 3) apply the analysis to assessments of wind patterns near the surface and for comparisons with atmospheric circulation models, 4) analyze shuttle radar data acquired for aeolian features on Earth to determine their radar characteristics, and 5) conduct geological mapping of two quadrangles. Wind, or aeolian, features are observed on Venus and aeolian processes play a role in modifying its surface. Analysis of features resulting from aeolian processes provides insight into characteristics of both the atmosphere and the surface. Wind related features identified on Venus include erosional landforms (yardangs), depositional dune fields, and features resulting from the interaction of the atmosphere and crater ejecta at the time of impact. The most abundant aeolian features are various wind streaks. Their discovery on Venus afforded the opportunity to learn about the interaction of the atmosphere and surface, both for the identification of sediments and in mapping near-surface winds.

On the application of neural networks to the classification of phase modulated waveforms

NASA Astrophysics Data System (ADS)

Buchenroth, Anthony; Yim, Joong Gon; Nowak, Michael; Chakravarthy, Vasu

2017-04-01

Accurate classification of phase modulated radar waveforms is a well-known problem in spectrum sensing. Identification of such waveforms aids situational awareness enabling radar and communications spectrum sharing. While various feature extraction and engineering approaches have sought to address this problem, the use of a machine learning algorithm that best utilizes these features is becomes foremost. In this effort, a comparison of a standard shallow and a deep learning approach are explored. Experiments provide insights into classifier architecture, training procedure, and performance.

Omics strategies for revealing Yersinia pestis virulence

PubMed Central

Yang, Ruifu; Du, Zongmin; Han, Yanping; Zhou, Lei; Song, Yajun; Zhou, Dongsheng; Cui, Yujun

2012-01-01

Omics has remarkably changed the way we investigate and understand life. Omics differs from traditional hypothesis-driven research because it is a discovery-driven approach. Mass datasets produced from omics-based studies require experts from different fields to reveal the salient features behind these data. In this review, we summarize omics-driven studies to reveal the virulence features of Yersinia pestis through genomics, trascriptomics, proteomics, interactomics, etc. These studies serve as foundations for further hypothesis-driven research and help us gain insight into Y. pestis pathogenesis. PMID:23248778

Analyzing Sub-Classifications of Glaucoma via SOM Based Clustering of Optic Nerve Images.

PubMed

Yan, Sanjun; Abidi, Syed Sibte Raza; Artes, Paul Habib

2005-01-01

We present a data mining framework to cluster optic nerve images obtained by Confocal Scanning Laser Tomography (CSLT) in normal subjects and patients with glaucoma. We use self-organizing maps and expectation maximization methods to partition the data into clusters that provide insights into potential sub-classification of glaucoma based on morphological features. We conclude that our approach provides a first step towards a better understanding of morphological features in optic nerve images obtained from glaucoma patients and healthy controls.

Disease Suppressive Soils: New Insights from the Soil Microbiome

USDA-ARS?s Scientific Manuscript database

In this review, we will present three currently-studied model systems with features representative of specific and general suppressiveness. Based on these systems, we will consider hypotheses about the fundamental nature of specific and general disease-suppressive soil microbial communities, explore...

Craniofacial and Dental Development in Costello Syndrome

PubMed Central

Goodwin, Alice F.; Oberoi, Snehlata; Landan, Maya; Charles, Cyril; Massie, Jessica C.; Fairley, Cecilia; Rauen, Katherine A.; Klein, Ophir D.

2014-01-01

Costello syndrome (CS) is a RASopathy characterized by a wide range of cardiac, musculoskeletal, dermatological, and developmental abnormalities. The RASopathies are defined as a group of syndromes caused by activated Ras/mitogen-activated protein kinase (MAPK) signaling. Specifically, CS is caused by activating mutations in HRAS. Although receptor tyrosine kinase (RTK) signaling, which is upstream of Ras/MAPK, is known to play a critical role in craniofacial and dental development, the craniofacial and dental features of CS have not been systematically defined in a large group of individuals. In order to address this gap in our understanding and fully characterize the CS phenotype, we evaluated the craniofacial and dental phenotype in a large cohort (n=41) of CS individuals. We confirmed that the craniofacial features common in CS include macrocephaly, bitemporal narrowing, convex facial profile, full cheeks, and large mouth. Additionally, CS patients have a characteristic dental phenotype that includes malocclusion with anterior open bite and posterior crossbite, enamel hypo-mineralization, delayed tooth development and eruption, gingival hyperplasia, thickening of the alveolar ridge, and high palate. Comparison of the craniofacial and dental phenotype in CS with other RASopathies, such as cardio-facio-cutaneous syndrome (CFC), provides insight into the complexities of Ras/MAPK signaling in human craniofacial and dental development. PMID:24668879

gRINN: a tool for calculation of residue interaction energies and protein energy network analysis of molecular dynamics simulations.

PubMed

Serçinoglu, Onur; Ozbek, Pemra

2018-05-25

Atomistic molecular dynamics (MD) simulations generate a wealth of information related to the dynamics of proteins. If properly analyzed, this information can lead to new insights regarding protein function and assist wet-lab experiments. Aiming to identify interactions between individual amino acid residues and the role played by each in the context of MD simulations, we present a stand-alone software called gRINN (get Residue Interaction eNergies and Networks). gRINN features graphical user interfaces (GUIs) and a command-line interface for generating and analyzing pairwise residue interaction energies and energy correlations from protein MD simulation trajectories. gRINN utilizes the features of NAMD or GROMACS MD simulation packages and automatizes the steps necessary to extract residue-residue interaction energies from user-supplied simulation trajectories, greatly simplifying the analysis for the end-user. A GUI, including an embedded molecular viewer, is provided for visualization of interaction energy time-series, distributions, an interaction energy matrix, interaction energy correlations and a residue correlation matrix. gRINN additionally offers construction and analysis of Protein Energy Networks, providing residue-based metrics such as degrees, betweenness-centralities, closeness centralities as well as shortest path analysis. gRINN is free and open to all users without login requirement at http://grinn.readthedocs.io.

Handwriting features of children with developmental coordination disorder--results of triangular evaluation.

PubMed

Rosenblum, Sara; Margieh, Jumana Aassy; Engel-Yeger, Batya

2013-11-01

Developmental coordination disorders (DCD) is one of the most common disorders affecting school-aged children. The study aimed to characterize the handwriting performance of children with DCD who write in Arabic, based on triangular evaluation. Participants included 58 children aged 11-12 years, 29 diagnosed with DCD based on the DSM-IV criteria and the M-ABC, and 29 matched typically developed controls. Children were asked to copy a paragraph on a sheet of paper affixed to a digitizer supplying objective measures of the handwriting process. The handwriting proficiency screening questionnaire (HPSQ) was completed by their teachers while observing their performance and followed by evaluation of their final written product. Results indicated that compared to controls, children with DCD required significantly more on-paper and in-air time per stroke while copying. In addition, global legibility, unrecognizable letters and spatial arrangement measures of their written product were significantly inferior. Significant group differences were also found between the HPSQ subscales scores. Furthermore, 82.8% of all participants were correctly classified into groups based on one discriminate function which included two handwriting performance measures. These study results strongly propose application of triangular standardized evaluation to receive better insight of handwriting deficit features of individual children with DCD who write in Arabic. Copyright © 2013 Elsevier Ltd. All rights reserved.

BMP signaling in dermal papilla cells is required for their hair follicle-inductive properties

PubMed Central

Rendl, Michael; Polak, Lisa; Fuchs, Elaine

2008-01-01

Hair follicle (HF) formation is initiated when epithelial stem cells receive cues from specialized mesenchymal dermal papilla (DP) cells. In culture, DP cells lose their HF-inducing properties, but during hair growth in vivo, they reside within the HF bulb and instruct surrounding epithelial progenitors to orchestrate the complex hair differentiation program. To gain insights into the molecular program that maintains DP cell fate, we previously purified DP cells and four neighboring populations and defined their cell-type-specific molecular signatures. Here, we exploit this information to show that the bulb microenvironment is rich in bone morphogenetic proteins (BMPs) that act on DP cells to maintain key signature features in vitro and hair-inducing activity in vivo. By employing a novel in vitro/in vivo hybrid knockout assay, we ablate BMP receptor 1a in purified DP cells. When DPs cannot receive BMP signals, they lose signature characteristics in vitro and fail to generate HFs when engrafted with epithelial stem cells in vivo. These results reveal that BMP signaling, in addition to its key role in epithelial stem cell maintenance and progenitor cell differentiation, is essential for DP cell function, and suggest that it is a critical feature of the complex epithelial–mesenchymal cross-talk necessary to make hair. PMID:18281466

Insights into the lithospheric architecture of Iberia and Morocco from teleseismic body-wave attenuation

NASA Astrophysics Data System (ADS)

Bezada, Maximiliano J.

2017-11-01

The long and often complicated tectonic history of continental lithosphere results in lateral strength heterogeneities which in turn affect the style and localization of deformation. In this study, we produce a model for the attenuation structure of Iberia and northern Morocco using a waveform-matching approach on P-wave data from teleseismic deep-focus earthquakes. We find that attenuation is correlated with zones of intraplate deformation and seismicity, but do not find a consistent relationship between attenuation and recent volcanism. The main features of our model are low to moderate Δt* in the undeformed Tertiary basins of Spain and high Δt* in areas deformed by the Alpine orogeny. Additionally, low Δt* is found in areas where the Alboran slab is thought to be attached to the Iberian and African lithosphere, and high Δt* where it has detached. These features are robust with respect to inversion parameters, and are consistent with independent data. Very mild backazimuthal dependence of the measurements and comparison with previous results suggest that the source of the attenuation is sub-crustal. In line with other recent studies, the range of Δt* we observe is much larger than can be expected from lithospheric thickness or temperature variations.

Whole genome sequencing of Gyeongbuk Araucana, a newly developed blue-egg laying chicken breed, reveals its origin and genetic characteristics.

PubMed

Jeong, Hyeonsoo; Kim, Kwondo; Caetano-Anollés, Kelsey; Kim, Heebal; Kim, Byung-Ki; Yi, Jun-Koo; Ha, Jae-Jung; Cho, Seoae; Oh, Dong Yep

2016-05-24

Chicken, Gallus gallus, is a valuable species both as a food source and as a model organism for scientific research. Here, we sequenced the genome of Gyeongbuk Araucana, a rare chicken breed with unique phenotypic characteristics including flight ability, large body size, and laying blue-shelled eggs, to identify its genomic features. We generated genomes of Gyeongbuk Araucana, Leghorn, and Korean Native Chicken at a total of 33.5, 35.82, and 33.23 coverage depth, respectively. Along with the genomes of 12 Chinese breeds, we identified genomic variants of 16.3 million SNVs and 2.3 million InDels in mapped regions. Additionally, through assembly of unmapped reads and selective sweep, we identified candidate genes that fall into heart, vasculature and muscle development and body growth categories, which provided insight into Gyeongbuk Araucana's phenotypic traits. Finally, genetic variation based on the transposable element insertion pattern was investigated to elucidate the features of transposable elements related to blue egg shell formation. This study presents results of the first genomic study on the Gyeongbuk Araucana breed; it has potential to serve as an invaluable resource for future research on the genomic characteristics of this chicken breed as well as others.

Clinical features and genetic diagnosis of hereditary spinocerebellar ataxia 3.

PubMed

Wang, Yaoguang; Yang, Xiaokai; Ma, Weide; Li, Jinxin; Zhang, Qingyuan; Xia, Shuqi; Wang, Hai; Zhang, Chenghui; Xu, Xiaomin; Zheng, Jiayong

2016-10-01

Spinocerebellar ataxia type 3 (SCA3) is a rare inherited autosomal dominant progressive neurological disorder, which results from a CAG‑repeat expansion in the gene encoding the deubiquitinating enzyme, ataxin‑3. At present, no effective treatment is available for this fatal disorder; however, certain studies have suggested that reducing the levels of mutant ataxin‑3 protein may reverse or halt the progression of disease in patients with SCA3. In the present study, clinical examinations were performed on a patient with SCA3 who exhibited disease features including coughing, expectoration and was bedridden with mobility limitation. CAG repetitions at SCA‑associated genes were detected in the patient's family by performing standard polymerase chain reaction (PCR) and triple‑repeat primed PCR. The numbers of CAG‑repeats within the two alleles of the gene of interest in the patient were 15 and 78. Notably, the patient's brother, who harbored 76 CAG‑repeats in one allele of the gene of interest, did not exhibit severe disease symptoms. These results suggest that the number of CAG‑repeats is a critical for determination of SCA3 disease severity and time of onset. In addition, the defined phenotypic characteristics of the patient in the present study provide useful insight for more accurate clinical diagnosis and genotyping of future patients.

Craniofacial and dental development in Costello syndrome.

PubMed

Goodwin, Alice F; Oberoi, Snehlata; Landan, Maya; Charles, Cyril; Massie, Jessica C; Fairley, Cecilia; Rauen, Katherine A; Klein, Ophir D

2014-06-01

Costello syndrome (CS) is a RASopathy characterized by a wide range of cardiac, musculoskeletal, dermatological, and developmental abnormalities. The RASopathies are defined as a group of syndromes caused by activated Ras/mitogen-activated protein kinase (MAPK) signaling. Specifically, CS is caused by activating mutations in HRAS. Although receptor tyrosine kinase (RTK) signaling, which is upstream of Ras/MAPK, is known to play a critical role in craniofacial and dental development, the craniofacial and dental features of CS have not been systematically defined in a large group of individuals. In order to address this gap in our understanding and fully characterize the CS phenotype, we evaluated the craniofacial and dental phenotype in a large cohort (n = 41) of CS individuals. We confirmed that the craniofacial features common in CS include macrocephaly, bitemporal narrowing, convex facial profile, full cheeks, and large mouth. Additionally, CS patients have a characteristic dental phenotype that includes malocclusion with anterior open bite and posterior crossbite, enamel hypo-mineralization, delayed tooth development and eruption, gingival hyperplasia, thickening of the alveolar ridge, and high palate. Comparison of the craniofacial and dental phenotype in CS with other RASopathies, such as cardio-facio-cutaneous syndrome (CFC), provides insight into the complexities of Ras/MAPK signaling in human craniofacial and dental development. © 2014 Wiley Periodicals, Inc.

The role of amino acid PET in the light of the new WHO classification 2016 for brain tumors.

PubMed

Suchorska, Bogdana; Albert, Nathalie L; Bauer, Elena K; Tonn, Jörg-Christian; Galldiks, Norbert

2018-04-26

Since its introduction in 2016, the revision of the World Health Organization (WHO) classification of central nervous system tumours has already changed the diagnostic and therapeutic approach in glial tumors. Blurring the lines between entities formerly labelled as "high-grade" or "low-grade", molecular markers define distinct biological subtypes with different clinical course. This new classification raises the demand for non-invasive imaging methods focussing on depicting metabolic processes. We performed a review of current literature on the use of amino acid PET (AA-PET) for obtaining diagnostic or prognostic information on glioma in the setting of the current WHO 2016 classification. So far, only a few studies have focussed on combining molecular genetic information and metabolic imaging using AA-PET. The current review summarizes the information available on "molecular grading" as well as prognostic information obtained from AA-PET and delivers an insight into a possible interrelation between metabolic imaging and glioma genetics. Within the framework of molecular characterization of gliomas, metabolic imaging using AA-PET is a promising tool for non-invasive characterisation of molecular features and to provide additional prognostic information. Further studies incorporating molecular and metabolic features are necessary to improve the explanatory power of AA-PET in glial tumors.

Adenomyosis: a life-cycle approach.

PubMed

Benagiano, Giuseppe; Brosens, Ivo; Habiba, Marwan

2015-03-01

The life-cycle approach to endometriosis highlighted unexpected features of the condition; the same approach was therefore applied to gain insight into the clinical features of adenomyosis and to draw a comparison with endometriosis. This is possible today thanks to new imaging techniques enabling non-invasive diagnosis of adenomyosis. The specificity and sensitivity of magnetic resonance imaging and transvaginal ultrasound remain uncertain. Unlike endometriosis, little information is available on the presence of classic adenomyosis in adolescents, except for rare cystic forms that may not represent the true disease. Adenomyosis is most likely to affect adult women, although most reported incidences are still based on post-hysterectomy studies, and are affected by diligence in histopathologic diagnosis and the adopted cut-off point. The traditionally accepted associations of adult adenomyosis, such as multiparity, a link to infertility and its effect on pregnancy are uncertain. Active adenomyosis has been found in pre- and peri-menopausal women and in postmenopausal women receiving tamoxifen. In conclusion, major diagnostic limitations and the systematic bias of hysterectomy make it difficult to draw firm conclusions from existing evidence. In addition, no information is available on the natural history of adenomyosis and no study has systematically evaluated its existence in adolescents. Copyright © 2014 Reproductive Healthcare Ltd. Published by Elsevier Ltd. All rights reserved.

Luminescence emission from nonpolar Al0.3Ga0.7N/GaN core-shell and core-multi-shell nanowires

NASA Astrophysics Data System (ADS)

Namvari, E.; Shojaei, S.; Asgari, A.

2017-12-01

In the present work, we theoretically study the possibility of luminescence emission from two systems of nonpolar Al0.3Ga0.7N/GaN Core-shell and core-multi-shell c-axis oriented nanowires with hexagonal cross section. To obtain energy levels and wave functions through the solution of Schrodinger-Poisson equations, numerical Self-consistent procedure has been employed. N-type doping has been considered to investigate the two-dimensional electron gas formation and its effect on luminescence. The detailed analysis of the results as a function of the various structural parameters has been carried out. The results presents an examination of the band to band luminescence feature and its changes with involved parameters. We found that the size of the system determines the feature of luminescence emission. As main finding, our calculations show that the intensity of luminescence spectrum in facet to facet route of NW cross section is significant than that of corner to corner route. In addition, no shift of the peak position is observed with changing the amount of doping. Our numerical calculations give more insights into the luminescence emission of nonpolar GaN/AlGaN core/shell nanowire and have many implications in experiment.

The structure of distractor-response bindings: Conditions for configural and elemental integration.

PubMed

Moeller, Birte; Frings, Christian; Pfister, Roland

2016-04-01

Human action control is influenced by bindings between perceived stimuli and responses carried out in their presence. Notably, responses given to a target stimulus can also be integrated with additional response-irrelevant distractor stimuli that accompany the target (distractor-response binding). Subsequently reencountering such a distractor then retrieves the associated response. Although a large body of evidence supports the existence of this effect, the specific structure of distractor-response bindings is still unclear. Here, we test the predictions derived from 2 possible assumptions about the structure of bindings between distractors and responses. According to a configural approach, the entire distractor object is integrated with a response, and only upon repetition of the entire distractor object the associated response would be retrieved. According to an elemental approach, one would predict integration of individual distractor features with the response and retrieval due to the repetition of an individual distractor feature. Four experiments indicate that both, configural and elemental bindings exist and specify boundary conditions for each type of binding. These findings provide detailed insights into the architecture of bindings between response-irrelevant stimuli and actions and thus allow for specifying how distractor stimuli influence human behavior. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

Femtosecond stimulated Raman evidence for charge-transfer character in pentacene singlet fission† †Electronic supplementary information (ESI) available: Actinic pump spectrum, discussion on ground state addition process, peak fitting procedure, transient absorption data, power dependence measurements, etalon pulse shaping, TIPS-pentacene FSRS data, and optimized geometry and frequency calculation results. See DOI: 10.1039/c7sc03496b

PubMed Central

Hart, Stephanie M.; Silva, W. Ruchira

2017-01-01

Singlet fission is a spin-allowed process in which an excited singlet state evolves into two triplet states. We use femtosecond stimulated Raman spectroscopy, an ultrafast vibrational technique, to follow the molecular structural evolution during singlet fission in order to determine the mechanism of this process. In crystalline pentacene, we observe the formation of an intermediate characterized by pairs of excited state peaks that are red- and blue-shifted relative to the ground state features. We hypothesize that these features arise from the formation of cationic and anionic species due to partial transfer of electron density from one pentacene molecule to a neighboring molecule. These observations provide experimental evidence for the role of states with significant charge-transfer character which facilitate the singlet fission process in pentacene. Our work both provides new insight into the singlet fission mechanism in pentacene and demonstrates the utility of structurally-sensitive time-resolved spectroscopic techniques in monitoring ultrafast processes. PMID:29675170

How does Subduction Interface Roughness influence Megathrust Earthquakes: Insights from Natural Data and Analogue Models

NASA Astrophysics Data System (ADS)

van Rijsingen, E.; Lallemand, S.; Peyret, M.; Corbi, F.; Funiciello, F.; Arcay, D.; Heuret, A.

2017-12-01

The role of subducting oceanic features on the seismogenic behavior of subduction zones has been increasingly addressed over the past years, although their exact relationship remains unclear. Do features like seamounts, fracture zones or submarine ridges act as barriers, prohibiting ruptures to propagate, or do they initiate megathrust earthquakes instead? With this question in mind, we aim to better understand the influence of subduction interface roughness on the location of an earthquake's hypocenter, rupture area and seismic asperity. Following the work on compiling a dual-wavelength subduction interface roughness (SubRough) database, we used this roughness proxy for a global comparison with large subduction earthquakes (MW > 7.5), which occurred since 1900 (SubQuake, new catalogue). We made a quantitative comparison between the earthquake data on the landward side of the trench and the roughness proxy on the seaward side, taking into account the most appropriate direction of roughness extrapolation. Main results show that areas with low roughness at long wavelengths (i.e. 80-100 km) are more prone to host large- to mega-earthquakes. In addition to this natural data study, we perform analogue experiments, which allow us to investigate the role subducting oceanic features play over the course of multiple seismic cycles. The experimental setup consists of a gelatin wedge and an underthrusting rigid aluminum plate (i.e. the analogues of the overriding and downgoing plates, respectively). By adding scaled 3D-printed topographic features (e.g. seamounts) on the downgoing plate, we are able to accurately monitor the initiation and propagation of ruptures with respect to the subducting features. Here we show the results of our natural data study, some preliminary results of the analogue models and our first conclusions on how the subduction interface roughness may influence the seismogenic potential of an area.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lackner, Florian; Chatterley, Adam S.; Pemmaraju, C. D.

Femtosecond extreme ultraviolet transient absorption spectroscopy is used to explore strong-field ionization induced dynamics in selenophene (C 4H 4Se). The dynamics are monitored in real-time from the viewpoint of the Se atom by recording the temporal evolution of element-specific spectral features near the Se 3d inner-shell absorption edge (~58 eV). The interpretation of the experimental results is supported by first-principles time-dependent density functional theory calculations. The experiments simultaneously capture the instantaneous population of stable molecular ions, the emergence and decay of excited cation states, and the appearance of atomic fragments. The experiments reveal, in particular, insight into the strong-field inducedmore » ring-opening dynamics in the selenophene cation, which are traced by the emergence of non-cyclic molecules as well as the liberation of Se + ions within an overall time scale of approximately 170 fs. In this study, we propose that both products may be associated with dynamics on the same electronic surfaces but with different degrees of vibrational excitation. The time-dependent inner-shell absorption features provide direct evidence for a complex relaxation mechanism that may be approximated by a two-step model, whereby the initially prepared, excited cyclic cation decays within τ 1 = 80 ± 30 fs into a transient molecular species, which then gives rise to the emergence of bare Se + and ring-open cations within an additional τ 2 = 80 ± 30 fs. The combined experimental and theoretical results suggest a close relationship between σ* excited cation states and the observed ring-opening reactions. In conclusion, the findings demonstrate that the combination of femtosecond time-resolved core-level spectroscopy with ab initio estimates of spectroscopic signatures provide new insights into complex, ultrafast photochemical reactions such as ring-opening dynamics in organic molecules in real-time and with simultaneous sensitivity for electronic and structural rearrangements.« less

Large Grooves in the South Polar Layered Deposits: Insights from Spacecraft Data and Terrestrial Analogs

NASA Technical Reports Server (NTRS)

Bridges, N. T.; Herkenhoff, K. E.

2000-01-01

The Martian polar layered deposits (PLD) are probably the best source of information about the recent climate history of Mars, but their origin and the mechanisms of accumulation are still a mystery. The polar layers are sedimentary deposits that most planetary scientists believe are composed of water ice and varying amounts of wind-blown dust, although their composition is poorly constrained. Interpretation of the observed polar stratigraphy in terms of global climate changes is complicated by the significant difference in surface ages between the north and south PLD inferred from crater statistics. The study reported here was undertaken as part of the landing site selection effort for the Mars Polar Lander (MPL) and Deep Space 2 (DS2) missions that made use of all available data. We used Mariner 9, Viking, and Mars Global Surveyor images of the south PLD in the area accessible to MPL and DS2 to evaluate the topography and morphology of grooves, terraced layers, and other features. Here we report on results from grooves that appear to have been carved by strong winds. Because these features are found throughout the interior of the PLD, where MPL and DS2 were targeted to land, their topographic characteristics were judged as important input for landing site safety assessment. The characteristics of the grooves also provide constraints and insights into aeolian processes in the polar regions and the effects these have on PLD ablation. Our results indicate that these grooves do not represent landing hazards at the scale of the images (approx. 80 m/pixel). Their topography and shape do not seem correlated with south PLD layering. No Earth analog of suitable scale exists, although the grooves bear some resemblance to smaller terrestrial deflation hollows found in soft sediment and ice. Additional information is contained in original extended abstract.

Direct observation of ring-opening dynamics in strong-field ionized selenophene using femtosecond inner-shell absorption spectroscopy

DOE PAGES

Lackner, Florian; Chatterley, Adam S.; Pemmaraju, C. D.; ...

2016-12-21

Femtosecond extreme ultraviolet transient absorption spectroscopy is used to explore strong-field ionization induced dynamics in selenophene (C 4H 4Se). The dynamics are monitored in real-time from the viewpoint of the Se atom by recording the temporal evolution of element-specific spectral features near the Se 3d inner-shell absorption edge (~58 eV). The interpretation of the experimental results is supported by first-principles time-dependent density functional theory calculations. The experiments simultaneously capture the instantaneous population of stable molecular ions, the emergence and decay of excited cation states, and the appearance of atomic fragments. The experiments reveal, in particular, insight into the strong-field inducedmore » ring-opening dynamics in the selenophene cation, which are traced by the emergence of non-cyclic molecules as well as the liberation of Se + ions within an overall time scale of approximately 170 fs. In this study, we propose that both products may be associated with dynamics on the same electronic surfaces but with different degrees of vibrational excitation. The time-dependent inner-shell absorption features provide direct evidence for a complex relaxation mechanism that may be approximated by a two-step model, whereby the initially prepared, excited cyclic cation decays within τ 1 = 80 ± 30 fs into a transient molecular species, which then gives rise to the emergence of bare Se + and ring-open cations within an additional τ 2 = 80 ± 30 fs. The combined experimental and theoretical results suggest a close relationship between σ* excited cation states and the observed ring-opening reactions. In conclusion, the findings demonstrate that the combination of femtosecond time-resolved core-level spectroscopy with ab initio estimates of spectroscopic signatures provide new insights into complex, ultrafast photochemical reactions such as ring-opening dynamics in organic molecules in real-time and with simultaneous sensitivity for electronic and structural rearrangements.« less

Biogeochemical Activity of Siderophilic Cyanobacteria and Insights from their Genomes Implications for the Development of New Biosignatures

NASA Technical Reports Server (NTRS)

Brown, I. I.; Bryant, D. A.; Thomas,-Keprta, K. L.; Tringe, S. G.; Sarkisova, S. A.; Galindo, C., Jr.; Malley, K.; Sosa, O.; Garrison, D. H.; McKay, David S.

2010-01-01

Verifying the links between genomie features in living organisms and their mineralization/demineralization activity will help to reveal traces of life on Earth and beyond. Among contemporary environments, iron-depositing hot springs (IDHS) may represent one of the most appropriate natural models for insights into ancient life since organisms may have originated on Earth and possibly Mars in association with hydrothennal activity and high [Fe(2+)]. Siderophilic or "iron-loving" cyanobacteria (CB) inhabiting IDHS may have genomic features and properties similar to those of ancient organisms because abundant Fe(2+) in IDHS has a strong potential to increase the magnitude of oxidative stress. That is why specific and/or additional proteins involved in Fe mineralization by siderophilic CB are expected. Inorganic polyphosphates (PPi) are known to increase the viability of prokaryotes Linder heavy metal concentrations and UV stress conditions. PPi have also been proposed as biosignatures. Ancient CB could have also been stressed by occasional migrations from the Fe(2+) rich Ocean to the basaltic land which was almost devoid of dissolved Fe(2+). Thus, the study of the adaptation reactions of siderophilic CB to fluctuation of dissolved Fe level may shed light on the paleophysiology of ancient oxygenic prokaryotes. Moreover, bioweathered Fe, Al, P, Cu, Ti and rare earth elements can be thought of as candidate organomarkers that document the effects of or ganic molecules in weathered rocks. However, the molecular mechanisms of the maintenance of Fe homeostasis in siderophilic CB, the role of PPi for this process and bioweathering activities are poorly understood. Here we present preliminary results describing a new mechanism of Fe mineralization in siderophilic CB, the effect of Fe on the generation of PPi bodies in siderophilic CB, their bioweathering activity and preliminary analysis of the diversity of proteins involved in the prevention of oxidative stress in phototrophs inhabiting IDHS.

