Structure of Cu/Ni Nanowires Obtained by Matrix Synthesis

NASA Astrophysics Data System (ADS)

Zhigalina, O. M.; Doludenko, I. M.; Khmelenin, D. N.; Zagorskiy, D. L.; Bedin, S. A.; Ivanov, I. M.

2018-05-01

The structure of layered Cu/Ni nanowires obtained by template synthesis in 100-nm channels of track membranes has been investigated by transmission and scanning electron microscopy. The phase composition and main structural features of individual nanowires are determined. It is shown that nanowires consist of alternating Ni ( Fm3m) and Cu ( Fm3m) layers with grains up to 100 nm in size. It is found that nanowires contain also copper oxide crystallites up to 20 nm in size. The elemental composition of individual layers and their mutual arrangement are determined.

Evaluating Sensory Processing in Fragile X Syndrome: Psychometric Analysis of the Brain Body Center Sensory Scales (BBCSS).

PubMed

Kolacz, Jacek; Raspa, Melissa; Heilman, Keri J; Porges, Stephen W

2018-06-01

Individuals with fragile X syndrome (FXS), especially those co-diagnosed with autism spectrum disorder (ASD), face many sensory processing challenges. However, sensory processing measures informed by neurophysiology are lacking. This paper describes the development and psychometric properties of a parent/caregiver report, the Brain-Body Center Sensory Scales (BBCSS), based on Polyvagal Theory. Parents/guardians reported on 333 individuals with FXS, 41% with ASD features. Factor structure using a split-sample exploratory-confirmatory design conformed to neurophysiological predictions. Internal consistency, test-retest, and inter-rater reliability were good to excellent. BBCSS subscales converged with the Sensory Profile and Sensory Experiences Questionnaire. However, data also suggest that BBCSS subscales reflect unique features related to sensory processing. Individuals with FXS and ASD features displayed more sensory challenges on most subscales.

Diagnosis of helicopter gearboxes using structure-based networks

NASA Technical Reports Server (NTRS)

Jammu, Vinay B.; Danai, Kourosh; Lewicki, David G.

1995-01-01

A connectionist network is introduced for fault diagnosis of helicopter gearboxes that incorporates knowledge of the gearbox structure and characteristics of the vibration features as its fuzzy weights. Diagnosis is performed by propagating the abnormal features of vibration measurements through this Structure-Based Connectionist Network (SBCN), the outputs of which represent the fault possibility values for individual components of the gearbox. The performance of this network is evaluated by applying it to experimental vibration data from an OH-58A helicopter gearbox. The diagnostic results indicate that the network performance is comparable to those obtained from supervised pattern classification.

Landscape Pattern Determines Neighborhood Size and Structure within a Lizard Population

PubMed Central

Ryberg, Wade A.; Hill, Michael T.; Painter, Charles W.; Fitzgerald, Lee A.

2013-01-01

Although defining population structure according to discrete habitat patches is convenient for metapopulation theories, taking this approach may overlook structure within populations continuously distributed across landscapes. For example, landscape features within habitat patches direct the movement of organisms and define the density distribution of individuals, which can generate spatial structure and localized dynamics within populations as well as among them. Here, we use the neighborhood concept, which describes population structure relative to the scale of individual movements, to illustrate how localized dynamics within a population of lizards (Sceloporus arenicolus) arise in response to variation in landscape pattern within a continuous habitat patch. Our results emphasize links between individual movements at small scales and the emergence of spatial structure within populations which resembles metapopulation dynamics at larger scales. We conclude that population dynamics viewed in a landscape context must consider the explicit distribution and movement of individuals within continuous habitat as well as among habitat patches. PMID:23441217

Multi-centre diagnostic classification of individual structural neuroimaging scans from patients with major depressive disorder.

PubMed

Mwangi, Benson; Ebmeier, Klaus P; Matthews, Keith; Steele, J Douglas

2012-05-01

Quantitative abnormalities of brain structure in patients with major depressive disorder have been reported at a group level for decades. However, these structural differences appear subtle in comparison with conventional radiologically defined abnormalities, with considerable inter-subject variability. Consequently, it has not been possible to readily identify scans from patients with major depressive disorder at an individual level. Recently, machine learning techniques such as relevance vector machines and support vector machines have been applied to predictive classification of individual scans with variable success. Here we describe a novel hybrid method, which combines machine learning with feature selection and characterization, with the latter aimed at maximizing the accuracy of machine learning prediction. The method was tested using a multi-centre dataset of T(1)-weighted 'structural' scans. A total of 62 patients with major depressive disorder and matched controls were recruited from referred secondary care clinical populations in Aberdeen and Edinburgh, UK. The generalization ability and predictive accuracy of the classifiers was tested using data left out of the training process. High prediction accuracy was achieved (~90%). While feature selection was important for maximizing high predictive accuracy with machine learning, feature characterization contributed only a modest improvement to relevance vector machine-based prediction (~5%). Notably, while the only information provided for training the classifiers was T(1)-weighted scans plus a categorical label (major depressive disorder versus controls), both relevance vector machine and support vector machine 'weighting factors' (used for making predictions) correlated strongly with subjective ratings of illness severity. These results indicate that machine learning techniques have the potential to inform clinical practice and research, as they can make accurate predictions about brain scan data from individual subjects. Furthermore, machine learning weighting factors may reflect an objective biomarker of major depressive disorder illness severity, based on abnormalities of brain structure.

Empowering Organizations: Approaches to Tobacco Control through Youth Empowerment Programs

ERIC Educational Resources Information Center

LeRoy, Lisa; Benet, Dana Jones; Mason, Theresa; Austin, W. David; Mills, Sherry

2004-01-01

Whereas most evaluations of youth empowerment focus on individual outcomes (i.e., were individual youths empowered?), this article focuses on the program as the unit of analysis and seeks to explain how organizational structures, program design features, and processes lead to organizational empowerment (OE). OE is defined as organizational efforts…

A sampling-based method for ranking protein structural models by integrating multiple scores and features.

PubMed

Shi, Xiaohu; Zhang, Jingfen; He, Zhiquan; Shang, Yi; Xu, Dong

2011-09-01

One of the major challenges in protein tertiary structure prediction is structure quality assessment. In many cases, protein structure prediction tools generate good structural models, but fail to select the best models from a huge number of candidates as the final output. In this study, we developed a sampling-based machine-learning method to rank protein structural models by integrating multiple scores and features. First, features such as predicted secondary structure, solvent accessibility and residue-residue contact information are integrated by two Radial Basis Function (RBF) models trained from different datasets. Then, the two RBF scores and five selected scoring functions developed by others, i.e., Opus-CA, Opus-PSP, DFIRE, RAPDF, and Cheng Score are synthesized by a sampling method. At last, another integrated RBF model ranks the structural models according to the features of sampling distribution. We tested the proposed method by using two different datasets, including the CASP server prediction models of all CASP8 targets and a set of models generated by our in-house software MUFOLD. The test result shows that our method outperforms any individual scoring function on both best model selection, and overall correlation between the predicted ranking and the actual ranking of structural quality.

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

Heritable Individual-Specific and Allele-Specific Chromatin Signatures in Humans

PubMed Central

McDaniell, Ryan; Lee, Bum-Kyu; Song, Lingyun; Liu, Zheng; Boyle, Alan P.; Erdos, Michael R.; Scott, Laura J.; Morken, Mario A.; Kucera, Katerina S.; Battenhouse, Anna; Keefe, Damian; Collins, Francis S.; Willard, Huntington F.; Lieb, Jason D.; Furey, Terrence S.; Crawford, Gregory E.; Iyer, Vishwanath R.; Birney, Ewan

2010-01-01

The extent to which variation in chromatin structure and transcription factor binding may influence gene expression, and thus underlie or contribute to variation in phenotype, is unknown. To address this question, we cataloged both individual-to-individual variation and differences between homologous chromosomes within the same individual (allele-specific variation) in chromatin structure and transcription factor binding in lymphoblastoid cells derived from individuals of geographically diverse ancestry. Ten percent of active chromatin sites were individual-specific; a similar proportion were allele-specific. Both individual-specific and allele-specific sites were commonly transmitted from parent to child, which suggests that they are heritable features of the human genome. Our study shows that heritable chromatin status and transcription factor binding differ as a result of genetic variation and may underlie phenotypic variation in humans. PMID:20299549

Discriminative latent models for recognizing contextual group activities.

PubMed

Lan, Tian; Wang, Yang; Yang, Weilong; Robinovitch, Stephen N; Mori, Greg

2012-08-01

In this paper, we go beyond recognizing the actions of individuals and focus on group activities. This is motivated from the observation that human actions are rarely performed in isolation; the contextual information of what other people in the scene are doing provides a useful cue for understanding high-level activities. We propose a novel framework for recognizing group activities which jointly captures the group activity, the individual person actions, and the interactions among them. Two types of contextual information, group-person interaction and person-person interaction, are explored in a latent variable framework. In particular, we propose three different approaches to model the person-person interaction. One approach is to explore the structures of person-person interaction. Differently from most of the previous latent structured models, which assume a predefined structure for the hidden layer, e.g., a tree structure, we treat the structure of the hidden layer as a latent variable and implicitly infer it during learning and inference. The second approach explores person-person interaction in the feature level. We introduce a new feature representation called the action context (AC) descriptor. The AC descriptor encodes information about not only the action of an individual person in the video, but also the behavior of other people nearby. The third approach combines the above two. Our experimental results demonstrate the benefit of using contextual information for disambiguating group activities.

Discriminative Latent Models for Recognizing Contextual Group Activities

PubMed Central

Lan, Tian; Wang, Yang; Yang, Weilong; Robinovitch, Stephen N.; Mori, Greg

2012-01-01

In this paper, we go beyond recognizing the actions of individuals and focus on group activities. This is motivated from the observation that human actions are rarely performed in isolation; the contextual information of what other people in the scene are doing provides a useful cue for understanding high-level activities. We propose a novel framework for recognizing group activities which jointly captures the group activity, the individual person actions, and the interactions among them. Two types of contextual information, group-person interaction and person-person interaction, are explored in a latent variable framework. In particular, we propose three different approaches to model the person-person interaction. One approach is to explore the structures of person-person interaction. Differently from most of the previous latent structured models, which assume a predefined structure for the hidden layer, e.g., a tree structure, we treat the structure of the hidden layer as a latent variable and implicitly infer it during learning and inference. The second approach explores person-person interaction in the feature level. We introduce a new feature representation called the action context (AC) descriptor. The AC descriptor encodes information about not only the action of an individual person in the video, but also the behavior of other people nearby. The third approach combines the above two. Our experimental results demonstrate the benefit of using contextual information for disambiguating group activities. PMID:22144516

Life events and borderline personality features: the influence of gene-environment interaction and gene-environment correlation.

PubMed

Distel, M A; Middeldorp, C M; Trull, T J; Derom, C A; Willemsen, G; Boomsma, D I

2011-04-01

Traumatic life events are generally more common in patients with borderline personality disorder (BPD) than in non-patients or patients with other personality disorders. This study investigates whether exposure to life events moderates the genetic architecture of BPD features. As the presence of genotype-environment correlation (rGE) can lead to spurious findings of genotype-environment interaction (G × E), we also test whether BPD features increase the likelihood of exposure to life events. The extent to which an individual is at risk to develop BPD was assessed with the Personality Assessment Inventory - Borderline features scale (PAI-BOR). Life events under study were a divorce/break-up, traffic accident, violent assault, sexual assault, robbery and job loss. Data were available for 5083 twins and 1285 non-twin siblings. Gene-environment interaction and correlation were assessed by using structural equation modelling (SEM) and the co-twin control design. There was evidence for both gene-environment interaction and correlation. Additive genetic influences on BPD features interacted with the exposure to sexual assault, with genetic variance being lower in exposed individuals. In individuals who had experienced a divorce/break-up, violent assault, sexual assault or job loss, environmental variance for BPD features was higher, leading to a lower heritability of BPD features in exposed individuals. Gene-environment correlation was present for some life events. The genes that influence BPD features thus also increased the likelihood of being exposed to certain life events. To our knowledge, this study is the first to test the joint effect of genetic and environmental influences and the exposure to life events on BPD features in the general population. Our results indicate the importance of both genetic vulnerability and life events.

The IVTANTHERMO-Online database for thermodynamic properties of individual substances with web interface

NASA Astrophysics Data System (ADS)

Belov, G. V.; Dyachkov, S. A.; Levashov, P. R.; Lomonosov, I. V.; Minakov, D. V.; Morozov, I. V.; Sineva, M. A.; Smirnov, V. N.

2018-01-01

The database structure, main features and user interface of an IVTANTHERMO-Online system are reviewed. This system continues the series of the IVTANTHERMO packages developed in JIHT RAS. It includes the database for thermodynamic properties of individual substances and related software for analysis of experimental results, data fitting, calculation and estimation of thermodynamical functions and thermochemistry quantities. In contrast to the previous IVTANTHERMO versions it has a new extensible database design, the client-server architecture, a user-friendly web interface with a number of new features for online and offline data processing.

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.

SIRU development. Volume 1: System development

NASA Technical Reports Server (NTRS)

Gilmore, J. P.; Cooper, R. J.

1973-01-01

A complete description of the development and initial evaluation of the Strapdown Inertial Reference Unit (SIRU) system is reported. System development documents the system mechanization with the analytic formulation for fault detection and isolation processing structure; the hardware redundancy design and the individual modularity features; the computational structure and facilities; and the initial subsystem evaluation results.

Encopresis: A Structural/Strategic Approach to Family Therapy.

ERIC Educational Resources Information Center

McColgan, Edgar B.; And Others

1985-01-01

Reports treatment of a 9-year-old boy with primary encopresis combining structural and strategic approaches. Describes organizational features of the family, the contextual approach to therapy, individual and collective responses to therapy, and follow-up at 3 months and 1 1/2 years. Discusses effects of therapy on encopresis and on other…

Document boundary determination using structural and lexical analysis

NASA Astrophysics Data System (ADS)

Taghva, Kazem; Cartright, Marc-Allen

2009-01-01

The document boundary determination problem is the process of identifying individual documents in a stack of papers. In this paper, we report on a classification system for automation of this process. The system employs features based on document structure and lexical content. We also report on experimental results to support the effectiveness of this system.

The relationship between structured and free play in the development of a mentally handicapped child: a case study.

PubMed

Hewson, S; McConkey, R; Jeffree, D

1980-01-01

This case study provides an individual illustration of the work of the Parental Involvement Project. A key feature of the approach used was the structured play situation. Thus, the case study also serves to demonstrate the role of structured play, and its relation to free play, in the development of a young, mentally handicapped child.

Feature engineering for MEDLINE citation categorization with MeSH.

PubMed

Jimeno Yepes, Antonio Jose; Plaza, Laura; Carrillo-de-Albornoz, Jorge; Mork, James G; Aronson, Alan R

2015-04-08

Research in biomedical text categorization has mostly used the bag-of-words representation. Other more sophisticated representations of text based on syntactic, semantic and argumentative properties have been less studied. In this paper, we evaluate the impact of different text representations of biomedical texts as features for reproducing the MeSH annotations of some of the most frequent MeSH headings. In addition to unigrams and bigrams, these features include noun phrases, citation meta-data, citation structure, and semantic annotation of the citations. Traditional features like unigrams and bigrams exhibit strong performance compared to other feature sets. Little or no improvement is obtained when using meta-data or citation structure. Noun phrases are too sparse and thus have lower performance compared to more traditional features. Conceptual annotation of the texts by MetaMap shows similar performance compared to unigrams, but adding concepts from the UMLS taxonomy does not improve the performance of using only mapped concepts. The combination of all the features performs largely better than any individual feature set considered. In addition, this combination improves the performance of a state-of-the-art MeSH indexer. Concerning the machine learning algorithms, we find that those that are more resilient to class imbalance largely obtain better performance. We conclude that even though traditional features such as unigrams and bigrams have strong performance compared to other features, it is possible to combine them to effectively improve the performance of the bag-of-words representation. We have also found that the combination of the learning algorithm and feature sets has an influence in the overall performance of the system. Moreover, using learning algorithms resilient to class imbalance largely improves performance. However, when using a large set of features, consideration needs to be taken with algorithms due to the risk of over-fitting. Specific combinations of learning algorithms and features for individual MeSH headings could further increase the performance of an indexing system.

Behavior and Performance on Long-Duration Spaceflights: Evidence from Analogue Environments

NASA Technical Reports Server (NTRS)

Palinkas, Lawrence A.; Gunderson, E. K. Eric; Johnson, Jeffrey C.; Holland, Albert W.

1999-01-01

Analyses of data collected in Antarctica since 1963 were conducted to identify features of behavior and performance likely to occur during long-duration missions in space.The influence of mission duration and station latitude on POMS mood scores was examined in 450 American men and women who overwintered in Antarctica between 1991 and 1998. The influence of crewmember social characteristics, personality traits, interpersonal needs, and station environments on measures of behavior and performance at the end of the austral winter was examined in 657 American men who overwintered between 1963 and 1974. Both data sets were used to examine the influence of crew social structure on individual performance. Results: Seasonal variations in mood appear to be associated with the altered diurnal cycle and psychological segmentation of the mission. Concurrent measures of personality, interpersonal needs, and coping styles are better predictors of depressed mood and peer-supervisor performance evaluations than baseline measures because of the unique features of the station social and physical environments and the absence of resources typically used to cope with stress elsewhere. Individuals in crews with a clique structure report significantly more depression, anxiety, anger, fatigue and confusion than individuals in crews with a core-periphery structure. Depressed mood is inversely associated with severity of station physical environment, supporting the existence of a positive or "salutogenic" effect for individuals seeking challenging experiences in extreme environments.

[Neighborhood environment quality, individual-level social capital, and depressive symptoms among adolescents].

PubMed

Asakura, Takashi

2011-09-01

We aimed to develop measures to assess features of neighborhood quality and individual social capital, as well as their associations with depressive symptoms among early adolescents. To determine whether relations of depressive symptoms with neighborhood quality might be contingent upon the level of individual cognitive social capital, neighborhood-by-cognitive social capital interaction terms were examined. A qualitative study was conducted to elicit the perceptions of early adolescents about their neighborhood environment. Subsequently, we recruited 2,002 eighth graders and asked for responses to a self-administered questionnaire. The variables analyzed in this study were the Center for Epidemiologic Studies-Depression scale (10 items), features of neighborhood quality, cognitive and structural individual social capital, and demographics. We adopted a generalized estimating equation regression model for the multivariate analysis. The analytic sample was 1,786 with no missing variable in the models. Seven subscales were devised to assess quality features of neighborhood environments with an examination of validity and reliability: "availability of services," "good neighborhood relations," "spaces for recreation," "insecurity and danger of accidents," "dirty-looking, squalid, unclean," "civic communities," and "aesthetic look." We also developed a scale of individual cognitive social capital, which consisted of three constructs: "social trust," "reciprocity," and "social norms." Additionally, the number of social activities in which subjects participated was counted as an indicator of the structural aspect of individual social capital. On examination with the generalized estimating equation regression model, "availability of services," "insecurity and danger of accidents," "dirty-looking, squalid, unclean," and cognitive social capital were significantly associated with the CES-D scores controlling for demographics. We also found a significant interplay between "dirty-looking, squalid, unclean" and the cognitive social capital for estimating scores of depressive symptoms. Improvement in features of neighborhood quality such as availability of services, cleanliness, and security and social order in terms of public policy as well as civic activities could contribute to promotion of mental health in adolescents. Individual cognitive social capital accumulated through experiencs of good social relationshisp in a community could also play important roles in maximizing mental health.

Detailed electromagnetic simulation for the structural color of butterfly wings.

PubMed

Lee, R Todd; Smith, Glenn S

2009-07-20

Many species of butterflies exhibit interesting optical phenomena due to structural color. The physical reason for this color is subwavelength features on the surface of a single scale. The exposed surface of a scale is covered with a ridge structure. The fully three-dimensional, periodic, finite-difference time-domain method is used to create a detailed electromagnetic model of a generic ridge. A novel method for presenting the three-dimensional observed color pattern is developed. Using these tools, the change in color that is a result of varying individual features of the scale is explored. Computational models are developed that are similar to three butterflies: Morpho rhetenor, Troides magellanus, and Ancyluris meliboeus.

Clustered marginalization of minorities during social transitions induced by co-evolution of behaviour and network structure

NASA Astrophysics Data System (ADS)

Schleussner, Carl-Friedrich; Donges, Jonathan F.; Engemann, Denis A.; Levermann, Anders

2016-08-01

Large-scale transitions in societies are associated with both individual behavioural change and restructuring of the social network. These two factors have often been considered independently, yet recent advances in social network research challenge this view. Here we show that common features of societal marginalization and clustering emerge naturally during transitions in a co-evolutionary adaptive network model. This is achieved by explicitly considering the interplay between individual interaction and a dynamic network structure in behavioural selection. We exemplify this mechanism by simulating how smoking behaviour and the network structure get reconfigured by changing social norms. Our results are consistent with empirical findings: The prevalence of smoking was reduced, remaining smokers were preferentially connected among each other and formed increasingly marginalized clusters. We propose that self-amplifying feedbacks between individual behaviour and dynamic restructuring of the network are main drivers of the transition. This generative mechanism for co-evolution of individual behaviour and social network structure may apply to a wide range of examples beyond smoking.

Clustered marginalization of minorities during social transitions induced by co-evolution of behaviour and network structure.