A Quantitative and Qualitative Exploration of Photoaversion in Achromatopsia

PubMed Central

Aboshiha, Jonathan; Kumaran, Neruban; Kalitzeos, Angelos; Hogg, Chris; Rubin, Gary; Michaelides, Michel

2017-01-01

Purpose Photoaversion (PA) is a disabling and ubiquitous feature of achromatopsia (ACHM). We aimed to help define the characteristics of this important symptom, and present the first published assessment of its impact on patients' lives, as well as quantitative and qualitative PA assessments. Methods Molecularly confirmed ACHM subjects were assessed for PA using four tasks: structured survey of patient experience, novel quantitative subjective measurement of PA, visual acuities in differing ambient lighting, and objective palpebral aperture-related PA testing. Results Photoaversion in ACHM was found to be the most significant symptom for a substantial proportion (38%) of patients. A novel subjective PA measurement technique was developed and demonstrated fidelity with more invasive paradigms without exposing often very photosensitive patients to brighter light intensities used elsewhere. An objective PA measurement was also refined for use in trials, indicating that higher light intensities than previously published are likely to be needed. Monocular testing, as required for trials, was also validated for the first time. Conclusions This study offers new insights into PA in ACHM. It provides the first structured evidence of the great significance of this symptom to patients, suggesting that PA should be considered as an additional outcome measure in therapeutic trials. It also offers new insights into the characteristics of PA in ACHM, and describes both subjective and objective measures of PA that could be employed in clinical trials. PMID:28715587

New insight on the anatomy and architecture of the avian neurocranium.

PubMed

Marugán-Lobón, Jesús; Buscalioni, Angela D

2009-03-01

This study aims to disentangle the main features of the avian neurocranium at high taxonomic scales using geometric morphometric tools. When surveying the variation across 60% of avian orders (sampled among 72 individuals), our results verify that the central nervous system has an important influence upon the architecture of the avian neurocranium, as in other very encephalized vertebrates such as mammals. When the avian brain expands relative to the cranial base it causes more "reptilian-like" neurocranial configurations to shape into rounder ones. This rounder appearance is achieved because the cranial base becomes relatively shorter and turns its flexure from concave to convex, at the same time forcing the foramen magnum to reorient ventrally instead of caudally. However, our analyses have also revealed that an important morphological difference between birds resides between the occiput and the cranial roof. This variation was unexpected since it had not been reported thus far, and entertains two plausible interpretations. Although it could be due to a trade-off between the relative sizes of the supraoccipital and the parietal bones, the presence of an additional bone (the intra- or post-parietal) between the latter two bones could also explain the variation congruently. This descriptive insight stresses the need for further developmental studies focused in understanding the evolutionary disparity of the avian neurocranium. (c) 2009 Wiley-Liss, Inc.

Is adermatoglyphia an additional feature of Kindler Syndrome?

PubMed

Almeida, Hiram Larangeira de; Goetze, Fernanda Mendes; Fong, Kenneth; Lai-Cheong, Joey; McGrath, John

2015-01-01

A typical feature of Kindler Syndrome is skin fragility; this condition in currently classified as a form of epidermolysis bullosa. We describe a rarely reported feature of two cases, one sporadic and one familial; both patients noticed acquired adermatoglyphia. The loss of dermatoglyphics could be an additional feature of this syndrome.

Are Psychopaths Morally Sensitive?

ERIC Educational Resources Information Center

Maxwell, Bruce; Le Sage, Leonie

2009-01-01

Philosophical and psychological opinion is divided over whether moral sensitivity, understood as the ability to pick out a situation's morally salient features, necessarily involves emotional engagement. This paper seeks to offer insight into this question. It reasons that if moral sensitivity does draw significantly on affective capacities of…

XML Tactical Chat (XTC): The Way Ahead for Navy Chat

DTIC Science & Technology

2007-09-01

multicast transmissions via sophisticated pruning algorithms, while allowing multicast packets to “ tunnel ” through IP routers. [Macedonia, Brutzman 1994...conference was Jabber Inc. who added some great insight into the power of Jabber. • Great features including blackberry handheld connectivity and

Single molecule image formation, reconstruction and processing: introduction.

PubMed

Ashok, Amit; Piestun, Rafael; Stallinga, Sjoerd

2016-07-01

The ability to image at the single molecule scale has revolutionized research in molecular biology. This feature issue presents a collection of articles that provides new insights into the fundamental limits of single molecule imaging and reports novel techniques for image formation and analysis.

American School & University. Volume 77, Number 3

ERIC Educational Resources Information Center

Agron, Joe, Ed.

2004-01-01

Each month, "American School & University" provides a mix of thought-provoking features, how-to-articles, industry reports, exclusive surveys, new sections, insightful columns, new product introductions and case histories to assist education officials in better performing their jobs. This November 2004 issue includes the following: "Honoring…

American School & University. Volume 77, Number 1

ERIC Educational Resources Information Center

Agron, Joe, Ed.

2004-01-01

Each month "American School & University" provides a mix of thought-provoking features, how-to-articles, industry reports, exclusive surveys, new sections, insightful columns, new product introductions and case histories to assist education officials in better performing their jobs. This September 2004 issue includes the following: "New…

American School & University. Volume 77, Number 10

ERIC Educational Resources Information Center

Agron, Joe, Ed.

2005-01-01

Each month, "American School & University" provides a mix of thought-provoking features, how-to-articles, industry reports, exclusive surveys, new sections, insightful columns, new product introductions and case histories to assist education officials in better performing their jobs. This May 2005 issue includes the following:…

Multiphase Method for Analysing Online Discussions

ERIC Educational Resources Information Center

Häkkinen, P.

2013-01-01

Several studies have analysed and assessed online performance and discourse using quantitative and qualitative methods. Quantitative measures have typically included the analysis of participation rates and learning outcomes in terms of grades. Qualitative measures of postings, discussions and context features aim to give insights into the nature…

American School & University. Volume 77, Number 11

ERIC Educational Resources Information Center

Agron, Joe, Ed.

2005-01-01

Each month, "American School & University" provides a mix of thought-provoking features, how-to-articles, industry reports, exclusive surveys, new sections, insightful columns, new product introductions and case histories to assist education officials in better performing their jobs. This March 2005 issue includes the following:…

American School & University. Volume 77, Number 4

ERIC Educational Resources Information Center

Agron, Joe, Ed.

2004-01-01

Each month, "American School & University" provides a mix of thought-provoking features, how-to-articles, industry reports, exclusive surveys, new sections, insightful columns, new product introductions and case histories to assist education officials in better performing their jobs. This December 2004 issue includes the following:…

Capacity for visual features in mental rotation

PubMed Central

Xu, Yangqing; Franconeri, Steven L.

2015-01-01

Although mental rotation is a core component of scientific reasoning, we still know little about its underlying mechanism. For instance - how much visual information can we rotate at once? Participants rotated a simple multi-part shape, requiring them to maintain attachments between features and moving parts. The capacity of this aspect of mental rotation was strikingly low – only one feature could remain attached to one part. Behavioral and eyetracking data showed that this single feature remained ‘glued’ via a singular focus of attention, typically on the object’s top. We argue that the architecture of the human visual system is not suited for keeping multiple features attached to multiple parts during mental rotation. Such measurement of the capacity limits may prove to be a critical step in dissecting the suite of visuospatial tools involved in mental rotation, leading to insights for improvement of pedagogy in science education contexts. PMID:26174781

Capacity for Visual Features in Mental Rotation.

PubMed

Xu, Yangqing; Franconeri, Steven L

2015-08-01

Although mental rotation is a core component of scientific reasoning, little is known about its underlying mechanisms. For instance, how much visual information can someone rotate at once? We asked participants to rotate a simple multipart shape, requiring them to maintain attachments between features and moving parts. The capacity of this aspect of mental rotation was strikingly low: Only one feature could remain attached to one part. Behavioral and eye-tracking data showed that this single feature remained "glued" via a singular focus of attention, typically on the object's top. We argue that the architecture of the human visual system is not suited for keeping multiple features attached to multiple parts during mental rotation. Such measurement of capacity limits may prove to be a critical step in dissecting the suite of visuospatial tools involved in mental rotation, leading to insights for improvement of pedagogy in science-education contexts. © The Author(s) 2015.

Angular description for 3D scattering centers

NASA Astrophysics Data System (ADS)

Bhalla, Rajan; Raynal, Ann Marie; Ling, Hao; Moore, John; Velten, Vincent J.

2006-05-01

The electromagnetic scattered field from an electrically large target can often be well modeled as if it is emanating from a discrete set of scattering centers (see Fig. 1). In the scattering center extraction tool we developed previously based on the shooting and bouncing ray technique, no correspondence is maintained amongst the 3D scattering center extracted at adjacent angles. In this paper we present a multi-dimensional clustering algorithm to track the angular and spatial behaviors of 3D scattering centers and group them into features. The extracted features for the Slicy and backhoe targets are presented. We also describe two metrics for measuring the angular persistence and spatial mobility of the 3D scattering centers that make up these features in order to gather insights into target physics and feature stability. We find that features that are most persistent are also the most mobile and discuss implications for optimal SAR imaging.

Autism and 15q11-q13 disorders: behavioral, genetic, and pathophysiological issues.

PubMed

Dykens, Elisabeth M; Sutcliffe, James S; Levitt, Pat

2004-01-01

New insights into biological factors that underlie autism may be gained by comparing autism to other neurodevelopmental disorders that have autistic features and relatively well-delineated genetic etiologies or neurobiological findings. This review moves beyond global diagnoses of autism and instead uses an endophenotypic approach to compare specific clusters of autistic symptomatology to features of chromosome 15q11-q13 disorders. Paternally or maternally derived deficiencies of 15q11-q13 result in Prader-Willi or Angelman syndromes, and we first use a global approach to review potential autism susceptibility genes in the 15q11-q13 region. We then use a more trait-based approach to suggest possible ties between specific phenotypic characteristics of autism and Prader-Willi syndrome, namely savant-like skills. We conclude with insights from pathophysiological studies that implicate altered development of specific neuron types and circuits in the cerebral cortex as part of the pathophysiological processes associated with autism and mental retardation. Copyright 2004 Wiley-Liss, Inc.

Amplification without instability: applying fluid dynamical insights in chemistry and biology

NASA Astrophysics Data System (ADS)

McCoy, Jonathan H.

2013-11-01

While amplification of small perturbations often arises from instability, transient amplification is possible locally even in asymptotically stable systems. That is, knowledge of a system's stability properties can mislead one's intuition for its transient behaviors. This insight, which has an interesting history in fluid dynamics, has more recently been rediscovered in ecology. Surprisingly, many nonlinear fluid dynamical and ecological systems share linear features associated with transient amplification of noise. This paper aims to establish that these features are widespread in many other disciplines concerned with noisy systems, especially chemistry, cell biology and molecular biology. Here, using classic nonlinear systems and the graphical language of network science, we explore how the noise amplification problem can be reframed in terms of activatory and inhibitory interactions between dynamical variables. The interaction patterns considered here are found in a great variety of systems, ranging from autocatalytic reactions and activator-inhibitor systems to influential models of nerve conduction, glycolysis, cell signaling and circadian rhythms.

Influence of hot spot features on the initiation characteristics of heterogeneous nitromethane

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dattelbaum, Dana M; Sheffield, Stephen A; Stahl, David B

2010-01-01

To gain insights into the critical hot spot features influencing energetic materials initiation characteristics, well-defined micron-scale particles have been intentionally introduced into the homogeneous explosive nitromethane (NM). Two types of potential hot spot origins have been examined - shock impedance mismatches using solid silica beads, and porosity using hollow microballoons - as well as their sizes and inter-particle separations. Here, we present the results of several series of gas gun-driven plate impact experiments on NM/particle mixtures with well-controlled shock inputs. Detailed insights into the nature of the reactive flow during the build-up to detonation have been obtained from the responsemore » of in-situ electromagnetic gauges, and the data have been used to establish Pop-plots (run-distance-to-detonation vs. shock input pressure) for the mixtures. Comparisons of sensitization effects and energy release characteristics relative to the initial shock front between the solid and hollow beads are presented.« less

A field study of the confluence between Negro and Solimões Rivers. Part 1: Hydrodynamics and sediment transport

NASA Astrophysics Data System (ADS)

Gualtieri, Carlo; Filizola, Naziano; de Oliveira, Marco; Santos, Andrè Martinelli; Ianniruberto, Marco

2018-01-01

Confluences are a common feature of riverine systems, where are located converging flow streamlines and potential mixing of separate flows. The confluence of the Negro and Solimões Rivers ranks among the largest on Earth and its study may provide some general insights into large confluence dynamics and processes. An investigation was recently conducted about that confluence in both low and high-flow conditions using acoustic Doppler velocity profiling (ADCP), water quality sampling and high-resolution seismic data. First, the study gained insights into the characterization of the basic hydrodynamics parameters about the confluence as well as of those affecting sediments transport. Second, the analysis of the results showed that common hydrodynamic features noted in previous confluence studies were herein observed. Finally, some differences between low-flow and relatively high-flow conditions about the transfer of momentum from the Solimões to the Negro side of the Amazon Channel were identified.

New insights on the origin of the High Velocity Peaks in the Galactic Bulge

NASA Astrophysics Data System (ADS)

Fernández-Trincado, J. G.; Robin, A. C.; Moreno, E.; Pérez-Villegas, A.; Pichardo, B.

2017-12-01

We provide new insight on the origin of the cold high-V_{los} peaks (˜200 kms^{-1}) in the Milky Way bulge discovered in the APOGEE commissioning data (Nidever et al. 2012). Here we show that such kinematic behaviour present in the field regions towards the Galactic bulge is not likely associated with orbits that build the boxy/peanut (B/P) bulge. To this purpose, a new set of test particle simulations of a kinematically cold stellar disk evolved in a 3D steady-state barred Milky Way galactic potential, has been analysed in detail. Especially bar particles trapped into the bar are identified through the orbital Jacobi energy E_{J}, which allows us to identify the building blocks of the B/P feature and investigate their kinematic properties. Finally, we present preliminary results showing that the high-V_{los} features observed towards the Milky Way bulge are a natural consequence of a large-scale midplane particle structure, which is unlikely associated with the Galactic bar.

Insight into resolution enhancement in generalized two-dimensional correlation spectroscopy.

PubMed

Ma, Lu; Sikirzhytski, Vitali; Hong, Zhenmin; Lednev, Igor K; Asher, Sanford A

2013-03-01

Generalized two-dimensional correlation spectroscopy (2D-COS) can be used to enhance spectral resolution in order to help differentiate highly overlapped spectral bands. Despite the numerous extensive 2D-COS investigations, the origin of the 2D spectral resolution enhancement mechanism(s) is not completely understood. In the work here, we studied the 2D-COS of simulated spectra in order to develop new insights into the dependence of 2D-COS spectral features on the overlapping band separations, their intensities and bandwidths, and their band intensity change rates. We found that the features in the 2D-COS maps that are derived from overlapping bands were determined by the spectral normalized half-intensities and the total intensity changes of the correlated bands. We identified the conditions required to resolve overlapping bands. In particular, 2D-COS peak resolution requires that the normalized half-intensities of a correlating band have amplitudes between the maxima and minima of the normalized half-intensities of the overlapping bands.

Insight into Resolution Enhancement in Generalized Two-Dimensional Correlation Spectroscopy

PubMed Central

Ma, Lu; Sikirzhytski, Vitali; Hong, Zhenmin; Lednev, Igor K.; Asher, Sanford A.

2014-01-01

Generalized two-dimensional correlation spectroscopy (2D COS) can be used to enhance spectral resolution in order to help differentiate highly overlapped spectral bands. Despite the numerous extensive 2D COS investigations, the origin of the 2D spectral resolution enhancement mechanism(s) are not completely understood. In the work here we studied the 2D COS of simulated spectra in order to develop new insights into the dependence of the 2D COS spectral features on the overlapping band separations, their intensities and bandwidths, and their band intensity change rates. We find that the features in the 2D COS maps that derive from overlapping bands are determined by the spectral normalized half-intensities and the total intensity changes of the correlated bands. We identify the conditions required to resolve overlapping bands. In particular, 2D COS peak resolution requires that the normalized half-intensities of a correlating band have amplitudes between the maxima and minima of the normalized half-intensities of the overlapping bands. PMID:23452492

Prediction of active sites of enzymes by maximum relevance minimum redundancy (mRMR) feature selection.

PubMed

Gao, Yu-Fei; Li, Bi-Qing; Cai, Yu-Dong; Feng, Kai-Yan; Li, Zhan-Dong; Jiang, Yang

2013-01-27

Identification of catalytic residues plays a key role in understanding how enzymes work. Although numerous computational methods have been developed to predict catalytic residues and active sites, the prediction accuracy remains relatively low with high false positives. In this work, we developed a novel predictor based on the Random Forest algorithm (RF) aided by the maximum relevance minimum redundancy (mRMR) method and incremental feature selection (IFS). We incorporated features of physicochemical/biochemical properties, sequence conservation, residual disorder, secondary structure and solvent accessibility to predict active sites of enzymes and achieved an overall accuracy of 0.885687 and MCC of 0.689226 on an independent test dataset. Feature analysis showed that every category of the features except disorder contributed to the identification of active sites. It was also shown via the site-specific feature analysis that the features derived from the active site itself contributed most to the active site determination. Our prediction method may become a useful tool for identifying the active sites and the key features identified by the paper may provide valuable insights into the mechanism of catalysis.

Deep Learning to Predict Falls in Older Adults Based on Daily-Life Trunk Accelerometry.

PubMed

Nait Aicha, Ahmed; Englebienne, Gwenn; van Schooten, Kimberley S; Pijnappels, Mirjam; Kröse, Ben

2018-05-22

Early detection of high fall risk is an essential component of fall prevention in older adults. Wearable sensors can provide valuable insight into daily-life activities; biomechanical features extracted from such inertial data have been shown to be of added value for the assessment of fall risk. Body-worn sensors such as accelerometers can provide valuable insight into fall risk. Currently, biomechanical features derived from accelerometer data are used for the assessment of fall risk. Here, we studied whether deep learning methods from machine learning are suited to automatically derive features from raw accelerometer data that assess fall risk. We used an existing dataset of 296 older adults. We compared the performance of three deep learning model architectures (convolutional neural network (CNN), long short-term memory (LSTM) and a combination of these two (ConvLSTM)) to each other and to a baseline model with biomechanical features on the same dataset. The results show that the deep learning models in a single-task learning mode are strong in recognition of identity of the subject, but that these models only slightly outperform the baseline method on fall risk assessment. When using multi-task learning, with gender and age as auxiliary tasks, deep learning models perform better. We also found that preprocessing of the data resulted in the best performance (AUC = 0.75). We conclude that deep learning models, and in particular multi-task learning, effectively assess fall risk on the basis of wearable sensor data.

Deep Learning to Predict Falls in Older Adults Based on Daily-Life Trunk Accelerometry

PubMed Central

Englebienne, Gwenn; Pijnappels, Mirjam

2018-01-01

Early detection of high fall risk is an essential component of fall prevention in older adults. Wearable sensors can provide valuable insight into daily-life activities; biomechanical features extracted from such inertial data have been shown to be of added value for the assessment of fall risk. Body-worn sensors such as accelerometers can provide valuable insight into fall risk. Currently, biomechanical features derived from accelerometer data are used for the assessment of fall risk. Here, we studied whether deep learning methods from machine learning are suited to automatically derive features from raw accelerometer data that assess fall risk. We used an existing dataset of 296 older adults. We compared the performance of three deep learning model architectures (convolutional neural network (CNN), long short-term memory (LSTM) and a combination of these two (ConvLSTM)) to each other and to a baseline model with biomechanical features on the same dataset. The results show that the deep learning models in a single-task learning mode are strong in recognition of identity of the subject, but that these models only slightly outperform the baseline method on fall risk assessment. When using multi-task learning, with gender and age as auxiliary tasks, deep learning models perform better. We also found that preprocessing of the data resulted in the best performance (AUC = 0.75). We conclude that deep learning models, and in particular multi-task learning, effectively assess fall risk on the basis of wearable sensor data. PMID:29786659

Simultaneously uncovering the patterns of brain regions involved in different story reading subprocesses.

PubMed

Wehbe, Leila; Murphy, Brian; Talukdar, Partha; Fyshe, Alona; Ramdas, Aaditya; Mitchell, Tom

2014-01-01

Story understanding involves many perceptual and cognitive subprocesses, from perceiving individual words, to parsing sentences, to understanding the relationships among the story characters. We present an integrated computational model of reading that incorporates these and additional subprocesses, simultaneously discovering their fMRI signatures. Our model predicts the fMRI activity associated with reading arbitrary text passages, well enough to distinguish which of two story segments is being read with 74% accuracy. This approach is the first to simultaneously track diverse reading subprocesses during complex story processing and predict the detailed neural representation of diverse story features, ranging from visual word properties to the mention of different story characters and different actions they perform. We construct brain representation maps that replicate many results from a wide range of classical studies that focus each on one aspect of language processing and offer new insights on which type of information is processed by different areas involved in language processing. Additionally, this approach is promising for studying individual differences: it can be used to create single subject maps that may potentially be used to measure reading comprehension and diagnose reading disorders.

New insights into hydrosilylation of unsaturated carbon-heteroatom (C═O, C═N) bonds by rhenium(V)-dioxo complexes.

PubMed

Huang, Liangfang; Wang, Wenmin; Wei, Xiaoqin; Wei, Haiyan

2015-04-23

The hydrosilylation of unsaturated carbon-heteroatom (C═O, C═N) bonds catalyzed by high-valent rhenium(V)-dioxo complex ReO2I(PPh3)2 (1) were studied computationally to determine the underlying mechanism. Our calculations revealed that the ionic outer-sphere pathway in which the organic substrate attacks the Si center in an η(1)-silane rhenium adduct to prompt the heterolytic cleavage of the Si-H bond is the most energetically favorable process for rhenium(V)-dioxo complex 1 catalyzed hydrosilylation of imines. The activation energy of the turnover-limiting step was calculated to be 22.8 kcal/mol with phenylmethanimine. This value is energetically more favorable than the [2 + 2] addition pathway by as much as 10.0 kcal/mol. Moreover, the ionic outer-sphere pathway competes with the [2 + 2] addition mechanism for rhenium(V)-dioxo complex 1 catalyzing the hydrosilylation of carbonyl compounds. Furthermore, the electron-donating group on the organic substrates would induce a better activity favoring the ionic outer-sphere mechanistic pathway. These findings highlight the unique features of high-valent transition-metal complexes as Lewis acids in activating the Si-H bond and catalyzing the reduction reactions.

Demographic Characteristics, Phenomenology, Comorbidity, and Family History in 200 Individuals With Body Dysmorphic Disorder

PubMed Central

Phillips, Katharine A.; Menard, William; Fay, Christina; Weisberg, Risa

2005-01-01

The authors examined characteristics of body dysmorphic disorder in the largest sample for which a wide range of clinical features has been reported. The authors also compared psychiatrically treated and untreated subjects. Body dysmorphic disorder usually began during adolescence, involved numerous body areas and behaviors, and was characterized by poor insight, high comorbidity rates, and high rates of functional impairment, suicidal ideation, and suicide attempts. There were far more similarities than differences between the currently treated and untreated subjects, although the treated subjects displayed better insight and had more comorbidity. PMID:16000674

Cross-cultural psychometric assessment of the VAGUS insight into psychosis scale - Spanish version.

PubMed

de León, Patricia Ponce; Gerretsen, Philip; Shah, Parita; Saracco-Alvarez, Ricardo; Graff-Guerrero, Ariel; Fresán, Ana

2018-01-01

Impaired insight into illness, a core feature of schizophrenia with negative clinical implications, is a multidimensional phenomenon existing on a continuum. However, the degree to which illness perception in distinct cultures influences the appraisal of insight into illness in schizophrenia remains unclear. As such, we aimed to determine if the psychometric properties of the VAGUS insight into psychosis scale (www.vagusonline.com), which was originally assessed in English speaking Canadians, were similar in a sample of Latino Mexican Spanish speaking patients with schizophrenia. To accomplish this, the VAGUS - Self-Report (SR) version was translated from English to Spanish and psychometrically evaluated in 95 participants. The Spanish version of the VAGUS-SR was internally consistent (ᾳ = 0.713), and demonstrated good convergent and discriminant validity with the subscales of the Positive and Negative Syndrome Scale. Factor analysis identified two components of insight, congruent with two of the components of the English version of the VAGUS-SR. In conclusion, the VAGUS-SR is a brief, novel, and valid measure of insight into illness in schizophrenia, which demonstrated similar psychometric properties in two culturally and linguistically distinct samples with schizophrenia. Future studies should assess whether the VAGUS demonstrates similar psychometric properties in non-Western cultures. Copyright © 2017 Elsevier B.V. All rights reserved.

Characteristics of Kodak Insight, an F-speed intraoral film.

PubMed

Ludlow, J B; Platin, E; Mol, A

2001-01-01

This study reports film speed, contrast, exposure latitude, resolution, and response to processing solution depletion of Kodak Insight intraoral film. Densitometric curves were generated by using International Standards Organization protocol. Additional curves were generated for Ultra-speed, Ektaspeed Plus, and Insight films developed in progressively depleted processing solutions. Eight observers viewed images of a resolution test tool for maximum resolution assessment. Images of an aluminum step-wedge were reviewed to determine useful exposure latitude. Insight's sensitivity in fresh automatic processor solutions places it in the F-speed group. An average gradient of 1.8 was found with all film types. Insight provided 93% of the useful exposure latitude of Ektaspeed Plus film. Insight maintained contrast in progressively depleted processing solutions. Like Ektaspeed Plus, Insight was able to resolve at least 20 line-pairs per millimeter. Under International Standards Organization conditions, Insight required only 77% of the exposure of Ektaspeed Plus film. Insight film provided stable contrast in depleted processing solutions.

Causes of death after fluid bolus resuscitation: new insights from FEAST

PubMed Central

2013-01-01

The Fluid Expansion as Supportive Therapy (FEAST study) was an extremely well conducted study that gave unexpected results. The investigators had reported that febrile children with impaired perfusion treated in low-income countries without access to intensive care are more likely to die if they receive bolus resuscitation with albumin or saline compared with no bolus resuscitation at all. In a secondary analysis of the trial, published in BMC Medicine, the authors found that increased mortality was evident in patients who presented with clinical features of severe shock in isolation or in conjunction with features of respiratory or neurological failure. The cause of excess deaths was primarily refractory shock and not fluid overload. These features are consistent with a potential cardiotoxic or ischemia-reperfusion injury following resuscitation with boluses of intravenous fluid. Although these effects may have been amplified by the absence of invasive monitoring, mechanical ventilation or vasopressors, the results provide compelling insights into the effects of intravenous fluid resuscitation and potential adverse effects that extend beyond the initial resuscitation period. These data add to the increasing body of literature about the safety and efficacy of intravenous resuscitation fluids, which may be applicable to management of other populations of critically ill patients. PMID:23497460

Is adermatoglyphia an additional feature of Kindler Syndrome?*

PubMed Central

de Almeida Jr, Hiram Larangeira; Goetze, Fernanda Mendes; Fong, Kenneth; Lai-Cheong, Joey; McGrath, John

2015-01-01

A typical feature of Kindler Syndrome is skin fragility; this condition in currently classified as a form of epidermolysis bullosa. We describe a rarely reported feature of two cases, one sporadic and one familial; both patients noticed acquired adermatoglyphia. The loss of dermatoglyphics could be an additional feature of this syndrome. PMID:26375235

Improving deep convolutional neural networks with mixed maxout units

PubMed Central

Liu, Fu-xian; Li, Long-yue

2017-01-01

Motivated by insights from the maxout-units-based deep Convolutional Neural Network (CNN) that “non-maximal features are unable to deliver” and “feature mapping subspace pooling is insufficient,” we present a novel mixed variant of the recently introduced maxout unit called a mixout unit. Specifically, we do so by calculating the exponential probabilities of feature mappings gained by applying different convolutional transformations over the same input and then calculating the expected values according to their exponential probabilities. Moreover, we introduce the Bernoulli distribution to balance the maximum values with the expected values of the feature mappings subspace. Finally, we design a simple model to verify the pooling ability of mixout units and a Mixout-units-based Network-in-Network (NiN) model to analyze the feature learning ability of the mixout models. We argue that our proposed units improve the pooling ability and that mixout models can achieve better feature learning and classification performance. PMID:28727737

American School & University. Volume 76, Number 6

ERIC Educational Resources Information Center

Agron, Joe, Ed.

2004-01-01

Each month "American School & University" provides a mix of thought-provoking features, how-to-articles, industry reports, exclusive surveys, new sections, insightful columns, new product introductions and case histories to assist education officials in better performing their jobs. This February 2004 issue includes the following: "The Color of…

American School & University. Volume 76, Number 13

ERIC Educational Resources Information Center

American School and University, 2004

2004-01-01

Each month "American School & University" provides a mix of thought-provoking features, how-to-articles, industry reports, exclusive surveys, new sections, insightful columns, new product introductions and case histories to assist education officials in better performing their jobs. This August 2004 issue includes the following: "Wireless World"…

Diamagnetic Anisotropy: Two Iron Complexes as Laboratory Examples

ERIC Educational Resources Information Center

Fernandez, Ignacio; Sanchez, Jorge Fernando Fernandez

2010-01-01

There are relatively few experiments describing the NMR properties of bis(amine) iron(II) phthalocyanine complexes. Several features make this experiment attractive: First, it nicely illustrates the diamagnetic anisotropy phenomena, providing both students and teachers an opportunity to gain insight into aspects such as phase correction and…

American School & University. Volume 77, Number 9

ERIC Educational Resources Information Center

Agron, Joe, Ed.

2005-01-01

Each month, "American School & University" provides a mix of thought-provoking features, how-to-articles, industry reports, exclusive surveys, new sections, insightful columns, new product introductions and case histories to assist education officials in better performing their jobs. This April 2005 issue includes the following: "Taking Pride"…

American School & University. Volume 77, Number 12

ERIC Educational Resources Information Center

Agron, Joe, Ed.

2005-01-01

Each month, "American School & University" provides a mix of thought-provoking features, how-to-articles, industry reports, exclusive surveys, new sections, insightful columns, new product introductions and case histories to assist education officials in better performing their jobs. This July 2005 issue includes the following: "Sweat Shop"…

American School & University. Volume 76, Number 9

ERIC Educational Resources Information Center

Agron, Joe, Ed.

2004-01-01

Each month "American School & University" provides a mix of thought-provoking features, how-to-articles, industry reports, exclusive surveys, new sections, insightful columns, new product introductions and case histories to assist education officials in better performing their jobs. This April 2004 issue includes the following: "Lifelong Learning"…

A Scaled-Projective Measure of Interpersonal Values

ERIC Educational Resources Information Center

Kilmann, Ralph H.

1975-01-01

The Kilmann Insight Test is a measure of the interpersonal value constructs. That is how the individual perceives and interprets the desirable and undesirable features of interpersonal behavior. The validity of the test is investigated by explaining its relationship to a self-report measure assessing similar values. (DEP)

The Structures of Life

ERIC Educational Resources Information Center

National Institute of General Medical Sciences (NIGMS), 2007

2007-01-01

This booklet reveals how structural biology provides insight into health and disease and is useful in developing new medications. It contains a general introduction to proteins, coverage of the techniques used to determine protein structures, and a chapter on structure-based drug design. The booklet features "Student Snapshots," designed to…

Pediatric brucellosis

PubMed Central

Bukhari, Elham E.

2018-01-01

Brucellosis remains the most common bacterial zoonotic infection in many countries worldwide. Despite being long recognized and controllable, the disease still causes substantial morbidity, affecting especially the young population. The aim of this review is to provide insight to the epidemiology, etiology, clinical features, diagnosis, and management of childhood brucellosis. PMID:29619483

Reflective Writing: Insights into What Lies beneath

ERIC Educational Resources Information Center

Kathpalia, Sujata S.; Heah, Carmel

2008-01-01

Educationists and writing practitioners consider reflection to be a defining feature of student portfolios (Fink 2003; Zubizarreta 2004; Jones and Shelton 2006). A writing portfolio without reflection is merely a collection of written work which does not contribute to "real" learning. Reflection in the portfolio approach happens when…

American School & University. Volume 76, Number 5

ERIC Educational Resources Information Center

Agron, Joe, Ed.

2004-01-01

Each month "American School & University" provides a mix of thought-provoking features, how-to-articles, industry reports, exclusive surveys, new sections, insightful columns, new product introductions and case histories to assist education officials in better performing their jobs. This January 2004 issue includes the following: "Optimism in…

American School & University. Volume 77, Number 6

ERIC Educational Resources Information Center

Agron, Joe, Ed.

2005-01-01

Each month, "American School & University" provides a mix of thought-provoking features, how-to-articles, industry reports, exclusive surveys, new sections, insightful columns, new product introductions and case histories to assist education officials in better performing their jobs. This February 2005 issue includes the following: "Under Fire"…

American School & University. Volume 77, Number 12

ERIC Educational Resources Information Center

Agron, Joe, Ed.

2005-01-01

Each month, "American School & University" provides a mix of thought-provoking features, how-to-articles, industry reports, exclusive surveys, new sections, insightful columns, new product introductions and case histories to assist education officials in better performing their jobs. This January 2005 issue includes the following: "Looking Ahead"…

Morphological Inheritance in Sandy Coastline Morphologies Subject to Long-Term Changes in Wave Climate: Surprising Insights from a Coastline Evolution Model

NASA Astrophysics Data System (ADS)

Murray, A. B.; Thomas, C.; Hurst, M. D.; Barkwith, A.; Ashton, A. D.; Ellis, M. A.

2014-12-01

Recent numerical modelling demonstrates that when sandy coastlines are affected predominantly by waves approaching from "high" angles (> ~45° between the coastline and wave crests at the offshore limit of shore-parallel contours), large-scale (kms to 100 kms) morphodynamic instabilities and finite-amplitude interactions can lead to the emergence of striking coastline features, including sand waves, capes and spits. The type of feature that emerges depends on the wave climate, defined as the angular distribution of wave influences on alongshore sediment transport. Under a constant wave climate, coastline morphology reaches a dynamical steady state; the cross-shore/alongshore aspect ratio and the general appearance of the features remains constant. In previous modelling involving wave-climate change, as well as comparisons between observed coastline morphologies and wave climates, it has been implicitly assumed that the morphology adjusts in a quasi-equilibrium fashion, so that at any time the coastline shape reflects the current forcing. However, here we present new model results showing pronounced path dependence in coastline morphodynamics. In experiments with a period of constant wave climate followed by a period of transition to a new wave climate and then a run-on phase, the features that exist during the run-on phase can be qualitatively and quantitatively different from those that would develop initially under the final wave climate. Although the features inherited from the past wave-climate history may in some case be true alternate stable states, in other cases the inherited features gradually decay toward the morphology that would be expected given the final wave climate. A suite of such experiments allows us to characterize how the e-folding timescale of this decay depends on 1) the initial wave climate, 2) the path through wave-climate space, and 3) the rate of transition. When the initial features are flying spits with cross-shore amplitudes of 6 - 8 km, e-folding times can be on the order of millennia or longer. These results could provide a new perspective when interpreting current and past coastline features. In addition, the complex paleo-coastline structure that develops in the coastal hinterlands in these experiments could be relevant to the structures observed in some coastal environments.

Vice President Sees Mars InSight Spacecraft in Colorado

NASA Image and Video Library

2017-10-27

Vice President Mike Pence joined NASA Associate Administrator for the Science Mission Directorate, Thomas Zurbuchen for a close-up view of NASA’s Mars InSight spacecraft during a visit to Lockheed Martin’s facility in Littleton, Colorado, on Thursday, October 26. InSight is being prepped for a May 2018 launch to the Red Planet, with a landing in November. It will study the deep interior of Mars, with a primary goal of helping scientists understand how rocky planets – including Earth – formed and evolved.   The vice president also visited a Lockheed Martin Virtual Reality lab, featuring demos of the company’s human exploration efforts. Lockheed Martin is the prime contractor building NASA’s Orion spacecraft, which will launch on the agency’s Space Launch System rocket, and take humans farther into the solar system than ever before.

Immunologic Insights on the Membrane Proximal External Region: A Major Human Immunodeficiency Virus Type-1 Vaccine Target

PubMed Central

Molinos-Albert, Luis M.; Clotet, Bonaventura; Blanco, Julià; Carrillo, Jorge

2017-01-01

Broadly neutralizing antibodies (bNAbs) targeting conserved regions within the human immunodeficiency virus type-1 (HIV-1) envelope glycoprotein (Env) can be generated by the human immune system and their elicitation by vaccination will be a key point to protect against the wide range of viral diversity. The membrane proximal external region (MPER) is a highly conserved region within the Env gp41 subunit, plays a major role in membrane fusion and is targeted by naturally induced bNAbs. Therefore, the MPER is considered as an attractive vaccine target. However, despite many attempts to design MPER-based immunogens, further study is still needed to understand its structural complexity, its amphiphilic feature, and its limited accessibility by steric hindrance. These particular features compromise the development of MPER-specific neutralizing responses during natural infection and limit the number of bNAbs isolated against this region, as compared with other HIV-1 vulnerability sites, and represent additional hurdles for immunogen development. Nevertheless, the analysis of MPER humoral responses elicited during natural infection as well as the MPER bNAbs isolated to date highlight that the human immune system is capable of generating MPER protective antibodies. Here, we discuss the recent advances describing the immunologic and biochemical features that make the MPER a unique HIV-1 vulnerability site, the different strategies to generate MPER-neutralizing antibodies in immunization protocols and point the importance of extending our knowledge toward new MPER epitopes by the isolation of novel monoclonal antibodies. This will be crucial for the redesign of immunogens able to skip non-neutralizing MPER determinants. PMID:28970835

Changes in exon–intron structure during vertebrate evolution affect the splicing pattern of exons

PubMed Central

Gelfman, Sahar; Burstein, David; Penn, Osnat; Savchenko, Anna; Amit, Maayan; Schwartz, Schraga; Pupko, Tal; Ast, Gil

2012-01-01

Exon–intron architecture is one of the major features directing the splicing machinery to the short exons that are located within long flanking introns. However, the evolutionary dynamics of exon–intron architecture and its impact on splicing is largely unknown. Using a comparative genomic approach, we analyzed 17 vertebrate genomes and reconstructed the ancestral motifs of both 3′ and 5′ splice sites, as also the ancestral length of exons and introns. Our analyses suggest that vertebrate introns increased in length from the shortest ancestral introns to the longest primate introns. An evolutionary analysis of splice sites revealed that weak splice sites act as a restrictive force keeping introns short. In contrast, strong splice sites allow recognition of exons flanked by long introns. Reconstruction of the ancestral state suggests these phenomena were not prevalent in the vertebrate ancestor, but appeared during vertebrate evolution. By calculating evolutionary rate shifts in exons, we identified cis-acting regulatory sequences that became fixed during the transition from early vertebrates to mammals. Experimental validations performed on a selection of these hexamers confirmed their regulatory function. We additionally revealed many features of exons that can discriminate alternative from constitutive exons. These features were integrated into a machine-learning approach to predict whether an exon is alternative. Our algorithm obtains very high predictive power (AUC of 0.91), and using these predictions we have identified and successfully validated novel alternatively spliced exons. Overall, we provide novel insights regarding the evolutionary constraints acting upon exons and their recognition by the splicing machinery. PMID:21974994

Does It Really Matter Where You Look When Walking on Stairs? Insights from a Dual-Task Study

PubMed Central

Miyasike-daSilva, Veronica; McIlroy, William E.

2012-01-01

Although the visual system is known to provide relevant information to guide stair locomotion, there is less understanding of the specific contributions of foveal and peripheral visual field information. The present study investigated the specific role of foveal vision during stair locomotion and ground-stairs transitions by using a dual-task paradigm to influence the ability to rely on foveal vision. Fifteen healthy adults (26.9±3.3 years; 8 females) ascended a 7-step staircase under four conditions: no secondary tasks (CONTROL); gaze fixation on a fixed target located at the end of the pathway (TARGET); visual reaction time task (VRT); and auditory reaction time task (ART). Gaze fixations towards stair features were significantly reduced in TARGET and VRT compared to CONTROL and ART. Despite the reduced fixations, participants were able to successfully ascend stairs and rarely used the handrail. Step time was increased during VRT compared to CONTROL in most stair steps. Navigating on the transition steps did not require more gaze fixations than the middle steps. However, reaction time tended to increase during locomotion on transitions suggesting additional executive demands during this phase. These findings suggest that foveal vision may not be an essential source of visual information regarding stair features to guide stair walking, despite the unique control challenges at transition phases as highlighted by phase-specific challenges in dual-tasking. Instead, the tendency to look at the steps in usual conditions likely provides a stable reference frame for extraction of visual information regarding step features from the entire visual field. PMID:22970297

Data for Quaternary faults, liquefaction features, and possible tectonic features in the Central and Eastern United States, east of the Rocky Mountain Front

USGS Publications Warehouse

Crone, Anthony J.; Wheeler, Russell L.

2000-01-01

The USGS is currently leading an effort to compile published geological information on Quaternary faults, folds, and earthquake-induced liquefaction in order to develop an internally consistent database on the locations, ages, and activity rates of major earthquake-related features throughout the United States. This report is the compilation for such features in the Central and Eastern United States (CEUS), which for the purposes of the compilation, is defined as the region extending from the Rocky Mountain Front eastward to the Atlantic seaboard. A key objective of this national compilation is to provide a comprehensive database of Quaternary features that might generate strong ground motion and therefore, should be considered in assessing the seismic hazard throughout the country. In addition to printed versions of regional and individual state compilations, the database will be available on the World-Wide Web, where it will be readily available to everyone. The primary purpose of these compilations and the derivative database is to provide a comprehensive, uniform source of geological information that can by used to complement the other types of data that are used in seismic-hazard assessments. Within our CEUS study area, which encompasses more than 60 percent of the continuous U.S., we summarize the geological information on 69 features that are categorized into four classes (Class A, B, C, and D) based on what is known about the feature's Quaternary activity. The CEUS contains only 13 features of tectonic origin for which there is convincing evidence of Quaternary activity (Class A features). Of the remaining 56 features, 11 require further study in order to confidently define their potential as possible sources of earthquake-induced ground motion (Class B), whereas the remaining features either lack convincing geologic evidence of Quaternary tectonic faulting or have been studied carefully enough to determine that they do not pose a significant seismic hazard (Classes C and D). The correlation between historical seismicity and Quaternary faults and liquefaction features in the CEUS is generally poor, which probably reflects the long return times between successive movements on individual structures. Some Quaternary faults and liquefaction features are located in aseismic areas or where historical seismicity is sparse. These relations indicate that the record of historical seismicity does not identify all potential seismic sources in the CEUS. Furthermore, geological studies of some currently aseismic faults have shown that the faults have generated strong earthquakes in the geologically recent past. Thus, the combination of geological information and seismological data can provide better insight into potential earthquake sources and thereby, contribute to better, more comprehensive seismic-hazard assessments.

Microscale Confinement features in microfluidic devices can affect biofilm

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kumar, Aloke; Karig, David K; Neethirajan, Suresh

2013-01-01

Biofilms are aggregations of microbes that are encased by extra-cellular polymeric substances (EPS) and adhere to surfaces and interfaces. Biofilm development on abiotic surfaces is a dynamic process, which typically proceeds through an initial phase of adhesion of plankntonic microbes to the substrate, followed by events such as growth, maturation and EPS secretion. However, the coupling of hydrodynamics, microbial adhesion and biofilm growth remain poorly understood. Here, we investigate the effect of semiconfined features on biofilm formation. Using a microfluidic device and fluorescent time-lapse microscopy, we establish that confinement features can significantly affect biofilm formation. Biofilm dynamics change not onlymore » as a function of confinement features, but also of the total fluid flow rate, and our combination of experimental results and numerical simulations reveal insights into the link between hydrodynamics and biofilm formation.« less

Mapping genomic features to functional traits through microbial whole genome sequences.

PubMed

Zhang, Wei; Zeng, Erliang; Liu, Dan; Jones, Stuart E; Emrich, Scott

2014-01-01

Recently, the utility of trait-based approaches for microbial communities has been identified. Increasing availability of whole genome sequences provide the opportunity to explore the genetic foundations of a variety of functional traits. We proposed a machine learning framework to quantitatively link the genomic features with functional traits. Genes from bacteria genomes belonging to different functional traits were grouped to Cluster of Orthologs (COGs), and were used as features. Then, TF-IDF technique from the text mining domain was applied to transform the data to accommodate the abundance and importance of each COG. After TF-IDF processing, COGs were ranked using feature selection methods to identify their relevance to the functional trait of interest. Extensive experimental results demonstrated that functional trait related genes can be detected using our method. Further, the method has the potential to provide novel biological insights.

Marketing and Advertising: Procter & Gamble Insights into Economics.

ERIC Educational Resources Information Center

Reinke, Robert; And Others

Featuring real-life examples that show economic principles at work, this document contains teaching units which are designed to supplement basic economics and consumer education textbooks in social studies, home economics, and business education classes. Written for grades 9-12, and adaptable for grades 7-8, the materials bring economic principles…

Twitteracy: Tweeting as a New Literacy Practice

ERIC Educational Resources Information Center

Greenhow, Christine; Gleason, Benjamin

2012-01-01

This article defines Twitter[TM]; outlines the features, affordances, and common uses; and conceptualizes "tweeting" as a literacy practice, comprising both traditional and new literacies, and impacting both informal and formal learning settings. Also provided is an overview of traditional and new literacies, and insights from a scan of the…

Understanding Game-Based Learning Cultures: Introduction to Special Issue

ERIC Educational Resources Information Center

Engerman, Jason A.; Carr-Chellman, Alison

2017-01-01

This special issue expands our understanding of teaching and learning through video game play, with specific attention to culture. The issue gives insight into the ways educators, researchers, and developers should be discussing and designing for impactful learner-centered game-based learning experiences. The issue features forward-thinking…

Radius Ratio Rule Rescue

ERIC Educational Resources Information Center

Michmerhuizen, Anna; Rose, Karine; Annankra, Wentiirim; Vander Griend, Douglas A.

2017-01-01

Making optimal pedagogical and predictive use of the radius ratio rule to distinguish between solid state structures that feature tetrahedral, octahedral and cubic holes requires several updated insights. A comparative analysis of the Born-Landé equation for lattice energy is developed to show that the rock salt structure is a suitable choice for…

The Development of Young Children's Understanding of the Process of Evaporation.

ERIC Educational Resources Information Center

Beveridge, Michael

1985-01-01

This investigation of the development of young children's concept of evaporation examines their intuitive explanations of real world events involving evaporation. A study of the effects of providing evidence contradicting their explanations and of directing their attention to relevant situational features provides insight into the development of…

Death as Insight into Life: Adolescents' Gothic Text Encounters

ERIC Educational Resources Information Center

Del Nero, Jennifer

2017-01-01

This qualitative case study explores adolescents' responses to texts containing death and destruction, a seminal trope of the Gothic literary genre. Participants read both classic and popular culture texts featuring characters grappling with death in their seventh grade reading classroom. Observations, interviews, and documents were collected and…

Oscillatory Dynamics Related to the Unagreement Pattern in Spanish

ERIC Educational Resources Information Center

Perez, Alejandro; Molinaro, Nicola; Mancini, Simona; Barraza, Paulo; Carreiras, Manuel

2012-01-01

Unagreement patterns consist in a person feature mismatch between subject and verb that is nonetheless grammatical in Spanish. The processing of this type of construction gives new insights into the understanding of agreement processes during language comprehension. Here, we contrasted oscillatory brain activity triggered by Unagreement in…

American School & University. Volume 76, Number 10

ERIC Educational Resources Information Center

Agron, Joe, Ed.

2004-01-01

Each month "American School & University" provides a mix of thought-provoking features, how-to-articles, industry reports, exclusive surveys, new sections, insightful columns, new product introductions and case histories to assist education officials in better performing their jobs. This May 2004 issue includes the following: "Taking The LEED"…

Home Visiting in Two Cultures

ERIC Educational Resources Information Center

Lamorey, Suzanne

2017-01-01

The home visiting component of early childhood education programs provides an important portal through which to observe family interactions as well as gain insights about the ethnotheories of the home visitor. Home visits were videotaped in the United States and in Turkey to analyze training and program effectiveness. One striking feature of this…

Selected Papers in School Finance: 1974.

ERIC Educational Resources Information Center

Office of Education (DHEW), Washington, DC.

Current school finance problems are discussed in three papers. The first presents an analysis of the Illinois school finance reform law, providing insights into the operation of the law and an evaluation method for examining finance laws in other states. In the second paper, the relationships between selected features of Michigan school districts…

STARS[R] Spring 2012 Quarterly Review: Framing Campus Sustainability

ERIC Educational Resources Information Center

Urbanski, Monika

2012-01-01

The Spring 2012 SQR: "Framing Campus Sustainability," features stories that frame the evolving concept of sustainability in higher education. Included in this issue are a snapshot of ratings-to-date, a focus on credits within the Operations (OP) category, and insights into how institutions are defining and interpreting the evolving…

Integrating legacy data to understand agroecosystem regional dynamics to catastrophic events

USDA-ARS?s Scientific Manuscript database

Multi-year extreme drought events are part of the history of the Earth system. Legacy data on the climate drivers, geomorphic features, and agroecosystem responses across a dynamically changing landscape throughout a region can provide important insights to a future where large-scale catastrophic ev...

The Arts in School Reform: Other Conversations.

ERIC Educational Resources Information Center

Burton, Judith M.

1994-01-01

Discusses why art is important in students' lives, features of artistry that captivate the mind, and reasons why arts should be fully integrated into school curricula. Change in art education should be grounded in substantive insights about artistic content, child development, teaching methods, and curriculum as a meeting ground. (SM)

Qualitative analysis of cognitive interviews with school children: A web-based food intake questionnaire

USDA-ARS?s Scientific Manuscript database

The use of computers to administer dietary assessment questionnaires has shown potential, particularly due to the variety of interactive features that can attract and sustain children's attention. Cognitive interviews can help researchers to gain insights into how children understand and elaborate t...

An Insight into E-Collections

ERIC Educational Resources Information Center

Albert, Angeline Sheba; Navaraj, A. Johnson

2006-01-01

The present paper gives a brief introduction about E-collections. It discusses the e-books, e-journals, utility, features, advantages and issues for the development of e-collections. E-books will offer a rich learning experience, reinforced with audio, video, 3D animation and collaborative learning tools. E-journals on the other hand are…

The Implications of Social Neuroscience for Social Disability

ERIC Educational Resources Information Center

McPartland, James C.; Pelphrey, Kevin A.

2012-01-01

Social disability represents a unifying feature in the diverse group of individuals with autism spectrum disorder (ASD). Social neuroscience is the study of brain mechanisms supporting interpersonal interaction. In this paper, we review brain imaging studies of the social brain and highlight practical applications of these scientific insights.…

Counseling and Psychotherapy: Theories and Interventions, Sixth Edition

ERIC Educational Resources Information Center

Capuzzi, David, Ed.; Stauffer, Mark D., Ed.

2016-01-01

Featuring important theories and trends not covered in other foundational texts, this book is designed to equip the next generation of counselors with the tools they need for understanding the core dimensions of the helping relationship. Topical experts provide contemporary information and insight on the following theories: psychoanalytic,…

Social Motor Synchronization: Insights for Understanding Social Behavior in Autism

ERIC Educational Resources Information Center

Fitzpatrick, Paula; Romero, Veronica; Amaral, Joseph L.; Duncan, Amie; Barnard, Holly; Richardson, Michael J.; Schmidt, R. C.

2017-01-01

Impairments in social interaction and communication are critical features of ASD but the underlying processes are poorly understood. An under-explored area is the social motor synchronization that happens when we coordinate our bodies with others. Here, we explored the relationships between dynamical measures of social motor synchronization and…

Genome-wide Hi-C analysis reveals extensive hierarchical chromatin interactions in rice.

PubMed

Dong, Qianli; Li, Ning; Li, Xiaochong; Yuan, Zan; Xie, Dejian; Wang, Xiaofei; Li, Jianing; Yu, Yanan; Wang, Jinbin; Ding, Baoxu; Zhang, Zhibin; Li, Changping; Bian, Yao; Zhang, Ai; Wu, Ying; Liu, Bao; Gong, Lei

2018-06-01

The non-random spatial packing of chromosomes in the nucleus plays a critical role in orchestrating gene expression and genome function. Here, we present a Hi-C analysis of the chromatin interaction patterns in rice (Oryza sativa L.) at hierarchical architectural levels. We confirm that rice chromosomes occupy their own territories with certain preferential inter-chromosomal associations. Moderate compartment delimitation and extensive TADs (Topologically Associated Domains) were determined to be associated with heterogeneous genomic compositions and epigenetic marks in the rice genome. We found subtle features including chromatin loops, gene loops, and off-/near-diagonal intensive interaction regions. Gene chromatin loops associated with H3K27me3 could be positively involved in gene expression. In addition to insulated enhancing effects for neighbor gene expression, the identified rice gene loops could bi-directionally (+/-) affect the expression of looped genes themselves. Finally, web-interleaved off-diagonal IHIs/KEEs (Interactive Heterochromatic Islands or KNOT ENGAGED ELEMENTs) could trap transposable elements (TEs) via the enrichment of silencing epigenetic marks. In parallel, the near-diagonal FIREs (Frequently Interacting Regions) could positively affect the expression of involved genes. Our results suggest that the chromatin packing pattern in rice is generally similar to that in Arabidopsis thaliana but with clear differences at specific structural levels. We conclude that genomic composition, epigenetic modification, and transcriptional activity could act in combination to shape global and local chromatin packing in rice. Our results confirm recent observations in rice and A. thaliana but also provide additional insights into the patterns and features of chromatin organization in higher plants. © 2018 The Authors. The Plant Journal published by John Wiley & Sons Ltd and Society for Experimental Biology.

Machine learning algorithm for automatic detection of CT-identifiable hyperdense lesions associated with traumatic brain injury

NASA Astrophysics Data System (ADS)

Keshavamurthy, Krishna N.; Leary, Owen P.; Merck, Lisa H.; Kimia, Benjamin; Collins, Scott; Wright, David W.; Allen, Jason W.; Brock, Jeffrey F.; Merck, Derek

2017-03-01

Traumatic brain injury (TBI) is a major cause of death and disability in the United States. Time to treatment is often related to patient outcome. Access to cerebral imaging data in a timely manner is a vital component of patient care. Current methods of detecting and quantifying intracranial pathology can be time-consuming and require careful review of 2D/3D patient images by a radiologist. Additional time is needed for image protocoling, acquisition, and processing. These steps often occur in series, adding more time to the process and potentially delaying time-dependent management decisions for patients with traumatic brain injury. Our team adapted machine learning and computer vision methods to develop a technique that rapidly and automatically detects CT-identifiable lesions. Specifically, we use scale invariant feature transform (SIFT)1 and deep convolutional neural networks (CNN)2 to identify important image features that can distinguish TBI lesions from background data. Our learning algorithm is a linear support vector machine (SVM)3. Further, we also employ tools from topological data analysis (TDA) for gleaning insights into the correlation patterns between healthy and pathological data. The technique was validated using 409 CT scans of the brain, acquired via the Progesterone for the Treatment of Traumatic Brain Injury phase III clinical trial (ProTECT_III) which studied patients with moderate to severe TBI4. CT data were annotated by a central radiologist and included patients with positive and negative scans. Additionally, the largest lesion on each positive scan was manually segmented. We reserved 80% of the data for training the SVM and used the remaining 20% for testing. Preliminary results are promising with 92.55% prediction accuracy (sensitivity = 91.15%, specificity = 93.45%), indicating the potential usefulness of this technique in clinical scenarios.

Insight change in psychosis: relationship with neurocognition, social cognition, clinical symptoms and phase of illness.

PubMed

Quee, P J; van der Meer, L; Krabbendam, L; de Haan, L; Cahn, W; Wiersma, D; van Beveren, N; Pijnenborg, G H M; Mulder, C L; Bruggeman, R; Aleman, A

2014-02-01

Impaired insight is an important and prevalent symptom of psychosis. It remains unclear whether cognitive disturbances hamper improvements in insight. We investigated the neurocognitive, social cognitive, and clinical correlates of changes in insight. One hundred and fifty-four patients with a psychotic disorder were assessed at baseline (T0 ) and after three years (T3 ) with the Birchwood Insight Scale, the Positive And Negative Syndrome Scale, measures of neurocognition and social cognition. Linear regression analyses were conducted to examine to what extend neurocognition, social cognition, clinical symptoms and phase of illness could uniquely predict insight change. Subsequently, changes in these factors were related to insight change. Better neurocognitive performance and fewer clinical symptoms at baseline explained insight improvements. The additional effect of clinical symptoms over and above the contribution of neurocognition was significant. Together, these factors explained 10% of the variance. Social cognition and phase of illness could not predict insight change. Changes in clinical symptoms, but not changes in neurocognitive performance were associated with insight change. Neurocognitive abilities may predict, in part, the development of insight in psychosis. © 2013 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Insight and analysis problem solving in microbes to machines.