PubMed

Schleussner, Carl-Friedrich; Donges, Jonathan F; Engemann, Denis A; Levermann, Anders

2016-08-11

Large-scale transitions in societies are associated with both individual behavioural change and restructuring of the social network. These two factors have often been considered independently, yet recent advances in social network research challenge this view. Here we show that common features of societal marginalization and clustering emerge naturally during transitions in a co-evolutionary adaptive network model. This is achieved by explicitly considering the interplay between individual interaction and a dynamic network structure in behavioural selection. We exemplify this mechanism by simulating how smoking behaviour and the network structure get reconfigured by changing social norms. Our results are consistent with empirical findings: The prevalence of smoking was reduced, remaining smokers were preferentially connected among each other and formed increasingly marginalized clusters. We propose that self-amplifying feedbacks between individual behaviour and dynamic restructuring of the network are main drivers of the transition. This generative mechanism for co-evolution of individual behaviour and social network structure may apply to a wide range of examples beyond smoking.

The Effects of Individual Differences on Learner's Navigation in a Courseware

ERIC Educational Resources Information Center

Somyürek, Sibel; Güyer, Tolga; Atasoy, Bilal

2008-01-01

One of the major features of a computer based instruction (CBI) is its non-linear structure allowing learners the opportunity of flexible navigation to accommodate their own needs. However, this non-linear structure may cause problems such as inefficient navigation, being lost or cognitive overhead for some learners. The aim of this study is to…

New Approach to Synthesis of Powder and Composite Materials by Electron Beam. Part 1. Technological Features of the Process

NASA Astrophysics Data System (ADS)

Rudskoy, A. I.; Kondrat'ev, S. Yu.; Sokolov, Yu. A.

2016-05-01

Possibilities of electron beam synthesis of structural and tool composite materials are considered. It is shown that a novel process involving mathematical modeling of each individual operation makes it possible to create materials with programmable structure and predictable properties from granules of various specified chemical compositions and sizes.

Visualizing spatial correlation: structural and electronic orders in iron-based superconductors on atomic scale

NASA Astrophysics Data System (ADS)

Maksov, Artem; Ziatdinov, Maxim; Li, Li; Sefat, Athena; Maksymovych, Petro; Kalinin, Sergei

Crystalline matter on the nanoscale level often exhibits strongly inhomogeneous structural and electronic orders, which have a profound effect on macroscopic properties. This may be caused by subtle interplay between chemical disorder, strain, magnetic, and structural order parameters. We present a novel approach based on combination of high resolution scanning tunneling microscopy/spectroscopy (STM/S) and deep data style analysis for automatic separation, extraction, and correlation of structural and electronic behavior which might lead us to uncovering the underlying sources of inhomogeneity in in iron-based family of superconductors (FeSe, BaFe2As2) . We identify STS spectral features using physically robust Bayesian linear unmixing, and show their direct relevance to the fundamental physical properties of the system, including electronic states associated with individual defects and impurities. We collect structural data from individual unit cells on the crystalline lattice, and calculate both global and local indicators of spatial correlation with electronic features, demonstrating, for the first time, a direct quantifiable connection between observed structural order parameters extracted from the STM data and electronic order parameters identified within the STS data. This research was sponsored by the Division of Materials Sciences and Engineering, Office of Science, Basic Energy Sciences, US DOE.

Support-vector-machine tree-based domain knowledge learning toward automated sports video classification

NASA Astrophysics Data System (ADS)

Xiao, Guoqiang; Jiang, Yang; Song, Gang; Jiang, Jianmin

2010-12-01

We propose a support-vector-machine (SVM) tree to hierarchically learn from domain knowledge represented by low-level features toward automatic classification of sports videos. The proposed SVM tree adopts a binary tree structure to exploit the nature of SVM's binary classification, where each internal node is a single SVM learning unit, and each external node represents the classified output type. Such a SVM tree presents a number of advantages, which include: 1. low computing cost; 2. integrated learning and classification while preserving individual SVM's learning strength; and 3. flexibility in both structure and learning modules, where different numbers of nodes and features can be added to address specific learning requirements, and various learning models can be added as individual nodes, such as neural networks, AdaBoost, hidden Markov models, dynamic Bayesian networks, etc. Experiments support that the proposed SVM tree achieves good performances in sports video classifications.

Including pride and its group-based, relational, and contextual features in theories of contempt.

PubMed

Sullivan, Gavin Brent

2017-01-01

Sentiment includes emotional and enduring attitudinal features of contempt, but explaining contempt as a mixture of basic emotion system affects does not adequately address the family resemblance structure of the concept. Adding forms of individual, group-based, and widely shared arrogance and contempt is necessary to capture the complex mixed feelings of proud superiority when "looking down upon" and acting harshly towards others.

ASTROS Enhancements. Volume I- ASTRO User’s Manual

DTIC Science & Technology

1993-03-01

alternative functions. The mechanisms by which these more advanced features are invoked are included in this manual but no attempt is made to provide... advanced topics are treated in the Programmer’s and Application Manuals which document the individual modules in the system and their interactions...of the more advanced features of the system without cluttering the discussion with details of the input structures. The detailed documentation of the

WONKA: objective novel complex analysis for ensembles of protein-ligand structures.

PubMed

Bradley, A R; Wall, I D; von Delft, F; Green, D V S; Deane, C M; Marsden, B D

2015-10-01

WONKA is a tool for the systematic analysis of an ensemble of protein-ligand structures. It makes the identification of conserved and unusual features within such an ensemble straightforward. WONKA uses an intuitive workflow to process structural co-ordinates. Ligand and protein features are summarised and then presented within an interactive web application. WONKA's power in consolidating and summarising large amounts of data is described through the analysis of three bromodomain datasets. Furthermore, and in contrast to many current methods, WONKA relates analysis to individual ligands, from which we find unusual and erroneous binding modes. Finally the use of WONKA as an annotation tool to share observations about structures is demonstrated. WONKA is freely available to download and install locally or can be used online at http://wonka.sgc.ox.ac.uk.

Computer ranking of the sequence of appearance of 73 features of the brain and related structures in staged human embryos during the sixth week of development.

PubMed

O'Rahilly, R; Müller, F; Hutchins, G M; Moore, G W

1987-09-01

The sequence of events in the development of the brain in human embryos, already published for stages 8-15, is here continued for stages 16 and 17. With the aid of a computerized bubble-sort algorithm, 71 individual embryos were ranked in ascending order of the features present. Whereas these numbered 100 in the previous study, the increasing structural complexity gave 27 new features in the two stages now under investigation. The chief characteristics of stage 16 (approximately 37 postovulatory days) are protruding basal nuclei, the caudal olfactory elevation (olfactory tubercle), the tectobulbar tracts, and ascending fibers to the cerebellum. The main features of stage 17 (approximately 41 postovulatory days) are the cortical nucleus of the amygdaloid body, an intermediate layer in the tectum mesencephali, the posterior commissure, and the habenulo-interpeduncular tract. In addition, a typical feature at stage 17 is the crescentic shape of the lens cavity.

Human action recognition with group lasso regularized-support vector machine

NASA Astrophysics Data System (ADS)

Luo, Huiwu; Lu, Huanzhang; Wu, Yabei; Zhao, Fei

2016-05-01

The bag-of-visual-words (BOVW) and Fisher kernel are two popular models in human action recognition, and support vector machine (SVM) is the most commonly used classifier for the two models. We show two kinds of group structures in the feature representation constructed by BOVW and Fisher kernel, respectively, since the structural information of feature representation can be seen as a prior for the classifier and can improve the performance of the classifier, which has been verified in several areas. However, the standard SVM employs L2-norm regularization in its learning procedure, which penalizes each variable individually and cannot express the structural information of feature representation. We replace the L2-norm regularization with group lasso regularization in standard SVM, and a group lasso regularized-support vector machine (GLRSVM) is proposed. Then, we embed the group structural information of feature representation into GLRSVM. Finally, we introduce an algorithm to solve the optimization problem of GLRSVM by alternating directions method of multipliers. The experiments evaluated on KTH, YouTube, and Hollywood2 datasets show that our method achieves promising results and improves the state-of-the-art methods on KTH and YouTube datasets.

Ecological forestry in an uneven-aged, late-successional forest: Simulated effects of contrasting treatments on structure and yield

Treesearch

Jacob J. Hanson; Craig G. Lorimer; Corey R. Halpin; Brian J. Palik

2012-01-01

Ecological forestry practices are designed to retain species and structural features important for maintaining ecosystem function but which may be deficient in conventionally managed stands. We used the spatially-explicit, individual tree model CANOPY to assess tradeoffs in enhanced ecological attributes vs. reductions in timber yield for a wide variety of treatments...

Iris-based medical analysis by geometric deformation features.

PubMed

Ma, Lin; Zhang, D; Li, Naimin; Cai, Yan; Zuo, Wangmeng; Wang, Kuanguan

2013-01-01

Iris analysis studies the relationship between human health and changes in the anatomy of the iris. Apart from the fact that iris recognition focuses on modeling the overall structure of the iris, iris diagnosis emphasizes the detecting and analyzing of local variations in the characteristics of irises. This paper focuses on studying the geometrical structure changes in irises that are caused by gastrointestinal diseases, and on measuring the observable deformations in the geometrical structures of irises that are related to roundness, diameter and other geometric forms of the pupil and the collarette. Pupil and collarette based features are defined and extracted. A series of experiments are implemented on our experimental pathological iris database, including manual clustering of both normal and pathological iris images, manual classification by non-specialists, manual classification by individuals with a medical background, classification ability verification for the proposed features, and disease recognition by applying the proposed features. The results prove the effectiveness and clinical diagnostic significance of the proposed features and a reliable recognition performance for automatic disease diagnosis. Our research results offer a novel systematic perspective for iridology studies and promote the progress of both theoretical and practical work in iris diagnosis.

GATOR: Requirements capturing of telephony features

NASA Technical Reports Server (NTRS)

Dankel, Douglas D., II; Walker, Wayne; Schmalz, Mark

1992-01-01

We are developing a natural language-based, requirements gathering system called GATOR (for the GATherer Of Requirements). GATOR assists in the development of more accurate and complete specifications of new telephony features. GATOR interacts with a feature designer who describes a new feature, set of features, or capability to be implemented. The system aids this individual in the specification process by asking for clarifications when potential ambiguities are present, by identifying potential conflicts with other existing features, and by presenting its understanding of the feature to the designer. Through user interaction with a model of the existing telephony feature set, GATOR constructs a formal representation of the new, 'to be implemented' feature. Ultimately GATOR will produce a requirements document and will maintain an internal representation of this feature to aid in future design and specification. This paper consists of three sections that describe (1) the structure of GATOR, (2) POND, GATOR's internal knowledge representation language, and (3) current research issues.

EEG resolutions in detecting and decoding finger movements from spectral analysis

PubMed Central

Xiao, Ran; Ding, Lei

2015-01-01

Mu/beta rhythms are well-studied brain activities that originate from sensorimotor cortices. These rhythms reveal spectral changes in alpha and beta bands induced by movements of different body parts, e.g., hands and limbs, in electroencephalography (EEG) signals. However, less can be revealed in them about movements of different fine body parts that activate adjacent brain regions, such as individual fingers from one hand. Several studies have reported spatial and temporal couplings of rhythmic activities at different frequency bands, suggesting the existence of well-defined spectral structures across multiple frequency bands. In the present study, spectral principal component analysis (PCA) was applied on EEG data, obtained from a finger movement task, to identify cross-frequency spectral structures. Features from identified spectral structures were examined in their spatial patterns, cross-condition pattern changes, detection capability of finger movements from resting, and decoding performance of individual finger movements in comparison to classic mu/beta rhythms. These new features reveal some similar, but more different spatial and spectral patterns as compared with classic mu/beta rhythms. Decoding results further indicate that these new features (91%) can detect finger movements much better than classic mu/beta rhythms (75.6%). More importantly, these new features reveal discriminative information about movements of different fingers (fine body-part movements), which is not available in classic mu/beta rhythms. The capability in decoding fingers (and hand gestures in the future) from EEG will contribute significantly to the development of non-invasive BCI and neuroprosthesis with intuitive and flexible controls. PMID:26388720

Effects of dynamic text in an AAC app on sight word reading for individuals with autism spectrum disorder.

PubMed

Caron, Jessica; Light, Janice; Holyfield, Christine; McNaughton, David

2018-06-01

The purpose of this study was to investigate the effects of Transition to Literacy (T2L) software features (i.e., dynamic text and speech output upon selection of a graphic symbol) within a grid display in an augmentative and alternative communication (AAC) app, on the sight word reading skills of individuals with autism spectrum disorders (ASD) and complex communication needs. The study implemented a single-subject multiple probe research design across one set of three participants. The same design was utilized with an additional set of two participants. As part of the intervention, the participants were exposed to an AAC app with the T2L features during a highly structured matching task. With only limited exposure to the features, the five participants all demonstrated increased accuracy of identification of 12 targeted sight words. This study provides preliminary evidence that redesigning AAC apps to include the provision of dynamic text combined with speech output, can positively impact the sight-word reading of participants during a structured task. This adaptation in AAC system design could be used to complement literacy instruction and to potentially infuse components of literacy learning into daily communication.

Clustered marginalization of minorities during social transitions induced by co-evolution of behaviour and network structure

PubMed Central

Schleussner, Carl-Friedrich; Donges, Jonathan F.; Engemann, Denis A.; Levermann, Anders

2016-01-01

Large-scale transitions in societies are associated with both individual behavioural change and restructuring of the social network. These two factors have often been considered independently, yet recent advances in social network research challenge this view. Here we show that common features of societal marginalization and clustering emerge naturally during transitions in a co-evolutionary adaptive network model. This is achieved by explicitly considering the interplay between individual interaction and a dynamic network structure in behavioural selection. We exemplify this mechanism by simulating how smoking behaviour and the network structure get reconfigured by changing social norms. Our results are consistent with empirical findings: The prevalence of smoking was reduced, remaining smokers were preferentially connected among each other and formed increasingly marginalized clusters. We propose that self-amplifying feedbacks between individual behaviour and dynamic restructuring of the network are main drivers of the transition. This generative mechanism for co-evolution of individual behaviour and social network structure may apply to a wide range of examples beyond smoking. PMID:27510641

Control-group feature normalization for multivariate pattern analysis of structural MRI data using the support vector machine.

PubMed

Linn, Kristin A; Gaonkar, Bilwaj; Satterthwaite, Theodore D; Doshi, Jimit; Davatzikos, Christos; Shinohara, Russell T

2016-05-15

Normalization of feature vector values is a common practice in machine learning. Generally, each feature value is standardized to the unit hypercube or by normalizing to zero mean and unit variance. Classification decisions based on support vector machines (SVMs) or by other methods are sensitive to the specific normalization used on the features. In the context of multivariate pattern analysis using neuroimaging data, standardization effectively up- and down-weights features based on their individual variability. Since the standard approach uses the entire data set to guide the normalization, it utilizes the total variability of these features. This total variation is inevitably dependent on the amount of marginal separation between groups. Thus, such a normalization may attenuate the separability of the data in high dimensional space. In this work we propose an alternate approach that uses an estimate of the control-group standard deviation to normalize features before training. We study our proposed approach in the context of group classification using structural MRI data. We show that control-based normalization leads to better reproducibility of estimated multivariate disease patterns and improves the classifier performance in many cases. Copyright © 2016 Elsevier Inc. All rights reserved.

Development of a brain MRI-based hidden Markov model for dementia recognition.

PubMed

Chen, Ying; Pham, Tuan D

2013-01-01

Dementia is an age-related cognitive decline which is indicated by an early degeneration of cortical and sub-cortical structures. Characterizing those morphological changes can help to understand the disease development and contribute to disease early prediction and prevention. But modeling that can best capture brain structural variability and can be valid in both disease classification and interpretation is extremely challenging. The current study aimed to establish a computational approach for modeling the magnetic resonance imaging (MRI)-based structural complexity of the brain using the framework of hidden Markov models (HMMs) for dementia recognition. Regularity dimension and semi-variogram were used to extract structural features of the brains, and vector quantization method was applied to convert extracted feature vectors to prototype vectors. The output VQ indices were then utilized to estimate parameters for HMMs. To validate its accuracy and robustness, experiments were carried out on individuals who were characterized as non-demented and mild Alzheimer's diseased. Four HMMs were constructed based on the cohort of non-demented young, middle-aged, elder and demented elder subjects separately. Classification was carried out using a data set including both non-demented and demented individuals with a wide age range. The proposed HMMs have succeeded in recognition of individual who has mild Alzheimer's disease and achieved a better classification accuracy compared to other related works using different classifiers. Results have shown the ability of the proposed modeling for recognition of early dementia. The findings from this research will allow individual classification to support the early diagnosis and prediction of dementia. By using the brain MRI-based HMMs developed in our proposed research, it will be more efficient, robust and can be easily used by clinicians as a computer-aid tool for validating imaging bio-markers for early prediction of dementia.

Modular and hierarchical structure of social contact networks

NASA Astrophysics Data System (ADS)

Ge, Yuanzheng; Song, Zhichao; Qiu, Xiaogang; Song, Hongbin; Wang, Yong

2013-10-01

Social contact networks exhibit overlapping qualities of communities, hierarchical structure and spatial-correlated nature. We propose a mixing pattern of modular and growing hierarchical structures to reconstruct social contact networks by using an individual’s geospatial distribution information in the real world. The hierarchical structure of social contact networks is defined based on the spatial distance between individuals, and edges among individuals are added in turn from the modular layer to the highest layer. It is a gradual process to construct the hierarchical structure: from the basic modular model up to the global network. The proposed model not only shows hierarchically increasing degree distribution and large clustering coefficients in communities, but also exhibits spatial clustering features of individual distributions. As an evaluation of the method, we reconstruct a hierarchical contact network based on the investigation data of a university. Transmission experiments of influenza H1N1 are carried out on the generated social contact networks, and results show that the constructed network is efficient to reproduce the dynamic process of an outbreak and evaluate interventions. The reproduced spread process exhibits that the spatial clustering of infection is accordant with the clustering of network topology. Moreover, the effect of individual topological character on the spread of influenza is analyzed, and the experiment results indicate that the spread is limited by individual daily contact patterns and local clustering topology rather than individual degree.

Implicit Learning of Recursive Context-Free Grammars

PubMed Central

Rohrmeier, Martin; Fu, Qiufang; Dienes, Zoltan

2012-01-01

Context-free grammars are fundamental for the description of linguistic syntax. However, most artificial grammar learning experiments have explored learning of simpler finite-state grammars, while studies exploring context-free grammars have not assessed awareness and implicitness. This paper explores the implicit learning of context-free grammars employing features of hierarchical organization, recursive embedding and long-distance dependencies. The grammars also featured the distinction between left- and right-branching structures, as well as between centre- and tail-embedding, both distinctions found in natural languages. People acquired unconscious knowledge of relations between grammatical classes even for dependencies over long distances, in ways that went beyond learning simpler relations (e.g. n-grams) between individual words. The structural distinctions drawn from linguistics also proved important as performance was greater for tail-embedding than centre-embedding structures. The results suggest the plausibility of implicit learning of complex context-free structures, which model some features of natural languages. They support the relevance of artificial grammar learning for probing mechanisms of language learning and challenge existing theories and computational models of implicit learning. PMID:23094021

When intensions do not map onto extensions: Individual differences in conceptualization.

PubMed

Hampton, James A; Passanisi, Alessia

2016-04-01

Concepts are represented in the mind through knowledge of their extensions (the class of items to which the concept applies) and intensions (features that distinguish that class of items). A common assumption among theories of concepts is that the 2 aspects are intimately related. Hence if there is systematic individual variation in concept representation, the variation should correlate between extensional and intensional measures. A pair of individuals with similar extensional beliefs about a given concept should also share similar intensional beliefs. To test this notion, exemplars (extensions) and features (intensions) of common categories were rated for typicality and importance respectively across 2 occasions. Within-subject consistency was greater than between-subjects consensus on each task, providing evidence for systematic individual variation. Furthermore, the similarity structure between individuals for each task was stable across occasions. However, across 5 samples, similarity between individuals for extensional judgments did not map onto similarity between individuals for intensional judgments. The results challenge the assumption common to many theories of conceptual representation that intensions determine extensions and support a hybrid view of concepts where there is a disconnection between the conceptual resources that are used for the 2 tasks. (c) 2016 APA, all rights reserved).

Comparative analysis of feature extraction methods in satellite imagery

NASA Astrophysics Data System (ADS)

Karim, Shahid; Zhang, Ye; Asif, Muhammad Rizwan; Ali, Saad

2017-10-01

Feature extraction techniques are extensively being used in satellite imagery and getting impressive attention for remote sensing applications. The state-of-the-art feature extraction methods are appropriate according to the categories and structures of the objects to be detected. Based on distinctive computations of each feature extraction method, different types of images are selected to evaluate the performance of the methods, such as binary robust invariant scalable keypoints (BRISK), scale-invariant feature transform, speeded-up robust features (SURF), features from accelerated segment test (FAST), histogram of oriented gradients, and local binary patterns. Total computational time is calculated to evaluate the speed of each feature extraction method. The extracted features are counted under shadow regions and preprocessed shadow regions to compare the functioning of each method. We have studied the combination of SURF with FAST and BRISK individually and found very promising results with an increased number of features and less computational time. Finally, feature matching is conferred for all methods.

Discrimination of artificial categories structured by family resemblances: a comparative study in people (Homo sapiens) and pigeons (Columba livia).

PubMed

Makino, Hiroshi; Jitsumori, Masako

2007-02-01

Adult humans (Homo sapiens) and pigeons (Columba livia) were trained to discriminate artificial categories that the authors created by mimicking 2 properties of natural categories. One was a family resemblance relationship: The highly variable exemplars, including those that did not have features in common, were structured by a similarity network with the features correlating to one another in each category. The other was a polymorphous rule: No single feature was essential for distinguishing the categories, and all the features overlapped between the categories. Pigeons learned the categories with ease and then showed a prototype effect in accord with the degrees of family resemblance for novel stimuli. Some evidence was also observed for interactive effects of learning of individual exemplars and feature frequencies. Humans had difficulty in learning the categories. The participants who learned the categories generally responded to novel stimuli in an all-or-none fashion on the basis of their acquired classification decision rules. The processes that underlie the classification performances of the 2 species are discussed.