PubMed

Clark, Kevin B

2015-11-01

A key feature for obtaining solutions to difficult problems, insight is oftentimes vaguely regarded as a special discontinuous intellectual process and/or a cognitive restructuring of problem representation or goal approach. However, this nearly century-old state of art devised by the Gestalt tradition to explain the non-analytical or non-trial-and-error, goal-seeking aptitude of primate mentality tends to neglect problem-solving capabilities of lower animal phyla, Kingdoms other than Animalia, and advancing smart computational technologies built from biological, artificial, and composite media. Attempting to provide an inclusive, precise definition of insight, two major criteria of insight, discontinuous processing and problem restructuring, are here reframed using terminology and statistical mechanical properties of computational complexity classes. Discontinuous processing becomes abrupt state transitions in algorithmic/heuristic outcomes or in types of algorithms/heuristics executed by agents using classical and/or quantum computational models. And problem restructuring becomes combinatorial reorganization of resources, problem-type substitution, and/or exchange of computational models. With insight bounded by computational complexity, humans, ciliated protozoa, and complex technological networks, for example, show insight when restructuring time requirements, combinatorial complexity, and problem type to solve polynomial and nondeterministic polynomial decision problems. Similar effects are expected from other problem types, supporting the idea that insight might be an epiphenomenon of analytical problem solving and consequently a larger information processing framework. Thus, this computational complexity definition of insight improves the power, external and internal validity, and reliability of operational parameters with which to classify, investigate, and produce the phenomenon for computational agents ranging from microbes to man-made devices. Copyright © 2015 Elsevier Ltd. All rights reserved.

Young People’s Preferences for an Asthma Self-Management App Highlight Psychological Needs: A Participatory Study

PubMed Central

Davis, Sharon; Calvo, Rafael Alejandro; Sawyer, Susan M

2017-01-01

Background Although the prevalence of mental illness among young people with asthma is known to be twice the rate of the wider population, none of the asthma apps reported have acknowledged or attempted to include psychological support features. This is perhaps because user involvement in the development of asthma apps has been scarce. User involvement, facilitated by participatory design methods, can begin to address these issues while contributing insights to our understanding of the psychological experience associated with asthma and how technology might improve quality of life. Objective The goal of this participatory user research study was to explore the experience, needs, and ideas of young people with asthma while allowing them to define requirements for an asthma app that would be engaging and effective at improving their well-being. Methods Young people aged 15-24 years with doctor-diagnosed asthma were invited to participate in a participatory workshop and to complete a workbook designed to elicit their thoughts and ideas about living with asthma, technology use, and the design of an app. Participants generated a number of artifacts (including collages, concept maps, and paper prototypes) designed to reify their ideas, tacit knowledge, and experience. Results A total of 20 participants (mean age 17.8 years; 60%, 12/20 female) representing a range from inadequately to well-controlled asthma completed a workbook and 13 of these also took part in a workshop (four workshops were held in total), resulting in 102 participant-generated artifacts. Theoretical thematic analysis resulted in a set of personal needs, feature ideas, and app characteristics considered relevant by young people for an asthma support app. The data revealed that psychological factors such as anxiety, and impediments to autonomy, competence, and relatedness (as consistent with self-determination theory [SDT]), were considered major influences on quality of life by young people with asthma. Furthermore, the incorporation of features pertaining to psychological experience was particularly valued by participants. Conclusions In addition to practical features for asthma management, an app for young people with asthma should include support for the mental health factors associated with lived experience (ie, anxiety, lack of autonomy, and social disconnectedness). We show how support for these factors can be translated into design features of an app for asthma. In addition to informing the development of asthma-support technologies for young people, these findings could have implications for technologies designed to support people with chronic illness more generally. PMID:28400353

The role of insight in exploratory psychodynamic psychotherapy.

PubMed

Høglend, P; Engelstad, V; Sørbye, O; Heyerdahl, O; Amlo, S

1994-12-01

Psychoanalytic theory holds that dynamic insight is used for self-observation and self-analysis during and after explorative therapy. Such self-analysis is held to lead to stable dynamic change. Within a sample of 43 moderately disturbed out-patients, pre-treatment level of insight was associated with treatment length, with not being an early or late drop-out, and with receiving additional psychotherapy during a four-year follow-up period. Pre-treatment level of insight turned out to be not directly correlated with outcome two and four years after therapy. However, level of insight was significantly correlated with outcome in interaction with treatment length. Gain of insight measured at two-year follow-up was the strongest predictor of overall dynamic change four years after therapy, compared with all the other outcome assessments made at two-year follow-up.

How self-reflection and self-certainty are related to neurocognitive functioning: an examination of cognitive insight in bipolar disorder.

PubMed

Van Camp, L S C; Oldenburg, J F E; Sabbe, B G C

2016-01-01

The pattern of associations between clinical insight, cognitive insight, and neurocognitive functioning was assessed in bipolar disorder patients. Data from 42 bipolar disorder patients were examined. Cognitive insight was measured using the Beck Cognitive Insight Scale (BCIS). The BCIS is a 15-item self-report instrument consisting of two subscales, self-reflectiveness and self-certainty. Clinical insight was measured by the use of the item G12 of the Positive and Negative Syndrome Scale. Neurocognitive functioning was assessed using the International Society for Bipolar Disorders-Battery for Assessment of Neurocognition. Correlation analyses revealed significant positive associations between self-reflectiveness and speed of processing, attention, working memory, visual learning, and reasoning and problem solving. The subscale self-certainty was negatively correlated to working memory, however, this correlation disappeared when we controlled for confounding variables. No correlations between clinical insight and neurocognition were found. In addition, there was no association between cognitive insight and clinical insight. Better neurocognitive functioning was more related to higher levels of self-reflectiveness than to diminished self-certainty.

DGIC Interconnection Insights | Distributed Generation Interconnection

Science.gov Websites

Center and Energy Analysis Group. NREL researchers examined PV project data from more than 30,000 solar permission to operate. "This report represents the first data-driven evaluation of how PV deployment additional insights on the research effort and report findings, check out STAT Chat (the "Solar

Creativity and Insight in Problem Solving

ERIC Educational Resources Information Center

Golnabi, Laura

2016-01-01

This paper analyzes the thought process involved in problem solving and its categorization as creative thinking as defined by psychologist R. Weisberg (2006). Additionally, the notion of insight, sometimes present in unconscious creative thinking and often leading to creative ideas, is discussed in the context of geometry problem solving. In…

Exploring potential Pluto-generated neutral tori

NASA Astrophysics Data System (ADS)

Smith, Howard T.; Hill, Matthew; KollMann, Peter; McHutt, Ralph

2015-11-01

The NASA New Horizons mission to Pluto is providing unprecedented insight into this mysterious outer solar system body. Escaping molecular nitrogen is of particular interest and possibly analogous to similar features observed at moons of Saturn and Jupiter. Such escaping N2 has the potential of creating molecular nitrogen and N (as a result of molecular dissociation) tori or partial toroidal extended particle distributions. The presence of these features would present the first confirmation of an extended toroidal neutral feature on a planetary scale in our solar system. While escape velocities are anticipated to be lower than those at Enceladus, Io or even Europa, particle lifetimes are much longer in Pluto’s orbit because as a result of much weaker solar interaction processes along Pluto’s orbit (on the order of tens of years). Thus, with a ~248 year orbit, Pluto may in fact be generating an extended toroidal feature along it orbit.For this work, we modify and apply our 3-D Monte Carlo neutral torus model (previously used at Saturn, Jupiter and Mercury) to study/analyze the theoretical possibility and scope of potential Pluto-generated neutral tori. Our model injects weighted particles and tracks their trajectories under the influence of all gravitational fields with interactions with other particles, solar photons and Pluto collisions. We present anticipated N2 and N tori based on current estimates of source characterization and environmental conditions. We also present an analysis of sensitivity to assumed initial conditions. Such results can provide insight into the Pluto system as well as valuable interpretation of New Horizon’s observational data.

Increasing Capacity for Innovation in Bureaucratic Primary Care Organizations: A Whole System Participatory Action Research Project

PubMed Central

Thomas, Paul; McDonnell, Juliet; McCulloch, Janette; While, Alison; Bosanquet, Nick; Ferlie, Ewan

2005-01-01

PURPOSE We wanted to identify what organizational features support innovation in Primary Care Groups (PCGs). METHODS Our study used a whole system participatory action research model. Four research teams provided complementary insights. Four case study PCGs were analyzed. Two had an intervention to help local facilitators reflect on their work. Data included 70 key informant interviews, observations of clinical governance interventions and committee meetings, analysis of written materials, surveys and telephone interviews of London Primary Care Organizations, interviews with 20 nurses, and interviews with 6 finance directors. A broad range of stakeholders reviewed data at annual conferences and formed conclusions about trustworthy principles. Sequential research phases were refocused in the light of these conclusions and in response to the changing political context. RESULTS Five features were associated with increased organizational capacity for innovation: (1) clear structures and a vision for corporate and clinical governance; (2) multiple opportunities for people to reflect and learn at all levels of the organization, and connections between these “learning spaces”; (3) both clinicians and managers in leadership roles that encourage participation; (4) the right timing for an initiative and its adaptation to the local context; and (5) external facilitation that provides opportunities for people to make sense of their experiences. Low morale was commonly attributed to 3 features: (1) overwhelming pace of reform, (2) inadequate staff experience and supportive infrastructure, and (3) financial deficits. CONCLUSIONS These features together may support innovation in other primary care bureaucracies. The research methodology enabled people from different backgrounds to make sense of diverse research insights. PMID:16046563

Increasing capacity for innovation in bureaucratic primary care organizations: a whole system participatory action research project.

PubMed

Thomas, Paul; McDonnell, Juliet; McCulloch, Janette; While, Alison; Bosanquet, Nick; Ferlie, Ewan

2005-01-01

We wanted to identify what organizational features support innovation in Primary Care Groups (PCGs). Our study used a whole system participatory action research model. Four research teams provided complementary insights. Four case study PCGs were analyzed. Two had an intervention to help local facilitators reflect on their work. Data included 70 key informant interviews, observations of clinical governance interventions and committee meetings, analysis of written materials, surveys and telephone interviews of London Primary Care Organizations, interviews with 20 nurses, and interviews with 6 finance directors. A broad range of stakeholders reviewed data at annual conferences and formed conclusions about trustworthy principles. Sequential research phases were refocused in the light of these conclusions and in response to the changing political context. Five features were associated with increased organizational capacity for innovation: (1) clear structures and a vision for corporate and clinical governance; (2) multiple opportunities for people to reflect and learn at all levels of the organization, and connections between these "learning spaces"; (3) both clinicians and managers in leadership roles that encourage participation; (4) the right timing for an initiative and its adaptation to the local context; and (5) external facilitation that provides opportunities for people to make sense of their experiences. Low morale was commonly attributed to 3 features: (1) overwhelming pace of reform, (2) inadequate staff experience and supportive infrastructure, and (3) financial deficits. These features together may support innovation in other primary care bureaucracies. The research methodology enabled people from different backgrounds to make sense of diverse research insights.

Educators' insights in using chronicle diabetes: a data management system for diabetes education.

PubMed

Wang, Jing; Siminerio, Linda M

2013-01-01

Diabetes educators lack data systems to monitor diabetes self-management education processes and programs. The purpose of the study is to explore diabetes educator's insights in using a diabetes education data management program: the Chronicle Diabetes system. We conducted 1 focus group with 8 diabetes educators who use the Chronicle system in western Pennsylvania. The focus group was audiotaped and transcribed verbatim. Themes were categorized according to system facilitators and barriers in using Chronicle. Educators report 4 system facilitators and 4 barrier features. System facilitators include (1) ability to extract data from Chronicle for education program recognition, (2) central location for collecting and documenting all patient and education data, (3) capability to monitor behavioral goal setting and clinical outcomes, and (4) use of a patient snapshot report that automatically summarizes behavioral goal setting and an education plan. Barriers reported are (1) initially time-consuming for data entry, (2) Health Insurance Portability and Accountability Act privacy concerns for e-mailing or downloading report, (3) need for special features (e.g., ability to attach a food diary), and (4) need to enhance existing features to standardize goal-setting process and incorporate psychosocial content. Educators favor capabilities for documenting program requirements, goal setting, and patient summaries. Barriers that need to be overcome are the amount of time needed for data entry, privacy, and special features. Diabetes educators conclude that a data management system such as Chronicle facilitates the education process and affords ease in documentation of meeting diabetes self-management education standards and recognition requirements.

Evolutionary ecology of specialization: insights from phylogenetic analysis

PubMed Central

Vamosi, Jana C.; Armbruster, W. Scott; Renner, Susanne S.

2014-01-01

In this Special feature, we assemble studies that illustrate phylogenetic approaches to studying salient questions regarding the effect of specialization on lineage diversification. The studies use an array of techniques involving a wide-ranging collection of biological systems (plants, butterflies, fish and amphibians are all represented). Their results reveal that macroevolutionary examination of specialization provides insight into the patterns of trade-offs in specialized systems; in particular, the genetic mechanisms of trade-offs appear to extend to very different aspects of life history in different groups. In turn, because a species may be a specialist from one perspective and a generalist in others, these trade-offs influence whether we perceive specialization to have effects on the evolutionary success of a lineage when we examine specialization only along a single axis. Finally, how geographical range influences speciation and extinction of specialist lineages remains a question offering much potential for further insight. PMID:25274367

Geological Mapping of the North Polar Region of Venus (V-1 Snegurochka Planitia): Significant Problems and Comparisons to the Earth's Archean

NASA Technical Reports Server (NTRS)

Head, James W.; Hurwitz, D. M.; Ivanov, M. A.; Basilevsky, A. T.; Kumar, P. Senthil

2008-01-01

The geological features, structures, thermal conditions, interpreted processes, and outstanding questions related to both the Earth's Archean and Venus share many similarities and we are using a problem-oriented approach to Venus mapping, guided by perspectives from the Archean record of the Earth, to gain new insight into both. The Earth's preserved and well-documented Archean record provides important insight into high heat-flux tectonic and magmatic environments and structures and Venus reveals the current configuration and recent geological record of analogous high-temperature environments unmodified by subsequent several billion years of segmentation and overprinting, as on Earth. We have problems on which progress might be made through comparison. Here we present the major goals of the geological mapping of the V-1 Snegurochka Planitia Quadrangle, and themes that could provide important insights into both planets:

Carnivore-specific SINEs (Can-SINEs): distribution, evolution, and genomic impact.

PubMed

Walters-Conte, Kathryn B; Johnson, Diana L E; Allard, Marc W; Pecon-Slattery, Jill

2011-01-01

Short interspersed nuclear elements (SINEs) are a type of class 1 transposable element (retrotransposon) with features that allow investigators to resolve evolutionary relationships between populations and species while providing insight into genome composition and function. Characterization of a Carnivora-specific SINE family, Can-SINEs, has, has aided comparative genomic studies by providing rare genomic changes, and neutral sequence variants often needed to resolve difficult evolutionary questions. In addition, Can-SINEs constitute a significant source of functional diversity with Carnivora. Publication of the whole-genome sequence of domestic dog, domestic cat, and giant panda serves as a valuable resource in comparative genomic inferences gleaned from Can-SINEs. In anticipation of forthcoming studies bolstered by new genomic data, this review describes the discovery and characterization of Can-SINE motifs as well as describes composition, distribution, and effect on genome function. As the contribution of noncoding sequences to genomic diversity becomes more apparent, SINEs and other transposable elements will play an increasingly large role in mammalian comparative genomics.

Carnivore-Specific SINEs (Can-SINEs): Distribution, Evolution, and Genomic Impact

PubMed Central

Johnson, Diana L.E.; Allard, Marc W.; Pecon-Slattery, Jill

2011-01-01

Short interspersed nuclear elements (SINEs) are a type of class 1 transposable element (retrotransposon) with features that allow investigators to resolve evolutionary relationships between populations and species while providing insight into genome composition and function. Characterization of a Carnivora-specific SINE family, Can-SINEs, has, has aided comparative genomic studies by providing rare genomic changes, and neutral sequence variants often needed to resolve difficult evolutionary questions. In addition, Can-SINEs constitute a significant source of functional diversity with Carnivora. Publication of the whole-genome sequence of domestic dog, domestic cat, and giant panda serves as a valuable resource in comparative genomic inferences gleaned from Can-SINEs. In anticipation of forthcoming studies bolstered by new genomic data, this review describes the discovery and characterization of Can-SINE motifs as well as describes composition, distribution, and effect on genome function. As the contribution of noncoding sequences to genomic diversity becomes more apparent, SINEs and other transposable elements will play an increasingly large role in mammalian comparative genomics. PMID:21846743

A Hyper-Heuristic Ensemble Method for Static Job-Shop Scheduling.

PubMed

Hart, Emma; Sim, Kevin

2016-01-01

We describe a new hyper-heuristic method NELLI-GP for solving job-shop scheduling problems (JSSP) that evolves an ensemble of heuristics. The ensemble adopts a divide-and-conquer approach in which each heuristic solves a unique subset of the instance set considered. NELLI-GP extends an existing ensemble method called NELLI by introducing a novel heuristic generator that evolves heuristics composed of linear sequences of dispatching rules: each rule is represented using a tree structure and is itself evolved. Following a training period, the ensemble is shown to outperform both existing dispatching rules and a standard genetic programming algorithm on a large set of new test instances. In addition, it obtains superior results on a set of 210 benchmark problems from the literature when compared to two state-of-the-art hyper-heuristic approaches. Further analysis of the relationship between heuristics in the evolved ensemble and the instances each solves provides new insights into features that might describe similar instances.

In Vitro Reconstitution of Metabolic Pathways: Insights into Nature’s Chemical Logic

PubMed Central

Lowry, Brian; Walsh, Christopher T.

2015-01-01

In vitro analysis of metabolic pathways is becoming a powerful method to gain a deeper understanding of Nature’s core biochemical transformations. With astounding advancements in biotechnology, purification of a metabolic pathway’s constitutive enzymatic components is becoming a tractable problem, and such in vitro studies allow scientists to capture the finer details of enzymatic reaction mechanisms, kinetics, and the identity of organic product molecules. In this review, we present eleven metabolic pathways that have been the subject of in vitro reconstitution studies in the literature in recent years. In addition, we have selected and analyzed subset of four case studies within these eleven examples that exemplify remarkable organic chemistry occurring within biology. These examples serves as tangible reminders that Nature’s biochemical routes obey the fundamental principles of organic chemistry, and the chemical mechanisms are reminiscent of those featured in traditional synthetic organic routes. The illustrations of biosynthetic chemistry depicted in this review may inspire the development of biomimetic chemistries via abiotic chemical techniques. PMID:26207083

Reviews Equipment: Data logger Book: Imagined Worlds Equipment: Mini data loggers Equipment: PICAXE-18M2 data logger Books: Engineering: A Very Short Introduction and To Engineer Is Human Book: Soap, Science, & Flat-Screen TVs Equipment: uLog and SensorLab Web Watch

NASA Astrophysics Data System (ADS)

2012-07-01

WE RECOMMEND Data logger Fourier NOVA LINK: data logging and analysis To Engineer is Human Engineering: essays and insights Soap, Science, & Flat-Screen TVs People, politics, business and science overlap uLog sensors and sensor adapter A new addition to the LogIT range offers simplicity and ease of use WORTH A LOOK Imagined Worlds Socio-scientific predictions for the future Mini light data logger and mini temperature data logger Small-scale equipment for schools SensorLab Plus LogIT's supporting software, with extra features HANDLE WITH CARE CAXE110P PICAXE-18M2 data logger Data logger 'on view' but disappoints Engineering: A Very Short Introduction A broad-brush treatment fails to satisfy WEB WATCH Two very different websites for students: advanced physics questions answered and a more general BBC science resource

Anions mediate ligand binding in Adineta vaga glutamate receptor ion channels

PubMed Central

Lomash, Suvendu; Chittori, Sagar; Brown, Patrick; Mayer, Mark L.

2014-01-01

SUMMARY AvGluR1, a glutamate receptor ion channel from the primitive eukaryote Adineta vaga, is activated by alanine, cysteine, methionine and phenylalanine which produce lectin-sensitive desensitizing responses like those to glutamate, aspartate and serine. AvGluR1 LBD crystal structures reveal a novel scheme for binding dissimilar ligands that may be utilized by distantly related odorant/chemosensory receptors. Arginine residues in domain 2 coordinate the γ-carboxyl group of glutamate, while in the alanine, methionine and serine complexes a chloride ion acts as a surrogate ligand, replacing the γ-carboxyl group. Removal of Cl− lowers affinity for these ligands, but not for glutamate, aspartate or for phenylalanine which occludes the anion binding site and binds with low affinity. AvGluR1 LBD crystal structures and sedimentation analysis also provide insights into the evolutionary link between prokaryotic and eukaryotic iGluRs and reveal features unique to both classes, emphasizing the need for additional structure based studies on iGluR-ligand interactions. PMID:23434404

Treating Sjögren's Syndrome: Insights for the Clinician

PubMed Central

Vitali, Claudio; Palombi, Gianluigi; Cataleta, Pierluigi

2010-01-01

Sjögren's syndrome (SS) is a systemic autoimmune disease that affects the exocrine glands, mainly the salivary and lachrymal glands, with consequent persistent dryness of the mouth and eyes. In addition to the clinical manifestations related to the exocrine gland involvement, a consistent prevalence of patients may present systemic manifestations. Some of these can be ascribed to the periepithelial extension of lymphocytic infiltration whilst others are determined by an immunomediated process affecting small- or medium-size vessels. While the use of tear and saliva substitutes and local or systemic stimulation of residual secretions represent the mainstays of the therapy of sicca component, different immunomodulating or immunosuppressive agents are usually required to treat extraglandular features, similarly to what happens in other connective tissue diseases. In the last few years, the advancement in the understanding the pathogenetic mechanisms of this disorder and the availability of new biologic target therapies seem to offer completely new therapeutic options. The use of B cell depleting or modulating therapies has achieved promising results. PMID:22870445

The oldest known snakes from the Middle Jurassic-Lower Cretaceous provide insights on snake evolution.

PubMed

Caldwell, Michael W; Nydam, Randall L; Palci, Alessandro; Apesteguía, Sebastián

2015-01-27

The previous oldest known fossil snakes date from ~100 million year old sediments (Upper Cretaceous) and are both morphologically and phylogenetically diverse, indicating that snakes underwent a much earlier origin and adaptive radiation. We report here on snake fossils that extend the record backwards in time by an additional ~70 million years (Middle Jurassic-Lower Cretaceous). These ancient snakes share features with fossil and modern snakes (for example, recurved teeth with labial and lingual carinae, long toothed suborbital ramus of maxillae) and with lizards (for example, pronounced subdental shelf/gutter). The paleobiogeography of these early snakes is diverse and complex, suggesting that snakes had undergone habitat differentiation and geographic radiation by the mid-Jurassic. Phylogenetic analysis of squamates recovers these early snakes in a basal polytomy with other fossil and modern snakes, where Najash rionegrina is sister to this clade. Ingroup analysis finds them in a basal position to all other snakes including Najash.

Vertically aligned carbon nanotubes as cytocompatible material for enhanced adhesion and proliferation of osteoblast-like cells.

PubMed

Giannona, Suna; Firkowska, Izabela; Rojas-Chapana, José; Giersig, Michael

2007-01-01

In this study, we describe the spatial organization of CAL-72 osteoblast-like cells on arrays of vertically aligned multi-walled carbon nanotubes (VACNTs). It was observed that, unlike cell growth on non-patterned surfaces, the cell attachment and spreading process on VACNTs was significantly enhanced. Additionally, since carbon nanotubes are known to possess resilient mechanical properties and are chemically stable, the effect of periodic arrays of VACNTs on CAL-72 osteoblast-like cells was also studied. The periodicity and alignment of VACNTs considerably influenced growth, shape and orientation of the cells by steering toward the nanopattern. This situation is of great interest for the potential application of VACNTs in bone bioenginnering. This data provides evidence that CAL-72 osteoblast-like cells can sense physical features at the nanoscale. These results give a fascinating insight into the ways in which cell growth can be influenced by man-made nanostructures and could provide a framework for achieving controlled cell guidance with controlled organization and special physical properties.

Biochemical and functional characterization of an albumin protein belonging to the hemopexin superfamily from Lens culinaris seeds.

PubMed

Scarafoni, Alessio; Gualtieri, Elisa; Barbiroli, Alberto; Carpen, Aristodemo; Negri, Armando; Duranti, Marcello

2011-09-14

The present paper reports the purification and biochemical characterization of an albumin identified in mature lentil seeds with high sequence similarity to pea PA2. These proteins are found in many edible seeds and are considered potentially detrimental for human health due to the potential allergenicity and lectin-like activity. Thus, the description of their possible presence in food and the assessment of the molecular properties are relevant. The M(r), pI, and N-terminal sequence of this protein have been determined. The work included the study of (i) the binding properties to hemine to assess the presence of hemopexin structural domains and (ii) the binding properties of the protein to thiamin. In addition, the structural changes induced by heating have been evaluated by means of spectroscopic techniques. Denaturation temperature has also been determined. The present work provides new insights about the structural molecular features and the ligand-binding properties and dynamics of this kind of seed albumin.

Learning Collaborative Sparse Representation for Grayscale-Thermal Tracking.

PubMed

Li, Chenglong; Cheng, Hui; Hu, Shiyi; Liu, Xiaobai; Tang, Jin; Lin, Liang

2016-09-27

Integrating multiple different yet complementary feature representations has been proved to be an effective way for boosting tracking performance. This paper investigates how to perform robust object tracking in challenging scenarios by adaptively incorporating information from grayscale and thermal videos, and proposes a novel collaborative algorithm for online tracking. In particular, an adaptive fusion scheme is proposed based on collaborative sparse representation in Bayesian filtering framework. We jointly optimize sparse codes and the reliable weights of different modalities in an online way. In addition, this work contributes a comprehensive video benchmark, which includes 50 grayscale-thermal sequences and their ground truth annotations for tracking purpose. The videos are with high diversity and the annotations were finished by one single person to guarantee consistency. Extensive experiments against other stateof- the-art trackers with both grayscale and grayscale-thermal inputs demonstrate the effectiveness of the proposed tracking approach. Through analyzing quantitative results, we also provide basic insights and potential future research directions in grayscale-thermal tracking.

Enhanced transformation of incidentally learned knowledge into explicit memory by dopaminergic modulation.

PubMed

Clos, Mareike; Sommer, Tobias; Schneider, Signe L; Rose, Michael

2018-01-01

During incidental learning statistical regularities are extracted from the environment without the intention to learn. Acquired implicit memory of these regularities can affect behavior in the absence of awareness. However, conscious insight in the underlying regularities can also develop during learning. Such emergence of explicit memory is an important learning mechanism that is assumed to involve prediction errors in the striatum and to be dopamine-dependent. Here we directly tested this hypothesis by manipulating dopamine levels during incidental learning in a modified serial reaction time task (SRTT) featuring a hidden regular sequence of motor responses in a placebo-controlled between-group study. Awareness for the sequential regularity was subsequently assessed using cued generation and additionally verified using free recall. The results demonstrated that dopaminergic modulation nearly doubled the amount of explicit sequence knowledge emerged during learning in comparison to the placebo group. This strong effect clearly argues for a causal role of dopamine-dependent processing for the development of awareness for sequential regularities during learning.

A high definition Mueller polarimetric endoscope for tissue characterisation

NASA Astrophysics Data System (ADS)

Qi, Ji; Elson, Daniel S.

2016-05-01

The contrast mechanism of medical endoscopy is mainly based on metrics of optical intensity and wavelength. As another fundamental property of light, polarization can not only reveal tissue scattering and absorption information from a different perspective, but can also provide insight into directional tissue birefringence properties to monitor pathological changes in collagen and elastin. Here we demonstrate a low cost wide field high definition Mueller polarimetric endoscope with minimal alterations to a rigid endoscope. We show that this novel endoscopic imaging modality is able to provide a number of image contrast mechanisms besides traditional unpolarized radiation intensity, including linear depolarization, circular depolarization, cross-polarization, directional birefringence and dichroism. This enhances tissue features of interest, and additionally reveals tissue micro-structure and composition, which is of central importance for tissue diagnosis and image guidance for surgery. The potential applications of the Mueller polarimetric endoscope include wide field early epithelial cancer diagnosis, surgical margin detection and energy-based tissue fusion monitoring, and could further benefit a wide range of endoscopic investigations through intra-operative guidance.