Theoretical and experimental analysis of the structural pattern responsible for the iridescence of Morpho butterflies.

PubMed

Siddique, Radwanul Hasan; Diewald, Silvia; Leuthold, Juerg; Hölscher, Hendrik

2013-06-17

Morpho butterflies are well-known for their iridescence originating from nanostructures in the scales of their wings. These optical active structures integrate three design principles leading to the wide angle reflection: alternating lamellae layers, "Christmas tree" like shape, and offsets between neighboring ridges. We study their individual effects rigorously by 2D FEM simulations of the nanostructures of the Morpho sulkowskyi butterfly and show how the reflection spectrum can be controlled by the design of the nanostructures. The width of the spectrum is broad (≈ 90 nm) for alternating lamellae layers (or "brunches") of the structure while the "Christmas tree" pattern together with a height offset between neighboring ridges reduces the directionality of the reflectance. Furthermore, we fabricated the simulated structures by e-beam lithography. The resulting samples mimicked all important optical features of the original Morpho butterfly scales and feature the intense blue iridescence with a wide angular range of reflection.

Analysis of macrolinguistic aspects of narratives from individuals with Alzheimer's disease, mild cognitive impairment, and no cognitive impairment.

PubMed

Toledo, Cíntia Matsuda; Aluísio, Sandra Maria; Dos Santos, Leandro Borges; Brucki, Sonia Maria Dozzi; Trés, Eduardo Sturzeneker; de Oliveira, Maira Okada; Mansur, Letícia Lessa

2018-01-01

The depiction of features in discourse production promotes accurate diagnosis and helps to establish the therapeutic intervention in cognitive impairment and dementia. We aimed to identify alterations in the macrolinguistic aspects of discourse using a new computational tool. Sixty individuals, aged 60 years and older, were distributed in three different groups: mild Alzheimer's disease (mAD), amnestic mild cognitive impairment, and healthy controls. A narrative created by individuals was analyzed through the Coh-Metrix-Dementia program, extracting the features of interest automatically. mAD showed worse overall performance compared to the other groups: less informative discourse, greater impairment in global coherence, greater modalization, and inferior narrative structure. It was not possible to discriminate between amnestic mild cognitive impairment and healthy controls. Our results are in line with the literature, verifying a pathological change in the macrostructure of discourse in mAD.

Structural diversity requires individual optimization of ethanol concentration in polysaccharide precipitation.

PubMed

Xu, Jun; Yue, Rui-Qi; Liu, Jing; Ho, Hing-Man; Yi, Tao; Chen, Hu-Biao; Han, Quan-Bin

2014-06-01

Ethanol precipitation is one of the most widely used methods for preparing natural polysaccharides, in which ethanol concentration significantly affects the precipitate yield, however, is usually set at 70-80%. Whether the standardization of ethanol concentration is appropriate has not been investigated. In the present study, the precipitation yields produced in varied ethanol concentrations (10-90%) were qualitatively and quantitatively evaluated by HPGPC (high-performance gel-permeation chromatography), using two series of standard glucans, namely dextrans and pullulans, as reference samples, and then eight natural samples. The results indicated that the response of a polysaccharide's chemical structure, with diversity in structural features and molecular sizes, to ethanol concentration is the decisive factor in precipitation of these glucans. Polysaccharides with different structural features, even though they have similar molecular weights, exhibit significantly different precipitation behaviors. For a specific glucan, the lower its molecular size, the higher the ethanol concentration needed for complete precipitation. The precipitate yield varied from 10% to 100% in 80% ethanol as the molecular size increased from 1kDa to 270kDa. This paper aims to draw scientists' attention to the fact that, in extracting natural polysaccharides by ethanol precipitation, the ethanol concentration must be individually optimized for each type of material. Copyright © 2014 Elsevier B.V. All rights reserved.

Structural power and the evolution of collective fairness in social networks.

PubMed

Santos, Fernando P; Pacheco, Jorge M; Paiva, Ana; Santos, Francisco C

2017-01-01

From work contracts and group buying platforms to political coalitions and international climate and economical summits, often individuals assemble in groups that must collectively reach decisions that may favor each part unequally. Here we quantify to which extent our network ties promote the evolution of collective fairness in group interactions, modeled by means of Multiplayer Ultimatum Games (MUG). We show that a single topological feature of social networks-which we call structural power-has a profound impact on the tendency of individuals to take decisions that favor each part equally. Increased fair outcomes are attained whenever structural power is high, such that the networks that tie individuals allow them to meet the same partners in different groups, thus providing the opportunity to strongly influence each other. On the other hand, the absence of such close peer-influence relationships dismisses any positive effect created by the network. Interestingly, we show that increasing the structural power of a network leads to the appearance of well-defined modules-as found in human social networks that often exhibit community structure-providing an interaction environment that maximizes collective fairness.

Bacterial chemoreceptors: high-performance signaling in networked arrays.

PubMed

Hazelbauer, Gerald L; Falke, Joseph J; Parkinson, John S

2008-01-01

Chemoreceptors are crucial components in the bacterial sensory systems that mediate chemotaxis. Chemotactic responses exhibit exquisite sensitivity, extensive dynamic range and precise adaptation. The mechanisms that mediate these high-performance functions involve not only actions of individual proteins but also interactions among clusters of components, localized in extensive patches of thousands of molecules. Recently, these patches have been imaged in native cells, important features of chemoreceptor structure and on-off switching have been identified, and new insights have been gained into the structural basis and functional consequences of higher order interactions among sensory components. These new data suggest multiple levels of molecular interactions, each of which contribute specific functional features and together create a sophisticated signaling device.

Bacterial chemoreceptors: high-performance signaling in networked arrays

PubMed Central

Hazelbauer, Gerald L.; Falke, Joseph J.; Parkinson, John S.

2010-01-01

Chemoreceptors are crucial components in the bacterial sensory systems that mediate chemotaxis. Chemotactic responses exhibit exquisite sensitivity, extensive dynamic range and precise adaptation. The mechanisms that mediate these high-performance functions involve not only actions of individual proteins but also interactions among clusters of components, localized in extensive patches of thousands of molecules. Recently, these patches have been imaged in native cells, important features of chemoreceptor structure and on–off switching have been identified, and new insights have been gained into the structural basis and functional consequences of higher order interactions among sensory components. These new data suggest multiple levels of molecular interactions, each of which contribute specific functional features and together create a sophisticated signaling device. PMID:18165013

A multimodal biometric authentication system based on 2D and 3D palmprint features

NASA Astrophysics Data System (ADS)

Aggithaya, Vivek K.; Zhang, David; Luo, Nan

2008-03-01

This paper presents a new personal authentication system that simultaneously exploits 2D and 3D palmprint features. Here, we aim to improve the accuracy and robustness of existing palmprint authentication systems using 3D palmprint features. The proposed system uses an active stereo technique, structured light, to capture 3D image or range data of the palm and a registered intensity image simultaneously. The surface curvature based method is employed to extract features from 3D palmprint and Gabor feature based competitive coding scheme is used for 2D representation. We individually analyze these representations and attempt to combine them with score level fusion technique. Our experiments on a database of 108 subjects achieve significant improvement in performance (Equal Error Rate) with the integration of 3D features as compared to the case when 2D palmprint features alone are employed.

Stories in Conversation.

ERIC Educational Resources Information Center

Hofer, Roberta Senner

Although conversational stories within one individual's corpus share the same structure, they have features that set them apart from one another. Based on the stories' general characteristics and the way they function in ongoing talk, they can be identified as: (1) durable personal experience narratives (PENs), which are often repeated during the…

Group Therapy Techniques for Sexually Abused Preteen Girls.

ERIC Educational Resources Information Center

Berman, Pearl

1990-01-01

Describes an open-ended, structured, highly intensive therapy group for sexually abused preteen girls that was the primary mode of treatment for 11 girls from low-income, rural White families with numerous problems. Unique features of the group included simultaneous group and individualized goals. (Author/BB)

Race and Residential Mobility: Individual Determinants and Structural Constraints.

ERIC Educational Resources Information Center

South, Scott J.; Deane, Glenn D.

1993-01-01

In 1979-80, residential mobility was lower among African Americans than non-African Americans after adjusting for differences in home ownership and sociodemographic characteristics. Both African-American and non-African-American mobility were influenced by life-cycle factors, housing characteristics, and metropolitan features, but African-American…

Discriminative analysis of schizophrenia using support vector machine and recursive feature elimination on structural MRI images.

PubMed

Lu, Xiaobing; Yang, Yongzhe; Wu, Fengchun; Gao, Minjian; Xu, Yong; Zhang, Yue; Yao, Yongcheng; Du, Xin; Li, Chengwei; Wu, Lei; Zhong, Xiaomei; Zhou, Yanling; Fan, Ni; Zheng, Yingjun; Xiong, Dongsheng; Peng, Hongjun; Escudero, Javier; Huang, Biao; Li, Xiaobo; Ning, Yuping; Wu, Kai

2016-07-01

Structural abnormalities in schizophrenia (SZ) patients have been well documented with structural magnetic resonance imaging (MRI) data using voxel-based morphometry (VBM) and region of interest (ROI) analyses. However, these analyses can only detect group-wise differences and thus, have a poor predictive value for individuals. In the present study, we applied a machine learning method that combined support vector machine (SVM) with recursive feature elimination (RFE) to discriminate SZ patients from normal controls (NCs) using their structural MRI data. We first employed both VBM and ROI analyses to compare gray matter volume (GMV) and white matter volume (WMV) between 41 SZ patients and 42 age- and sex-matched NCs. The method of SVM combined with RFE was used to discriminate SZ patients from NCs using significant between-group differences in both GMV and WMV as input features. We found that SZ patients showed GM and WM abnormalities in several brain structures primarily involved in the emotion, memory, and visual systems. An SVM with a RFE classifier using the significant structural abnormalities identified by the VBM analysis as input features achieved the best performance (an accuracy of 88.4%, a sensitivity of 91.9%, and a specificity of 84.4%) in the discriminative analyses of SZ patients. These results suggested that distinct neuroanatomical profiles associated with SZ patients might provide a potential biomarker for disease diagnosis, and machine-learning methods can reveal neurobiological mechanisms in psychiatric diseases.

A novel approach to internal crown characterization for coniferous tree species classification

NASA Astrophysics Data System (ADS)

Harikumar, A.; Bovolo, F.; Bruzzone, L.

2016-10-01

The knowledge about individual trees in forest is highly beneficial in forest management. High density small foot- print multi-return airborne Light Detection and Ranging (LiDAR) data can provide a very accurate information about the structural properties of individual trees in forests. Every tree species has a unique set of crown structural characteristics that can be used for tree species classification. In this paper, we use both the internal and external crown structural information of a conifer tree crown, derived from a high density small foot-print multi-return LiDAR data acquisition for species classification. Considering the fact that branches are the major building blocks of a conifer tree crown, we obtain the internal crown structural information using a branch level analysis. The structure of each conifer branch is represented using clusters in the LiDAR point cloud. We propose the joint use of the k-means clustering and geometric shape fitting, on the LiDAR data projected onto a novel 3-dimensional space, to identify branch clusters. After mapping the identified clusters back to the original space, six internal geometric features are estimated using a branch-level analysis. The external crown characteristics are modeled by using six least correlated features based on cone fitting and convex hull. Species classification is performed using a sparse Support Vector Machines (sparse SVM) classifier.

Health care, human worth and the limits of the particular.

PubMed Central

Cherry, C

1997-01-01

An ethics concerned with health care developments and systems must be historically continuous, especially as it concerns the application to managed structures of key moral-epistemic concepts such as care, love and empathy. These concepts are traditionally most at home in the personal, individual domain. Human beings have non-instrumental worth just because they are human beings and not by virtue of their capacities. Managed health care systems tend to abstract from this worth in respect of both individuals' distinctness and individual identity. The first, a common feature of quantitative approaches to health care assessment and delivery, is avoidable. The second, by contrast, is necessarily sacrificed in impersonally managed structures. Failure to distinguish the two encourages confusion and distress, and the demand for impossible medico-moral relationships. PMID:9358352

Influence of Perceptual Saliency Hierarchy on Learning of Language Structures: An Artificial Language Learning Experiment

PubMed Central

Gong, Tao; Lam, Yau W.; Shuai, Lan

2016-01-01

Psychological experiments have revealed that in normal visual perception of humans, color cues are more salient than shape cues, which are more salient than textural patterns. We carried out an artificial language learning experiment to study whether such perceptual saliency hierarchy (color > shape > texture) influences the learning of orders regulating adjectives of involved visual features in a manner either congruent (expressing a salient feature in a salient part of the form) or incongruent (expressing a salient feature in a less salient part of the form) with that hierarchy. Results showed that within a few rounds of learning participants could learn the compositional segments encoding the visual features and the order between them, generalize the learned knowledge to unseen instances with the same or different orders, and show learning biases for orders that are congruent with the perceptual saliency hierarchy. Although the learning performances for both the biased and unbiased orders became similar given more learning trials, our study confirms that this type of individual perceptual constraint could contribute to the structural configuration of language, and points out that such constraint, as well as other factors, could collectively affect the structural diversity in languages. PMID:28066281

Influence of Perceptual Saliency Hierarchy on Learning of Language Structures: An Artificial Language Learning Experiment.

PubMed

Gong, Tao; Lam, Yau W; Shuai, Lan

2016-01-01

Psychological experiments have revealed that in normal visual perception of humans, color cues are more salient than shape cues, which are more salient than textural patterns. We carried out an artificial language learning experiment to study whether such perceptual saliency hierarchy (color > shape > texture) influences the learning of orders regulating adjectives of involved visual features in a manner either congruent (expressing a salient feature in a salient part of the form) or incongruent (expressing a salient feature in a less salient part of the form) with that hierarchy. Results showed that within a few rounds of learning participants could learn the compositional segments encoding the visual features and the order between them, generalize the learned knowledge to unseen instances with the same or different orders, and show learning biases for orders that are congruent with the perceptual saliency hierarchy. Although the learning performances for both the biased and unbiased orders became similar given more learning trials, our study confirms that this type of individual perceptual constraint could contribute to the structural configuration of language, and points out that such constraint, as well as other factors, could collectively affect the structural diversity in languages.

Human Hippocampal Structure: A Novel Biomarker Predicting Mnemonic Vulnerability to, and Recovery from, Sleep Deprivation

PubMed Central

Goldstein-Piekarski, Andrea N.; Greer, Stephanie M.; Stark, Shauna; Stark, Craig E.

2016-01-01

Sleep deprivation impairs the formation of new memories. However, marked interindividual variability exists in the degree to which sleep loss compromises learning, the mechanistic reasons for which are unclear. Furthermore, which physiological sleep processes restore learning ability following sleep deprivation are similarly unknown. Here, we demonstrate that the structural morphology of human hippocampal subfields represents one factor determining vulnerability (and conversely, resilience) to the impact of sleep deprivation on memory formation. Moreover, this same measure of brain morphology was further associated with the quality of nonrapid eye movement slow wave oscillations during recovery sleep, and by way of such activity, determined the success of memory restoration. Such findings provide a novel human biomarker of cognitive susceptibility to, and recovery from, sleep deprivation. Moreover, this metric may be of special predictive utility for professions in which memory function is paramount yet insufficient sleep is pervasive (e.g., aviation, military, and medicine). SIGNIFICANCE STATEMENT Sleep deprivation does not impact all people equally. Some individuals show cognitive resilience to the effects of sleep loss, whereas others express striking vulnerability, the reasons for which remain largely unknown. Here, we demonstrate that structural features of the human brain, specifically those within the hippocampus, accurately predict which individuals are susceptible (or conversely, resilient) to memory impairments caused by sleep deprivation. Moreover, this same structural feature determines the success of memory restoration following subsequent recovery sleep. Therefore, structural properties of the human brain represent a novel biomarker predicting individual vulnerability to (and recovery from) the effects of sleep loss, one with occupational relevance in professions where insufficient sleep is pervasive yet memory function is paramount. PMID:26911684

Fiberprint: A subject fingerprint based on sparse code pooling for white matter fiber analysis.

PubMed

Kumar, Kuldeep; Desrosiers, Christian; Siddiqi, Kaleem; Colliot, Olivier; Toews, Matthew

2017-09-01

White matter characterization studies use the information provided by diffusion magnetic resonance imaging (dMRI) to draw cross-population inferences. However, the structure, function, and white matter geometry vary across individuals. Here, we propose a subject fingerprint, called Fiberprint, to quantify the individual uniqueness in white matter geometry using fiber trajectories. We learn a sparse coding representation for fiber trajectories by mapping them to a common space defined by a dictionary. A subject fingerprint is then generated by applying a pooling function for each bundle, thus providing a vector of bundle-wise features describing a particular subject's white matter geometry. These features encode unique properties of fiber trajectories, such as their density along prominent bundles. An analysis of data from 861 Human Connectome Project subjects reveals that a fingerprint based on approximately 3000 fiber trajectories can uniquely identify exemplars from the same individual. We also use fingerprints for twin/sibling identification, our observations consistent with the twin data studies of white matter integrity. Our results demonstrate that the proposed Fiberprint can effectively capture the variability in white matter fiber geometry across individuals, using a compact feature vector (dimension of 50), making this framework particularly attractive for handling large datasets. Copyright © 2017 Elsevier Inc. All rights reserved.

Observations of the structure and evolution of solar flares with a soft X-ray telescope

NASA Technical Reports Server (NTRS)

Vorpahl, J. A.; Gibson, E. G.; Landecker, P. B.; Mckenzie, D. L.; Underwood, J. M.

1975-01-01

Soft X ray flare events were observed with the S-056 X-ray telescope that was part of the ATM complement of instruments aboard SKYLAB. Analyses of these data are reported. The observations are summarized and a detailed discussion of the X-ray flare structures is presented. The data indicated that soft X-ray emitted by a flare come primarily from an intense well-defined core surrounded by a region of fainter, more diffuse emission. An analysis of flare evolution indicates evidence for preliminary heating and energy release prior to the main phase of the flare. Core features are found to be remarkably stable and retain their shape throughout a flare. Most changes in the overall configuration seem to be result of the appearance, disappearance or change in brightness of individual features, rather than the restructuring or reorientation of these features. Brief comparisons with several theories are presented.

Diffeomorphic functional brain surface alignment: Functional demons.

PubMed

Nenning, Karl-Heinz; Liu, Hesheng; Ghosh, Satrajit S; Sabuncu, Mert R; Schwartz, Ernst; Langs, Georg

2017-08-01

Aligning brain structures across individuals is a central prerequisite for comparative neuroimaging studies. Typically, registration approaches assume a strong association between the features used for alignment, such as macro-anatomy, and the variable observed, such as functional activation or connectivity. Here, we propose to use the structure of intrinsic resting state fMRI signal correlation patterns as a basis for alignment of the cortex in functional studies. Rather than assuming the spatial correspondence of functional structures between subjects, we have identified locations with similar connectivity profiles across subjects. We mapped functional connectivity relationships within the brain into an embedding space, and aligned the resulting maps of multiple subjects. We then performed a diffeomorphic alignment of the cortical surfaces, driven by the corresponding features in the joint embedding space. Results show that functional alignment based on resting state fMRI identifies functionally homologous regions across individuals with higher accuracy than alignment based on the spatial correspondence of anatomy. Further, functional alignment enables measurement of the strength of the anatomo-functional link across the cortex, and reveals the uneven distribution of this link. Stronger anatomo-functional dissociation was found in higher association areas compared to primary sensory- and motor areas. Functional alignment based on resting state features improves group analysis of task based functional MRI data, increasing statistical power and improving the delineation of task-specific core regions. Finally, a comparison of the anatomo-functional dissociation between cohorts is demonstrated with a group of left and right handed subjects. Copyright © 2017 Elsevier Inc. All rights reserved.

Genetic diversity, genetic structure and demographic history of Cycas simplicipinna (Cycadaceae) assessed by DNA sequences and SSR markers

PubMed Central

2014-01-01

Background Cycas simplicipinna (T. Smitinand) K. Hill. (Cycadaceae) is an endangered species in China. There were seven populations and 118 individuals that we could collect were genotyped in this study. Here, we assessed the genetic diversity, genetic structure and demographic history of this species. Results Analyses of data of DNA sequences (two maternally inherited intergenic spacers of chloroplast, cpDNA and one biparentally inherited internal transcribed spacer region ITS4-ITS5, nrDNA) and sixteen microsatellite loci (SSR) were conducted in the species. Of the 118 samples, 86 individuals from the seven populations were used for DNA sequencing and 115 individuals from six populations were used for the microsatellite study. We found high genetic diversity at the species level, low genetic diversity within each of the seven populations and high genetic differentiation among the populations. There was a clear genetic structure within populations of C. simplicipinna. A demographic history inferred from DNA sequencing data indicates that C. simplicipinna experienced a recent population contraction without retreating to a common refugium during the last glacial period. The results derived from SSR data also showed that C. simplicipinna underwent past effective population contraction, likely during the Pleistocene. Conclusions Some genetic features of C. simplicipinna such as having high genetic differentiation among the populations, a clear genetic structure and a recent population contraction could provide guidelines for protecting this endangered species from extinction. Furthermore, the genetic features with population dynamics of the species in our study would help provide insights and guidelines for protecting other endangered species effectively. PMID:25016306

Dynamic Social Impact: The Creation of Culture by Communication.

ERIC Educational Resources Information Center

Latane, Bibb

1996-01-01

Presents a theory of how individuals located in social space influence each other to create higher order patterns of cultural structure. Presents the theory as five propositions and six derivations, arguing that Dynamic Social Impact Theory accounts for four key features of culture: regional clustering, correlations among cultural elements,…

Joint source based analysis of multiple brain structures in studying major depressive disorder

NASA Astrophysics Data System (ADS)

Ramezani, Mahdi; Rasoulian, Abtin; Hollenstein, Tom; Harkness, Kate; Johnsrude, Ingrid; Abolmaesumi, Purang

2014-03-01

We propose a joint Source-Based Analysis (jSBA) framework to identify brain structural variations in patients with Major Depressive Disorder (MDD). In this framework, features representing position, orientation and size (i.e. pose), shape, and local tissue composition are extracted. Subsequently, simultaneous analysis of these features within a joint analysis method is performed to generate the basis sources that show signi cant di erences between subjects with MDD and those in healthy control. Moreover, in a cross-validation leave- one-out experiment, we use a Fisher Linear Discriminant (FLD) classi er to identify individuals within the MDD group. Results show that we can classify the MDD subjects with an accuracy of 76% solely based on the information gathered from the joint analysis of pose, shape, and tissue composition in multiple brain structures.

Consumers' Preferences for Electronic Nicotine Delivery System Product Features: A Structured Content Analysis.

PubMed

Kistler, Christine E; Crutchfield, Trisha M; Sutfin, Erin L; Ranney, Leah M; Berman, Micah L; Zarkin, Gary A; Goldstein, Adam O

2017-06-07

To inform potential governmental regulations, we aimed to develop a list of electronic nicotine delivery system (ENDS) product features important to U.S. consumers by age and gender. We employed qualitative data methods. Participants were eligible if they had used an ENDS at least once. Groups were selected by age and gender (young adult group aged 18-25, n = 11; middle-age group aged 26-64, n = 9; and women's group aged 26-64, n = 9). We conducted five individual older adult interviews (aged 68-80). Participants discussed important ENDS features. We conducted a structured content analysis of the group and interview responses. Of 34 participants, 68% were white and 56% were female. Participants mentioned 12 important ENDS features, including: (1) user experience; (2) social acceptability; (3) cost; (4) health risks/benefits; (5) ease of use; (6) flavors; (7) smoking cessation aid; (8) nicotine content; (9) modifiability; (10) ENDS regulation; (11) bridge between tobacco cigarettes; (12) collectability. The most frequently mentioned ENDS feature was modifiability for young adults, user experience for middle-age and older adults, and flavor for the women's group. This study identified multiple features important to ENDS consumers. Groups differed in how they viewed various features by age and gender. These results can inform ongoing regulatory efforts.

Consumers’ Preferences for Electronic Nicotine Delivery System Product Features: A Structured Content Analysis

PubMed Central

Kistler, Christine E.; Crutchfield, Trisha M.; Sutfin, Erin L.; Ranney, Leah M.; Berman, Micah L.; Zarkin, Gary A.; Goldstein, Adam O.

2017-01-01

To inform potential governmental regulations, we aimed to develop a list of electronic nicotine delivery system (ENDS) product features important to U.S. consumers by age and gender. We employed qualitative data methods. Participants were eligible if they had used an ENDS at least once. Groups were selected by age and gender (young adult group aged 18–25, n = 11; middle-age group aged 26–64, n = 9; and women’s group aged 26–64, n = 9). We conducted five individual older adult interviews (aged 68–80). Participants discussed important ENDS features. We conducted a structured content analysis of the group and interview responses. Of 34 participants, 68% were white and 56% were female. Participants mentioned 12 important ENDS features, including: (1) user experience; (2) social acceptability; (3) cost; (4) health risks/benefits; (5) ease of use; (6) flavors; (7) smoking cessation aid; (8) nicotine content; (9) modifiability; (10) ENDS regulation; (11) bridge between tobacco cigarettes; (12) collectability. The most frequently mentioned ENDS feature was modifiability for young adults, user experience for middle-age and older adults, and flavor for the women’s group. This study identified multiple features important to ENDS consumers. Groups differed in how they viewed various features by age and gender. These results can inform ongoing regulatory efforts. PMID:28590444

Diagnostic Analyzer for Gearboxes (DAG): User's Guide. Version 3.1 for Microsoft Windows 3.1

NASA Technical Reports Server (NTRS)

Jammu, Vinay B.; Kourosh, Danai

1997-01-01

This documentation describes the Diagnostic Analyzer for Gearboxes (DAG) software for performing fault diagnosis of gearboxes. First, the user would construct a graphical representation of the gearbox using the gear, bearing, shaft, and sensor tools contained in the DAG software. Next, a set of vibration features obtained by processing the vibration signals recorded from the gearbox using a signal analyzer is required. Given this information, the DAG software uses an unsupervised neural network referred to as the Fault Detection Network (FDN) to identify the occurrence of faults, and a pattern classifier called Single Category-Based Classifier (SCBC) for abnormality scaling of individual vibration features. The abnormality-scaled vibration features are then used as inputs to a Structure-Based Connectionist Network (SBCN) for identifying faults in gearbox subsystems and components. The weights of the SBCN represent its diagnostic knowledge and are derived from the structure of the gearbox graphically presented in DAG. The outputs of SBCN are fault possibility values between 0 and 1 for individual subsystems and components in the gearbox with a 1 representing a definite fault and a 0 representing normality. This manual describes the steps involved in creating the diagnostic gearbox model, along with the options and analysis tools of the DAG software.

Multilevel depth and image fusion for human activity detection.

PubMed

Ni, Bingbing; Pei, Yong; Moulin, Pierre; Yan, Shuicheng

2013-10-01

Recognizing complex human activities usually requires the detection and modeling of individual visual features and the interactions between them. Current methods only rely on the visual features extracted from 2-D images, and therefore often lead to unreliable salient visual feature detection and inaccurate modeling of the interaction context between individual features. In this paper, we show that these problems can be addressed by combining data from a conventional camera and a depth sensor (e.g., Microsoft Kinect). We propose a novel complex activity recognition and localization framework that effectively fuses information from both grayscale and depth image channels at multiple levels of the video processing pipeline. In the individual visual feature detection level, depth-based filters are applied to the detected human/object rectangles to remove false detections. In the next level of interaction modeling, 3-D spatial and temporal contexts among human subjects or objects are extracted by integrating information from both grayscale and depth images. Depth information is also utilized to distinguish different types of indoor scenes. Finally, a latent structural model is developed to integrate the information from multiple levels of video processing for an activity detection. Extensive experiments on two activity recognition benchmarks (one with depth information) and a challenging grayscale + depth human activity database that contains complex interactions between human-human, human-object, and human-surroundings demonstrate the effectiveness of the proposed multilevel grayscale + depth fusion scheme. Higher recognition and localization accuracies are obtained relative to the previous methods.

Ultrastructural diversity between centrioles of eukaryotes.

PubMed

Gupta, Akshari; Kitagawa, Daiju

2018-02-16

Several decades of centriole research have revealed the beautiful symmetry present in these microtubule-based organelles, which are required to form centrosomes, cilia, and flagella in many eukaryotes. Centriole architecture is largely conserved across most organisms, however, individual centriolar features such as the central cartwheel or microtubule walls exhibit considerable variability when examined with finer resolution. Here, we review the ultrastructural characteristics of centrioles in commonly studied organisms, highlighting the subtle and not-so-subtle differences between specific structural components of these centrioles. Additionally, we survey some non-canonical centriole structures that have been discovered in various species, from the coaxial bicentrioles of protists and lower land plants to the giant irregular centrioles of the fungus gnat Sciara. Finally, we speculate on the functional significance of these differences between centrioles, and the contribution of individual structural elements such as the cartwheel or microtubules towards the stability of centrioles.Centriole structure, cartwheel, triplet microtubules, SAS-6, centrosome.

The influence of structural stigma and rejection sensitivity on young sexual minority men's daily tobacco and alcohol use

PubMed Central

Pachankis, John E.; Hatzenbuehler, Mark L.; Starks, Tyrel J.

2018-01-01

Stigma occurs at both individual and structural levels, but existing research tends to examine the effect of individual and structural forms of stigma in isolation, rather than considering potential synergistic effects. To address this gap, our study examined whether stigma at the individual level, namely gay-related rejection sensitivity, interacts with structural stigma to predict substance use among young sexual minority men. Sexual minority (n = 119) participants completed online measures of our constructs (e.g., rejection sensitivity). Participants currently resided across a broad array of geographic areas (i.e., 24 U.S. states), and had attended high school in 28 states, allowing us to capture sufficient variance in current and past forms of structural stigma, defined as (1) a lack of state-level policies providing equal opportunities for heterosexual and sexual minority individuals and (2) negative state-aggregated attitudes toward sexual minorities. To measure daily substance use, we utilized a daily diary approach, whereby all participants were asked to indicate whether they used tobacco or alcohol on nine consecutive days. Results indicated that structural stigma interacted with rejection sensitivity to predict tobacco and alcohol use, and that this relationship depended on the developmental timing of exposure to structural stigma. In contrast, rejection sensitivity did not mediate the relationship between structural stigma and substance use. These results suggest that psychological predispositions, such as rejection sensitivity, interact with features of the social environment, such as structural stigma, to predict important health behaviors among young sexual minority men. These results add to a growing body of research documenting the multiple levels through which stigma interacts to produce negative health outcomes among sexual minority individuals. PMID:24507912

The Impact of Individual Differences, Types of Model and Social Settings on Block Building Performance among Chinese Preschoolers.

PubMed

Tian, Mi; Deng, Zhu; Meng, Zhaokun; Li, Rui; Zhang, Zhiyi; Qi, Wenhui; Wang, Rui; Yin, Tingting; Ji, Menghui

2018-01-01

Children's block building performances are used as indicators of other abilities in multiple domains. In the current study, we examined individual differences, types of model and social settings as influences on children's block building performance. Chinese preschoolers ( N = 180) participated in a block building activity in a natural setting, and performance was assessed with multiple measures in order to identify a range of specific skills. Using scores generated across these measures, three dependent variables were analyzed: block building skills, structural balance and structural features. An overall MANOVA showed that there were significant main effects of gender and grade level across most measures. Types of model showed no significant effect in children's block building. There was a significant main effect of social settings on structural features, with the best performance in the 5-member group, followed by individual and then the 10-member block building. These findings suggest that boys performed better than girls in block building activity. Block building performance increased significantly from 1st to 2nd year of preschool, but not from second to third. The preschoolers created more representational constructions when presented with a model made of wooden rather than with a picture. There was partial evidence that children performed better when working with peers in a small group than when working alone or working in a large group. It is suggested that future study should examine other modalities rather than the visual one, diversify the samples and adopt a longitudinal investigation.

Correlation of the lung microbiota with metabolic profiles in bronchoalveolar lavage fluid in HIV infection.

PubMed

Cribbs, Sushma K; Uppal, Karan; Li, Shuzhao; Jones, Dean P; Huang, Laurence; Tipton, Laura; Fitch, Adam; Greenblatt, Ruth M; Kingsley, Lawrence; Guidot, David M; Ghedin, Elodie; Morris, Alison

2016-01-20

While 16S ribosomal RNA (rRNA) sequencing has been used to characterize the lung's bacterial microbiota in human immunodeficiency virus (HIV)-infected individuals, taxonomic studies provide limited information on bacterial function and impact on the host. Metabolic profiles can provide functional information on host-microbe interactions in the lungs. We investigated the relationship between the respiratory microbiota and metabolic profiles in the bronchoalveolar lavage fluid of HIV-infected and HIV-uninfected outpatients. Targeted sequencing of the 16S rRNA gene was used to analyze the bacterial community structure and liquid chromatography-high-resolution mass spectrometry was used to detect features in bronchoalveolar lavage fluid. Global integration of all metabolic features with microbial species was done using sparse partial least squares regression. Thirty-nine HIV-infected subjects and 20 HIV-uninfected controls without acute respiratory symptoms were enrolled. Twelve mass-to-charge ratio (m/z) features from C18 analysis were significantly different between HIV-infected individuals and controls (false discovery rate (FDR) = 0.2); another 79 features were identified by network analysis. Further metabolite analysis demonstrated that four features were significantly overrepresented in the bronchoalveolar lavage (BAL) fluid of HIV-infected individuals compared to HIV-uninfected, including cystine, two complex carbohydrates, and 3,5-dibromo-L-tyrosine. There were 231 m/z features significantly associated with peripheral blood CD4 cell counts identified using sparse partial least squares regression (sPLS) at a variable importance on projection (VIP) threshold of 2. Twenty-five percent of these 91 m/z features were associated with various microbial species. Bacteria from families Caulobacteraceae, Staphylococcaceae, Nocardioidaceae, and genus Streptococcus were associated with the greatest number of features. Glycerophospholipid and lineolate pathways correlated with these bacteria. In bronchoalveolar lavage fluid, specific metabolic profiles correlated with bacterial organisms known to play a role in the pathogenesis of pneumonia in HIV-infected individuals. These findings suggest that microbial communities and their interactions with the host may have functional metabolic impact in the lung.

ELUCIDATING BRAIN CONNECTIVITY NETWORKS IN MAJOR DEPRESSIVE DISORDER USING CLASSIFICATION-BASED SCORING.

PubMed

Sacchet, Matthew D; Prasad, Gautam; Foland-Ross, Lara C; Thompson, Paul M; Gotlib, Ian H

2014-04-01

Graph theory is increasingly used in the field of neuroscience to understand the large-scale network structure of the human brain. There is also considerable interest in applying machine learning techniques in clinical settings, for example, to make diagnoses or predict treatment outcomes. Here we used support-vector machines (SVMs), in conjunction with whole-brain tractography, to identify graph metrics that best differentiate individuals with Major Depressive Disorder (MDD) from nondepressed controls. To do this, we applied a novel feature-scoring procedure that incorporates iterative classifier performance to assess feature robustness. We found that small-worldness , a measure of the balance between global integration and local specialization, most reliably differentiated MDD from nondepressed individuals. Post-hoc regional analyses suggested that heightened connectivity of the subcallosal cingulate gyrus (SCG) in MDDs contributes to these differences. The current study provides a novel way to assess the robustness of classification features and reveals anomalies in large-scale neural networks in MDD.

Abnormal semantic knowledge in a case of developmental amnesia.

PubMed

Blumenthal, Anna; Duke, Devin; Bowles, Ben; Gilboa, Asaf; Rosenbaum, R Shayna; Köhler, Stefan; McRae, Ken

2017-07-28

An important theory holds that semantic knowledge can develop independently of episodic memory. One strong source of evidence supporting this independence comes from the observation that individuals with early hippocampal damage leading to developmental amnesia generally perform normally on standard tests of semantic memory, despite their profound impairment in episodic memory. However, one aspect of semantic memory that has not been explored is conceptual structure. We built on the theoretically important distinction between intrinsic features of object concepts (e.g., shape, colour, parts) and extrinsic features (e.g., how something is used, where it is typically located). The accrual of extrinsic feature knowledge that is important for concepts such as chair or spoon may depend on binding mechanisms in the hippocampus. We tested HC, an individual with developmental amnesia due to a well-characterized lesion of the hippocampus, on her ability to generate semantic features for object concepts. HC generated fewer extrinsic features than controls, but a similar number of intrinsic features than controls. We also tested her on typicality ratings. Her typicality ratings were abnormal for nonliving things (which more strongly depend on extrinsic features), but normal for living things (which more strongly depend on intrinsic features). In contrast, NB, who has MTL but not hippocampal damage due to surgery, showed no impairments in either task. These results suggest that episodic and semantic memory are not entirely independent, and that the hippocampus is important for learning some aspects of conceptual knowledge. Copyright © 2017 Elsevier Ltd. All rights reserved.

The Role of the Pulmonary Embolism Response Team: How to Build One, Who to Include, Scenarios, Organization, and Algorithms.

PubMed

Galmer, Andrew; Weinberg, Ido; Giri, Jay; Jaff, Michael; Weinberg, Mitchell

2017-09-01

Pulmonary embolism response teams (PERTs) are multidisciplinary response teams aimed at delivering a range of diagnostic and therapeutic modalities to patients with pulmonary embolism. These teams have gained traction on a national scale. However, despite sharing a common goal, individual PERT programs are quite individualized-varying in their methods of operation, team structures, and practice patterns. The tendency of such response teams is to become intensely structured, algorithmic, and inflexible. However, in their current form, PERT programs are quite the opposite. They are being creatively customized to meet the needs of the individual institution based on available resources, skills, personnel, and institutional goals. After a review of the essential core elements needed to create and operate a PERT team in any form, this article will discuss the more flexible feature development of the nascent PERT team. These include team planning, member composition, operational structure, benchmarking, market analysis, and rudimentary financial operations. Copyright © 2017 Elsevier Inc. All rights reserved.

3DNALandscapes: a database for exploring the conformational features of DNA.

PubMed

Zheng, Guohui; Colasanti, Andrew V; Lu, Xiang-Jun; Olson, Wilma K

2010-01-01

3DNALandscapes, located at: http://3DNAscapes.rutgers.edu, is a new database for exploring the conformational features of DNA. In contrast to most structural databases, which archive the Cartesian coordinates and/or derived parameters and images for individual structures, 3DNALandscapes enables searches of conformational information across multiple structures. The database contains a wide variety of structural parameters and molecular images, computed with the 3DNA software package and known to be useful for characterizing and understanding the sequence-dependent spatial arrangements of the DNA sugar-phosphate backbone, sugar-base side groups, base pairs, base-pair steps, groove structure, etc. The data comprise all DNA-containing structures--both free and bound to proteins, drugs and other ligands--currently available in the Protein Data Bank. The web interface allows the user to link, report, plot and analyze this information from numerous perspectives and thereby gain insight into DNA conformation, deformability and interactions in different sequence and structural contexts. The data accumulated from known, well-resolved DNA structures can serve as useful benchmarks for the analysis and simulation of new structures. The collective data can also help to understand how DNA deforms in response to proteins and other molecules and undergoes conformational rearrangements.

Empathizing, systemizing, and autistic traits: latent structure in individuals with autism, their parents, and general population controls.

PubMed

Grove, Rachel; Baillie, Andrew; Allison, Carrie; Baron-Cohen, Simon; Hoekstra, Rosa A

2013-05-01

The search for genes involved in autism spectrum conditions (ASC) may have been hindered by the assumption that the different symptoms that define the condition can be attributed to the same causal mechanism. Instead the social and nonsocial aspects of ASC may have distinct causes at genetic, cognitive, and neural levels. It has been posited that the core features of ASC can be explained by a deficit in empathizing alongside intact or superior systemizing; the drive to understand and derive rules about a system. First-degree relatives also show some mild manifestations that parallel the defining features of ASC, termed the broader autism phenotype. Factor analyses were conducted to assess whether the latent structure of empathizing, systemizing, and autistic traits differs across samples with a high (individuals on the spectrum), medium (first-degree relatives) or low (general population controls) genetic vulnerability to autism. Results highlighted a two-factor model, confirming an empathizing and a systemizing factor. The relationship between these two factors was significantly stronger in first-degree relatives and the autism group compared with controls. The same model provided the best fit among the three groups, suggesting a similar latent structure irrespective of genetic vulnerability. However, results also suggest that although these traits are relatively independent in the general population, they are substantially correlated in individuals with ASC and their parents. This implies that there is substantially more overlap between systemizing and empathizing among individuals with an increased genetic liability to autism. This has potential implications for the genetic, environmental, and cognitive explanations of autism spectrum conditions. © 2013 American Psychological Association

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

The Process of Change in Higher Education Institutions. AAHE-ERIC/Higher Education Research Report, No. 7, 1982.

ERIC Educational Resources Information Center

Nordvall, Robert C.

Conditions that inhibit change in higher education institutions and various models of the change process are described. Attention is also directed to: organizational character, structural features, planning procedures, key individuals in the change process, and practical advice about change. The major change models for higher education…

It's all coming back to me now: perception and memory in amnesia.

PubMed

Baxter, Mark G

2012-07-12

Medial temporal lobe (MTL) structures may constitute a representational hierarchy, rather than a dedicated system for memory. Barense et al. (2012) show that intact memory for object features can interfere with perception of complex objects in individuals with MTL amnesia. Copyright © 2012 Elsevier Inc. All rights reserved.

Two models for microsimulation of family life cycle and family structure.

PubMed

Bertino, S; Pinnelli, A; Vichi, M

1988-01-01

2 models are proposed for the microsimulation of the family and analysis of family structure and life cycle. These models were devised primarily for teaching purposes. The families are composed of 3 generations (parents, grandparents, children). Cohabitation is not considered. The 1st model is governed by a transition mechanism based on the rules of a Markov multidimensional, nonhonogeneous chain. The 2nd model is based on stochastic point processes. Input data comprise annual mortality probability according to 1) sex, 2) age, 3) civil status, 4) annual probability of 1st marriage, 5) age combinations between the spouses, and 6) the probability of having 1, 2, or 3 children at 6 months intervals from the previous event (marriage or birth of nth child). The applications of the 1st model are presented using 2 mortality and fertility hypotheses (high and low) and a nuptiality hypothesis (West European nature). The various features of family composition are analyzed according to the duration of a couple's marriage and the age of the individual, as well as the characteristic features of the individual and family life cycle given these 2 demographic conditions.

Electronic fingerprints of DNA bases on graphene.