Gene Ontology annotations at SGD: new data sources and annotation methods

PubMed Central

Hong, Eurie L.; Balakrishnan, Rama; Dong, Qing; Christie, Karen R.; Park, Julie; Binkley, Gail; Costanzo, Maria C.; Dwight, Selina S.; Engel, Stacia R.; Fisk, Dianna G.; Hirschman, Jodi E.; Hitz, Benjamin C.; Krieger, Cynthia J.; Livstone, Michael S.; Miyasato, Stuart R.; Nash, Robert S.; Oughtred, Rose; Skrzypek, Marek S.; Weng, Shuai; Wong, Edith D.; Zhu, Kathy K.; Dolinski, Kara; Botstein, David; Cherry, J. Michael

2008-01-01

The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org/) collects and organizes biological information about the chromosomal features and gene products of the budding yeast Saccharomyces cerevisiae. Although published data from traditional experimental methods are the primary sources of evidence supporting Gene Ontology (GO) annotations for a gene product, high-throughput experiments and computational predictions can also provide valuable insights in the absence of an extensive body of literature. Therefore, GO annotations available at SGD now include high-throughput data as well as computational predictions provided by the GO Annotation Project (GOA UniProt; http://www.ebi.ac.uk/GOA/). Because the annotation method used to assign GO annotations varies by data source, GO resources at SGD have been modified to distinguish data sources and annotation methods. In addition to providing information for genes that have not been experimentally characterized, GO annotations from independent sources can be compared to those made by SGD to help keep the literature-based GO annotations current. PMID:17982175

Structural insights into substrate and inhibitor binding sites in human indoleamine 2,3-dioxygenase 1

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lewis-Ballester, Ariel; Pham, Khoa N.; Batabyal, Dipanwita

Human indoleamine 2,3-dioxygenase 1 (hIDO1) is an attractive cancer immunotherapeutic target owing to its role in promoting tumoral immune escape. However, drug development has been hindered by limited structural information. Here, we report the crystal structures of hIDO1 in complex with its substrate, Trp, an inhibitor, epacadostat, and/or an effector, indole ethanol (IDE). The data reveal structural features of the active site (Sa) critical for substrate activation; in addition, they disclose a new inhibitor-binding mode and a distinct small molecule binding site (Si). Structure-guided mutation of a critical residue, F270, to glycine perturbs the Si site, allowing structural determination ofmore » an inhibitory complex, where both the Sa and Si sites are occupied by Trp. The Si site offers a novel target site for allosteric inhibitors and a molecular explanation for the previously baffling substrate-inhibition behavior of the enzyme. Taken together, the data open exciting new avenues for structure-based drug design.« less

Advanced Ultrasound Technologies for Diagnosis and Therapy.

PubMed

Rix, Anne; Lederle, Wiltrud; Theek, Benjamin; Lammers, Twan; Moonen, Chrit; Schmitz, Georg; Kiessling, Fabian

2018-05-01

Ultrasound is among the most rapidly advancing imaging techniques. Functional methods such as elastography have been clinically introduced, and tissue characterization is improved by contrast-enhanced scans. Here, novel superresolution techniques provide unique morphologic and functional insights into tissue vascularization. Functional analyses are complemented by molecular ultrasound imaging, to visualize markers of inflammation and angiogenesis. The full potential of diagnostic ultrasound may become apparent by integrating these multiple imaging features in radiomics approaches. Emerging interest in ultrasound also results from its therapeutic potential. Various applications of tumor ablation with high-intensity focused ultrasound are being clinically evaluated, and its performance strongly benefits from the integration into MRI. Additionally, oscillating microbubbles mediate sonoporation to open biologic barriers, thus improving the delivery of drugs or nucleic acids that are coadministered or coformulated with microbubbles. This article provides an overview of recent developments in diagnostic and therapeutic ultrasound, highlighting multiple innovation tracks and their translational potential. © 2018 by the Society of Nuclear Medicine and Molecular Imaging.

Real-time dual-band haptic music player for mobile devices.

PubMed

Hwang, Inwook; Lee, Hyeseon; Choi, Seungmoon

2013-01-01

We introduce a novel dual-band haptic music player for real-time simultaneous vibrotactile playback with music in mobile devices. Our haptic music player features a new miniature dual-mode actuator that can produce vibrations consisting of two principal frequencies and a real-time vibration generation algorithm that can extract vibration commands from a music file for dual-band playback (bass and treble). The algorithm uses a "haptic equalizer" and provides plausible sound-to-touch modality conversion based on human perceptual data. In addition, we present a user study carried out to evaluate the subjective performance (precision, harmony, fun, and preference) of the haptic music player, in comparison with the current practice of bass-band-only vibrotactile playback via a single-frequency voice-coil actuator. The evaluation results indicated that the new dual-band playback outperforms the bass-only rendering, also providing several insights for further improvements. The developed system and experimental findings have implications for improving the multimedia experience with mobile devices.

Dynamics of Viremia in Primary HIV-1 infection in Africans: Insights from Analyses of Host and Viral Correlates

PubMed Central

Prentice, Heather A.; Price, Matthew A.; Porter, Travis R.; Cormier, Emmanuel; Mugavero, Michael J.; Kamali, Anatoli; Karita, Etienne; Lakhi, Shabir; Sanders, Eduard J.; Anzala, Omu; Amornkul, Pauli N.; Allen, Susan; Hunter, Eric; Kaslow, Richard A.; Gilmour, Jill; Tang, Jianming

2014-01-01

In HIV-1 infection, plasma viral load (VL) has dual implications for pathogenesis and public health. Based on well-known patterns of HIV-1 evolution and immune escape, we hypothesized that VL is an evolving quantitative trait that depends heavily on duration of infection (DOI), demographic features, human leukocyte antigen (HLA) genotypes and viral characteristics. Prospective data from 421 African seroconverters with at least four eligible visits did show relatively steady VL beyond 3 months of untreated infection, but host and viral factors independently associated with cross-sectional and longitudinal VL often varied by analytical approaches and sliding time windows. Specifically, the effects of age, HLA-B*53 and infecting HIV-1 subtypes (A1, C and others) on VL were either sporadic or highly sensitive to time windows. These observations were strengthened by the addition of 111 seroconverters with 2–3 eligible VL results, suggesting that DOI should be a critical parameter in epidemiological and clinical studies. PMID:24418560

Advances in the Study of Heart Development and Disease Using Zebrafish

PubMed Central

Brown, Daniel R.; Samsa, Leigh Ann; Qian, Li; Liu, Jiandong

2016-01-01

Animal models of cardiovascular disease are key players in the translational medicine pipeline used to define the conserved genetic and molecular basis of disease. Congenital heart diseases (CHDs) are the most common type of human birth defect and feature structural abnormalities that arise during cardiac development and maturation. The zebrafish, Danio rerio, is a valuable vertebrate model organism, offering advantages over traditional mammalian models. These advantages include the rapid, stereotyped and external development of transparent embryos produced in large numbers from inexpensively housed adults, vast capacity for genetic manipulation, and amenability to high-throughput screening. With the help of modern genetics and a sequenced genome, zebrafish have led to insights in cardiovascular diseases ranging from CHDs to arrhythmia and cardiomyopathy. Here, we discuss the utility of zebrafish as a model system and summarize zebrafish cardiac morphogenesis with emphasis on parallels to human heart diseases. Additionally, we discuss the specific tools and experimental platforms utilized in the zebrafish model including forward screens, functional characterization of candidate genes, and high throughput applications. PMID:27335817

Research with parthenogenetic stem cells will help decide whether a safer clinical use is possible.

PubMed

Muñoz, M; Penarossa, G; Caamaño, J N; Díez, C; Brevini, T A L; Gómez, E

2015-04-01

The derivation and use of parthenogenetic stem cells (pESCs) are envisaged as a reliable alternative to conventional embryonic stem cells. Similar to embryonic stem cells in their proliferation, expression of pluripotency markers and capacity to multilineage differentiation, pESCs are at a lower risk of immune rejection within stem cell-based therapeutics. Moreover, pESCs represent an important model system to study the effect of paternally imprinted genes on cell differentiation. However, currently available information about the genetic and epigenetic behaviour of pESCs is limited. Thus, a detailed look at the biology of parthenogenetic (PG) embryos and PG-derived cell lines would allow gaining insight into the full potential of pESC in biotechnology. In this commentary article we review some features related to the biology of PG embryos and pESCs. In addition, novel traits on bovine pESCs (bpESCs) are discussed. Copyright © 2013 John Wiley & Sons, Ltd.

Anti-cooperative ligand binding and dimerisation in the glycopeptide antibiotic dalbavancin† †Electronic supplementary information (ESI) available. See DOI: 10.1039/C3OB42428F Click here for additional data file.

PubMed Central

Cheng, Mu; Ziora, Zyta M.; Hansford, Karl A.; Blaskovich, Mark A.; Butler, Mark S.

2014-01-01

Dalbavancin, a semi-synthetic glycopeptide with enhanced antibiotic activity compared to vancomycin and teicoplanin, binds to the C-terminal lysyl-d-alanyl-d-alanine subunit of Lipid II, inhibiting peptidoglycan biosynthesis. In this study, micro-calorimetry and electrospray ionization (ESI)-MS have been used to investigate the relationship between oligomerisation of dalbavancin and binding of a Lipid II peptide mimic, diacetyl-Lys-d-Ala-d-Ala (Ac2-Kaa). Dalbavancin dimerised strongly in an anti-cooperative manner with ligand-binding, as was the case for ristocetin A, but not for vancomycin and teicoplanin. Dalbavancin and ristocetin A both adopt an ‘closed’ conformation upon ligand binding, suggesting anti-cooperative dimerisation with ligand-binding may be a general feature of dalbavancin/ristocetin A-like glycopeptides. Understanding these effects may provide insight into design of novel dalbavancin derivatives with cooperative ligand-binding and dimerisation characteristics that could enhance antibiotic activity. PMID:24608916

Lybatides from Lycium barbarum Contain An Unusual Cystine-stapled Helical Peptide Scaffold.

PubMed

Tan, Wei Liang; Wong, Ka H; Lei, Jian; Sakai, Naoki; Tan, Hong Wei; Hilgenfeld, Rolf; Tam, James P

2017-07-12

Cysteine-rich peptides (CRPs) of 2-6 kDa are generally thermally and proteolytically stable because of their multiple cross-bracing disulfide bonds. Here, we report the discovery and characterization of two novel cystine-stapled CRPs, designated lybatide 1 and 2 (lyba1 and lyba2), from the cortex of Lycium barbarum root. Lybatides, 32 to 33 amino acids in length, are hyperstable and display a novel disulfide connectivity with a cysteine motif of C-C-C-C-CC-CC which contains two pairs of adjacent cysteines (-CC-CC). X-ray structure analysis revealed the presence of a single cystine-stabilized (α + π)-helix in lyba2, a rare feature of CRPs. Together, our results suggest that lybatides, one of the smallest four-disulfide-constrained plant CRPs, is a new family of CRPs. Additionally, this study provides new insights into the molecular diversity of plant cysteine-rich peptides and the unusual lybatide scaffold could be developed as a useful template for peptide engineering and therapeutic development.

The Diversity of Ribonuclease P: Protein and RNA Catalysts with Analogous Biological Functions

PubMed Central

Klemm, Bradley P.; Wu, Nancy; Chen, Yu; Liu, Xin; Kaitany, Kipchumba J.; Howard, Michael J.; Fierke, Carol A.

2016-01-01

Ribonuclease P (RNase P) is an essential endonuclease responsible for catalyzing 5’ end maturation in precursor transfer RNAs. Since its discovery in the 1970s, RNase P enzymes have been identified and studied throughout the three domains of life. Interestingly, RNase P is either RNA-based, with a catalytic RNA subunit, or a protein-only (PRORP) enzyme with differential evolutionary distribution. The available structural data, including the active site data, provides insight into catalysis and substrate recognition. The hydrolytic and kinetic mechanisms of the two forms of RNase P enzymes are similar, yet features unique to the RNA-based and PRORP enzymes are consistent with different evolutionary origins. The various RNase P enzymes, in addition to their primary role in tRNA 5’ maturation, catalyze cleavage of a variety of alternative substrates, indicating a diversification of RNase P function in vivo. The review concludes with a discussion of recent advances and interesting research directions in the field. PMID:27187488

The special features of tree ring gas chronologies

NASA Astrophysics Data System (ADS)

Ageev, Boris G.; Gruzdev, Aleksandr N.; Sapozhnikova, Valeria A.

2015-11-01

Stem wood is known to contain significant amounts of gases. However, literature data on the functional role of the gases are lacking. The results of our experiments show that porous wood structure is capable of annual accumulation (sorption) of the stem gas components that include H2O vapor and plant cell-respired CO2. This allows for development of additional chronologies to be used for gaining a deeper insight into the behavior of the stem gases. An analysis of the vacuum-extracted wood tree ring CO2 and H2O has revealed that the CO2 and H2O chronologies are associated with interannual variations in the total pressure of the gas components in the tree rings and are characterized by short-period cycles independent of tree age and by long-period variations with tree age. Our investigations led us to propose a procedure for using the CO2 content as a marker of year-to-year variations in the total pressure of the residual gas components found in wood tree rings.

A physiologically based model for tramadol pharmacokinetics in horses.

PubMed

Abbiati, Roberto Andrea; Cagnardi, Petra; Ravasio, Giuliano; Villa, Roberto; Manca, Davide

2017-09-21

This work proposes an application of a minimal complexity physiologically based pharmacokinetic model to predict tramadol concentration vs time profiles in horses. Tramadol is an opioid analgesic also used for veterinary treatments. Researchers and medical doctors can profit from the application of mathematical models as supporting tools to optimize the pharmacological treatment of animal species. The proposed model is based on physiology but adopts the minimal compartmental architecture necessary to describe the experimental data. The model features a system of ordinary differential equations, where most of the model parameters are either assigned or individualized for a given horse, using literature data and correlations. Conversely, residual parameters, whose value is unknown, are regressed exploiting experimental data. The model proved capable of simulating pharmacokinetic profiles with accuracy. In addition, it provides further insights on un-observable tramadol data, as for instance tramadol concentration in the liver or hepatic metabolism and renal excretion extent. Copyright © 2017 Elsevier Ltd. All rights reserved.

Molecular biology of Fanconi anaemia--an old problem, a new insight.

PubMed

Ahmad, Shamim I; Hanaoka, Fumio; Kirk, Sandra H

2002-05-01

Fanconi anaemia (FA) comprises a group of autosomal recessive disorders resulting from mutations in one of eight genes (FANCA, FANCB, FANCC, FANCD1, FANCD2, FANCE, FANCF and FANCG). Although caused by relatively simple mutations, the disease shows a complex phenotype, with a variety of features including developmental abnormalities and ultimately severe anaemia and/or leukemia leading to death in the mid teens. Since 1992 all but two of the genes have been identified, and molecular analysis of their products has revealed a complex mode of action. Many of the proteins form a nuclear multisubunit complex that appears to be involved in the repair of double-strand DNA breaks. Additionally, at least one of the proteins, FANCC, influences apoptotic pathways in response to oxidative damage. Further analysis of the FANC proteins will provide vital information on normal cell responses to damage and allow therapeutic strategies to be developed that will hopefully supplant bone marrow transplantation. Copyright 2002 Wiley Periodicals, Inc.

Article and process for producing an article

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lacy, Benjamin Paul; Jacala, Ariel Caesar Prepena; Kottilingam, Srikanth Chandrudu

An article and a process of producing an article are provided. The article includes a base material, a cooling feature arrangement positioned on the base material, the cooling feature arrangement including an additive-structured material, and a cover material. The cooling feature arrangement is between the base material and the cover material. The process of producing the article includes manufacturing a cooling feature arrangement by an additive manufacturing technique, and then positioning the cooling feature arrangement between a base material and a cover material.

Additivity of Feature-Based and Symmetry-Based Grouping Effects in Multiple Object Tracking

PubMed Central

Wang, Chundi; Zhang, Xuemin; Li, Yongna; Lyu, Chuang

2016-01-01

Multiple object tracking (MOT) is an attentional process wherein people track several moving targets among several distractors. Symmetry, an important indicator of regularity, is a general spatial pattern observed in natural and artificial scenes. According to the “laws of perceptual organization” proposed by Gestalt psychologists, regularity is a principle of perceptual grouping, such as similarity and closure. A great deal of research reported that feature-based similarity grouping (e.g., grouping based on color, size, or shape) among targets in MOT tasks can improve tracking performance. However, no additive feature-based grouping effects have been reported where the tracking objects had two or more features. “Additive effect” refers to a greater grouping effect produced by grouping based on multiple cues instead of one cue. Can spatial symmetry produce a similar grouping effect similar to that of feature similarity in MOT tasks? Are the grouping effects based on symmetry and feature similarity additive? This study includes four experiments to address these questions. The results of Experiments 1 and 2 demonstrated the automatic symmetry-based grouping effects. More importantly, an additive grouping effect of symmetry and feature similarity was observed in Experiments 3 and 4. Our findings indicate that symmetry can produce an enhanced grouping effect in MOT and facilitate the grouping effect based on color or shape similarity. The “where” and “what” pathways might have played an important role in the additive grouping effect. PMID:27199875

Martian Oceans: Old Debate - New Insights

NASA Technical Reports Server (NTRS)

Oehler, Dorothy Z.; Allen, Carlton C.

2014-01-01

The possibility of an ancient ocean in the northern lowlands of Mars has been discussed for decades [1-14], but the subject remains controversial [15-20]. Among the many unique features of the northern lowlands is the extensive development of "giant polygons" - polygonal landforms that range from 1 to 20 km across. The kilometer-scale size of these features distinguishes them from a variety of smaller polygons (usually < 250 m) on Mars that have been compared to terrestrial analogs such as ice-wedge and desiccation features. However, until recently, geologists were aware of no examples of polygons on Earth comparable in scale to the giant polygons of Mars, so there were no good analogs from which to draw interpretations. That picture has changed with 3D seismic data acquired by the petroleum industry in exploration of offshore basins. The new data reveal kilometer-scale polygonal features in more than 50 offshore basins on Earth]. These features provide a credible analog for the giant polygons of Mars.

Deep feature learning for knee cartilage segmentation using a triplanar convolutional neural network.

PubMed

Prasoon, Adhish; Petersen, Kersten; Igel, Christian; Lauze, François; Dam, Erik; Nielsen, Mads

2013-01-01

Segmentation of anatomical structures in medical images is often based on a voxel/pixel classification approach. Deep learning systems, such as convolutional neural networks (CNNs), can infer a hierarchical representation of images that fosters categorization. We propose a novel system for voxel classification integrating three 2D CNNs, which have a one-to-one association with the xy, yz and zx planes of 3D image, respectively. We applied our method to the segmentation of tibial cartilage in low field knee MRI scans and tested it on 114 unseen scans. Although our method uses only 2D features at a single scale, it performs better than a state-of-the-art method using 3D multi-scale features. In the latter approach, the features and the classifier have been carefully adapted to the problem at hand. That we were able to get better results by a deep learning architecture that autonomously learns the features from the images is the main insight of this study.

Towards the Complete Characterization of Marine-Terminating Glacier Outlet Systems

NASA Astrophysics Data System (ADS)

Mayer, L. A.; Jakobsson, M.; Mix, A. C.; Jerram, K.; Hogan, K.; Heffron, E.; Muenchow, A.

2016-12-01

The Petermann Glacier Experiment was aimed at understanding past variations in Petermann Glacier and their relationship to changes in climatic and oceanographic conditions. A critical component of the experiment was a comprehensive program conducted on the icebreaker Oden to map submarine glacial landforms, offering insight into past ice dynamics and establishing the overall geomorphological context of the region. Concurrent water-column mapping provided remarkable insight into modern glacial, oceanographic, and biological processes suggesting that a carefully designed experiment could provide a near-complete characterization of marine-terminating glacier outlet systems. Water-column mapping revealed seeps emanating from several seafloor regions. These features appeared along common depth zones and may represent fresh water emanating from a submerged aquifer; initial pore water analyses of cores also imply a fresh water flux into the fjord system. Water-column data also show a spatially consistent but variable distribution of a strong mid-water scattering layer, a biological response possibly tracing the inflow of Atlantic water into the fjord and enhanced by input from local outlet glaciers. The continuous nature of these acoustic records over 30 days offers a complete 4-D picture of the distribution of the scattering layer (and perhaps internal circulation patterns and water-mass interactions) with a spatial and temporal distribution far beyond that achievable by traditional oceanographic stations. Additional, higher-resolution water-column imaging around local outlet glaciers presents a clear picture of subglacial sediment-laden meltwater plumes. Thus in addition to the paleoceanographic information they provided, the acoustic systems deployed captured a 4D-view of many of the modern geological, oceanographic and ecological processes within and adjacent to the Petermann Glacier marine system. With the addition of seafloor and water-column sampling, long-term oceanographic moorings, a much more robust biological program (to understand what we are mapping in the water-column) and, the ability to extend our measurements under the ice sheet, we stand poised to truly characterize and hopefully understand the processes at work in front of marine-terminating outlet glaciers.

Analyzing the Language of Therapist Empathy in Motivational Interview based Psychotherapy

PubMed Central

Xiao, Bo; Can, Dogan; Georgiou, Panayiotis G.; Atkins, David; Narayanan, Shrikanth S.

2016-01-01

Empathy is an important aspect of social communication, especially in medical and psychotherapy applications. Measures of empathy can offer insights into the quality of therapy. We use an N-gram language model based maximum likelihood strategy to classify empathic versus non-empathic utterances and report the precision and recall of classification for various parameters. High recall is obtained with unigram while bigram features achieved the highest F1-score. Based on the utterance level models, a group of lexical features are extracted at the therapy session level. The effectiveness of these features in modeling session level annotator perceptions of empathy is evaluated through correlation with expert-coded session level empathy scores. Our combined feature set achieved a correlation of 0.558 between predicted and expert-coded empathy scores. Results also suggest that the longer term empathy perception process may be more related to isolated empathic salient events. PMID:27602411

Provincialising the World Culture Theory Debate: Critical Insights from a Margin

ERIC Educational Resources Information Center

Takayama, Keita

2015-01-01

Neo-institutionalist theory of global "isomorphism", or so-called World Culture Theory (WCT), has been much debated in comparative education. One notable feature of the debate is that the vast majority of its participants belong to a handful of closely knit comparative education communities. Ironically enough then, a debate that…

Different Approaches to Dual Enrollment: Understanding Program Features and Their Implications. Insight

ERIC Educational Resources Information Center

Edwards, Linsey; Hughes, Katherine L.; Weisberg, Alan

2011-01-01

Dual enrollment programs allow high school students to take college courses and earn college credit. While dual enrollment has historically focused on high-achieving students, these programs can have significant benefits for underperforming students as well, particularly if integrated with a career focus. This research shows that student…

Making Sense of Cluster Analysis: Revelations from Pakistani Science Classes

ERIC Educational Resources Information Center

Pell, Tony; Hargreaves, Linda

2011-01-01

Cluster analysis has been applied to quantitative data in educational research over several decades and has been a feature of the Maurice Galton's research in primary and secondary classrooms. It has offered potentially useful insights for teaching yet its implications for practice are rarely implemented. It has been subject also to negative…

The Ecological Rationality of Delay Tolerance: Insights from Capuchin Monkeys

ERIC Educational Resources Information Center

Addessi, Elsa; Paglieri, Fabio; Focaroli, Valentina

2011-01-01

Both human and non-human animals often face decisions between options available at different times, and the capacity of delaying gratification has usually been considered one of the features distinguishing humans from other animals. However, this characteristic can widely vary across individuals, species, and types of task and it is still unclear…

A Multi-Level Model of Moral Thinking Based on Neuroscience and Moral Psychology

ERIC Educational Resources Information Center

Jeong, Changwoo; Han, Hye Min

2011-01-01

Developments in neurobiology are providing new insights into the biological and physical features of human thinking, and brain-activation imaging methods such as functional magnetic resonance imaging have become the most dominant research techniques to approach the biological part of thinking. With the aid of neurobiology, there also have been…

Autism and 15q11-q13 Disorders: Behavioral, Genetic, and Pathophysiological Issues

ERIC Educational Resources Information Center

Dykens, Elisabeth M.; Sutcliffe, James S.; Levitt, Pat

2004-01-01

New insights into biological factors that underlie autism may be gained by comparing autism to other neurodevelopmental disorders that have autistic features and relatively well-delineated genetic etiologies or neurobiological findings. This review moves beyond global diagnoses of autism and instead uses an endophenotypic approach to compare…

Dissipative Work in Thermodynamics

ERIC Educational Resources Information Center

Anacleto, Joaquim; Pereira, Mario G.; Ferreira, J. M.

2011-01-01

This work explores the concept of dissipative work and shows that such a kind of work is an invariant non-negative quantity. This feature is then used to get a new insight into adiabatic irreversible processes; for instance, why the final temperature in any adiabatic irreversible process is always higher than that attained in a reversible process…

The Mental Timeline in Discourse Organization and Processing

ERIC Educational Resources Information Center

Lee, Choonkyu

2012-01-01

Early language research has revealed important insights into the building blocks of language, such as morphosyntactic features and rules and truth-conditions of sentences. Once we situate language in real-life use, however, a wide range of factors come into play. Language interacts not only with the surrounding linguistic context but also with the…

Did Language Evolve Like the Vertebrate Eye?

ERIC Educational Resources Information Center

Botha, Rudolf P.

2002-01-01

Offers a critical appraisal of the way in which the idea that human language or some of its features evolved like the vertebrate eye by natural selection is articulated in Pinker and Bloom's (1990) selectionist account of language evolution. Argues that this account is less than insightful because it fails to draw some of the conceptual…

Traditional Ecological Knowledge and Global Environmental Change: Research findings and policy implications

PubMed Central

Gómez-Baggethun, Erik; Corbera, Esteve; Reyes-García, Victoria

2015-01-01

This paper introduces the special feature of Ecology and Society entitled “Traditional Ecological Knowledge and Global Environmental Change. The special feature addresses two main research themes. The first theme concerns the resilience of Traditional Ecological Knowledge (hereafter TEK) and the conditions that might explain its loss or persistence in the face of global change. The second theme relates to new findings regarding the way in which TEK strengthens community resilience to respond to the multiple stressors of global environmental change. Those themes are analyzed using case studies from Africa, Asia, America and Europe. Theoretical insights and empirical findings from the studies suggest that despite the generalized worldwide trend of TEK erosion, substantial pockets of TEK persist in both developing and developed countries. A common trend on the studies presented here is hybridization, where traditional knowledge, practices, and beliefs are merged with novel forms of knowledge and technologies to create new knowledge systems. The findings also reinforce previous hypotheses pointing at the importance of TEK systems as reservoirs of experiential knowledge that can provide important insights for the design of adaptation and mitigation strategies to cope with global environmental change. Based on the results from papers in this feature, we discuss policy directions that might help to promote maintenance and restoration of living TEK systems as sources of social-ecological resilience. PMID:26097492

Prevalence of body dysmorphic disorder and associated features in German adolescents: A self-report survey.

PubMed

Möllmann, Anne; Dietel, Fanny A; Hunger, Antje; Buhlmann, Ulrike

2017-08-01

Prior research has not yet investigated the prevalence of body dysmorphic disorder (BDD) in adolescents and young adults based on criteria from the Diagnostic and Statistical Manual of Mental Disorders, fifth edition (DSM-5). In the current study, the point prevalence of BDD, comorbid symptoms, and associated features, such as appearance-related suicidality, level of insight or history of plastic surgeries, were examined in a non-clinical sample of German adolescents and young adults (n=308), between 15 and 21 years old, using self-report measures. Eleven participants (3.6%; 95% CI=[1.9, 5.8]) met DSM-5 criteria for BDD. Self-reported BDD (vs. no-BDD) was related to respondents showing significantly more obsessive-compulsive (OC) symptoms and lower degrees of insight regarding appearance concerns. Significantly more adolescents and young adults with vs. without self-reported BDD (36.4% vs. 8.8%) reported appearance-related suicidal ideation. In conclusion, body dysmorphic symptoms are common in adolescents and young adults and are associated with high rates of comorbid symptoms and suicidal ideation. Copyright © 2017 Elsevier Ireland Ltd. All rights reserved.

Born Pupils? Natural Pedagogy and Cultural Pedagogy.