PubMed

Ahmed, Towfiq; Kilina, Svetlana; Das, Tanmoy; Haraldsen, Jason T; Rehr, John J; Balatsky, Alexander V

2012-02-08

We calculate the electronic local density of states (LDOS) of DNA nucleotide bases (A,C,G,T), deposited on graphene. We observe significant base-dependent features in the LDOS in an energy range within a few electronvolts of the Fermi level. These features can serve as electronic fingerprints for the identification of individual bases in scanning tunneling spectroscopy (STS) experiments that perform image and site dependent spectroscopy on biomolecules. Thus the fingerprints of DNA-graphene hybrid structures may provide an alternative route to DNA sequencing using STS. © 2012 American Chemical Society

Facades structure detection by geometric moment

NASA Astrophysics Data System (ADS)

Jiang, Diqiong; Chen, Hui; Song, Rui; Meng, Lei

2017-06-01

This paper proposes a novel method for extracting facades structure from real-world pictures by using local geometric moment. Compared with existing methods, the proposed method has advantages of easy-to-implement, low computational cost, and robustness to noises, such as uneven illumination, shadow, and shade from other objects. Besides, our method is faster and has a lower space complexity, making it feasible for mobile devices and the situation where real-time data processing is required. Specifically, a facades structure modal is first proposed to support the use of our special noise reduction method, which is based on a self-adapt local threshold with Gaussian weighted average for image binarization processing and the feature of the facades structure. Next, we divide the picture of the building into many individual areas, each of which represents a door or a window in the picture. Subsequently we calculate the geometric moment and centroid for each individual area, for identifying those collinear ones based on the feature vectors, each of which is thereafter replaced with a line. Finally, we comprehensively analyze all the geometric moment and centroid to find out the facades structure of the building. We compare our result with other methods and especially report the result from the pictures taken in bad environmental conditions. Our system is designed for two application, i.e, the reconstruction of facades based on higher resolution ground-based on imagery, and the positional system based on recognize the urban building.

Computer ranking of the sequence of appearance of 40 features of the brain and related structures in staged human embryos during the seventh week of development.

PubMed

O'Rahilly, R; Müller, F; Hutchins, G M; Moore, G W

1988-08-01

The sequence of events in the development of the brain in human embryos, already published for stages 8-17, is here continued for stages 18 and 19. With the aid of a computerized bubble-sort algorithm, 58 individual embryos were ranked in ascending order of the features present. The increasing structural complexity provided 40 new features in these two stages. The chief characteristics of stage 18 (approximately 44 postovulatory days) are rapidly growing basal nuclei; appearance of the extraventricular bulge of the cerebellum (flocculus), of the superior cerebellar peduncle, and of follicles in the epiphysis cerebri; and the presence of vomeronasal organ and ganglion, of the bucconasal membrane, and of isolated semicircular ducts. The main features of stage 19 (approximately 48 days) are the cochlear nuclei, the ganglion of the nervus terminalis, nuclei of the prosencephalic septum, the appearance of the subcommissural organ, the presence of villi in the choroid plexuses of the fourth and lateral ventricles, and the stria medullaris thalami.

Building theory-based concepts: four-year-olds preferentially seek explanations for features of kinds.

PubMed

Cimpian, Andrei; Petro, Gina

2014-05-01

Is the structure of human concepts continuous across development, or does it undergo qualitative transformations? Extensive evidence with adults has demonstrated that they are motivated to understand why categories have the features they do. To investigate whether young children display a similar motivation-an issue that bears on the question of continuity vs. transformation in conceptual structure-we conducted three studies involving 4-year-olds (N=90) and adults (N=124). Experiments 1 and 2 suggested that 4-year-olds indeed display a strong motivation to explain why categories have the features they do. Specifically, when provided with the option of asking "why?" about features of novel categories vs. features of individuals from other novel categories, children preferred to ask "why?" about the category features. Moreover, children's explanatory preference was specific to facts about categories per se and did not extend to facts that were merely presented in the context of multiple category instances. Experiment 3 also ruled out the possibility that the category facts were preferred because these facts were more surprising. In sum, these three studies reveal an early-emerging motivation to make sense of the categories encountered in the world and, more generally, speak to the richness of children's conceptual representations. Copyright © 2014 Elsevier B.V. All rights reserved.

Development of a brain MRI-based hidden Markov model for dementia recognition

PubMed Central

2013-01-01

Background Dementia is an age-related cognitive decline which is indicated by an early degeneration of cortical and sub-cortical structures. Characterizing those morphological changes can help to understand the disease development and contribute to disease early prediction and prevention. But modeling that can best capture brain structural variability and can be valid in both disease classification and interpretation is extremely challenging. The current study aimed to establish a computational approach for modeling the magnetic resonance imaging (MRI)-based structural complexity of the brain using the framework of hidden Markov models (HMMs) for dementia recognition. Methods Regularity dimension and semi-variogram were used to extract structural features of the brains, and vector quantization method was applied to convert extracted feature vectors to prototype vectors. The output VQ indices were then utilized to estimate parameters for HMMs. To validate its accuracy and robustness, experiments were carried out on individuals who were characterized as non-demented and mild Alzheimer's diseased. Four HMMs were constructed based on the cohort of non-demented young, middle-aged, elder and demented elder subjects separately. Classification was carried out using a data set including both non-demented and demented individuals with a wide age range. Results The proposed HMMs have succeeded in recognition of individual who has mild Alzheimer's disease and achieved a better classification accuracy compared to other related works using different classifiers. Results have shown the ability of the proposed modeling for recognition of early dementia. Conclusion The findings from this research will allow individual classification to support the early diagnosis and prediction of dementia. By using the brain MRI-based HMMs developed in our proposed research, it will be more efficient, robust and can be easily used by clinicians as a computer-aid tool for validating imaging bio-markers for early prediction of dementia. PMID:24564961

Reinforcement learning algorithms for robotic navigation in dynamic environments.

PubMed

Yen, Gary G; Hickey, Travis W

2004-04-01

The purpose of this study was to examine improvements to reinforcement learning (RL) algorithms in order to successfully interact within dynamic environments. The scope of the research was that of RL algorithms as applied to robotic navigation. Proposed improvements include: addition of a forgetting mechanism, use of feature based state inputs, and hierarchical structuring of an RL agent. Simulations were performed to evaluate the individual merits and flaws of each proposal, to compare proposed methods to prior established methods, and to compare proposed methods to theoretically optimal solutions. Incorporation of a forgetting mechanism did considerably improve the learning times of RL agents in a dynamic environment. However, direct implementation of a feature-based RL agent did not result in any performance enhancements, as pure feature-based navigation results in a lack of positional awareness, and the inability of the agent to determine the location of the goal state. Inclusion of a hierarchical structure in an RL agent resulted in significantly improved performance, specifically when one layer of the hierarchy included a feature-based agent for obstacle avoidance, and a standard RL agent for global navigation. In summary, the inclusion of a forgetting mechanism, and the use of a hierarchically structured RL agent offer substantially increased performance when compared to traditional RL agents navigating in a dynamic environment.

Predicting Gene Structure Changes Resulting from Genetic Variants via Exon Definition Features.

PubMed

Majoros, William H; Holt, Carson; Campbell, Michael S; Ware, Doreen; Yandell, Mark; Reddy, Timothy E

2018-04-25

Genetic variation that disrupts gene function by altering gene splicing between individuals can substantially influence traits and disease. In those cases, accurately predicting the effects of genetic variation on splicing can be highly valuable for investigating the mechanisms underlying those traits and diseases. While methods have been developed to generate high quality computational predictions of gene structures in reference genomes, the same methods perform poorly when used to predict the potentially deleterious effects of genetic changes that alter gene splicing between individuals. Underlying that discrepancy in predictive ability are the common assumptions by reference gene finding algorithms that genes are conserved, well-formed, and produce functional proteins. We describe a probabilistic approach for predicting recent changes to gene structure that may or may not conserve function. The model is applicable to both coding and noncoding genes, and can be trained on existing gene annotations without requiring curated examples of aberrant splicing. We apply this model to the problem of predicting altered splicing patterns in the genomes of individual humans, and we demonstrate that performing gene-structure prediction without relying on conserved coding features is feasible. The model predicts an unexpected abundance of variants that create de novo splice sites, an observation supported by both simulations and empirical data from RNA-seq experiments. While these de novo splice variants are commonly misinterpreted by other tools as coding or noncoding variants of little or no effect, we find that in some cases they can have large effects on splicing activity and protein products, and we propose that they may commonly act as cryptic factors in disease. The software is available from geneprediction.org/SGRF. bmajoros@duke.edu. Supplementary information is available at Bioinformatics online.

What is a 'good' job? Modelling job quality for blue collar workers.

PubMed

Jones, Wendy; Haslam, Roger; Haslam, Cheryl

2017-01-01

This paper proposes a model of job quality, developed from interviews with blue collar workers: bus drivers, manufacturing operatives and cleaners (n  =  80). The model distinguishes between core features, important for almost all workers, and 'job fit' features, important to some but not others, or where individuals might have different preferences. Core job features found important for almost all interviewees included job security, personal safety and having enough pay to meet their needs. 'Job fit' features included autonomy and the opportunity to form close relationships. These showed more variation between participants; priorities were influenced by family commitments, stage of life and personal preference. The resulting theoretical perspective indicates the features necessary for a job to be considered 'good' by the person doing it, whilst not adversely affecting their health. The model should have utility as a basis for measuring and improving job quality and the laudable goal of creating 'good jobs'. Practitioner Summary: Good work can contribute positively to health and well-being, but there is a lack of agreement regarding the concept of a 'good' job. A model of job quality has been constructed based on semi-structured worker interviews (n  =  80). The model emphasises the need to take into account variation between individuals in their preferred work characteristics.

Clustering Suicide Attempters: Impulsive-Ambivalent, Well-Planned, or Frequent.

PubMed

Lopez-Castroman, Jorge; Nogue, Erika; Guillaume, Sebastien; Picot, Marie Christine; Courtet, Philippe

2016-06-01

Attempts to predict suicidal behavior within high-risk populations have so far shown insufficient accuracy. Although several psychosocial and clinical features have been consistently associated with suicide attempts, investigations of latent structure in well-characterized populations of suicide attempters are lacking. We analyzed a sample of 1,009 hospitalized suicide attempters that were recruited between 1999 and 2012. Eleven clinically relevant items related to the characteristics of suicidal behavior were submitted to a Hierarchical Ascendant Classification. Phenotypic profiles were compared between the resulting clusters. A decisional tree was constructed to facilitate the differentiation of individuals classified within the first 2 clusters. Most individuals were included in a cluster characterized by less lethal means and planning ("impulse-ambivalent"). A second cluster featured more carefully planned attempts ("well-planned"), more alcohol or drug use before the attempt, and more precautions to avoid interruptions. Finally, a small, third cluster included individuals reporting more attempts ("frequent"), more often serious or violent attempts, and an earlier age at first attempt. Differences across clusters by demographic and clinical characteristics were also found, particularly with the third cluster whose participants had experienced high levels of childhood abuse. Cluster analysis consistently supported 3 distinct clusters of individuals with specific features in their suicidal behaviors and phenotypic profiles that could help clinicians to better focus prevention strategies. © Copyright 2016 Physicians Postgraduate Press, Inc.

Evidence for shared cognitive processing of pitch in music and language.

PubMed

Perrachione, Tyler K; Fedorenko, Evelina G; Vinke, Louis; Gibson, Edward; Dilley, Laura C

2013-01-01

Language and music epitomize the complex representational and computational capacities of the human mind. Strikingly similar in their structural and expressive features, a longstanding question is whether the perceptual and cognitive mechanisms underlying these abilities are shared or distinct--either from each other or from other mental processes. One prominent feature shared between language and music is signal encoding using pitch, conveying pragmatics and semantics in language and melody in music. We investigated how pitch processing is shared between language and music by measuring consistency in individual differences in pitch perception across language, music, and three control conditions intended to assess basic sensory and domain-general cognitive processes. Individuals' pitch perception abilities in language and music were most strongly related, even after accounting for performance in all control conditions. These results provide behavioral evidence, based on patterns of individual differences, that is consistent with the hypothesis that cognitive mechanisms for pitch processing may be shared between language and music.

Automated renal histopathology: digital extraction and quantification of renal pathology

NASA Astrophysics Data System (ADS)

Sarder, Pinaki; Ginley, Brandon; Tomaszewski, John E.

2016-03-01

The branch of pathology concerned with excess blood serum proteins being excreted in the urine pays particular attention to the glomerulus, a small intertwined bunch of capillaries located at the beginning of the nephron. Normal glomeruli allow moderate amount of blood proteins to be filtered; proteinuric glomeruli allow large amount of blood proteins to be filtered. Diagnosis of proteinuric diseases requires time intensive manual examination of the structural compartments of the glomerulus from renal biopsies. Pathological examination includes cellularity of individual compartments, Bowman's and luminal space segmentation, cellular morphology, glomerular volume, capillary morphology, and more. Long examination times may lead to increased diagnosis time and/or lead to reduced precision of the diagnostic process. Automatic quantification holds strong potential to reduce renal diagnostic time. We have developed a computational pipeline capable of automatically segmenting relevant features from renal biopsies. Our method first segments glomerular compartments from renal biopsies by isolating regions with high nuclear density. Gabor texture segmentation is used to accurately define glomerular boundaries. Bowman's and luminal spaces are segmented using morphological operators. Nuclei structures are segmented using color deconvolution, morphological processing, and bottleneck detection. Average computation time of feature extraction for a typical biopsy, comprising of ~12 glomeruli, is ˜69 s using an Intel(R) Core(TM) i7-4790 CPU, and is ~65X faster than manual processing. Using images from rat renal tissue samples, automatic glomerular structural feature estimation was reproducibly demonstrated for 15 biopsy images, which contained 148 individual glomeruli images. The proposed method holds immense potential to enhance information available while making clinical diagnoses.

Neuroanatomy of Individual Differences in Language in Adult Males with Autism

PubMed Central

Lai, Meng-Chuan; Lombardo, Michael V.; Ecker, Christine; Chakrabarti, Bhismadev; Suckling, John; Bullmore, Edward T.; Happé, Francesca; Murphy, Declan G. M.; Baron-Cohen, Simon

2015-01-01

One potential source of heterogeneity within autism spectrum conditions (ASC) is language development and ability. In 80 high-functioning male adults with ASC, we tested if variations in developmental and current structural language are associated with current neuroanatomy. Groups with and without language delay differed behaviorally in early social reciprocity, current language, but not current autistic features. Language delay was associated with larger total gray matter (GM) volume, smaller relative volume at bilateral insula, ventral basal ganglia, and right superior, middle, and polar temporal structures, and larger relative volume at pons and medulla oblongata in adulthood. Despite this heterogeneity, those with and without language delay showed significant commonality in morphometric features when contrasted with matched neurotypical individuals (n = 57). In ASC, better current language was associated with increased GM volume in bilateral temporal pole, superior temporal regions, dorsolateral fronto-parietal and cerebellar structures, and increased white matter volume in distributed frontal and insular regions. Furthermore, current language–neuroanatomy correlation patterns were similar across subgroups with or without language delay. High-functioning adult males with ASC show neuroanatomical variations associated with both developmental and current language characteristics. This underscores the importance of including both developmental and current language as specifiers for ASC, to help clarify heterogeneity. PMID:25249409

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).

The σ law of evolutionary dynamics in community-structured population.

PubMed

Tang, Changbing; Li, Xiang; Cao, Lang; Zhan, Jingyuan

2012-08-07

Evolutionary game dynamics in finite populations provide a new framework to understand the selection of traits with frequency-dependent fitness. Recently, a simple but fundamental law of evolutionary dynamics, which we call σ law, describes how to determine the selection between two competing strategies: in most evolutionary processes with two strategies, A and B, strategy A is favored over B in weak selection if and only if σR+S>T+σP. This relationship holds for a wide variety of structured populations with mutation rate and weak selection under certain assumptions. In this paper, we propose a model of games based on a community-structured population and revisit this law under the Moran process. By calculating the average payoffs of A and B individuals with the method of effective sojourn time, we find that σ features not only the structured population characteristics, but also the reaction rate between individuals. That is to say, an interaction between two individuals are not uniform, and we can take σ as a reaction rate between any two individuals with the same strategy. We verify this viewpoint by the modified replicator equation with non-uniform interaction rates in a simplified version of the prisoner's dilemma game (PDG). Copyright © 2012 Elsevier Ltd. All rights reserved.

Landscape Features Shape Genetic Structure in Threatened Northern Spotted Owls

USGS Publications Warehouse

Funk, W. Chris; Forsman, Eric D.; Mullins, Thomas D.; Haig, Susan M.

2008-01-01

Several recent studies have shown that landscape features can strongly affect spatial patterns of gene flow and genetic variation. Understanding landscape effects on genetic variation is important in conservation for defining management units and understanding movement patterns. The landscape may have little effect on gene flow, however, in highly mobile species such as birds. We tested for genetic breaks associated with landscape features in the northern spotted owl (Strix occidentalis caurina), a threatened subspecies associated with old forests in the U.S. Pacific Northwest and extreme southwestern Canada. We found little evidence for distinct genetic breaks in northern spotted owls using a large microsatellite dataset (352 individuals from across the subspecies' range genotyped at 10 loci). Nonetheless, dry low-elevation valleys and the Cascade and Olympic Mountains restrict gene flow, while the Oregon Coast Range facilitates it. The wide Columbia River is not a barrier to gene flow. In addition, inter-individual genetic distance and latitude were negatively related, likely reflecting northward colonization following Pleistocene glacial recession. Our study shows that landscape features may play an important role in shaping patterns of genetic variation in highly vagile taxa such as birds.

Accurate predictions of population-level changes in sequence and structural properties of HIV-1 Env using a volatility-controlled diffusion model

PubMed Central

DeLeon, Orlando; Hodis, Hagit; O’Malley, Yunxia; Johnson, Jacklyn; Salimi, Hamid; Zhai, Yinjie; Winter, Elizabeth; Remec, Claire; Eichelberger, Noah; Van Cleave, Brandon; Puliadi, Ramya; Harrington, Robert D.; Stapleton, Jack T.; Haim, Hillel

2017-01-01

The envelope glycoproteins (Envs) of HIV-1 continuously evolve in the host by random mutations and recombination events. The resulting diversity of Env variants circulating in the population and their continuing diversification process limit the efficacy of AIDS vaccines. We examined the historic changes in Env sequence and structural features (measured by integrity of epitopes on the Env trimer) in a geographically defined population in the United States. As expected, many Env features were relatively conserved during the 1980s. From this state, some features diversified whereas others remained conserved across the years. We sought to identify “clues” to predict the observed historic diversification patterns. Comparison of viruses that cocirculate in patients at any given time revealed that each feature of Env (sequence or structural) exists at a defined level of variance. The in-host variance of each feature is highly conserved among individuals but can vary between different HIV-1 clades. We designate this property “volatility” and apply it to model evolution of features as a linear diffusion process that progresses with increasing genetic distance. Volatilities of different features are highly correlated with their divergence in longitudinally monitored patients. Volatilities of features also correlate highly with their population-level diversification. Using volatility indices measured from a small number of patient samples, we accurately predict the population diversity that developed for each feature over the course of 30 years. Amino acid variants that evolved at key antigenic sites are also predicted well. Therefore, small “fluctuations” in feature values measured in isolated patient samples accurately describe their potential for population-level diversification. These tools will likely contribute to the design of population-targeted AIDS vaccines by effectively capturing the diversity of currently circulating strains and addressing properties of variants expected to appear in the future. PMID:28384158

Structural hierarchy of autism spectrum disorder symptoms: an integrative framework.

PubMed

Kim, Hyunsik; Keifer, Cara M; Rodriguez-Seijas, Craig; Eaton, Nicholas R; Lerner, Matthew D; Gadow, Kenneth D

2018-01-01

In an attempt to resolve questions regarding the symptom classification of autism spectrum disorder (ASD), previous research generally aimed to demonstrate superiority of one model over another. Rather than adjudicating which model may be optimal, we propose an alternative approach that integrates competing models using Goldberg's bass-ackwards method, providing a comprehensive understanding of the underlying symptom structure of ASD. The study sample comprised 3,825 individuals, consecutive referrals to a university hospital developmental disabilities specialty clinic or a child psychiatry outpatient clinic. This study analyzed DSM-IV-referenced ASD symptom statements from parent and teacher versions of the Child and Adolescent Symptom Inventory-4R. A series of exploratory structural equation models was conducted in order to produce interpretable latent factors that account for multivariate covariance. Results indicated that ASD symptoms were structured into an interpretable hierarchy across multiple informants. This hierarchy includes five levels; key features of ASD bifurcate into different constructs with increasing specificity. This is the first study to examine an underlying structural hierarchy of ASD symptomatology using the bass-ackwards method. This hierarchy demonstrates how core features of ASD relate at differing levels of resolution, providing a model for conceptualizing ASD heterogeneity and a structure for integrating divergent theories of cognitive processes and behavioral features that define the disorder. These findings suggest that a more coherent and complete understanding of the structure of ASD symptoms may be reflected in a metastructure rather than at one level of resolution. © 2017 Association for Child and Adolescent Mental Health.

A comparative study of family-specific protein-ligand complex affinity prediction based on random forest approach

NASA Astrophysics Data System (ADS)

Wang, Yu; Guo, Yanzhi; Kuang, Qifan; Pu, Xuemei; Ji, Yue; Zhang, Zhihang; Li, Menglong

2015-04-01

The assessment of binding affinity between ligands and the target proteins plays an essential role in drug discovery and design process. As an alternative to widely used scoring approaches, machine learning methods have also been proposed for fast prediction of the binding affinity with promising results, but most of them were developed as all-purpose models despite of the specific functions of different protein families, since proteins from different function families always have different structures and physicochemical features. In this study, we proposed a random forest method to predict the protein-ligand binding affinity based on a comprehensive feature set covering protein sequence, binding pocket, ligand structure and intermolecular interaction. Feature processing and compression was respectively implemented for different protein family datasets, which indicates that different features contribute to different models, so individual representation for each protein family is necessary. Three family-specific models were constructed for three important protein target families of HIV-1 protease, trypsin and carbonic anhydrase respectively. As a comparison, two generic models including diverse protein families were also built. The evaluation results show that models on family-specific datasets have the superior performance to those on the generic datasets and the Pearson and Spearman correlation coefficients ( R p and Rs) on the test sets are 0.740, 0.874, 0.735 and 0.697, 0.853, 0.723 for HIV-1 protease, trypsin and carbonic anhydrase respectively. Comparisons with the other methods further demonstrate that individual representation and model construction for each protein family is a more reasonable way in predicting the affinity of one particular protein family.