PubMed

Heyes, Cecilia

2016-03-01

The theory of natural pedagogy is an important focus of research on the evolution and development of cultural learning. It proposes that we are born pupils; that human children genetically inherit a package of psychological adaptations that make them receptive to teaching. In this article, I first examine the components of the package-eye contact, contingencies, infant-directed speech, gaze cuing, and rational imitation-asking in each case whether current evidence indicates that the component is a reliable feature of infant behavior and a genetic adaptation for teaching. I then discuss three fundamental insights embodied in the theory: Imitation is not enough for cumulative cultural inheritance, the extra comes from blind trust, and tweaking is a powerful source of cognitive change. Combining the results of the empirical review with these insights, I argue that human receptivity to teaching is founded on nonspecific genetic adaptations for social bonding and social learning and acquires its species- and functionally specific features through the operation of domain-general processes of learning in sociocultural contexts. We engage, not in natural pedagogy, but in cultural pedagogy. © The Author(s) 2016.

Emerging insights into recurrent and metastatic human papillomavirus‐related oropharyngeal squamous cell carcinoma

PubMed Central

Faraji, Farhoud; Eisele, David W.

2017-01-01

ABSTRACT Objective To review recent literature on human papillomavirus‐related (HPV‐positive) oropharyngeal squamous cell carcinoma (OPC) and focus on implications of recurrent and metastatic disease. Methods Primary articles from 1990 to 2016 indexed in MEDLINE (1) pertaining to the epidemiology of HPV‐positive OPC and (2) providing clinical insight into recurrent and metastatic OPC. Results The incidence of HPV‐positive OPC is increasing globally. HPV‐positive OPC is a subtype with distinct molecular and clinical features including enhanced treatment response and improved overall survival. While disease recurrence is less common in patients with HPV‐positive OPC, up to 36% of patients experience treatment failure within eight years. Recurrent and metastatic OPC has historically signified poor prognosis, however recent data are challenging this dogma. Here, we discuss recurrent and metastatic OPC in the context of HPV tumor status. Conclusion HPV‐positive OPC exhibits distinct genetic, cellular, epidemiological, and clinical features from HPV‐negative OPC. HPV tumor status is emerging as a marker indicative of improved prognosis after disease progression in both locoregionally recurrent and distant metastatic OPC. Level of Evidence N/A. PMID:28894817

Insights into heliobacterial photosynthesis and physiology from the genome of Heliobacterium modesticaldum.

PubMed

Sattley, W Matthew; Blankenship, Robert E

2010-06-01

The complete annotated genome sequence of Heliobacterium modesticaldum strain Ice1 provides our first glimpse into the genetic potential of the Heliobacteriaceae, a unique family of anoxygenic phototrophic bacteria. H. modesticaldum str. Ice1 is the first completely sequenced phototrophic representative of the Firmicutes, and heliobacteria are the only phototrophic members of this large bacterial phylum. The H. modesticaldum genome consists of a single 3.1-Mb circular chromosome with no plasmids. Of special interest are genomic features that lend insight to the physiology and ecology of heliobacteria, including the genetic inventory of the photosynthesis gene cluster. Genes involved in transport, photosynthesis, and central intermediary metabolism are described and catalogued. The obligately heterotrophic metabolism of heliobacteria is a key feature of the physiology and evolution of these phototrophs. The conspicuous absence of recognizable genes encoding the enzyme ATP-citrate lyase prevents autotrophic growth via the reverse citric acid cycle in heliobacteria, thus being a distinguishing differential characteristic between heliobacteria and green sulfur bacteria. The identities of electron carriers that enable energy conservation by cyclic light-driven electron transfer remain in question.

Linking user and staff perspectives in the evaluation of innovative transition projects for youth with disabilities.

PubMed

McAnaney, Donal F; Wynne, Richard F

2016-06-01

A key challenge in formative evaluation is to gather appropriate evidence to inform the continuous improvement of initiatives. In the absence of outcome data, the programme evaluator often must rely on the perceptions of beneficiaries and staff in generating insight into what is making a difference. The article describes the approach adopted in an evaluation of 15 innovative projects supporting school-leavers with disabilities in making the transition to education, work and life in community settings. Two complementary processes provided an insight into what project staff and leadership viewed as the key project activities and features that facilitated successful transition as well as the areas of quality of life (QOL) that participants perceived as having been impacted positively by the projects. A comparison was made between participants' perceptions of QOL impact with the views of participants in services normally offered by the wider system. This revealed that project participants were significantly more positive in their views than participants in traditional services. In addition, the processes and activities of the more highly rated projects were benchmarked against less highly rated projects and also with usually available services. Even in the context of a range of intervening variables such as level and complexity of participant needs and variations in the stage of development of individual projects, the benchmarking process indicated a number of project characteristics that were highly valued by participants. © The Author(s) 2016.

The 360 photography: a new anatomical insight of the sphenoid bone. Interest for anatomy teaching and skull base surgery.

PubMed

Jacquesson, Timothée; Mertens, Patrick; Berhouma, Moncef; Jouanneau, Emmanuel; Simon, Emile

2017-01-01

Skull base architecture is tough to understand because of its 3D complex shape and its numerous foramen, reliefs or joints. It is especially true for the sphenoid bone whom central location hinged with most of skull base components is unique. Recently, technological progress has led to develop new pedagogical tools. This way, we bought a new real-time three-dimensional insight of the sphenoid bone that could be useful for the teacher, the student and the surgeon. High-definition photography was taken all around an isolated dry skull base bone prepared with Beauchêne's technique. Pictures were then computed to provide an overview with rotation and magnification on demand. From anterior, posterior, lateral or oblique views and from in out looks, anatomical landmarks and subtleties were described step by step. Thus, the sella turcica, the optic canal, the superior orbital fissure, the sphenoid sinus, the vidian canal, pterygoid plates and all foramen were clearly placed relative to the others at each face of the sphenoid bone. In addition to be the first report of the 360 Photography tool, perspectives are promising as the development of a real-time interactive tridimensional space featuring the sphenoid bone. It allows to turn around the sphenoid bone and to better understand its own special shape, numerous foramen, neurovascular contents and anatomical relationships. This new technological tool may further apply for surgical planning and mostly for strengthening a basic anatomical knowledge firstly introduced.

Buddhism and neuroethics: the ethics of pharmaceutical cognitive enhancement.

PubMed

Fenton, Andrew

2009-08-01

This paper integrates some Buddhist moral values, attitudes and self-cultivation techniques into a discussion of the ethics of cognitive enhancement technologies - in particular, pharmaceutical enhancements. Many Buddhists utilize meditation techniques that are both integral to their practice and are believed to enhance the cognitive and affective states of experienced practitioners. Additionally, Mahāyāna Buddhism's teaching on skillful means permits a liberal use of methods or techniques in Buddhist practice that yield insight into our selfnature or aid in alleviating or eliminating duhkha (i.e. dissatisfaction). These features of many, if not most, Buddhist traditions will inform much of the Buddhist assessment of pharmaceutical enhancements offered in this paper. Some Buddhist concerns about the effects and context of the use of pharmaceutical enhancements will be canvassed in the discussion. Also, the author will consider Buddhist views of the possible harms that may befall human and nonhuman research subjects, interference with a recipient's karma, the artificiality of pharmaceutical enhancements, and the possible motivations or intentions of healthy individuals pursuing pharmacological enhancement. Perhaps surprisingly, none of these concerns will adequately ground a reflective Buddhist opposition to the further development and continued use of pharmaceutical enhancements, either in principle or in practice. The author argues that Buddhists, from at least certain traditions - particularly Mahāyāna Buddhist traditions - should advocate the development or use of pharmaceutical enhancements if a consequence of their use is further insight into our self-nature or the reduction or alleviation of duhkha.

Morphology, development, and evolution of fetal membranes and placentation in squamate reptiles.

PubMed

Blackburn, Daniel G; Flemming, Alexander F

2009-09-15

Current studies on fetal membranes of reptiles are providing insight into three major historical transformations: evolution of the amniote egg, evolution of viviparity, and evolution of placentotrophy. Squamates (lizards and snakes) are ideal for such studies because their fetal membranes sustain embryos in oviparous species and contribute to placentas in viviparous species. Ultrastructure of the fetal membranes in oviparous corn snakes (Pituophis guttatus) shows that the chorioallantois is specialized for gas exchange and the omphalopleure, for water absorption. Transmission and scanning electron microscopic studies of viviparous thamnophine snakes (Thamnophis, Storeria) have revealed morphological specializations for gas exchange and absorption in the intra-uterine environment that represent modifications of features found in oviparous species. Thus, fetal membranes in oviparous species show morphological differentiation for distinct functions that have been recruited and enhanced under viviparous conditions. The ultimate in specialization of fetal membranes is found in viviparous skinks of South America (Mabuya) and Africa (Trachylepis, Eumecia), in which placentotrophy accounts for nearly all of the nutrients for development. Ongoing research on these lizards has revealed morphological specializations of the chorioallantoic placenta through which nutrient transfer is accomplished. In addition, African Trachylepis show an invasive form of implantation, in which uterine epithelium is replaced by invading chorionic cells. Ongoing analysis of these lizards shows how integration of multiple lines of evidence can provide insight into the evolution of developmental and reproductive specializations once thought to be confined to eutherian mammals.

3.3 Å structure of Niemann–Pick C1 protein reveals insights into the function of the C-terminal luminal domain in cholesterol transport

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Xiaochun; Lu, Feiran; Trinh, Michael N.

Niemann–Pick C1 (NPC1) and NPC2 proteins are indispensable for the export of LDL-derived cholesterol from late endosomes. Mutations in these proteins result in Niemann–Pick type C disease, a lysosomal storage disease. Despite recent reports of the NPC1 structure depicting its overall architecture, the function of its C-terminal luminal domain (CTD) remains poorly understood even though 45% of NPC disease-causing mutations are in this domain. Here, we report a crystal structure at 3.3 Å resolution of NPC1* (residues 314–1,278), which—in contrast to previous lower resolution structures—features the entire CTD well resolved. Notably, all eight cysteines of the CTD form four disulfidemore » bonds, one of which (C909–C914) enforces a specific loop that in turn mediates an interaction with a loop of the N-terminal domain (NTD). Importantly, this loop and its interaction with the NTD were not observed in any previous structures due to the lower resolution. Our mutagenesis experiments highlight the physiological relevance of the CTD–NTD interaction, which might function to keep the NTD in the proper orientation for receiving cholesterol from NPC2. Additionally, this structure allows us to more precisely map all of the disease-causing mutations, allowing future molecular insights into the pathogenesis of NPC disease.« less

A decade of decoding reward-related fMRI signals and where we go from here.

PubMed

Kahnt, Thorsten

2017-06-04

Information about potential rewards in the environment is essential for guiding adaptive behavior, and understanding neural reward processes may provide insights into neuropsychiatric dysfunctions. Over the past 10 years, multivoxel pattern analysis (MVPA) techniques have been used to study brain areas encoding information about expected and experienced outcomes. These studies have identified reward signals throughout the brain, including the striatum, medial prefrontal cortex, orbitofrontal cortex, dorsolateral prefrontal cortex, and parietal cortex. This review article discusses some of the assumptions and models that are used to interpret results from these studies, and how they relate to findings from animal electrophysiology. The article reviews and summarizes some of the key findings from MVPA studies on reward. In particular, it first focuses on studies that, in addition to mapping out the brain areas that process rewards, have provided novel insights into the coding mechanisms of value and reward. Then, it discusses examples of how multivariate imaging approaches are being used more recently to decode features of expected rewards that go beyond value, such as the identity of an expected outcome or the action required to obtain it. The study of such complex and multifaceted reward representations highlights the key advantage of using representational methods, which are uniquely able to reveal these signals and may narrow the gap between animal and human research. Applied in a clinical context, MVPA may advance our understanding of neuropsychiatric disorders and the development of novel treatment strategies. Copyright © 2017 Elsevier Inc. All rights reserved.

A proposal for overcoming problems in teaching interviewing skills to medical students.

PubMed

Benbassat, Jochanan; Baumal, Reuben

2009-08-01

The objective of this paper is to draw attention to four features that distinguish the pedagogy of patient interviewing from the teaching of other clinical skills: (a) students are not naïve to the skill to be learned, (b) they encounter role models with a wide variability in interviewing styles, (c) clinical teachers are not usually specialists in the behavioral sciences, including patient interviewing, and (d) the validity of the methods used for assessment of interviewing skills is uncertain. We propose to adjust the teaching of patient interviewing to these features by (a) gaining an insight into the students' views and using these views as a point of departure for discussions of patient interviewing; (b) helping students to understand why different clinicians use different communication styles; (c) providing the clinical tutors with additional training that will help them function as both specialists who share their expertise with the students and facilitators of small-group learning; and (d) using assessment methods that encourage joint deliberation by the learner and the examiner, rather than a judgmental right-wrong dualism by the examiner alone. The teaching approach that we suggest is consistent with current theories of adult learning, and it occurs in an egalitarian rather than a hierarchical environment. Hopefully, students will also adopt such egalitarian attitudes toward patients, thereby reducing the tendency to a paternalistic communication style.

A Multi-Functional Microelectrode Array Featuring 59760 Electrodes, 2048 Electrophysiology Channels, Stimulation, Impedance Measurement and Neurotransmitter Detection Channels.

PubMed

Dragas, Jelena; Viswam, Vijay; Shadmani, Amir; Chen, Yihui; Bounik, Raziyeh; Stettler, Alexander; Radivojevic, Milos; Geissler, Sydney; Obien, Marie; Müller, Jan; Hierlemann, Andreas

2017-06-01

Biological cells are characterized by highly complex phenomena and processes that are, to a great extent, interdependent. To gain detailed insights, devices designed to study cellular phenomena need to enable tracking and manipulation of multiple cell parameters in parallel; they have to provide high signal quality and high spatiotemporal resolution. To this end, we have developed a CMOS-based microelectrode array system that integrates six measurement and stimulation functions, the largest number to date. Moreover, the system features the largest active electrode array area to date (4.48×2.43 mm 2 ) to accommodate 59,760 electrodes, while its power consumption, noise characteristics, and spatial resolution (13.5 μm electrode pitch) are comparable to the best state-of-the-art devices. The system includes: 2,048 action-potential (AP, bandwidth: 300 Hz to 10 kHz) recording units, 32 local-field-potential (LFP, bandwidth: 1 Hz to 300 Hz) recording units, 32 current recording units, 32 impedance measurement units, and 28 neurotransmitter detection units, in addition to the 16 dual-mode voltage-only or current/voltage-controlled stimulation units. The electrode array architecture is based on a switch matrix, which allows for connecting any measurement/stimulation unit to any electrode in the array and for performing different measurement/stimulation functions in parallel.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yin, Zhiqi; Shi, Ke; Banerjee, Surajit

Integration of the reverse-transcribed viral DNA into the host genome is an essential step in the life cycle of retroviruses. Retrovirus integrase catalyses insertions of both ends of the linear viral DNA into a host chromosome. Integrase from HIV-1 and closely related retroviruses share the three-domain organization, consisting of a catalytic core domain flanked by amino- and carboxy-terminal domains essential for the concerted integration reaction. Although structures of the tetrameric integrase–DNA complexes have been reported for integrase from prototype foamy virus featuring an additional DNA-binding domain and longer interdomain linkers, the architecture of a canonical three-domain integrase bound to DNAmore » remained elusive. In this paper, we report a crystal structure of the three-domain integrase from Rous sarcoma virus in complex with viral and target DNAs. The structure shows an octameric assembly of integrase, in which a pair of integrase dimers engage viral DNA ends for catalysis while another pair of non-catalytic integrase dimers bridge between the two viral DNA molecules and help capture target DNA. The individual domains of the eight integrase molecules play varying roles to hold the complex together, making an extensive network of protein–DNA and protein–protein contacts that show both conserved and distinct features compared with those observed for prototype foamy virus integrase. Finally, our work highlights the diversity of retrovirus intasome assembly and provides insights into the mechanisms of integration by HIV-1 and related retroviruses.« less

Animal Toxins Providing Insights into TRPV1 Activation Mechanism

PubMed Central

Geron, Matan; Hazan, Adina

2017-01-01

Beyond providing evolutionary advantages, venoms offer unique research tools, as they were developed to target functionally important proteins and pathways. As a key pain receptor in the nociceptive pathway, transient receptor potential vanilloid 1 (TRPV1) of the TRP superfamily has been shown to be a target for several toxins, as a way of producing pain to deter predators. Importantly, TRPV1 is involved in thermoregulation, inflammation, and acute nociception. As such, toxins provide tools to understand TRPV1 activation and modulation, a critical step in advancing pain research and the development of novel analgesics. Indeed, the phytotoxin capsaicin, which is the spicy chemical in chili peppers, was invaluable in the original cloning and characterization of TRPV1. The unique properties of each subsequently characterized toxin have continued to advance our understanding of functional, structural, and biophysical characteristics of TRPV1. By building on previous reviews, this work aims to provide a comprehensive summary of the advancements made in TRPV1 research in recent years by employing animal toxins, in particular DkTx, RhTx, BmP01, Echis coloratus toxins, APHCs and HCRG21. We examine each toxin’s functional aspects, behavioral effects, and structural features, all of which have contributed to our current knowledge of TRPV1. We additionally discuss the key features of TRPV1’s outer pore domain, which proves to be the target of the currently discussed toxins. PMID:29035314

Microcalcifications in breast cancer: novel insights into the molecular mechanism and functional consequence of mammary mineralisation

PubMed Central

Cox, R F; Hernandez-Santana, A; Ramdass, S; McMahon, G; Harmey, J H; Morgan, M P

2012-01-01

Background: Mammographic microcalcifications represent one of the most reliable features of nonpalpable breast cancer yet remain largely unexplored and poorly understood. Methods: We report a novel model to investigate the in vitro mineralisation potential of a panel of mammary cell lines. Primary mammary tumours were produced by implanting tumourigenic cells into the mammary fat pads of female BALB/c mice. Results: Hydroxyapatite (HA) was deposited only by the tumourigenic cell lines, indicating mineralisation potential may be associated with cell phenotype in this in vitro model. We propose a mechanism for mammary mineralisation, which suggests that the balance between enhancers and inhibitors of physiological mineralisation are disrupted. Inhibition of alkaline phosphatase and phosphate transport prevented mineralisation, demonstrating that mineralisation is an active cell-mediated process. Hydroxyapatite was found to enhance in vitro tumour cell migration, while calcium oxalate had no effect, highlighting potential consequences of calcium deposition. In addition, HA was also deposited in primary mammary tumours produced by implanting the tumourigenic cells into the mammary fat pads of female BALB/c mice. Conclusion: This work indicates that formation of mammary HA is a cell-specific regulated process, which creates an osteomimetic niche potentially enhancing breast tumour progression. Our findings point to the cells mineralisation potential and the microenvironment regulating it, as a significant feature of breast tumour development. PMID:22233923

Prediction of protein interaction hot spots using rough set-based multiple criteria linear programming.

PubMed

Chen, Ruoying; Zhang, Zhiwang; Wu, Di; Zhang, Peng; Zhang, Xinyang; Wang, Yong; Shi, Yong

2011-01-21

Protein-protein interactions are fundamentally important in many biological processes and it is in pressing need to understand the principles of protein-protein interactions. Mutagenesis studies have found that only a small fraction of surface residues, known as hot spots, are responsible for the physical binding in protein complexes. However, revealing hot spots by mutagenesis experiments are usually time consuming and expensive. In order to complement the experimental efforts, we propose a new computational approach in this paper to predict hot spots. Our method, Rough Set-based Multiple Criteria Linear Programming (RS-MCLP), integrates rough sets theory and multiple criteria linear programming to choose dominant features and computationally predict hot spots. Our approach is benchmarked by a dataset of 904 alanine-mutated residues and the results show that our RS-MCLP method performs better than other methods, e.g., MCLP, Decision Tree, Bayes Net, and the existing HotSprint database. In addition, we reveal several biological insights based on our analysis. We find that four features (the change of accessible surface area, percentage of the change of accessible surface area, size of a residue, and atomic contacts) are critical in predicting hot spots. Furthermore, we find that three residues (Tyr, Trp, and Phe) are abundant in hot spots through analyzing the distribution of amino acids. Copyright © 2010 Elsevier Ltd. All rights reserved.

Deformation associated with ghost craters and basins in volcanic smooth plains on Mercury: Strain analysis and implications for plains evolution

NASA Astrophysics Data System (ADS)

Klimczak, Christian; Watters, Thomas R.; Ernst, Carolyn M.; Freed, Andrew M.; Byrne, Paul K.; Solomon, Sean C.; Blair, David M.; Head, James W.

2012-09-01

Since its insertion into orbit about Mercury in March 2011, the MESSENGER spacecraft has imaged most previously unseen regions of the planet in unprecedented detail, revealing extensive regions of contiguous smooth plains at high northern latitudes and surrounding the Caloris basin. These smooth plains, thought to be emplaced by flood volcanism, are populated with several hundred ghost craters and basins, nearly to completely buried impact features having rims for which the surface expressions are now primarily rings of deformational landforms. Associated with some ghost craters are interior groups of graben displaying mostly polygonal patterns. The origin of these graben is not yet fully understood, but comparison with numerical models suggests that the majority of such features are the result of stresses from local thermal contraction. In this paper, we highlight a previously unreported category of ghost craters, quantify extensional strains across graben-bearing ghost craters, and make use of graben geometries to gain insights into the subsurface geology of smooth plains areas. In particular, the style and mechanisms of graben development imply that flooding of impact craters and basins led to substantial pooling of lavas, to thicknesses of ˜1.5 km. In addition, surface strains derived from groups of graben are generally in agreement with theoretically and numerically derived strains for thermal contraction.

Where does subduction initiate and die? Insights from global convection models with continental drift

NASA Astrophysics Data System (ADS)

Ulvrova, Martina; Williams, Simon; Coltice, Nicolas; Tackley, Paul

2017-04-01

Plate tectonics is a prominent feature on Earth. Together with the underlying convecting mantle, plates form a self-organized system. In order to understand the dynamics of the coupled system, subduction of the lithospheric plates plays the key role since it links the exterior with the interior of the planet. In this work we study subduction initiation and death with respect to the position of the continental rafts. Using thermo-mechanical numerical calculations we investigate global convection models featuring self-consistent plate tectonics and continental drifting employing a pseudo-plastic rheology and testing the effect of a free surface. We consider uncompressible mantle convection in Boussinesq approximation that is basaly and internaly heated. Our calculations indicate that the presence of the continents alterns stress distribution within a certain distance from the margins. Intra-oceanic subudction initiation is favorable during super-continent cycles while the initiation at passive continental margin prevails when continents are dispersed. The location of subduction initiation is additionally controlled by the lithospheric strength. Very weak lithosphere results in domination of intra-oceanic subduction initiation. The subduction zones die more easily in the vicinity of the continent due to the strong rheological contrast between the oceanic and continental lithosphere. In order to compare our findings with subduction positions through time recorded on Earth, we analyse subduction birth in global plate reconstruction back to 410 My.

Experimental and theoretical study of the electronic spectrum of the BAr2 complex: Transition to the excited valence B(2s2p2 2D) state

NASA Astrophysics Data System (ADS)

Krumrine, Jennifer R.; Alexander, Millard H.; Yang, Xin; Dagdigian, Paul J.

2000-03-01

The 2s2p22D←2s22p 2P valence transition in the BAr2 cluster is investigated in a collaborative experimental and theoretical study. Laser fluorescence excitation spectra of a supersonic expansion of B atoms entrained in Ar at high source backing pressures display several features not assignable to the BAr complex. Resonance fluorescence is not observed, but instead emission from the lower 3s state. Size-selected fluorescence depletion spectra show that these features in the excitation spectrum are primarily due to the BAr2 complex. This electronic transition within BAr2 is modeled theoretically, similarly to our earlier study of the 3s←2p transition [M. H. Alexander et al., J. Chem. Phys. 106, 6320 (1997)]. The excited potential energy surfaces of the fivefold degenerate B(2s2p22D) state within the ternary complex are computed in a pairwise-additive model employing diatomic BAr potential energy curves which reproduce our previous experimental observations on the electronic states emanating from the B(2D)+Ar asymptote. The simulated absorption spectrum reproduces reasonably well the observed fluorescence depletion spectrum. The theoretical model lends insight into the energetics of the approach of B to multiple Ar atoms, and how the orientation of B p-orbitals governs the stability of the complex.

Geophysical surveys and archaeological insights at Fort Pierre Chouteau, a frontier trading post on the Middle Missouri

NASA Astrophysics Data System (ADS)

Patton, Margaret Maurine

Fort Pierre Chouteau in present day South Dakota was the most important fur trading post of the American Fur Company in the 1830s, serving as a regional hub for the fur trade. The Fort was sold to the U.S. Military in 1855 for use as a base in the Sioux Wars but was abandoned in 1856. Geophysical surveys and previous excavations indicate evidence of both occupations. Geophysics is an important tool for determining the extent of archaeological sites, yet the relationships between geophysical anomalies and excavation features may not be readily evident. Initial geophysical surveys (Kvamme 2007) were completed to determine the extent of the fur trading Fort, and additional surveys in August 2012 used magnetometry and electrical resistance to determine if evidence of military structures exists outside of the Fort. This study examines connections between excavation features and geophysical anomalies in order to better interpret anomalies inside the Fort palisade. The palisade builder's trench, adobe pavement, post holes, and unknown structures are characterized through the analysis of the excavations and anomalies. The location of one of the military structures outside of the palisade is also identified. As many sites have histories of excavations prior to any geophysical surveys, combining the two sets of information is important in order to more fully understand site layout and the archaeological causes of geophysical anomalies.

Connecting the Interstellar Gas and Dust Properties in Distant Galaxies Using Quasar Absorption Systems

NASA Technical Reports Server (NTRS)

Aller, Monique C.; Dwek, Eliahu; Kulkarni, Varsha P.; York, Donald G.; Welty, Daniel E.; Vladilo, Giovanni; Som, Debopam; Lackey, Kyle; Dwek, Eli; Beiranvand, Nassim;

Hydrogen bond dynamics of superheated water and methanol by ultrafast IR-pump and EUV-photoelectron probe spectroscopy.

PubMed

Vöhringer-Martinez, E; Link, O; Lugovoy, E; Siefermann, K R; Wiederschein, F; Grubmüller, H; Abel, B

2014-09-28

Supercritical water and methanol have recently drawn much attention in the field of green chemistry. It is crucial to an understanding of supercritical solvents to know their dynamics and to what extent hydrogen (H) bonds persist in these fluids. Here, we show that with femtosecond infrared (IR) laser pulses water and methanol can be heated to temperatures near and above their critical temperature Tc and their molecular dynamics can be studied via ultrafast photoelectron spectroscopy at liquid jet interfaces with high harmonics radiation. As opposed to previous studies, the main focus here is the comparison between the hydrogen bonded systems of methanol and water and their interpretation by theory. Superheated water initially forms a dense hot phase with spectral features resembling those of monomers in gas phase water. On longer timescales, this phase was found to build hot aggregates, whose size increases as a function of time. In contrast, methanol heated to temperatures near Tc initially forms a broad distribution of aggregate sizes and some gas. These experimental features are also found and analyzed in extended molecular dynamics simulations. Additionally, the simulations enabled us to relate the origin of the different behavior of these two hydrogen-bonded liquids to the nature of the intermolecular potentials. The combined experimental and theoretical approach delivers new insights into both superheated phases and may contribute to understand their different chemical reactivities.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Harmony, S.C.; Steiner, J.L.; Stumpf, H.J.

The PIUS advanced reactor is a 640-MWe pressurized water reactor developed by Asea Brown Boveri (ABB). A unique feature of the PIUS concept is the absence of mechanical control and shutdown rods. Reactivity is controlled by coolant boron concentration and the temperature of the moderator coolant. As part of the preapplication and eventual design certification process, advanced reactor applicants are required to submit neutronic and thermal-hydraulic safety analyses over a sufficient range of normal operation, transient conditions, and specified accident sequences. Los Alamos is supporting the US Nuclear Regulatory Commission`s preapplication review of the PIUS reactor. A fully one-dimensional modelmore » of the PIUS reactor has been developed for the Transient Reactor Analysis Code, TRACPF1/MOD2. Early in 1992, ABB submitted a Supplemental Information Package describing recent design modifications. An important feature of the PIUS Supplement design was the addition of an active scram system that will function for most transient and accident conditions. A one-dimensional Transient Reactor Analysis Code baseline calculation of the PIUS Supplement design were performed for a break in the main steam line at the outlet nozzle of the loop 3 steam generator. Sensitivity studies were performed to explore the robustness of the PIUS concept to severe off-normal conditions following a main steam line break. The sensitivity study results provide insights into the robustness of the design.« less

Prediction of Protein-Protein Interaction Sites by Random Forest Algorithm with mRMR and IFS

PubMed Central

Li, Bi-Qing; Feng, Kai-Yan; Chen, Lei; Huang, Tao; Cai, Yu-Dong

2012-01-01

Prediction of protein-protein interaction (PPI) sites is one of the most challenging problems in computational biology. Although great progress has been made by employing various machine learning approaches with numerous characteristic features, the problem is still far from being solved. In this study, we developed a novel predictor based on Random Forest (RF) algorithm with the Minimum Redundancy Maximal Relevance (mRMR) method followed by incremental feature selection (IFS). We incorporated features of physicochemical/biochemical properties, sequence conservation, residual disorder, secondary structure and solvent accessibility. We also included five 3D structural features to predict protein-protein interaction sites and achieved an overall accuracy of 0.672997 and MCC of 0.347977. Feature analysis showed that 3D structural features such as Depth Index (DPX) and surface curvature (SC) contributed most to the prediction of protein-protein interaction sites. It was also shown via site-specific feature analysis that the features of individual residues from PPI sites contribute most to the determination of protein-protein interaction sites. It is anticipated that our prediction method will become a useful tool for identifying PPI sites, and that the feature analysis described in this paper will provide useful insights into the mechanisms of interaction. PMID:22937126

Small-World Network Spectra in Mean-Field Theory

NASA Astrophysics Data System (ADS)

Grabow, Carsten; Grosskinsky, Stefan; Timme, Marc

2012-05-01

Collective dynamics on small-world networks emerge in a broad range of systems with their spectra characterizing fundamental asymptotic features. Here we derive analytic mean-field predictions for the spectra of small-world models that systematically interpolate between regular and random topologies by varying their randomness. These theoretical predictions agree well with the actual spectra (obtained by numerical diagonalization) for undirected and directed networks and from fully regular to strongly random topologies. These results may provide analytical insights to empirically found features of dynamics on small-world networks from various research fields, including biology, physics, engineering, and social science.

Applications of alignment-free methods in epigenomics.

PubMed

Pinello, Luca; Lo Bosco, Giosuè; Yuan, Guo-Cheng

2014-05-01

Epigenetic mechanisms play an important role in the regulation of cell type-specific gene activities, yet how epigenetic patterns are established and maintained remains poorly understood. Recent studies have supported a role of DNA sequences in recruitment of epigenetic regulators. Alignment-free methods have been applied to identify distinct sequence features that are associated with epigenetic patterns and to predict epigenomic profiles. Here, we review recent advances in such applications, including the methods to map DNA sequence to feature space, sequence comparison and prediction models. Computational studies using these methods have provided important insights into the epigenetic regulatory mechanisms.

Establishing a learning foundation in a dynamically changing world: Insights from artificial language work

NASA Astrophysics Data System (ADS)

Gonzales, Kalim

It is argued that infants build a foundation for learning about the world through their incidental acquisition of the spatial and temporal regularities surrounding them. A challenge is that learning occurs across multiple contexts whose statistics can greatly differ. Two artificial language studies with 12-month-olds demonstrate that infants come prepared to parse statistics across contexts using the temporal and perceptual features that distinguish one context from another. These results suggest that infants can organize their statistical input with a wider range of features that typically considered. Possible attention, decision making, and memory mechanisms are discussed.

Characterizing Black Hole Mergers

NASA Technical Reports Server (NTRS)

Baker, John; Boggs, William Darian; Kelly, Bernard

2010-01-01

Binary black hole mergers are a promising source of gravitational waves for interferometric gravitational wave detectors. Recent advances in numerical relativity have revealed the predictions of General Relativity for the strong burst of radiation generated in the final moments of binary coalescence. We explore features in the merger radiation which characterize the final moments of merger and ringdown. Interpreting the waveforms in terms of an rotating implicit radiation source allows a unified phenomenological description of the system from inspiral through ringdown. Common features in the waveforms allow quantitative description of the merger signal which may provide insights for observations large-mass black hole binaries.

The Manifest Association Structure of the Single-Factor Model: Insights from Partial Correlations

ERIC Educational Resources Information Center

Salgueiro, Maria de Fatima; Smith, Peter W. F.; McDonald, John W.

2008-01-01

The association structure between manifest variables arising from the single-factor model is investigated using partial correlations. The additional insights to the practitioner provided by partial correlations for detecting a single-factor model are discussed. The parameter space for the partial correlations is presented, as are the patterns of…

Geological Mapping of Fortuna Tessera (V-2): Venus and Earth's Archean Process Comparisons

NASA Technical Reports Server (NTRS)

Head, James W.; Hurwitz,D. M.; Ivanov, M. A.; Basilevsky, A. T.; Kumar, P. Senthil

2008-01-01

The geological features, structures, thermal conditions, interpreted processes, and outstanding questions related to both the Earth's Archean and Venus share many similarities and we are using a problem-oriented approach to Venus mapping, guided by insight from the Archean record of the Earth, to gain new insight into the evolution of Venus and Earth's Archean. The Earth's preserved and well-documented Archean record provides important insight into high heat-flux tectonic and magmatic environments and structures and the surface of Venus reveals the current configuration and recent geological record of analogous high-temperature environments unmodified by subsequent several billion years of segmentation and overprinting, as on Earth. Elsewhere we have addressed the nature of the Earth's Archean, the similarities to and differences from Venus, and the specific Venus and Earth-Archean problems on which progress might be made through comparison. Here we present the major goals of the Venus-Archean comparison and show how preliminary mapping of the geology of the V-2 Fortuna Tessera quadrangle is providing insight on these problems. We have identified five key themes and questions common to both the Archean and Venus, the assessment of which could provide important new insights into the history and processes of both planets.

Persistent homology of time-dependent functional networks constructed from coupled time series

NASA Astrophysics Data System (ADS)

Stolz, Bernadette J.; Harrington, Heather A.; Porter, Mason A.

2017-04-01

We use topological data analysis to study "functional networks" that we construct from time-series data from both experimental and synthetic sources. We use persistent homology with a weight rank clique filtration to gain insights into these functional networks, and we use persistence landscapes to interpret our results. Our first example uses time-series output from networks of coupled Kuramoto oscillators. Our second example consists of biological data in the form of functional magnetic resonance imaging data that were acquired from human subjects during a simple motor-learning task in which subjects were monitored for three days during a five-day period. With these examples, we demonstrate that (1) using persistent homology to study functional networks provides fascinating insights into their properties and (2) the position of the features in a filtration can sometimes play a more vital role than persistence in the interpretation of topological features, even though conventionally the latter is used to distinguish between signal and noise. We find that persistent homology can detect differences in synchronization patterns in our data sets over time, giving insight both on changes in community structure in the networks and on increased synchronization between brain regions that form loops in a functional network during motor learning. For the motor-learning data, persistence landscapes also reveal that on average the majority of changes in the network loops take place on the second of the three days of the learning process.

Three-dimensional radar imaging of structures and craters in the Martian polar caps.

PubMed

Putzig, Nathaniel E; Smith, Isaac B; Perry, Matthew R; Foss, Frederick J; Campbell, Bruce A; Phillips, Roger J; Seu, Roberto

2018-07-01

Over the last decade, observations acquired by the Shallow Radar (SHARAD) sounder on individual passes of the Mars Reconnaissance Orbiter have revealed the internal structure of the Martian polar caps and provided new insights into the formation of the icy layers within and their relationship to climate. However, a complete picture of the cap interiors has been hampered by interfering reflections from off-nadir surface features and signal losses associated with sloping structures and scattering. Foss et al. (2017) addressed these limitations by assembling three-dimensional data volumes of SHARAD observations from thousands of orbital passes over each polar region and applying geometric corrections simultaneously. The radar volumes provide unprecedented views of subsurface features, readily imaging structures previously inferred from time-intensive manual analysis of single-orbit data (e.g., trough-bounding surfaces, a buried chasma, and a basal unit in the north, massive carbon-dioxide ice deposits and discontinuous layered sequences in the south). Our new mapping of the carbon-dioxide deposits yields a volume of 16,500 km 3 , 11% larger than the prior estimate. In addition, the radar volumes newly reveal other structures, including what appear to be buried impact craters with no surface expression. Our first assessment of 21 apparent craters at the base of the north polar layered deposits suggests a Hesperian age for the substrate, consistent with that of the surrounding plains as determined from statistics of surface cratering rates. Planned mapping of similar features throughout both polar volumes may provide new constraints on the age of the icy layered deposits. The radar volumes also provide new topographic data between the highest latitudes observed by the Mars Orbiter Laser Altimeter and those observed by SHARAD. In general, mapping of features in these radar volumes is placing new constraints on the nature and evolution of the polar deposits and associated climate changes.

Cost-effectiveness of Rotavirus vaccination in Vietnam

PubMed Central

Kim, Sun-Young; Goldie, Sue J; Salomon, Joshua A

2009-01-01

Background Rotavirus is the most common cause of severe diarrhea leading to hospitalization or disease-specific death among young children. New rotavirus vaccines have recently been approved. Some previous studies have provided broad qualitative insights into the health and economic consequences of introducing the vaccines into low-income countries, representing several features of rotavirus infection, such as varying degrees of severity and age-dependency of clinical manifestation, in their model-based analyses. We extend this work to reflect additional features of rotavirus (e.g., the possibility of reinfection and varying degrees of partial immunity conferred by natural infection), and assess the influence of the features on the cost-effectiveness of rotavirus vaccination. Methods We developed a Markov model that reflects key features of rotavirus infection, using the most recent data available. We applied the model to the 2004 Vietnamese birth cohort and re-evaluated the cost-effectiveness (2004 US dollars per disability-adjusted life year [DALY]) of rotavirus vaccination (Rotarix®) compared to no vaccination, from both societal and health care system perspectives. We conducted univariate sensitivity analyses and also performed a probabilistic sensitivity analysis, based on Monte Carlo simulations drawing parameter values from the distributions assigned to key uncertain parameters. Results Rotavirus vaccination would not completely protect young children against rotavirus infection due to the partial nature of vaccine immunity, but would effectively reduce severe cases of rotavirus gastroenteritis (outpatient visits, hospitalizations, or deaths) by about 67% over the first 5 years of life. Under base-case assumptions (94% coverage and $5 per dose), the incremental cost per DALY averted from vaccination compared to no vaccination would be $540 from the societal perspective and $550 from the health care system perspective. Conclusion Introducing rotavirus vaccines would be a cost-effective public health intervention in Vietnam. However, given the uncertainty about vaccine efficacy and potential changes in rotavirus epidemiology in local settings, further clinical research and re-evaluation of rotavirus vaccination programs may be necessary as new information emerges. PMID:19159483

Genome-wide association meta-analysis of neuropathologic features of Alzheimer's disease and related dementias.

PubMed

Beecham, Gary W; Hamilton, Kara; Naj, Adam C; Martin, Eden R; Huentelman, Matt; Myers, Amanda J; Corneveaux, Jason J; Hardy, John; Vonsattel, Jean-Paul; Younkin, Steven G; Bennett, David A; De Jager, Philip L; Larson, Eric B; Crane, Paul K; Kamboh, M Ilyas; Kofler, Julia K; Mash, Deborah C; Duque, Linda; Gilbert, John R; Gwirtsman, Harry; Buxbaum, Joseph D; Kramer, Patricia; Dickson, Dennis W; Farrer, Lindsay A; Frosch, Matthew P; Ghetti, Bernardino; Haines, Jonathan L; Hyman, Bradley T; Kukull, Walter A; Mayeux, Richard P; Pericak-Vance, Margaret A; Schneider, Julie A; Trojanowski, John Q; Reiman, Eric M; Schellenberg, Gerard D; Montine, Thomas J

2014-09-01

Alzheimer's disease (AD) and related dementias are a major public health challenge and present a therapeutic imperative for which we need additional insight into molecular pathogenesis. We performed a genome-wide association study and analysis of known genetic risk loci for AD dementia using neuropathologic data from 4,914 brain autopsies. Neuropathologic data were used to define clinico-pathologic AD dementia or controls, assess core neuropathologic features of AD (neuritic plaques, NPs; neurofibrillary tangles, NFTs), and evaluate commonly co-morbid neuropathologic changes: cerebral amyloid angiopathy (CAA), Lewy body disease (LBD), hippocampal sclerosis of the elderly (HS), and vascular brain injury (VBI). Genome-wide significance was observed for clinico-pathologic AD dementia, NPs, NFTs, CAA, and LBD with a number of variants in and around the apolipoprotein E gene (APOE). GalNAc transferase 7 (GALNT7), ATP-Binding Cassette, Sub-Family G (WHITE), Member 1 (ABCG1), and an intergenic region on chromosome 9 were associated with NP score; and Potassium Large Conductance Calcium-Activated Channel, Subfamily M, Beta Member 2 (KCNMB2) was strongly associated with HS. Twelve of the 21 non-APOE genetic risk loci for clinically-defined AD dementia were confirmed in our clinico-pathologic sample: CR1, BIN1, CLU, MS4A6A, PICALM, ABCA7, CD33, PTK2B, SORL1, MEF2C, ZCWPW1, and CASS4 with 9 of these 12 loci showing larger odds ratio in the clinico-pathologic sample. Correlation of effect sizes for risk of AD dementia with effect size for NFTs or NPs showed positive correlation, while those for risk of VBI showed a moderate negative correlation. The other co-morbid neuropathologic features showed only nominal association with the known AD loci. Our results discovered new genetic associations with specific neuropathologic features and aligned known genetic risk for AD dementia with specific neuropathologic changes in the largest brain autopsy study of AD and related dementias.

Three-dimensional radar imaging of structures and craters in the Martian polar caps

NASA Astrophysics Data System (ADS)

Putzig, Nathaniel E.; Smith, Isaac B.; Perry, Matthew R.; Foss, Frederick J.; Campbell, Bruce A.; Phillips, Roger J.; Seu, Roberto

2018-07-01

Over the last decade, observations acquired by the Shallow Radar (SHARAD) sounder on individual passes of the Mars Reconnaissance Orbiter have revealed the internal structure of the Martian polar caps and provided new insights into the formation of the icy layers within and their relationship to climate. However, a complete picture of the cap interiors has been hampered by interfering reflections from off-nadir surface features and signal losses associated with sloping structures and scattering. Foss et al. (The Leading Edge 36, 43-57, 2017, https://doi.org/10.1190/tle36010043.1) addressed these limitations by assembling three-dimensional data volumes of SHARAD observations from thousands of orbital passes over each polar region and applying geometric corrections simultaneously. The radar volumes provide unprecedented views of subsurface features, readily imaging structures previously inferred from time-intensive manual analysis of single-orbit data (e.g., trough-bounding surfaces, a buried chasma, and a basal unit in the north, massive carbon-dioxide ice deposits and discontinuous layered sequences in the south). Our new mapping of the carbon-dioxide deposits yields a volume of 16,500 km3, 11% larger than the prior estimate. In addition, the radar volumes newly reveal other structures, including what appear to be buried impact craters with no surface expression. Our first assessment of 21 apparent craters at the base of the north polar layered deposits suggests a Hesperian age for the substrate, consistent with that of the surrounding plains as determined from statistics of surface cratering rates. Planned mapping of similar features throughout both polar volumes may provide new constraints on the age of the icy layered deposits. The radar volumes also provide new topographic data between the highest latitudes observed by the Mars Orbiter Laser Altimeter and those observed by SHARAD. In general, mapping of features in these radar volumes is placing new constraints on the nature and evolution of the polar deposits and associated climate changes.

76 FR 10482 - Special Conditions: Boeing Model 787-8 Airplane; Overhead Flightcrew-Rest Compartment Occupiable...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-02-25

... Boeing Model 787-8 airplane. This airplane will have novel or unusual design features associated with an... standards for this design feature. These special conditions contain the additional safety standards that the... airworthiness standards. Additional special conditions will be issued for other novel or unusual design features...

Visual scan-path analysis with feature space transient fixation moments

NASA Astrophysics Data System (ADS)

Dempere-Marco, Laura; Hu, Xiao-Peng; Yang, Guang-Zhong

2003-05-01

The study of eye movements provides useful insight into the cognitive processes underlying visual search tasks. The analysis of the dynamics of eye movements has often been approached from a purely spatial perspective. In many cases, however, it may not be possible to define meaningful or consistent dynamics without considering the features underlying the scan paths. In this paper, the definition of the feature space has been attempted through the concept of visual similarity and non-linear low dimensional embedding, which defines a mapping from the image space into a low dimensional feature manifold that preserves the intrinsic similarity of image patterns. This has enabled the definition of perceptually meaningful features without the use of domain specific knowledge. Based on this, this paper introduces a new concept called Feature Space Transient Fixation Moments (TFM). The approach presented tackles the problem of feature space representation of visual search through the use of TFM. We demonstrate the practical values of this concept for characterizing the dynamics of eye movements in goal directed visual search tasks. We also illustrate how this model can be used to elucidate the fundamental steps involved in skilled search tasks through the evolution of transient fixation moments.

The influence of repressor DNA binding site architecture on transcriptional control.

PubMed

Park, Dan M; Kiley, Patricia J

2014-08-26

How the architecture of DNA binding sites dictates the extent of repression of promoters is not well understood. Here, we addressed the importance of the number and information content of the three direct repeats (DRs) in the binding and repression of the icdA promoter by the phosphorylated form of the global Escherichia coli repressor ArcA (ArcA-P). We show that decreasing the information content of the two sites with the highest information (DR1 and DR2) eliminated ArcA binding to all three DRs and ArcA repression of icdA. Unexpectedly, we also found that DR3 occupancy functions principally in repression, since mutation of this low-information-content site both eliminated DNA binding to DR3 and significantly weakened icdA repression, despite the fact that binding to DR1 and DR2 was intact. In addition, increasing the information content of any one of the three DRs or addition of a fourth DR increased ArcA-dependent repression but perturbed signal-dependent regulation of repression. Thus, our data show that the information content and number of DR elements are critical architectural features for maintaining a balance between high-affinity binding and signal-dependent regulation of icdA promoter function in response to changes in ArcA-P levels. Optimization of such architectural features may be a common strategy to either dampen or enhance the sensitivity of DNA binding among the members of the large OmpR/PhoB family of regulators as well as other transcription factors. In Escherichia coli, the response regulator ArcA maintains homeostasis of redox carriers under O2-limiting conditions through a comprehensive repression of carbon oxidation pathways that require aerobic respiration to recycle redox carriers. Although a binding site architecture comprised of a variable number of sequence recognition elements has been identified within the promoter regions of ArcA-repressed operons, it is unclear how this variable architecture dictates transcriptional regulation. By dissecting the role of multiple sequence elements within the icdA promoter, we provide insight into the design principles that allow ArcA to repress transcription within diverse promoter contexts. Our data suggest that the arrangement of recognition elements is tailored to achieve sufficient repression of a given promoter while maintaining appropriate signal-dependent regulation of repression, providing insight into how diverse binding site architectures link changes in O2 with the fine-tuning of carbon oxidation pathway levels. Copyright © 2014 Park and Kiley.

Dreaming and insight

PubMed Central

Edwards, Christopher L.; Ruby, Perrine M.; Malinowski, Josie E.; Bennett, Paul D.; Blagrove, Mark T.

2013-01-01

This paper addresses claims that dreams can be a source of personal insight. Whereas there has been anecdotal backing for such claims, there is now tangential support from findings of the facilitative effect of sleep on cognitive insight, and of REM sleep in particular on emotional memory consolidation. Furthermore, the presence in dreams of metaphorical representations of waking life indicates the possibility of novel insight as an emergent feature of such metaphorical mappings. In order to assess whether personal insight can occur as a result of the consideration of dream content, 11 dream group discussion sessions were conducted which followed the Ullman Dream Appreciation technique, one session for each of 11 participants (10 females, 1 male; mean age = 19.2 years). Self-ratings of deepened self-perception and personal gains from participation in the group sessions showed that the Ullman technique is an effective procedure for establishing connections between dream content and recent waking life experiences, although wake life sources were found for only 14% of dream report text. The mean Exploration-Insight score on the Gains from Dream Interpretation questionnaire was very high and comparable to outcomes from the well-established Hill (1996) therapist-led dream interpretation method. This score was associated between-subjects with pre-group positive Attitude Toward Dreams (ATD). The need to distinguish “aha” experiences as a result of discovering a waking life source for part of a dream, from “aha” experiences of personal insight as a result of considering dream content, is discussed. Difficulties are described in designing a control condition to which the dream report condition can be compared. PMID:24550849

Modeling the complex pathology of Alzheimer’s disease in Drosophila

PubMed Central

Fernandez-Funez, Pedro; de Mena, Lorena; Rincon-Limas, Diego E.

2015-01-01

Alzheimer’s disease (AD) is the leading cause of dementia and the most common neurodegenerative disorder. AD is mostly a sporadic disorder and its main risk factor is age, but mutations in three genes that promote the accumulation of the amyloid-β (Aβ42) peptide revealed the critical role of Amyloid precursor protein (APP) processing in AD. Neurofibrillary tangles enriched in tau are the other pathological hallmark of AD, but the lack of causative tau mutations still puzzles researchers. Here, we describe the contribution of a powerful invertebrate model, the fruit fly Drosophila melanogaster, to uncovering the function and pathogenesis of human APP, Aβ42, and tau. APP and tau participate in many complex cellular processes, although their main function is microtubule stabilization and the to-and-fro transport of axonal vesicles. Additionally, expression of secreted Aβ42 induces prominent neuronal death in Drosophila, a critical feature of AD, making this model a popular choice for identifying intrinsic and extrinsic factors mediating Aβ42 neurotoxicity. Overall, Drosophila has made significant contributions to better understand the complex pathology of AD, although additional insight can be expected from combining multiple transgenes, performing genome-wide loss-of-function screens, and testing anti-tau therapies alone or in combination with Aβ42. PMID:26024860

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brady, Michael P.; Ievlev, Anton V.; Fayek, Mostafa

Hydrogen gas is formed when Mg corrodes in water; however, the manner and extent to which the hydrogen may also enter the Mg metal is poorly understood. Such knowledge is critical as stress corrosion cracking (SCC)/embrittlement phenomena limit many otherwise promising structural and functional uses of Mg. Here, we report via D 2O/D isotopic tracer and H 2O exposures with characterization by secondary ion mass spectrometry, inelastic neutron scattering vibrational spectrometry, electron microscopy, and atom probe tomography techniques direct evidence that hydrogen rapidly penetrated tens of micrometers into Mg metal after only 4 h of exposure to water at roommore » temperature. Further, technologically important microalloying additions of <1 wt % Zr and Nd used to improve the manufacturability and mechanical properties of Mg significantly increased the extent of hydrogen ingress, whereas Al additions in the 2–3 wt % range did not. Segregation of hydrogen species was observed at regions of high Mg/Zr/Nd nanoprecipitate density and at Mg(Zr) metastable solid solution microstructural features. We also report evidence that this ingressed hydrogen was unexpectedly present in the alloy as nanoconfined, molecular H 2. These new insights provide a basis for strategies to design Mg alloys to resist SCC in aqueous environments as well as potentially impact functional uses such as hydrogen storage where increased hydrogen uptake is desired.« less

Mental Illness Stigma Expressed by Police to Police.

PubMed

Stuart, Heather

2017-01-01

This paper describes mental health related stigma expressed by police to police using a newly developed 11-item Police Officer Stigma Scale and reports on the preliminary psychometric properties (factor structure and internal reliability) of this scale. The scale used an indirect measurement approach adapted from the Perceived Devaluation and Discrimination Scale. Five themes appropriate to police culture were adapted and six additional items were added. Responses were rated on a 5-point agreement scale with an additional don't know option. Data were collected from officers attending a mandatory workshop (90.5% response). Exploratory factor analysis showed the scale to be unidimensional and internally reliable (Cronbach's alpha was 0.82). The most endorsed items pertained to avoiding disclosure to a supervisor/manager or to a colleague (85% agreement), that most officers would expect discrimination at work (62%), and that most officers would not want a supervisor or manager who had a mental illness (62%). Findings highlight that (a) Police-to-police mental illness stigma may be a particularly strong feature of police cultures; (b) police should be a focus for targeted anti-stigma interventions; and (c) though further psychometric testing is needed, the Police Office Stigma Scale may provide important insights into the nature and functioning of police-to-police stigma in police cultures in future research.

A new insight into the phase transition in the early Universe with two Higgs doublets

NASA Astrophysics Data System (ADS)

Bernon, Jérémy; Bian, Ligong; Jiang, Yun

2018-05-01

We study the electroweak phase transition in the alignment limit of the CP-conserving two-Higgs-doublet model (2HDM) of Type I and Type II. The effective potential is evaluated at one-loop, where the thermal potential includes Daisy corrections and is reliably approximated by means of a sum of Bessel functions. Both 1-stage and 2-stage electroweak phase transitions are shown to be possible, depending on the pattern of the vacuum development as the Universe cools down. For the 1-stage case focused on in this paper, we analyze the properties of phase transition and discover that the field value of the electroweak symmetry breaking vacuum at the critical temperature at which the first order phase transition occurs is largely correlated with the vacuum depth of the 1-loop potential at zero temperature. We demonstrate that a strong first order electroweak phase transition (SFOEWPT) in the 2HDM is achievable and establish benchmark scenarios leading to different testable signatures at colliders. In addition, we verify that an enhanced triple Higgs coupling (including loop corrections) is a typical feature of the SFOPT driven by the additional doublet. As a result, SFOEWPT might be able to be probed at the LHC and future lepton colliders through Higgs pair production.

Cognitive insight: A systematic review.

PubMed

Van Camp, L S C; Sabbe, B G C; Oldenburg, J F E

2017-07-01

Cognitive insight is the ability to re-evaluate thoughts and beliefs in order to make thoughtful conclusions. It differs from clinical insight, as it focuses on more general metacognitive processes. Therefore, it could be relevant to diverse disorders and non-clinical subjects. There is a growing body of research on cognitive insight in individuals with and without psychosis. This review has summarised the current state of the art regarding this topic. We conclude that while cognitive insight in its current form seems valid for use in individuals with psychosis, it is less so for individuals without psychosis. Additionally, higher cognitive insight not always leads to better psychological functioning. For instance, higher levels of self-reflection are often associated with depressive mood. We therefore recommend the sub-components of cognitive insight to be studied separately. Also, it is unclear what position cognitive insight takes within the spectrum of metacognitive processes and how it relates to other self-related concepts that have been defined previously in literature. Combining future and past research on cognitive insight and its analogue concepts will help in the formation of a uniform definition that fits all subjects discussed here. Copyright © 2017. Published by Elsevier Ltd.

Burkholderia pseudomallei Colony Morphotypes Show a Synchronized Metabolic Pattern after Acute Infection

PubMed Central

Steinmetz, Ivo; Lalk, Michael

2016-01-01

Background Burkholderia pseudomallei is a water and soil bacterium and the causative agent of melioidosis. A characteristic feature of this bacterium is the formation of different colony morphologies which can be isolated from environmental samples as well as from clinical samples, but can also be induced in vitro. Previous studies indicate that morphotypes can differ in a number of characteristics such as resistance to oxidative stress, cellular adhesion and intracellular replication. Yet the metabolic features of B. pseudomallei and its different morphotypes have not been examined in detail so far. Therefore, this study aimed to characterize the exometabolome of B. pseudomallei morphotypes and the impact of acute infection on their metabolic characteristics. Methods and Principal Findings We applied nuclear magnetic resonance spectroscopy (1H-NMR) in a metabolic footprint approach to compare nutrition uptake and metabolite secretion of starvation induced morphotypes of the B. pseudomallei strains K96243 and E8. We observed gluconate production and uptake in all morphotype cultures. Our study also revealed that among all morphotypes amino acids could be classified with regard to their fast and slow consumption. In addition to these shared metabolic features, the morphotypes varied highly in amino acid uptake profiles, secretion of branched chain amino acid metabolites and carbon utilization. After intracellular passage in vitro or murine acute infection in vivo, we observed a switch of the various morphotypes towards a single morphotype and a synchronization of nutrient uptake and metabolite secretion. Conclusion To our knowledge, this study provides first insights into the basic metabolism of B. pseudomallei and its colony morphotypes. Furthermore, our data suggest, that acute infection leads to the synchronization of B. pseudomallei colony morphology and metabolism through yet unknown host signals and bacterial mechanisms. PMID:26943908

CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms.