Structural analysis of natural textures.

PubMed

Vilnrotter, F M; Nevatia, R; Price, K E

1986-01-01

Many textures can be described structurally, in terms of the individual textural elements and their spatial relationships. This paper describes a system to generate useful descriptions of natural textures in these terms. The basic approach is to determine an initial, partial description of the elements using edge features. This description controls the extraction of the texture elements. The elements are grouped by type, and spatial relationships between elements are computed. The descriptions are shown to be useful for recognition of the textures, and for reconstruction of periodic textures.

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

G.A> Valentine; F.V. Perry

The distribution and characteristics of individual basaltic volcanoes in the waning Southwestern Nevada Volcanic Field provide insight into the changing physical nature of magmatism and the controls on volcano location. During Pliocene-Pleistocene times the volumes of individual volcanoes have decreased by more than one order of magnitude, as have fissure lengths and inferred lava effusion rates. Eruptions evolved from Hawaiian-style eruptions with extensive lavas to eruptions characterized by small pulses of lava and Strombolian to violent Strombolian mechanisms. These trends indicate progressively decreasing partial melting and length scales, or magmatic footprints, of mantle source zones for individual volcanoes. The locationmore » of each volcano is determined by the location of its magmatic footprint at depth, and only by shallow structural and topographic features that are within that footprint. The locations of future volcanoes in a waning system are less likely to be determined by large-scale topography or structures than were older, larger volume volcanoes.« less

ARC-1979-A79-7029

NASA Image and Video Library

1979-02-28

This mosaic of Jupiter was assembled from nine individual photos taken through an orange filter by Voyager 1 on Feb. 6, 1979, when the spacecraft was 4.7 million miles (7.8 million kilometers) from Jupiter. Distortion of the mosaic, especially where portions of the limb have been fitted together, is caused by rotation of the planet during the 96-second intervals between individual pictures. The large atmospheric feature just below and to the right of center is the Great Red Spot. The complex structure of the cloud formations seen over the entire planet gives some hint of the equally complex motions in the Voyager 1 time-lapse photography. The smallest atomospheric features seen in this view are approximately 85 miles (140 kilometers) across. Voyager project is managed and controlled by Jet Propulsion Laboratory for NASA's Office of Space Science. (JPL ref. No. P-21146)

Conceptual Structure within and between Modalities

PubMed Central

Dilkina, Katia; Lambon Ralph, Matthew A.

2012-01-01

Current views of semantic memory share the assumption that conceptual representations are based on multimodal experience, which activates distinct modality-specific brain regions. This proposition is widely accepted, yet little is known about how each modality contributes to conceptual knowledge and how the structure of this contribution varies across these multiple information sources. We used verbal feature lists, features from drawings, and verbal co-occurrence statistics from latent semantic analysis to examine the informational structure in four domains of knowledge: perceptual, functional, encyclopedic, and verbal. The goals of the analysis were three-fold: (1) to assess the structure within individual modalities; (2) to compare structures between modalities; and (3) to assess the degree to which concepts organize categorically or randomly. Our results indicated significant and unique structure in all four modalities: perceptually, concepts organize based on prominent features such as shape, size, color, and parts; functionally, they group based on use and interaction; encyclopedically, they arrange based on commonality in location or behavior; and verbally, they group associatively or relationally. Visual/perceptual knowledge gives rise to the strongest hierarchical organization and is closest to classic taxonomic structure. Information is organized somewhat similarly in the perceptual and encyclopedic domains, which differs significantly from the structure in the functional and verbal domains. Notably, the verbal modality has the most unique organization, which is not at all categorical but also not random. The idiosyncrasy and complexity of conceptual structure across modalities raise the question of how all of these modality-specific experiences are fused together into coherent, multifaceted yet unified concepts. Accordingly, both methodological and theoretical implications of the present findings are discussed. PMID:23293593

The autonomy of biological individuals and artificial models.

PubMed

Moreno, Alvaro; Etxeberria, Arantza; Umerez, Jon

2008-02-01

This paper aims to offer an overview of the meaning of autonomy for biological individuals and artificial models rooted in a specific perspective that pays attention to the historical and structural aspects of its origins and evolution. Taking autopoiesis and the recursivity characteristic of its circular logic as a starting point, we depart from some of its consequences to claim that the theory of autonomy should also take into account historical and structural features. Autonomy should not be considered only in internal or constitutive terms, the largely neglected interactive aspects stemming from it should be equally addressed. Artificial models contribute to get a better understanding of the role of autonomy for life and the varieties of its organization and phenomenological diversity.

Experimental analysis for fabrication of high-aspect-ratio piezoelectric ceramic structure by micro-powder injection molding process

NASA Astrophysics Data System (ADS)

Han, Jun Sae; Gal, Chang Woo; Park, Jae Man; Kim, Jong Hyun; Park, Seong Jin

2018-04-01

Aspect ratio effects in the micro-powder injection molding process were experimentally analyzed for fabrication of high-aspect-ratio piezoelectric ceramic structure. The mechanisms of critical defects have been studied according to individual manufacturing steps. In the molding process, incomplete filling phenomenon determines the critical aspect ratios of a micro pattern. According to mold temperature, an incomplete filling phenomenon has been analyzed with respect to different pattern sizes and aspect ratio. In demolding and drying process, the capillary behavior of sacrificial polymeric mold insert determines the critical aspect ratio of a micro pattern. With respect to pattern dimensions, slumping behavior has been analyzed. Based on our current systems, micro PZT feature has stability when it has lower aspect ratio than 5. Under optimized processing conditions, 20 μm and 40 μm ceramic rod array feature which has 5 of aspect ratio were successfully fabricated by the developed process. Further modification points to fabricate the smaller and higher feature were specifically addressed.

EIT in resonator chains: similarities and differences with atomic media

NASA Technical Reports Server (NTRS)

Matsko, A. B.; Maleki, L.; Savchenkov, A. A.; Ilchenko, V. S.

2004-01-01

We theoretically study a parallel configuration of two interacting whispering gallery mode optical resonators and show a narrow-band modal structure as a basis for a widely tunable delay line. For the optimum coupling configuration the system can possess an unusually narrow spectral feature with a much narrower bandwidth than the loaded bandwidth of each individual resonator.

Component Structure of Individual Differences in True and False Recognition of Faces

ERIC Educational Resources Information Center

Bartlett, James C.; Shastri, Kalyan K.; Abdi, Herve; Neville-Smith, Marsha

2009-01-01

Principal-component analyses of 4 face-recognition studies uncovered 2 independent components. The first component was strongly related to false-alarm errors with new faces as well as to facial "conjunctions" that recombine features of previously studied faces. The second component was strongly related to hits as well as to the conjunction/new…

bpRNA: large-scale automated annotation and analysis of RNA secondary structure.

PubMed

Danaee, Padideh; Rouches, Mason; Wiley, Michelle; Deng, Dezhong; Huang, Liang; Hendrix, David

2018-05-09

While RNA secondary structure prediction from sequence data has made remarkable progress, there is a need for improved strategies for annotating the features of RNA secondary structures. Here, we present bpRNA, a novel annotation tool capable of parsing RNA structures, including complex pseudoknot-containing RNAs, to yield an objective, precise, compact, unambiguous, easily-interpretable description of all loops, stems, and pseudoknots, along with the positions, sequence, and flanking base pairs of each such structural feature. We also introduce several new informative representations of RNA structure types to improve structure visualization and interpretation. We have further used bpRNA to generate a web-accessible meta-database, 'bpRNA-1m', of over 100 000 single-molecule, known secondary structures; this is both more fully and accurately annotated and over 20-times larger than existing databases. We use a subset of the database with highly similar (≥90% identical) sequences filtered out to report on statistical trends in sequence, flanking base pairs, and length. Both the bpRNA method and the bpRNA-1m database will be valuable resources both for specific analysis of individual RNA molecules and large-scale analyses such as are useful for updating RNA energy parameters for computational thermodynamic predictions, improving machine learning models for structure prediction, and for benchmarking structure-prediction algorithms.

Brain properties predict proximity to symptom onset in sporadic Alzheimer's disease.

PubMed

Vogel, Jacob W; Vachon-Presseau, Etienne; Pichet Binette, Alexa; Tam, Angela; Orban, Pierre; La Joie, Renaud; Savard, Mélissa; Picard, Cynthia; Poirier, Judes; Bellec, Pierre; Breitner, John C S; Villeneuve, Sylvia

2018-06-01

See Tijms and Visser (doi:10.1093/brain/awy113) for a scientific commentary on this article.Alzheimer's disease is preceded by a lengthy 'preclinical' stage spanning many years, during which subtle brain changes occur in the absence of overt cognitive symptoms. Predicting when the onset of disease symptoms will occur is an unsolved challenge in individuals with sporadic Alzheimer's disease. In individuals with autosomal dominant genetic Alzheimer's disease, the age of symptom onset is similar across generations, allowing the prediction of individual onset times with some accuracy. We extend this concept to persons with a parental history of sporadic Alzheimer's disease to test whether an individual's symptom onset age can be informed by the onset age of their affected parent, and whether this estimated onset age can be predicted using only MRI. Structural and functional MRIs were acquired from 255 ageing cognitively healthy subjects with a parental history of sporadic Alzheimer's disease from the PREVENT-AD cohort. Years to estimated symptom onset was calculated as participant age minus age of parental symptom onset. Grey matter volume was extracted from T1-weighted images and whole-brain resting state functional connectivity was evaluated using degree count. Both modalities were summarized using a 444-region cortical-subcortical atlas. The entire sample was divided into training (n = 138) and testing (n = 68) sets. Within the training set, individuals closer to or beyond their parent's symptom onset demonstrated reduced grey matter volume and altered functional connectivity, specifically in regions known to be vulnerable in Alzheimer's disease. Machine learning was used to identify a weighted set of imaging features trained to predict years to estimated symptom onset. This feature set alone significantly predicted years to estimated symptom onset in the unseen testing data. This model, using only neuroimaging features, significantly outperformed a similar model instead trained with cognitive, genetic, imaging and demographic features used in a traditional clinical setting. We next tested if these brain properties could be generalized to predict time to clinical progression in a subgroup of 26 individuals from the Alzheimer's Disease Neuroimaging Initiative, who eventually converted either to mild cognitive impairment or to Alzheimer's dementia. The feature set trained on years to estimated symptom onset in the PREVENT-AD predicted variance in time to clinical conversion in this separate longitudinal dataset. Adjusting for participant age did not impact any of the results. These findings demonstrate that years to estimated symptom onset or similar measures can be predicted from brain features and may help estimate presymptomatic disease progression in at-risk individuals.

The Impact of Individual Differences, Types of Model and Social Settings on Block Building Performance among Chinese Preschoolers

PubMed Central

Tian, Mi; Deng, Zhu; Meng, Zhaokun; Li, Rui; Zhang, Zhiyi; Qi, Wenhui; Wang, Rui; Yin, Tingting; Ji, Menghui

2018-01-01

Children’s block building performances are used as indicators of other abilities in multiple domains. In the current study, we examined individual differences, types of model and social settings as influences on children’s block building performance. Chinese preschoolers (N = 180) participated in a block building activity in a natural setting, and performance was assessed with multiple measures in order to identify a range of specific skills. Using scores generated across these measures, three dependent variables were analyzed: block building skills, structural balance and structural features. An overall MANOVA showed that there were significant main effects of gender and grade level across most measures. Types of model showed no significant effect in children’s block building. There was a significant main effect of social settings on structural features, with the best performance in the 5-member group, followed by individual and then the 10-member block building. These findings suggest that boys performed better than girls in block building activity. Block building performance increased significantly from 1st to 2nd year of preschool, but not from second to third. The preschoolers created more representational constructions when presented with a model made of wooden rather than with a picture. There was partial evidence that children performed better when working with peers in a small group than when working alone or working in a large group. It is suggested that future study should examine other modalities rather than the visual one, diversify the samples and adopt a longitudinal investigation. PMID:29441031

Topology and layout optimization of discrete and continuum structures

NASA Technical Reports Server (NTRS)

Bendsoe, Martin P.; Kikuchi, Noboru

1993-01-01

The basic features of the ground structure method for truss structure an continuum problems are described. Problems with a large number of potential structural elements are considered using the compliance of the structure as the objective function. The design problem is the minimization of compliance for a given structural weight, and the design variables for truss problems are the cross-sectional areas of the individual truss members, while for continuum problems they are the variable densities of material in each of the elements of the FEM discretization. It is shown how homogenization theory can be applied to provide a relation between material density and the effective material properties of a periodic medium with a known microstructure of material and voids.

Conditions for building a community of practice in an advanced physics laboratory

NASA Astrophysics Data System (ADS)

Irving, Paul W.; Sayre, Eleanor C.

2014-06-01

We use the theory of communities of practice and the concept of accountable disciplinary knowledge to describe how a learning community develops in the context of an upper-division physics laboratory course. The change in accountable disciplinary knowledge motivates students' enculturation into a community of practice. The enculturation process is facilitated by four specific structural features of the course and supported by a primary instructional choice. The four structural features are "paucity of instructor time," "all in a room together," "long and difficult experiments," and "same experiments at different times." The instructional choice is the encouragement of the sharing and development of knowledge and understanding by the instructor. The combination of the instructional choice and structural features promotes the development of the learning community in which students engage in authentic practices of a physicist. This results in a classroom community that can provide students with the opportunity to have an accelerated trajectory towards being a more central participant of the community of a practice of physicists. We support our claims with video-based observations of laboratory classroom interactions and individual, semistructured interviews with students about their laboratory experiences and physics identity.

Segmentation and texture analysis of structural biomarkers using neighborhood-clustering-based level set in MRI of the schizophrenic brain.

PubMed

Latha, Manohar; Kavitha, Ganesan

2018-02-03

Schizophrenia (SZ) is a psychiatric disorder that especially affects individuals during their adolescence. There is a need to study the subanatomical regions of SZ brain on magnetic resonance images (MRI) based on morphometry. In this work, an attempt was made to analyze alterations in structure and texture patterns in images of the SZ brain using the level-set method and Laws texture features. T1-weighted MRI of the brain from Center of Biomedical Research Excellence (COBRE) database were considered for analysis. Segmentation was carried out using the level-set method. Geometrical and Laws texture features were extracted from the segmented brain stem, corpus callosum, cerebellum, and ventricle regions to analyze pattern changes in SZ. The level-set method segmented multiple brain regions, with higher similarity and correlation values compared with an optimized method. The geometric features obtained from regions of the corpus callosum and ventricle showed significant variation (p < 0.00001) between normal and SZ brain. Laws texture feature identified a heterogeneous appearance in the brain stem, corpus callosum and ventricular regions, and features from the brain stem were correlated with Positive and Negative Syndrome Scale (PANSS) score (p < 0.005). A framework of geometric and Laws texture features obtained from brain subregions can be used as a supplement for diagnosis of psychiatric disorders.

Retrieval from long-term memory reduces working memory representations for visual features and their bindings.

PubMed

van Lamsweerde, Amanda E; Beck, Melissa R; Elliott, Emily M

2015-02-01

The ability to remember feature bindings is an important measure of the ability to maintain objects in working memory (WM). In this study, we investigated whether both object- and feature-based representations are maintained in WM. Specifically, we tested the hypotheses that retaining a greater number of feature representations (i.e., both as individual features and bound representations) results in a more robust representation of individual features than of feature bindings, and that retrieving information from long-term memory (LTM) into WM would cause a greater disruption to feature bindings. In four experiments, we examined the effects of retrieving a word from LTM on shape and color-shape binding change detection performance. We found that binding changes were more difficult to detect than individual-feature changes overall, but that the cost of retrieving a word from LTM was the same for both individual-feature and binding changes.

A persistent homology approach to collective behavior in insect swarms

NASA Astrophysics Data System (ADS)

Sinhuber, Michael; Ouellette, Nicholas T.

Various animals from birds and fish to insects tend to form aggregates, displaying self-organized collective swarming behavior. Due to their frequent occurrence in nature and their implications for engineered, collective systems, these systems have been investigated and modeled thoroughly for decades. Common approaches range from modeling them with coupled differential equations on the individual level up to continuum approaches. We present an alternative, topology-based approach for describing swarming behavior at the macroscale rather than the microscale. We study laboratory swarms of Chironomus riparius, a flying, non-biting midge. To obtain the time-resolved three-dimensional trajectories of individual insects, we use a multi-camera stereoimaging and particle-tracking setup. To investigate the swarming behavior in a topological sense, we employ a persistent homology approach to identify persisting structures and features in the insect swarm that elude a direct, ensemble-averaging approach. We are able to identify features of sub-clusters in the swarm that show behavior distinct from that of the remaining swarm members. The coexistence of sub-swarms with different features resembles some non-biological systems such as active colloids or even thermodynamic systems.

Photovoltaic module and interlocked stack of photovoltaic modules

DOEpatents

Wares, Brian S.

2014-09-02

One embodiment relates to an arrangement of photovoltaic modules configured for transportation. The arrangement includes a plurality of photovoltaic modules, each photovoltaic module including a frame. A plurality of individual male alignment features and a plurality of individual female alignment features are included on each frame. Adjacent photovoltaic modules are interlocked by multiple individual male alignment features on a first module of the adjacent photovoltaic modules fitting into and being surrounded by corresponding individual female alignment features on a second module of the adjacent photovoltaic modules. Other embodiments, features and aspects are also disclosed.

Exploring How Different Features of Animations of Sodium Chloride Dissolution Affect Students' Explanations

NASA Astrophysics Data System (ADS)

Kelly, Resa M.; Jones, Loretta L.

2007-10-01

Animations of molecular structure and dynamics are often used to help students understand the abstract ideas of chemistry. This qualitative study investigated how the features of two different styles of molecular-level animation affected students' explanations of how sodium chloride dissolves in water. In small group sessions 18 college-level general chemistry students dissolved table salt in water, after which they individually viewed two animations of salt dissolution. Before and after viewing each animation the participants provided pictorial, written, and oral explanations of the process at the macroscopic and molecular levels. The students then discussed the animations as a group. An analysis of the data showed that students incorporated some of the microscopic structural and functional features from the animations into their explanations. However, oral explanations revealed that in many cases, participants who drew or wrote correct explanations did not comprehend their meanings. Students' drawings may have reflected only what they had seen, rather than a cohesive understanding. Students' explanations given after viewing the animations improved, but some prior misconceptions were retained and in some cases, new misconceptions appeared. Students reported that they found the animations useful in learning; however, they sometimes missed essential features when they watched the animation alone.

Distributed acoustic cues for caller identity in macaque vocalization.

PubMed

Fukushima, Makoto; Doyle, Alex M; Mullarkey, Matthew P; Mishkin, Mortimer; Averbeck, Bruno B

2015-12-01

Individual primates can be identified by the sound of their voice. Macaques have demonstrated an ability to discern conspecific identity from a harmonically structured 'coo' call. Voice recognition presumably requires the integrated perception of multiple acoustic features. However, it is unclear how this is achieved, given considerable variability across utterances. Specifically, the extent to which information about caller identity is distributed across multiple features remains elusive. We examined these issues by recording and analysing a large sample of calls from eight macaques. Single acoustic features, including fundamental frequency, duration and Weiner entropy, were informative but unreliable for the statistical classification of caller identity. A combination of multiple features, however, allowed for highly accurate caller identification. A regularized classifier that learned to identify callers from the modulation power spectrum of calls found that specific regions of spectral-temporal modulation were informative for caller identification. These ranges are related to acoustic features such as the call's fundamental frequency and FM sweep direction. We further found that the low-frequency spectrotemporal modulation component contained an indexical cue of the caller body size. Thus, cues for caller identity are distributed across identifiable spectrotemporal components corresponding to laryngeal and supralaryngeal components of vocalizations, and the integration of those cues can enable highly reliable caller identification. Our results demonstrate a clear acoustic basis by which individual macaque vocalizations can be recognized.

Distributed acoustic cues for caller identity in macaque vocalization

PubMed Central

Doyle, Alex M.; Mullarkey, Matthew P.; Mishkin, Mortimer; Averbeck, Bruno B.

2015-01-01

Individual primates can be identified by the sound of their voice. Macaques have demonstrated an ability to discern conspecific identity from a harmonically structured ‘coo’ call. Voice recognition presumably requires the integrated perception of multiple acoustic features. However, it is unclear how this is achieved, given considerable variability across utterances. Specifically, the extent to which information about caller identity is distributed across multiple features remains elusive. We examined these issues by recording and analysing a large sample of calls from eight macaques. Single acoustic features, including fundamental frequency, duration and Weiner entropy, were informative but unreliable for the statistical classification of caller identity. A combination of multiple features, however, allowed for highly accurate caller identification. A regularized classifier that learned to identify callers from the modulation power spectrum of calls found that specific regions of spectral–temporal modulation were informative for caller identification. These ranges are related to acoustic features such as the call’s fundamental frequency and FM sweep direction. We further found that the low-frequency spectrotemporal modulation component contained an indexical cue of the caller body size. Thus, cues for caller identity are distributed across identifiable spectrotemporal components corresponding to laryngeal and supralaryngeal components of vocalizations, and the integration of those cues can enable highly reliable caller identification. Our results demonstrate a clear acoustic basis by which individual macaque vocalizations can be recognized. PMID:27019727

Peer Assessment for Learning from a Social Perspective: The Influence of Interpersonal Variables and Structural Features

ERIC Educational Resources Information Center

van Gennip, Nanine A. E.; Segers, Mien S. R.; Tillema, Harm H.

2009-01-01

This paper reports a systematic literature review examining empirical studies on the effects of peer assessment for learning. Peer assessment is fundamentally a social process whose core activity is feedback given to and received from others, aimed at enhancing the performance of each individual group member and/or the group as a whole. This makes…

Investigating Neuroanatomical Features in Top Athletes at the Single Subject Level.

PubMed

Taubert, Marco; Wenzel, Uwe; Draganski, Bogdan; Kiebel, Stefan J; Ragert, Patrick; Krug, Jürgen; Villringer, Arno

2015-01-01

In sport events like Olympic Games or World Championships competitive athletes keep pushing the boundaries of human performance. Compared to team sports, high achievements in many athletic disciplines depend solely on the individual's performance. Contrasting previous research looking for expertise-related differences in brain anatomy at the group level, we aim to demonstrate changes in individual top athlete's brain, which would be averaged out in a group analysis. We compared structural magnetic resonance images (MRI) of three professional track-and-field athletes to age-, gender- and education-matched control subjects. To determine brain features specific to these top athletes, we tested for significant deviations in structural grey matter density between each of the three top athletes and a carefully matched control sample. While total brain volumes were comparable between athletes and controls, we show regional grey matter differences in striatum and thalamus. The demonstrated brain anatomy patterns remained stable and were detected after 2 years with Olympic Games in between. We also found differences in the fusiform gyrus in two top long jumpers. We interpret our findings in reward-related areas as correlates of top athletes' persistency to reach top-level skill performance over years.

Time drawings: Spatial representation of temporal concepts.

PubMed

Leone, María Juliana; Salles, Alejo; Pulver, Alejandro; Golombek, Diego Andrés; Sigman, Mariano

2018-03-01

Time representation is a fundamental property of human cognition. Ample evidence shows that time (and numbers) are represented in space. However, how the conceptual mapping varies across individuals, scales, and temporal structures remains largely unknown. To investigate this issue, we conducted a large online study consisting in five experiments that addressed different time scales and topology: Zones of time, Seasons, Days of the week, Parts of the day and Timeline. Participants were asked to map different kinds of time events to a location in space and to determine their size and color. Results showed that time is organized in space in a hierarchical progression: some features appear to be universal (i.e. selection order), others are shaped by how time is organized in distinct cultures (i.e. location order) and, finally, some aspects vary depending on individual features such as age, gender, and chronotype (i.e. size and color). Copyright © 2018 Elsevier Inc. All rights reserved.

Empowering organizations: approaches to tobacco control through youth empowerment programs.

PubMed

LeRoy, Lisa; Benet, Dana Jones; Mason, Theresa; Austin, W David; Mills, Sherry

2004-10-01

Whereas most evaluations of youth empowerment focus on individual outcomes (i.e., were individual youths empowered?), this article focuses on the program as the unit of analysis and seeks to explain how organizational structures, program design features, and processes lead to organizational empowerment (OE). OE is defined as organizational efforts that generate psychological empowerment among members and organizational effectiveness needed for goal achievement. Case studies of five American Legacy Foundation-funded tobacco control youth empowerment programs were conducted during the first 2 years of implementation. Using an OE framework, the authors assessed program design features of the youth empowerment programs that contributed to or detracted from processes leading to OE. Comparing and contrasting the programs led to the identification of models and strategies that contribute to OE. Ecological influences of the state contexts (i.e., political climate, history of tobacco control, and public health infrastructure) were also examined.

Proceedings From the Turner Resource Network Symposium: The Crossroads of Health Care Research and Health Care Delivery

PubMed Central

Backeljauw, Philippe F.; Bondy, Carolyn; Chernausek, Steven D.; Cernich, Joseph T.; Cole, David A.; Fasciano, Laura P.; Foodim, Joan; Hawley, Scott; Hong, David S.; Knickmeyer, Rebecca C.; Kruszka, Paul; Lin, Angela E.; Lippe, Barbara M.; Lorigan, Gary A.; Maslen, Cheryl L.; Mauras, Nelly; Page, David C.; Pemberton, Victoria L.; Prakash, Siddharth K.; Quigley, Charmian A.; Ranallo, Kelly C.; Reiss, Allan L.; Sandberg, David E.; Scurlock, Cindy; Silberbach, Michael

2016-01-01

Turner syndrome, a congenital condition that affects ∼1/2,500 births, results from absence or structural alteration of the second sex chromosome. There has been substantial effort by numerous clinical and genetic research groups to delineate the clinical, pathophysiological, cytogenetic, and molecular features of this multisystem condition. Questions about the molecular-genetic and biological basis of many of the clinical features remain unanswered, and health care providers and families seek improved care for affected individuals. The inaugural “Turner Resource Network (TRN) Symposium” brought together individuals with Turner syndrome and their families, advocacy group leaders, clinicians, basic scientists, physician-scientists, trainees and other stakeholders with interest in the well-being of individuals and families living with the condition. The goal of this symposium was to establish a structure for a TRN that will be a patient-powered organization involving those living with Turner syndrome, their families, clinicians, and scientists. The TRN will identify basic and clinical questions that might be answered with registries, clinical trials, or through bench research to promote and advocate for best practices and improved care for individuals with Turner syndrome. The symposium concluded with the consensus that two rationales justify the creation of a TRN: inadequate attention has been paid to the health and psychosocial issues facing girls and women who live with Turner syndrome;investigations into the susceptibility to common disorders such as cardiovascular or autoimmune diseases caused by sex chromosome deficiencies will increase understanding of disease susceptibilities in the general population. PMID:25920614

A cognitive-affective system theory of personality: reconceptualizing situations, dispositions, dynamics, and invariance in personality structure.

PubMed

Mischel, W; Shoda, Y

1995-04-01

A theory was proposed to reconcile paradoxical findings on the invariance of personality and the variability of behavior across situations. For this purpose, individuals were assumed to differ in (a) the accessibility of cognitive-affective mediating units (such as encodings, expectancies and beliefs, affects, and goals) and (b) the organization of relationships through which these units interact with each other and with psychological features of situations. The theory accounts for individual differences in predictable patterns of variability across situations (e.g., if A then she X, but if B then she Y), as well as for overall average levels of behavior, as essential expressions or behavioral signatures of the same underlying personality system. Situations, personality dispositions, dynamics, and structure were reconceptualized from this perspective.

Improved data visualization techniques for analyzing macromolecule structural changes.

PubMed

Kim, Jae Hyun; Iyer, Vidyashankara; Joshi, Sangeeta B; Volkin, David B; Middaugh, C Russell

2012-10-01

The empirical phase diagram (EPD) is a colored representation of overall structural integrity and conformational stability of macromolecules in response to various environmental perturbations. Numerous proteins and macromolecular complexes have been analyzed by EPDs to summarize results from large data sets from multiple biophysical techniques. The current EPD method suffers from a number of deficiencies including lack of a meaningful relationship between color and actual molecular features, difficulties in identifying contributions from individual techniques, and a limited ability to be interpreted by color-blind individuals. In this work, three improved data visualization approaches are proposed as techniques complementary to the EPD. The secondary, tertiary, and quaternary structural changes of multiple proteins as a function of environmental stress were first measured using circular dichroism, intrinsic fluorescence spectroscopy, and static light scattering, respectively. Data sets were then visualized as (1) RGB colors using three-index EPDs, (2) equiangular polygons using radar charts, and (3) human facial features using Chernoff face diagrams. Data as a function of temperature and pH for bovine serum albumin, aldolase, and chymotrypsin as well as candidate protein vaccine antigens including a serine threonine kinase protein (SP1732) and surface antigen A (SP1650) from S. pneumoniae and hemagglutinin from an H1N1 influenza virus are used to illustrate the advantages and disadvantages of each type of data visualization technique. Copyright © 2012 The Protein Society.

Improved data visualization techniques for analyzing macromolecule structural changes

PubMed Central

Kim, Jae Hyun; Iyer, Vidyashankara; Joshi, Sangeeta B; Volkin, David B; Middaugh, C Russell

2012-01-01

The empirical phase diagram (EPD) is a colored representation of overall structural integrity and conformational stability of macromolecules in response to various environmental perturbations. Numerous proteins and macromolecular complexes have been analyzed by EPDs to summarize results from large data sets from multiple biophysical techniques. The current EPD method suffers from a number of deficiencies including lack of a meaningful relationship between color and actual molecular features, difficulties in identifying contributions from individual techniques, and a limited ability to be interpreted by color-blind individuals. In this work, three improved data visualization approaches are proposed as techniques complementary to the EPD. The secondary, tertiary, and quaternary structural changes of multiple proteins as a function of environmental stress were first measured using circular dichroism, intrinsic fluorescence spectroscopy, and static light scattering, respectively. Data sets were then visualized as (1) RGB colors using three-index EPDs, (2) equiangular polygons using radar charts, and (3) human facial features using Chernoff face diagrams. Data as a function of temperature and pH for bovine serum albumin, aldolase, and chymotrypsin as well as candidate protein vaccine antigens including a serine threonine kinase protein (SP1732) and surface antigen A (SP1650) from S. pneumoniae and hemagglutinin from an H1N1 influenza virus are used to illustrate the advantages and disadvantages of each type of data visualization technique. PMID:22898970

A wirelessly programmable actuation and sensing system for structural health monitoring

NASA Astrophysics Data System (ADS)

Long, James; Büyüköztürk, Oral

2016-04-01

Wireless sensor networks promise to deliver low cost, low power and massively distributed systems for structural health monitoring. A key component of these systems, particularly when sampling rates are high, is the capability to process data within the network. Although progress has been made towards this vision, it remains a difficult task to develop and program 'smart' wireless sensing applications. In this paper we present a system which allows data acquisition and computational tasks to be specified in Python, a high level programming language, and executed within the sensor network. Key features of this system include the ability to execute custom application code without firmware updates, to run multiple users' requests concurrently and to conserve power through adjustable sleep settings. Specific examples of sensor node tasks are given to demonstrate the features of this system in the context of structural health monitoring. The system comprises of individual firmware for nodes in the wireless sensor network, and a gateway server and web application through which users can remotely submit their requests.

Animal Construction as a Free Boundary Problem: Evidence of Fractal Scaling Laws

NASA Astrophysics Data System (ADS)

Nicolis, S. C.

2014-12-01

We suggest that the main features of animal construction can be understood as the sum of locally independent actions of non-interacting individuals subjected to the global constraints imposed by the nascent structure. We first formulate an analytically tractable oscopic description of construction which predicts a 1/3 power law for how the length of the structure grows with time. We further show how the power law is modified when biases in random walk performed by the constructors as well as halting times between consecutive construction steps are included.

Design of an activity landscape view taking compound-based feature probabilities into account.

PubMed

Zhang, Bijun; Vogt, Martin; Bajorath, Jürgen

2014-09-01

Activity landscapes (ALs) of compound data sets are rationalized as graphical representations that integrate similarity and potency relationships between active compounds. ALs enable the visualization of structure-activity relationship (SAR) information and are thus computational tools of interest for medicinal chemistry. For AL generation, similarity and potency relationships are typically evaluated in a pairwise manner and major AL features are assessed at the level of compound pairs. In this study, we add a conditional probability formalism to AL design that makes it possible to quantify the probability of individual compounds to contribute to characteristic AL features. Making this information graphically accessible in a molecular network-based AL representation is shown to further increase AL information content and helps to quickly focus on SAR-informative compound subsets. This feature probability-based AL variant extends the current spectrum of AL representations for medicinal chemistry applications.

Towards in vivo focal cortical dysplasia phenotyping using quantitative MRI.

PubMed

Adler, Sophie; Lorio, Sara; Jacques, Thomas S; Benova, Barbora; Gunny, Roxana; Cross, J Helen; Baldeweg, Torsten; Carmichael, David W

2017-01-01

Focal cortical dysplasias (FCDs) are a range of malformations of cortical development each with specific histopathological features. Conventional radiological assessment of standard structural MRI is useful for the localization of lesions but is unable to accurately predict the histopathological features. Quantitative MRI offers the possibility to probe tissue biophysical properties in vivo and may bridge the gap between radiological assessment and ex-vivo histology. This review will cover histological, genetic and radiological features of FCD following the ILAE classification and will explain how quantitative voxel- and surface-based techniques can characterise these features. We will provide an overview of the quantitative MRI measures available, their link with biophysical properties and finally the potential application of quantitative MRI to the problem of FCD subtyping. Future research linking quantitative MRI to FCD histological properties should improve clinical protocols, allow better characterisation of lesions in vivo and tailored surgical planning to the individual.

SMOQ: a tool for predicting the absolute residue-specific quality of a single protein model with support vector machines

PubMed Central

2014-01-01

Background It is important to predict the quality of a protein structural model before its native structure is known. The method that can predict the absolute local quality of individual residues in a single protein model is rare, yet particularly needed for using, ranking and refining protein models. Results We developed a machine learning tool (SMOQ) that can predict the distance deviation of each residue in a single protein model. SMOQ uses support vector machines (SVM) with protein sequence and structural features (i.e. basic feature set), including amino acid sequence, secondary structures, solvent accessibilities, and residue-residue contacts to make predictions. We also trained a SVM model with two new additional features (profiles and SOV scores) on 20 CASP8 targets and found that including them can only improve the performance when real deviations between native and model are higher than 5Å. The SMOQ tool finally released uses the basic feature set trained on 85 CASP8 targets. Moreover, SMOQ implemented a way to convert predicted local quality scores into a global quality score. SMOQ was tested on the 84 CASP9 single-domain targets. The average difference between the residue-specific distance deviation predicted by our method and the actual distance deviation on the test data is 2.637Å. The global quality prediction accuracy of the tool is comparable to other good tools on the same benchmark. Conclusion SMOQ is a useful tool for protein single model quality assessment. Its source code and executable are available at: http://sysbio.rnet.missouri.edu/multicom_toolbox/. PMID:24776231

SMOQ: a tool for predicting the absolute residue-specific quality of a single protein model with support vector machines.

PubMed

Cao, Renzhi; Wang, Zheng; Wang, Yiheng; Cheng, Jianlin

2014-04-28

It is important to predict the quality of a protein structural model before its native structure is known. The method that can predict the absolute local quality of individual residues in a single protein model is rare, yet particularly needed for using, ranking and refining protein models. We developed a machine learning tool (SMOQ) that can predict the distance deviation of each residue in a single protein model. SMOQ uses support vector machines (SVM) with protein sequence and structural features (i.e. basic feature set), including amino acid sequence, secondary structures, solvent accessibilities, and residue-residue contacts to make predictions. We also trained a SVM model with two new additional features (profiles and SOV scores) on 20 CASP8 targets and found that including them can only improve the performance when real deviations between native and model are higher than 5Å. The SMOQ tool finally released uses the basic feature set trained on 85 CASP8 targets. Moreover, SMOQ implemented a way to convert predicted local quality scores into a global quality score. SMOQ was tested on the 84 CASP9 single-domain targets. The average difference between the residue-specific distance deviation predicted by our method and the actual distance deviation on the test data is 2.637Å. The global quality prediction accuracy of the tool is comparable to other good tools on the same benchmark. SMOQ is a useful tool for protein single model quality assessment. Its source code and executable are available at: http://sysbio.rnet.missouri.edu/multicom_toolbox/.

Inkjet Printing of Functional and Structural Materials: Fluid Property Requirements, Feature Stability, and Resolution

NASA Astrophysics Data System (ADS)

Derby, Brian

2010-08-01

Inkjet printing is viewed as a versatile manufacturing tool for applications in materials fabrication in addition to its traditional role in graphics output and marking. The unifying feature in all these applications is the dispensing and precise positioning of very small volumes of fluid (1-100 picoliters) on a substrate before transformation to a solid. The application of inkjet printing to the fabrication of structures for structural or functional materials applications requires an understanding as to how the physical processes that operate during inkjet printing interact with the properties of the fluid precursors used. Here we review the current state of understanding of the mechanisms of drop formation and how this defines the fluid properties that are required for a given liquid to be printable. The interactions between individual drops and the substrate as well as between adjacent drops are important in defining the resolution and accuracy of printed objects. Pattern resolution is limited by the extent to which a liquid drop spreads on a substrate and how spreading changes with the overlap of adjacent drops to form continuous features. There are clearly defined upper and lower bounds to the width of a printed continuous line, which can be defined in terms of materials and process variables. Finer-resolution features can be achieved through appropriate patterning and structuring of the substrate prior to printing, which is essential if polymeric semiconducting devices are to be fabricated. Low advancing and receding contact angles promote printed line stability but are also more prone to solute segregation or “coffee staining” on drying.

Metacognitive impairment in active cocaine use disorder is associated with individual differences in brain structure

PubMed Central

Moeller, Scott J.; Fleming, Stephen M.; Gan, Gabriela; Zilverstand, Anna; Malaker, Pias; Uquillas, Federico d’Oleire; Schneider, Kristin E.; Preston-Campbell, Rebecca; Parvaz, Muhammad A.; Maloney, Thomas; Alia-Klein, Nelly; Goldstein, Rita Z.

2016-01-01

Dysfunctional self-awareness has been posited as a key feature of drug addiction, contributing to compromised control over addictive behaviors. In the present investigation, we showed that, compared with healthy controls (n=13) and even individuals with remitted cocaine use disorder (n=14), individuals with active cocaine use disorder (n=8) exhibited deficits in basic metacognition, defined as a weaker link between objective performance and self-reported confidence of performance on a visuo-perceptual accuracy task. This metacognitive deficit was accompanied by gray matter volume decreases, also most pronounced in individuals with active cocaine use disorder, in the rostral anterior cingulate cortex, a region necessary for this function in health. Our results thus provide a direct unbiased measurement – not relying on long-term memory or multifaceted choice behavior – of metacognition deficits in drug addiction, which are further mapped onto structural deficits in a brain region that subserves metacognitive accuracy in health and self-awareness in drug addiction. Impairments of metacognition could provide a basic mechanism underlying the higher-order self-awareness deficits in addiction, particularly among recent, active users. PMID:26948669

Shaping skeletal growth by modular regulatory elements in the Bmp5 gene.

PubMed

Guenther, Catherine; Pantalena-Filho, Luiz; Kingsley, David M

2008-12-01

Cartilage and bone are formed into a remarkable range of shapes and sizes that underlie many anatomical adaptations to different lifestyles in vertebrates. Although the morphological blueprints for individual cartilage and bony structures must somehow be encoded in the genome, we currently know little about the detailed genomic mechanisms that direct precise growth patterns for particular bones. We have carried out large-scale enhancer surveys to identify the regulatory architecture controlling developmental expression of the mouse Bmp5 gene, which encodes a secreted signaling molecule required for normal morphology of specific skeletal features. Although Bmp5 is expressed in many skeletal precursors, different enhancers control expression in individual bones. Remarkably, we show here that different enhancers also exist for highly restricted spatial subdomains along the surface of individual skeletal structures, including ribs and nasal cartilages. Transgenic, null, and regulatory mutations confirm that these anatomy-specific sequences are sufficient to trigger local changes in skeletal morphology and are required for establishing normal growth rates on separate bone surfaces. Our findings suggest that individual bones are composite structures whose detailed growth patterns are built from many smaller lineage and gene expression domains. Individual enhancers in BMP genes provide a genomic mechanism for controlling precise growth domains in particular cartilages and bones, making it possible to separately regulate skeletal anatomy at highly specific locations in the body.

Computer ranking of the sequence of appearance of 100 features of the brain and related structures in staged human embryos during the first 5 weeks of development.

PubMed

O'Rahilly, R; Müller, F; Hutchins, G M; Moore, G W

1984-11-01

The sequence of events in the development of the brain in staged human embryos was investigated in much greater detail than in previous studies by listing 100 features in 165 embryos of the first 5 weeks. Using a computerized bubble-sort algorithm, individual embryos were ranked in ascending order of the features present. This procedure made feasible an appreciation of the slight variation found in the developmental features. The vast majority of features appeared during either one or two stages (about 2 or 3 days). In general, the soundness of the Carnegie system of embryonic staging was amply confirmed. The rhombencephalon was found to show increasing complexity around stage 13, and the postoptic portion of the diencephalon underwent considerable differentiation by stage 15. The need for similar investigations of other systems of the body is emphasized, and the importance of such studies in assessing the timing of congenital malformations and in clarifying syndromic clusters is suggested.

Semantic memory: a feature-based analysis and new norms for Italian.

PubMed

Montefinese, Maria; Ambrosini, Ettore; Fairfield, Beth; Mammarella, Nicola

2013-06-01

Semantic norms for properties produced by native speakers are valuable tools for researchers interested in the structure of semantic memory and in category-specific semantic deficits in individuals following brain damage. The aims of this study were threefold. First, we sought to extend existing semantic norms by adopting an empirical approach to category (Exp. 1) and concept (Exp. 2) selection, in order to obtain a more representative set of semantic memory features. Second, we extensively outlined a new set of semantic production norms collected from Italian native speakers for 120 artifactual and natural basic-level concepts, using numerous measures and statistics following a feature-listing task (Exp. 3b). Finally, we aimed to create a new publicly accessible database, since only a few existing databases are publicly available online.

[Morphochemical changes in the substantia nigra cellular structures in Parkinson's disease].