PubMed

Terfve, Camille; Cokelaer, Thomas; Henriques, David; MacNamara, Aidan; Goncalves, Emanuel; Morris, Melody K; van Iersel, Martijn; Lauffenburger, Douglas A; Saez-Rodriguez, Julio

2012-10-18

Cells process signals using complex and dynamic networks. Studying how this is performed in a context and cell type specific way is essential to understand signaling both in physiological and diseased situations. Context-specific medium/high throughput proteomic data measured upon perturbation is now relatively easy to obtain but formalisms that can take advantage of these features to build models of signaling are still comparatively scarce. Here we present CellNOptR, an open-source R software package for building predictive logic models of signaling networks by training networks derived from prior knowledge to signaling (typically phosphoproteomic) data. CellNOptR features different logic formalisms, from Boolean models to differential equations, in a common framework. These different logic model representations accommodate state and time values with increasing levels of detail. We provide in addition an interface via Cytoscape (CytoCopteR) to facilitate use and integration with Cytoscape network-based capabilities. Models generated with this pipeline have two key features. First, they are constrained by prior knowledge about the network but trained to data. They are therefore context and cell line specific, which results in enhanced predictive and mechanistic insights. Second, they can be built using different logic formalisms depending on the richness of the available data. Models built with CellNOptR are useful tools to understand how signals are processed by cells and how this is altered in disease. They can be used to predict the effect of perturbations (individual or in combinations), and potentially to engineer therapies that have differential effects/side effects depending on the cell type or context.

CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms

PubMed Central

2012-01-01

Background Cells process signals using complex and dynamic networks. Studying how this is performed in a context and cell type specific way is essential to understand signaling both in physiological and diseased situations. Context-specific medium/high throughput proteomic data measured upon perturbation is now relatively easy to obtain but formalisms that can take advantage of these features to build models of signaling are still comparatively scarce. Results Here we present CellNOptR, an open-source R software package for building predictive logic models of signaling networks by training networks derived from prior knowledge to signaling (typically phosphoproteomic) data. CellNOptR features different logic formalisms, from Boolean models to differential equations, in a common framework. These different logic model representations accommodate state and time values with increasing levels of detail. We provide in addition an interface via Cytoscape (CytoCopteR) to facilitate use and integration with Cytoscape network-based capabilities. Conclusions Models generated with this pipeline have two key features. First, they are constrained by prior knowledge about the network but trained to data. They are therefore context and cell line specific, which results in enhanced predictive and mechanistic insights. Second, they can be built using different logic formalisms depending on the richness of the available data. Models built with CellNOptR are useful tools to understand how signals are processed by cells and how this is altered in disease. They can be used to predict the effect of perturbations (individual or in combinations), and potentially to engineer therapies that have differential effects/side effects depending on the cell type or context. PMID:23079107

Integrative Data Analysis of Multi-Platform Cancer Data with a Multimodal Deep Learning Approach.

PubMed

Liang, Muxuan; Li, Zhizhong; Chen, Ting; Zeng, Jianyang

2015-01-01

Identification of cancer subtypes plays an important role in revealing useful insights into disease pathogenesis and advancing personalized therapy. The recent development of high-throughput sequencing technologies has enabled the rapid collection of multi-platform genomic data (e.g., gene expression, miRNA expression, and DNA methylation) for the same set of tumor samples. Although numerous integrative clustering approaches have been developed to analyze cancer data, few of them are particularly designed to exploit both deep intrinsic statistical properties of each input modality and complex cross-modality correlations among multi-platform input data. In this paper, we propose a new machine learning model, called multimodal deep belief network (DBN), to cluster cancer patients from multi-platform observation data. In our integrative clustering framework, relationships among inherent features of each single modality are first encoded into multiple layers of hidden variables, and then a joint latent model is employed to fuse common features derived from multiple input modalities. A practical learning algorithm, called contrastive divergence (CD), is applied to infer the parameters of our multimodal DBN model in an unsupervised manner. Tests on two available cancer datasets show that our integrative data analysis approach can effectively extract a unified representation of latent features to capture both intra- and cross-modality correlations, and identify meaningful disease subtypes from multi-platform cancer data. In addition, our approach can identify key genes and miRNAs that may play distinct roles in the pathogenesis of different cancer subtypes. Among those key miRNAs, we found that the expression level of miR-29a is highly correlated with survival time in ovarian cancer patients. These results indicate that our multimodal DBN based data analysis approach may have practical applications in cancer pathogenesis studies and provide useful guidelines for personalized cancer therapy.

A quantitative brain map of experimental cerebral malaria pathology.

PubMed

Strangward, Patrick; Haley, Michael J; Shaw, Tovah N; Schwartz, Jean-Marc; Greig, Rachel; Mironov, Aleksandr; de Souza, J Brian; Cruickshank, Sheena M; Craig, Alister G; Milner, Danny A; Allan, Stuart M; Couper, Kevin N

2017-03-01

The murine model of experimental cerebral malaria (ECM) has been utilised extensively in recent years to study the pathogenesis of human cerebral malaria (HCM). However, it has been proposed that the aetiologies of ECM and HCM are distinct, and, consequently, no useful mechanistic insights into the pathogenesis of HCM can be obtained from studying the ECM model. Therefore, in order to determine the similarities and differences in the pathology of ECM and HCM, we have performed the first spatial and quantitative histopathological assessment of the ECM syndrome. We demonstrate that the accumulation of parasitised red blood cells (pRBCs) in brain capillaries is a specific feature of ECM that is not observed during mild murine malaria infections. Critically, we show that individual pRBCs appear to occlude murine brain capillaries during ECM. As pRBC-mediated congestion of brain microvessels is a hallmark of HCM, this suggests that the impact of parasite accumulation on cerebral blood flow may ultimately be similar in mice and humans during ECM and HCM, respectively. Additionally, we demonstrate that cerebrovascular CD8+ T-cells appear to co-localise with accumulated pRBCs, an event that corresponds with development of widespread vascular leakage. As in HCM, we show that vascular leakage is not dependent on extensive vascular destruction. Instead, we show that vascular leakage is associated with alterations in transcellular and paracellular transport mechanisms. Finally, as in HCM, we observed axonal injury and demyelination in ECM adjacent to diverse vasculopathies. Collectively, our data therefore shows that, despite very different presentation, and apparently distinct mechanisms, of parasite accumulation, there appear to be a number of comparable features of cerebral pathology in mice and in humans during ECM and HCM, respectively. Thus, when used appropriately, the ECM model may be useful for studying specific pathological features of HCM.

Controllable Grid Interface for Testing Ancillary Service Controls and Fault Performance of Utility-Scale Wind Power Generation: Preprint

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gevorgian, Vahan; Koralewicz, Przemyslaw; Wallen, Robb

The rapid expansion of wind power has led many transmission system operators to demand modern wind power plants to comply with strict interconnection requirements. Such requirements involve various aspects of wind power plant operation, including fault ride-through and power quality performance as well as the provision of ancillary services to enhance grid reliability. During recent years, the National Renewable Energy Laboratory (NREL) of the U.S. Department of Energy has developed a new, groundbreaking testing apparatus and methodology to test and demonstrate many existing and future advanced controls for wind generation (and other renewable generation technologies) on the multimegawatt scale andmore » medium-voltage levels. This paper describes the capabilities and control features of NREL's 7-MVA power electronic grid simulator (also called a controllable grid interface, or CGI) that enables testing many active and reactive power control features of modern wind turbine generators -- including inertial response, primary and secondary frequency responses, and voltage regulation -- under a controlled, medium-voltage grid environment. In particular, this paper focuses on the specifics of testing the balanced and unbalanced fault ride-through characteristics of wind turbine generators under simulated strong and weak medium-voltage grid conditions. In addition, this paper provides insights on the power hardware-in-the-loop feature implemented in the CGI to emulate (in real time) the conditions that might exist in various types of electric power systems under normal operations and/or contingency scenarios. Using actual test examples and simulation results, this paper describes the value of CGI as an ultimate modeling validation tool for all types of 'grid-friendly' controls by wind generation.« less

The geomorphic impact of glaciers as indicated by tors in North Sweden (Aurivaara, 68° N)

NASA Astrophysics Data System (ADS)

André, Marie-Françoise

2004-02-01

Geomorphological investigations carried out on 15 tor-like features located on the Aurivaara plateau (North Sweden, 68° N) provide new insights in the greatly debated age of these landforms. Erratics and till trapped deep in the tor joints support a pre-Weichselian age for tor formation. Moreover, the occurrence of various weathering stages in allochtonous material, the joint width up to 1.5 m (requiring long-term weathering), and the frequent association of tors with pediment-like forms, suggest pre-Quaternary tor formation. The juxtaposition of fresh erratics and in situ old weathering features (mushroom rocks, concentrically weathered well-rounded corestones, and grus) indicates a predominantly cold-based regime for the Scandinavian ice sheet, with erratics carried by the overlying moving ice being repeatedly deposited on tor summits during deglaciation phases. The relationships between tors and ice action indicated for the Aurivaara plateau result in the proposal of a morphodynamical succession of five tor subtypes ranging from the preservation of well-rounded corestones still embedded in grus (suggesting negligible glacial erosion) to the almost complete removal of tor features by ice scouring. A comparison with tors in similar geological and topographical contexts from the unglaciated Dartmoor area allows a tentative evaluation of an average overall glacial erosion of 0-10 m on the northern Sweden plateaus, in sharp contrast with the 190 m overdeepening of the nearby Torneträsk basin. Thus, this case study of Swedish tors provides additional support to the recent interpretations of relict landscapes in previously glaciated areas and is in accordance with the classical «model» of glacial selective erosion established in the Nordic and Arctic mountains.

Sports Stars: Analyzing the Performance of Astronomers at Visualization-based Discovery

NASA Astrophysics Data System (ADS)

Fluke, C. J.; Parrington, L.; Hegarty, S.; MacMahon, C.; Morgan, S.; Hassan, A. H.; Kilborn, V. A.

2017-05-01

In this data-rich era of astronomy, there is a growing reliance on automated techniques to discover new knowledge. The role of the astronomer may change from being a discoverer to being a confirmer. But what do astronomers actually look at when they distinguish between “sources” and “noise?” What are the differences between novice and expert astronomers when it comes to visual-based discovery? Can we identify elite talent or coach astronomers to maximize their potential for discovery? By looking to the field of sports performance analysis, we consider an established, domain-wide approach, where the expertise of the viewer (i.e., a member of the coaching team) plays a crucial role in identifying and determining the subtle features of gameplay that provide a winning advantage. As an initial case study, we investigate whether the SportsCode performance analysis software can be used to understand and document how an experienced Hi astronomer makes discoveries in spectral data cubes. We find that the process of timeline-based coding can be applied to spectral cube data by mapping spectral channels to frames within a movie. SportsCode provides a range of easy to use methods for annotation, including feature-based codes and labels, text annotations associated with codes, and image-based drawing. The outputs, including instance movies that are uniquely associated with coded events, provide the basis for a training program or team-based analysis that could be used in unison with discipline specific analysis software. In this coordinated approach to visualization and analysis, SportsCode can act as a visual notebook, recording the insight and decisions in partnership with established analysis methods. Alternatively, in situ annotation and coding of features would be a valuable addition to existing and future visualization and analysis packages.

Caves, Carbonates and Climate: Karst Landscape Development through Environmental Forcing, Little Cayman Island

NASA Astrophysics Data System (ADS)

Hsia, S.; Ouellette, G., Jr.; Manfrino, C.

2016-12-01

The Cayman Islands are situated in the west-central Caribbean Sea, between Cuba and the Yucatan Peninsula. Little Cayman Island (LCI) is relatively underdeveloped and understudied in comparison to its sister islands, Grand Cayman and Cayman Brac, and hosts less than 200 permanent residents over a 30 square kilometer area. However, like its sister islands, LCI is a small carbonate platform derived from reef building during the Oligocene, Miocene, and Quaternary. The shared geologic history of the Cayman Islands along with minimal human disturbance makes LCI an ideal site to study an island karst landscape. Conduction of field surveys, stratigraphic and petrologic comparisons between primary lithologic formations, and compilation of a geospatial inventory of karst features and lithology of LCI using GIS revealed novel insights into landscape evolution on LCI. In addition to surface karst surveys, several caves on the island were mapped. Cave morphologies suggest that evolution of LCI karst features have been driven by both hydroclimate, as well as salt and freshwater mixing, modulated by sea level fluctuations. These findings are mirrored in the lithology of partially dolomitized Miocene carbonates, which contain paleo-karst fill features and reveal hydroclimate influence, as well as enhanced resistance to dissolution in the present day, ostensibly from submersion in Mg-rich sea waters prior to the Quaternary. These findings shed light on the complex relationship of climate, geology, and karst landscape development on this particular carbonate island. This information is critical in anticipating structural and hydrogeological integrity on LCI under future climate change scenarios and serves as an example of the interplay linking climate and geologic processes to karst landscape development on small carbonate islands.

Classifying eating disorders based on "healthy" and "unhealthy" perfectionism and impulsivity.

PubMed

Slof-Op't Landt, Margarita C T; Claes, Laurence; van Furth, Eric F

2016-07-01

Perfectionism and impulsivity are associated with eating disorders (EDs). The current study examines whether clinically relevant subgroups of women with EDs can be identified based on "healthy" and "unhealthy" perfectionism and impulsivity. Latent profile analyses (LPA) were performed on data of 844 patients (DSM-IV diagnosis: 381 anorexia nervosa, 146 bulimia nervosa, 56 binge-eating disorder, 261 ED not otherwise specified). "Healthy" and "unhealthy" forms of perfectionism and impulsivity were assessed by the Frost Multidimensional Perfectionism Scale and the Dickman Impulsivity Inventory, respectively. The Eating Disorder Examination Questionnaire was completed to assess ED psychopathology. Furthermore, in 229 patients additional ED symptoms, depression, self-esteem, obsessive-compulsive symptoms, and personality features were assessed. The LPA revealed four profiles; 1. "Healthy Impulsivity" (HI; n = 191), 2. "Unhealthy Impulsivity" (UI; n = 238), 3. "Healthy and Unhealthy Perfectionism" (HP + UP; n = 153), 4. "Healthy Perfectionism" (HP; n = 262). Patients belonging to the "HP + UP" and the "UI" classes reported higher levels of ED psychopathology. More severe comorbid symptoms (depressive, obsessive-compulsive and self-esteem) were found in the patients belonging to the "HP + UP" class. Patients from the "HP + UP" and "HP" classes had higher scores for the personality features Harm Avoidance, Persistence and Cooperativeness. Women with EDs could be meaningfully grouped according to perfectionism and impulsivity. These findings can be used to improve treatment matching and intervention strategies. The use of dimensional features, like perfectionism and impulsivity, in ED research, may enable the identification of fundamental underlying mechanisms and provide more insight into potential mechanisms that may drive or maintain disordered eating. © 2016 Wiley Periodicals, Inc. (Int J Eat Disord 2016; 49:673-680). © 2016 Wiley Periodicals, Inc.

Disease Prediction based on Functional Connectomes using a Scalable and Spatially-Informed Support Vector Machine

PubMed Central

Watanabe, Takanori; Kessler, Daniel; Scott, Clayton; Angstadt, Michael; Sripada, Chandra

2014-01-01

Substantial evidence indicates that major psychiatric disorders are associated with distributed neural dysconnectivity, leading to strong interest in using neuroimaging methods to accurately predict disorder status. In this work, we are specifically interested in a multivariate approach that uses features derived from whole-brain resting state functional connectomes. However, functional connectomes reside in a high dimensional space, which complicates model interpretation and introduces numerous statistical and computational challenges. Traditional feature selection techniques are used to reduce data dimensionality, but are blind to the spatial structure of the connectomes. We propose a regularization framework where the 6-D structure of the functional connectome (defined by pairs of points in 3-D space) is explicitly taken into account via the fused Lasso or the GraphNet regularizer. Our method only restricts the loss function to be convex and margin-based, allowing non-differentiable loss functions such as the hinge-loss to be used. Using the fused Lasso or GraphNet regularizer with the hinge-loss leads to a structured sparse support vector machine (SVM) with embedded feature selection. We introduce a novel efficient optimization algorithm based on the augmented Lagrangian and the classical alternating direction method, which can solve both fused Lasso and GraphNet regularized SVM with very little modification. We also demonstrate that the inner subproblems of the algorithm can be solved efficiently in analytic form by coupling the variable splitting strategy with a data augmentation scheme. Experiments on simulated data and resting state scans from a large schizophrenia dataset show that our proposed approach can identify predictive regions that are spatially contiguous in the 6-D “connectome space,” offering an additional layer of interpretability that could provide new insights about various disease processes. PMID:24704268

New insights into the effects of biomaterial chemistry and topography on the morphology of kidney epithelial cells.

PubMed

Hulshof, Frits; Schophuizen, Carolien; Mihajlovic, Milos; van Blitterswijk, Clemens; Masereeuw, Rosalinde; de Boer, Jan; Stamatialis, Dimitrios

2018-02-01

Increasing incidence of renal pathology in the western world calls for innovative research for the development of cell-based therapies such as a bioartificial kidney (BAK) device. To fulfil the multitude of kidney functions, the core component of the BAK is a living membrane consisting of a tight kidney cell monolayer with preserved functional organic ion transporters cultured on a polymeric membrane surface. This membrane, on one side, is in contact with blood and therefore should have excellent blood compatibility, whereas the other side should facilitate functional monolayer formation. This work investigated the effect of membrane chemistry and surface topography on kidney epithelial cells to improve the formation of a functional monolayer. To achieve this, microtopographies were fabricated with high resolution and reproducibility on polystyrene films and on polyethersulfone-polyvinyl pyrrolidone (PES-PVP) porous membranes. A conditionally immortalized proximal tubule epithelial cell line (ciPTEC) was cultured on both, and subsequently, the cell morphology and monolayer formation were assessed. Our results showed that L-dopamine coating of the PES-PVP was sufficient to support ciPTEC monolayer formation. The polystyrene topographies with large features were able to align the cells in various patterns without significantly disruption of monolayer formation; however, the PES-PVP topographies with large features disrupted the monolayer. In contrast, the PES-PVP membranes with small features and with large spacing supported well the ciPTEC monolayer formation. In addition, the topographical PES-PVP membranes were compatible as a substrate membrane to measure organic cation transporter activity in Transwell® systems. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Integrated web visualizations for protein-protein interaction databases.

PubMed

Jeanquartier, Fleur; Jean-Quartier, Claire; Holzinger, Andreas

2015-06-16

Understanding living systems is crucial for curing diseases. To achieve this task we have to understand biological networks based on protein-protein interactions. Bioinformatics has come up with a great amount of databases and tools that support analysts in exploring protein-protein interactions on an integrated level for knowledge discovery. They provide predictions and correlations, indicate possibilities for future experimental research and fill the gaps to complete the picture of biochemical processes. There are numerous and huge databases of protein-protein interactions used to gain insights into answering some of the many questions of systems biology. Many computational resources integrate interaction data with additional information on molecular background. However, the vast number of diverse Bioinformatics resources poses an obstacle to the goal of understanding. We present a survey of databases that enable the visual analysis of protein networks. We selected M=10 out of N=53 resources supporting visualization, and we tested against the following set of criteria: interoperability, data integration, quantity of possible interactions, data visualization quality and data coverage. The study reveals differences in usability, visualization features and quality as well as the quantity of interactions. StringDB is the recommended first choice. CPDB presents a comprehensive dataset and IntAct lets the user change the network layout. A comprehensive comparison table is available via web. The supplementary table can be accessed on http://tinyurl.com/PPI-DB-Comparison-2015. Only some web resources featuring graph visualization can be successfully applied to interactive visual analysis of protein-protein interaction. Study results underline the necessity for further enhancements of visualization integration in biochemical analysis tools. Identified challenges are data comprehensiveness, confidence, interactive feature and visualization maturing.

Comparative genomics of bdelloid rotifers: Insights from desiccating and nondesiccating species

PubMed Central

Almeida, Pedro; Wilson, Christopher G.; Smith, Thomas P.; Fontaneto, Diego; Crisp, Alastair; Micklem, Gos; Tunnacliffe, Alan

2018-01-01

Bdelloid rotifers are a class of microscopic invertebrates that have existed for millions of years apparently without sex or meiosis. They inhabit a variety of temporary and permanent freshwater habitats globally, and many species are remarkably tolerant of desiccation. Bdelloids offer an opportunity to better understand the evolution of sex and recombination, but previous work has emphasised desiccation as the cause of several unusual genomic features in this group. Here, we present high-quality whole-genome sequences of 3 bdelloid species: Rotaria macrura and R. magnacalcarata, which are both desiccation intolerant, and Adineta ricciae, which is desiccation tolerant. In combination with the published assembly of A. vaga, which is also desiccation tolerant, we apply a comparative genomics approach to evaluate the potential effects of desiccation tolerance and asexuality on genome evolution in bdelloids. We find that ancestral tetraploidy is conserved among all 4 bdelloid species, but homologous divergence in obligately aquatic Rotaria genomes is unexpectedly low. This finding is contrary to current models regarding the role of desiccation in shaping bdelloid genomes. In addition, we find that homologous regions in A. ricciae are largely collinear and do not form palindromic repeats as observed in the published A. vaga assembly. Consequently, several features interpreted as genomic evidence for long-term ameiotic evolution are not general to all bdelloid species, even within the same genus. Finally, we substantiate previous findings of high levels of horizontally transferred nonmetazoan genes in both desiccating and nondesiccating bdelloid species and show that this unusual feature is not shared by other animal phyla, even those with desiccation-tolerant representatives. These comparisons call into question the proposed role of desiccation in mediating horizontal genetic transfer. PMID:29689044

A quantitative brain map of experimental cerebral malaria pathology

PubMed Central

Schwartz, Jean-Marc; Greig, Rachel; Mironov, Aleksandr; de Souza, J. Brian; Cruickshank, Sheena M.; Craig, Alister G.; Milner, Danny A.; Allan, Stuart M.

2017-01-01

The murine model of experimental cerebral malaria (ECM) has been utilised extensively in recent years to study the pathogenesis of human cerebral malaria (HCM). However, it has been proposed that the aetiologies of ECM and HCM are distinct, and, consequently, no useful mechanistic insights into the pathogenesis of HCM can be obtained from studying the ECM model. Therefore, in order to determine the similarities and differences in the pathology of ECM and HCM, we have performed the first spatial and quantitative histopathological assessment of the ECM syndrome. We demonstrate that the accumulation of parasitised red blood cells (pRBCs) in brain capillaries is a specific feature of ECM that is not observed during mild murine malaria infections. Critically, we show that individual pRBCs appear to occlude murine brain capillaries during ECM. As pRBC-mediated congestion of brain microvessels is a hallmark of HCM, this suggests that the impact of parasite accumulation on cerebral blood flow may ultimately be similar in mice and humans during ECM and HCM, respectively. Additionally, we demonstrate that cerebrovascular CD8+ T-cells appear to co-localise with accumulated pRBCs, an event that corresponds with development of widespread vascular leakage. As in HCM, we show that vascular leakage is not dependent on extensive vascular destruction. Instead, we show that vascular leakage is associated with alterations in transcellular and paracellular transport mechanisms. Finally, as in HCM, we observed axonal injury and demyelination in ECM adjacent to diverse vasculopathies. Collectively, our data therefore shows that, despite very different presentation, and apparently distinct mechanisms, of parasite accumulation, there appear to be a number of comparable features of cerebral pathology in mice and in humans during ECM and HCM, respectively. Thus, when used appropriately, the ECM model may be useful for studying specific pathological features of HCM. PMID:28273147

Quantitative proteome profile of water deficit stress responses in eastern cottonwood ( Populus deltoides) leaves

DOE Office of Scientific and Technical Information (OSTI.GOV)

Abraham, Paul E.; Garcia, Benjamin J.; Gunter, Lee E.

Drought stress is a recurring feature of world climate and the single most important factor influencing agricultural yield worldwide. Plants display highly variable, species-specific responses to drought and these responses are multifaceted, requiring physiological and morphological changes influenced by genetic and molecular mechanisms. Moreover, the reproducibility of water deficit studies is very cumbersome, which significantly impedes research on drought tolerance, because how a plant responds is highly influenced by the timing, duration, and intensity of the water deficit. Despite progress in the identification of drought-related mechanisms in many plants, the molecular basis of drought resistance remains to be fully understoodmore » in trees, particularly in poplar species because their wide geographic distribution results in varying tolerances to drought. Herein, we aimed to better understand this complex phenomenon in eastern cottonwood ( Populus deltoides) by performing a detailed contrast of the proteome changes between two different water deficit experiments to identify functional intersections and divergences in proteome responses. We investigated plants subjected to cyclic water deficit and compared these responses to plants subjected to prolonged acute water deficit. In total, we identified 108,012 peptide sequences across both experiments that provided insight into the quantitative state of 22,737 Populus gene models and 8,199 functional protein groups in response to drought. Together, these datasets provide the most comprehensive insight into proteome drought responses in poplar to date and a direct proteome comparison between short period dehydration shock and cyclic, post-drought re-watering. Altogether, this investigation provides novel insights into drought avoidance mechanisms that are distinct from progressive drought stress. Additionally, we identified proteins that have been associated as drought-relevant in previous studies. Importantly, we highlight the RD26 transcription factor as a gene regulated at both the transcript and protein level, regardless of species and drought condition, and, thus, represents a key, universal drought marker for Populus species.« less

Quantitative proteome profile of water deficit stress responses in eastern cottonwood ( Populus deltoides) leaves

DOE PAGES

Abraham, Paul E.; Garcia, Benjamin J.; Gunter, Lee E.; ...

2018-02-15

Drought stress is a recurring feature of world climate and the single most important factor influencing agricultural yield worldwide. Plants display highly variable, species-specific responses to drought and these responses are multifaceted, requiring physiological and morphological changes influenced by genetic and molecular mechanisms. Moreover, the reproducibility of water deficit studies is very cumbersome, which significantly impedes research on drought tolerance, because how a plant responds is highly influenced by the timing, duration, and intensity of the water deficit. Despite progress in the identification of drought-related mechanisms in many plants, the molecular basis of drought resistance remains to be fully understoodmore » in trees, particularly in poplar species because their wide geographic distribution results in varying tolerances to drought. Herein, we aimed to better understand this complex phenomenon in eastern cottonwood ( Populus deltoides) by performing a detailed contrast of the proteome changes between two different water deficit experiments to identify functional intersections and divergences in proteome responses. We investigated plants subjected to cyclic water deficit and compared these responses to plants subjected to prolonged acute water deficit. In total, we identified 108,012 peptide sequences across both experiments that provided insight into the quantitative state of 22,737 Populus gene models and 8,199 functional protein groups in response to drought. Together, these datasets provide the most comprehensive insight into proteome drought responses in poplar to date and a direct proteome comparison between short period dehydration shock and cyclic, post-drought re-watering. Altogether, this investigation provides novel insights into drought avoidance mechanisms that are distinct from progressive drought stress. Additionally, we identified proteins that have been associated as drought-relevant in previous studies. Importantly, we highlight the RD26 transcription factor as a gene regulated at both the transcript and protein level, regardless of species and drought condition, and, thus, represents a key, universal drought marker for Populus species.« less

On brain activity mapping: insights and lessons from Brain Decoding Project to map memory patterns in the hippocampus.

PubMed

Tsien, Joe Z; Li, Meng; Osan, Remus; Chen, Guifen; Lin, Longnian; Wang, Phillip Lei; Frey, Sabine; Frey, Julietta; Zhu, Dajiang; Liu, Tianming; Zhao, Fang; Kuang, Hui

2013-09-01

The BRAIN project recently announced by the president Obama is the reflection of unrelenting human quest for cracking the brain code, the patterns of neuronal activity that define who we are and what we are. While the Brain Activity Mapping proposal has rightly emphasized on the need to develop new technologies for measuring every spike from every neuron, it might be helpful to consider both the theoretical and experimental aspects that would accelerate our search for the organizing principles of the brain code. Here we share several insights and lessons from the similar proposal, namely, Brain Decoding Project that we initiated since 2007. We provide a specific example in our initial mapping of real-time memory traces from one part of the memory circuit, namely, the CA1 region of the mouse hippocampus. We show how innovative behavioral tasks and appropriate mathematical analyses of large datasets can play equally, if not more, important roles in uncovering the specific-to-general feature-coding cell assembly mechanism by which episodic memory, semantic knowledge, and imagination are generated and organized. Our own experiences suggest that the bottleneck of the Brain Project is not only at merely developing additional new technologies, but also the lack of efficient avenues to disseminate cutting edge platforms and decoding expertise to neuroscience community. Therefore, we propose that in order to harness unique insights and extensive knowledge from various investigators working in diverse neuroscience subfields, ranging from perception and emotion to memory and social behaviors, the BRAIN project should create a set of International and National Brain Decoding Centers at which cutting-edge recording technologies and expertise on analyzing large datasets analyses can be made readily available to the entire community of neuroscientists who can apply and schedule to perform cutting-edge research.