PubMed

Salkov, V N; Khudoerkov, R M; Voronkov, D N; Sobolev, V B; Kutukova, K A

to clarify the features of morphochemical changes in the substantia nigra cellular structures in Parkinson's disease. The structural characteristics of the substantia nigra were studied microscopically and quantified using computer morphometric methods at brain autopsies of individuals with Parkinson's disease who had died from intercurrent diseases and those who had no evidence of neurological disorders in their history (a control group). This investigation could clarify the features of morphochemical changes in both the neural network structures and the glial populations of the substantia nigra in Parkinson's disease. The number of neurons containing tyrosine hydroxylase (a marker of dopamine neurons) in the compact part of the substantia nigra (a ventral region) was smaller and the density distribution of Lewy bodies was higher in the patients with Parkinson's disease than in the control group. The accumulation of iron (II) compounds in the cellular elements and neuropile and the increased expression of glial fibrillary acidic protein in Parkinson's disease were more pronounced than those in the controls. Postmortem diagnosis in Parkinson's disease should be based on a full description of a set of neuronal and glial morphochemical and structural changes in the substantia nigra rather than on the identification of cellular markers for the neurodegenerative process.

Perception of Leitmotives in Richard Wagner's Der Ring des Nibelungen.

PubMed

Baker, David J; Müllensiefen, Daniel

2017-01-01

The music of Richard Wagner tends to generate very diverse judgments indicative of the complex relationship between listeners and the sophisticated musical structures in Wagner's music. This paper presents findings from two listening experiments using the music from Wagner's Der Ring des Nibelungen that explores musical as well as individual listener parameters to better understand how listeners are able to hear leitmotives, a compositional device closely associated with Wagner's music. Results confirm findings from a previous experiment showing that specific expertise with Wagner's music can account for a greater portion of the variance in an individual's ability to recognize and remember musical material compared to measures of generic musical training. Results also explore how acoustical distance of the leitmotives affects memory recognition using a chroma similarity measure. In addition, we show how characteristics of the compositional structure of the leitmotives contributes to their salience and memorability. A final model is then presented that accounts for the aforementioned individual differences factors, as well as parameters of musical surface and structure. Our results suggest that that future work in music perception may consider both individual differences variables beyond musical training, as well as symbolic features and audio commonly used in music information retrieval in order to build robust models of musical perception and cognition.

Perception of Leitmotives in Richard Wagner's Der Ring des Nibelungen

PubMed Central

Baker, David J.; Müllensiefen, Daniel

2017-01-01

The music of Richard Wagner tends to generate very diverse judgments indicative of the complex relationship between listeners and the sophisticated musical structures in Wagner's music. This paper presents findings from two listening experiments using the music from Wagner's Der Ring des Nibelungen that explores musical as well as individual listener parameters to better understand how listeners are able to hear leitmotives, a compositional device closely associated with Wagner's music. Results confirm findings from a previous experiment showing that specific expertise with Wagner's music can account for a greater portion of the variance in an individual's ability to recognize and remember musical material compared to measures of generic musical training. Results also explore how acoustical distance of the leitmotives affects memory recognition using a chroma similarity measure. In addition, we show how characteristics of the compositional structure of the leitmotives contributes to their salience and memorability. A final model is then presented that accounts for the aforementioned individual differences factors, as well as parameters of musical surface and structure. Our results suggest that that future work in music perception may consider both individual differences variables beyond musical training, as well as symbolic features and audio commonly used in music information retrieval in order to build robust models of musical perception and cognition. PMID:28522981

Recombinant PrPSc shares structural features with brain-derived PrPSc suggesting that they have a similar architecture: Insights from limited proteolysis

USDA-ARS?s Scientific Manuscript database

An extensive body of experimental and spectroscopic evidence supports the hypothesis that PrPSc is a multimer of 4-rung ß-solenoids, and that individual PrPSc solenoids stack to form amyloid fibers. We recently used limited proteolysis to map the ß-strands and connecting loops that make up the PrPSc...

Experimental evolution of multicellularity using microbial pseudo-organisms.

PubMed

Queller, David C; Strassmann, Joan E

2013-02-23

In a major evolutionary transition to a new level of organization, internal conflicts must be controlled before the transition can truly be successful. One such transition is that from single cells to multicellularity. Conflicts among cells in multicellular organisms can be greatly reduced if they consist of genetically identical clones. However, mutations to cheaters that experience one round of within-individual selection could still be a problem, particularly for certain life cycles. We propose an experimental evolution method to investigate this issue, using micro-organisms to construct multicellular pseudo-organisms, which can be evolved under different artificial life cycles. These experiments can be used to test the importance of various life cycle features in maintaining cooperation. They include structured reproduction, in which small propagule size reduces within-individual genetic variation. They also include structured growth, which increases local relatedness within individual bodies. Our method provides a novel way to test how different life cycles favour cooperation, even for life cycles that do not exist.

Subjective face recognition difficulties, aberrant sensibility, sleeping disturbances and aberrant eating habits in families with Asperger syndrome

PubMed Central

Nieminen-von Wendt, Taina; Paavonen, Juulia E; Ylisaukko-Oja, Tero; Sarenius, Susan; Källman, Tiia; Järvelä, Irma; von Wendt, Lennart

2005-01-01

Background The present study was undertaken in order to determine whether a set of clinical features, which are not included in the DSM-IV or ICD-10 for Asperger Syndrome (AS), are associated with AS in particular or whether they are merely a familial trait that is not related to the diagnosis. Methods Ten large families, a total of 138 persons, of whom 58 individuals fulfilled the diagnostic criteria for AS and another 56 did not to fulfill these criteria, were studied using a structured interview focusing on the possible presence of face recognition difficulties, aberrant sensibility and eating habits and sleeping disturbances. Results The prevalence for face recognition difficulties was 46.6% in individuals with AS compared with 10.7% in the control group. The corresponding figures for subjectively reported presence of aberrant sensibilities were 91.4% and 46.6%, for sleeping disturbances 48.3% and 23.2% and for aberrant eating habits 60.3% and 14.3%, respectively. Conclusion An aberrant processing of sensory information appears to be a common feature in AS. The impact of these and other clinical features that are not incorporated in the ICD-10 and DSM-IV on our understanding of AS may hitherto have been underestimated. These associated clinical traits may well be reflected by the behavioural characteristics of these individuals. PMID:15826308

X-ray crystallographic studies of RNase A variants engineered at the most destabilizing positions of the main hydrophobic core: further insight into protein stability.

PubMed

Kurpiewska, Katarzyna; Font, Josep; Ribó, Marc; Vilanova, Maria; Lewiński, Krzysztof

2009-11-15

To investigate the structural origin of decreased pressure and temperature stability, the crystal structure of bovine pancreatic ribonuclease A variants V47A, V54A, V57A, I81A, I106A, and V108A was solved at 1.4-2.0 A resolution and compared with the structure of wild-type protein. The introduced mutations had only minor influence on the global structure of ribonuclease A. The structural changes had individual character that depends on the localization of mutated residue, however, they seemed to expand from mutation site to the rest of the structure. Several different parameters have been evaluated to find correlation with decrease of free energy of unfolding DeltaDeltaG(T), and the most significant correlation was found for main cavity volume change. Analysis of the difference distance matrices revealed that the ribonuclease A molecule is organized into five relatively rigid subdomains with individual response to mutation. This behavior consistent with results of unfolding experiments is an intrinsic feature of ribonuclease A that might be surviving remnants of folding intermediates and reflects the dynamic nature of the molecule. 2009 Wiley-Liss, Inc.

Correlations in Scattered X-Ray Laser Pulses Reveal Nanoscale Structural Features of Viruses

NASA Astrophysics Data System (ADS)

Kurta, Ruslan P.; Donatelli, Jeffrey J.; Yoon, Chun Hong; Berntsen, Peter; Bielecki, Johan; Daurer, Benedikt J.; DeMirci, Hasan; Fromme, Petra; Hantke, Max Felix; Maia, Filipe R. N. C.; Munke, Anna; Nettelblad, Carl; Pande, Kanupriya; Reddy, Hemanth K. N.; Sellberg, Jonas A.; Sierra, Raymond G.; Svenda, Martin; van der Schot, Gijs; Vartanyants, Ivan A.; Williams, Garth J.; Xavier, P. Lourdu; Aquila, Andrew; Zwart, Peter H.; Mancuso, Adrian P.

2017-10-01

We use extremely bright and ultrashort pulses from an x-ray free-electron laser (XFEL) to measure correlations in x rays scattered from individual bioparticles. This allows us to go beyond the traditional crystallography and single-particle imaging approaches for structure investigations. We employ angular correlations to recover the three-dimensional (3D) structure of nanoscale viruses from x-ray diffraction data measured at the Linac Coherent Light Source. Correlations provide us with a comprehensive structural fingerprint of a 3D virus, which we use both for model-based and ab initio structure recovery. The analyses reveal a clear indication that the structure of the viruses deviates from the expected perfect icosahedral symmetry. Our results anticipate exciting opportunities for XFEL studies of the structure and dynamics of nanoscale objects by means of angular correlations.

Structural and functional correlates of motor imagery BCI performance: Insights from the patterns of fronto-parietal attention network.

PubMed

Zhang, Tao; Liu, Tiejun; Li, Fali; Li, Mengchen; Liu, Dongbo; Zhang, Rui; He, Hui; Li, Peiyang; Gong, Jinnan; Luo, Cheng; Yao, Dezhong; Xu, Peng

2016-07-01

Motor imagery (MI)-based brain-computer interfaces (BCIs) have been widely used for rehabilitation of motor abilities and prosthesis control for patients with motor impairments. However, MI-BCI performance exhibits a wide variability across subjects, and the underlying neural mechanism remains unclear. Several studies have demonstrated that both the fronto-parietal attention network (FPAN) and MI are involved in high-level cognitive processes that are crucial for the control of BCIs. Therefore, we hypothesized that the FPAN may play an important role in MI-BCI performance. In our study, we recorded multi-modal datasets consisting of MI electroencephalography (EEG) signals, T1-weighted structural and resting-state functional MRI data for each subject. MI-BCI performance was evaluated using the common spatial pattern to extract the MI features from EEG signals. One cortical structural feature (cortical thickness (CT)) and two measurements (degree centrality (DC) and eigenvector centrality (EC)) of node centrality were derived from the structural and functional MRI data, respectively. Based on the information extracted from the EEG and MRI, a correlation analysis was used to elucidate the relationships between the FPAN and MI-BCI performance. Our results show that the DC of the right ventral intraparietal sulcus, the EC and CT of the left inferior parietal lobe, and the CT of the right dorsolateral prefrontal cortex were significantly associated with MI-BCI performance. Moreover, the receiver operating characteristic analysis and machine learning classification revealed that the EC and CT of the left IPL could effectively predict the low-aptitude BCI users from the high-aptitude BCI users with 83.3% accuracy. Those findings consistently reveal that the individuals who have efficient FPAN would perform better on MI-BCI. Our findings may deepen the understanding of individual variability in MI-BCI performance, and also may provide a new biomarker to predict individual MI-BCI performance. Copyright © 2016 Elsevier Inc. All rights reserved.

Small-scale Magnetic Flux Emergence in the Quiet Sun

NASA Astrophysics Data System (ADS)

Moreno-Insertis, F.; Martinez-Sykora, J.; Hansteen, V. H.; Muñoz, D.

2018-06-01

Small bipolar magnetic features are observed to appear in the interior of individual granules in the quiet Sun, signaling the emergence of tiny magnetic loops from the solar interior. We study the origin of those features as part of the magnetoconvection process in the top layers of the convection zone. Two quiet-Sun magnetoconvection models, calculated with the radiation-magnetohydrodynamic (MHD) Bifrost code and with domain stretching from the top layers of the convection zone to the corona, are analyzed. Using 3D visualization as well as a posteriori spectral synthesis of Stokes parameters, we detect the repeated emergence of small magnetic elements in the interior of granules, as in the observations. Additionally, we identify the formation of organized horizontal magnetic sheets covering whole granules. Our approach is twofold, calculating statistical properties of the system, like joint probability density functions (JPDFs), and pursuing individual events via visualization tools. We conclude that the small magnetic loops surfacing within individual granules in the observations may originate from sites at or near the downflows in the granular and mesogranular levels, probably in the first 1 or 1.5 Mm below the surface. We also document the creation of granule-covering magnetic sheet-like structures through the sideways expansion of a small subphotospheric magnetic concentration picked up and pulled out of the interior by a nascent granule. The sheet-like structures that we found in the models may match the recent observations of Centeno et al.

Novel measures of linkage disequilibrium that correct the bias due to population structure and relatedness.

PubMed

Mangin, B; Siberchicot, A; Nicolas, S; Doligez, A; This, P; Cierco-Ayrolles, C

2012-03-01

Among the several linkage disequilibrium measures known to capture different features of the non-independence between alleles at different loci, the most commonly used for diallelic loci is the r(2) measure. In the present study, we tackled the problem of the bias of r(2) estimate, which results from the sample structure and/or the relatedness between genotyped individuals. We derived two novel linkage disequilibrium measures for diallelic loci that are both extensions of the usual r(2) measure. The first one, r(S)(2), uses the population structure matrix, which consists of information about the origins of each individual and the admixture proportions of each individual genome. The second one, r(V)(2), includes the kinship matrix into the calculation. These two corrections can be applied together in order to correct for both biases and are defined either on phased or unphased genotypes.We proved that these novel measures are linked to the power of association tests under the mixed linear model including structure and kinship corrections. We validated them on simulated data and applied them to real data sets collected on Vitis vinifera plants. Our results clearly showed the usefulness of the two corrected r(2) measures, which actually captured 'true' linkage disequilibrium unlike the usual r(2) measure.

Design and evaluation of a modular lower limb exoskeleton for rehabilitation.

PubMed

Dos Santos, Wilian M; Nogueira, Samuel L; de Oliveira, Gustavo C; Pena, Guido G; Siqueira, Adriano A G

2017-07-01

This paper deals with the evaluation of an exoskeleton designed for assisting individuals to rehabilitate compromised lower limb movements resulting from stroke or incomplete spinal cord injury. The exoskeleton is composed of lightweight tubular structures and six free joints that provide a modular feature to the system. This feature allows the exoskeleton to be adapted to assist the movement of one or more patient joints. The actuation of the exoskeleton is also modular, and can be performed passively, by means of springs and dampers, or actively through actuators. In addition, its telescopic tubular links, developed to adjust the size of the links in order to align the joints of the exoskeleton with patient joints, allows the exoskeleton to be adjustable to fit different patients. Experiments considering the interaction between a healthy subject and the exoskeleton are performed to evaluate the influence of the exoskeleton structure on kinematic and muscular activity profiles during walking.

Streaks, multiplets, and holes: High-resolution spatio-temporal behavior of Parkfield seismicity

USGS Publications Warehouse

Waldhauser, F.; Ellsworth, W.L.; Schaff, D.P.; Cole, A.

2004-01-01

Double-difference locations of ???8000 earthquakes from 1969-2002 on the Parkfield section of the San Andreas Fault reveal detailed fault structures and seismicity that is, although complex, highly organized in both space and time. Distinctive features of the seismicity include: 1) multiple recurrence of earthquakes of the same size at precisely the same location on the fault (multiplets), implying frictional or geometric controls on their location and size; 2) sub-horizontal alignments of hypocenters along the fault plane (streaks), suggestive of rheological transitions within the fault zone and/or stress concentrations between locked and creeping areas; 3) regions devoid of microearthquakes with typical dimensions of 1-5 km (holes), one of which contains the M6 1966 Parkfield earthquake hypocenter. These features represent long lived structures that persist through many cycles of individual event. Copyright 2004 by the American Geophysical Union.

A new procedure for dynamic adaption of three-dimensional unstructured grids

NASA Technical Reports Server (NTRS)

Biswas, Rupak; Strawn, Roger

1993-01-01

A new procedure is presented for the simultaneous coarsening and refinement of three-dimensional unstructured tetrahedral meshes. This algorithm allows for localized grid adaption that is used to capture aerodynamic flow features such as vortices and shock waves in helicopter flowfield simulations. The mesh-adaption algorithm is implemented in the C programming language and uses a data structure consisting of a series of dynamically-allocated linked lists. These lists allow the mesh connectivity to be rapidly reconstructed when individual mesh points are added and/or deleted. The algorithm allows the mesh to change in an anisotropic manner in order to efficiently resolve directional flow features. The procedure has been successfully implemented on a single processor of a Cray Y-MP computer. Two sample cases are presented involving three-dimensional transonic flow. Computed results show good agreement with conventional structured-grid solutions for the Euler equations.

Individual differences in brain structure and resting brain function underlie cognitive styles: evidence from the Embedded Figures Test.

PubMed

Hao, Xin; Wang, Kangcheng; Li, Wenfu; Yang, Wenjing; Wei, Dongtao; Qiu, Jiang; Zhang, Qinglin

2013-01-01

Cognitive styles can be characterized as individual differences in the way people perceive, think, solve problems, learn, and relate to others. Field dependence/independence (FDI) is an important and widely studied dimension of cognitive styles. Although functional imaging studies have investigated the brain activation of FDI cognitive styles, the combined structural and functional correlates with individual differences in a large sample have never been investigated. In the present study, we investigated the neural correlates of individual differences in FDI cognitive styles by analyzing the correlations between Embedded Figures Test (EFT) score and structural neuroimaging data [regional gray matter volume (rGMV) was assessed using voxel-based morphometry (VBM)]/functional neuroimaging data [resting-brain functions were measured by amplitude of low-frequency fluctuation (ALFF)] throughout the whole brain. Results showed that the increased rGMV in the left inferior parietal lobule (IPL) was associated with the EFT score, which might be the structural basis of effective local processing. Additionally, a significant positive correlation between ALFF and EFT score was found in the fronto-parietal network, including the left inferior parietal lobule (IPL) and the medial prefrontal cortex (mPFC). We speculated that the left IPL might be associated with superior feature identification, and mPFC might be related to cognitive inhibition of global processing bias. These results suggested that the underlying neuroanatomical and functional bases were linked to the individual differences in FDI cognitive styles and emphasized the important contribution of superior local processing ability and cognitive inhibition to field-independent style.

Individual Differences in Brain Structure and Resting Brain Function Underlie Cognitive Styles: Evidence from the Embedded Figures Test

PubMed Central

Hao, Xin; Wang, Kangcheng; Li, Wenfu; Yang, Wenjing; Wei, Dongtao; Qiu, Jiang; Zhang, Qinglin

2013-01-01

Cognitive styles can be characterized as individual differences in the way people perceive, think, solve problems, learn, and relate to others. Field dependence/independence (FDI) is an important and widely studied dimension of cognitive styles. Although functional imaging studies have investigated the brain activation of FDI cognitive styles, the combined structural and functional correlates with individual differences in a large sample have never been investigated. In the present study, we investigated the neural correlates of individual differences in FDI cognitive styles by analyzing the correlations between Embedded Figures Test (EFT) score and structural neuroimaging data [regional gray matter volume (rGMV) was assessed using voxel-based morphometry (VBM)] / functional neuroimaging data [resting-brain functions were measured by amplitude of low-frequency fluctuation (ALFF)] throughout the whole brain. Results showed that the increased rGMV in the left inferior parietal lobule (IPL) was associated with the EFT score, which might be the structural basis of effective local processing. Additionally, a significant positive correlation between ALFF and EFT score was found in the fronto-parietal network, including the left inferior parietal lobule (IPL) and the medial prefrontal cortex (mPFC). We speculated that the left IPL might be associated with superior feature identification, and mPFC might be related to cognitive inhibition of global processing bias. These results suggested that the underlying neuroanatomical and functional bases were linked to the individual differences in FDI cognitive styles and emphasized the important contribution of superior local processing ability and cognitive inhibition to field-independent style. PMID:24348991

Left nucleus accumbens atrophy in deficit schizophrenia: A preliminary study.

PubMed

De Rossi, Pietro; Dacquino, Claudia; Piras, Fabrizio; Caltagirone, Carlo; Spalletta, Gianfranco

2016-08-30

A question that remains to be answered is whether schizophrenia can be characterized by a single etiopathophysiology or whether separate sub-syndromes should be differentiated to define specific mechanisms for each sub-type. Individuals affected by the deficit subtype of schizophrenia (DSZ) display avolitional/amotivational features that respond poorly to conventional treatments. Characterizing DSZ from a neuroanatomical point of view may help clarify this issue and develop new treatment strategies. To determine if DSZ is associated with structural alterations in specific deep grey matter structures linked to its key clinical features, 22 DSZ patients, 22 non-deficit schizophrenia (NDSZ) patients and 22 healthy controls (HC) were recruited for a case-control cross-sectional study. High-resolution magnetic resonance imaging was performed in all subjects and volumes of deep grey matter structures were measured using FreeSurfer. DSZ patients displayed smaller left accumbens volumes compared to both NDSZ patients and HC. Moreover, age and duration of illness were significantly associated with lower volume of the left accumbens in DSZ but not in NDSZ. Findings indicate that DSZ is associated with lower volume of the nucleus accumbens in the dominant hemisphere. This is consistent with the psychopathological features and functional impairments present in DSZ and thus indicates a potential mechanism. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Comparison of Topographic Profiles Across Venus' Coronae and Craters: Implications for Corona Origin Hypothesis

NASA Astrophysics Data System (ADS)

Stoddard, P. R.; Jurdy, D. M.

2006-12-01

Venus' surface hosts nearly 1000 unambiguous impact craters, ranging in diameter from 1.5 to 280 km. Although the majority of these are pristine, slightly less than 200 have been modified by either volcanic or tectonic activity or both. In addition, numerous researchers have identified hundreds of ring-like features of varying morphology, termed "coronae." These have typically been thought of as having a diapiric or volcanic origin. Recently, however, based on the circular to quasi-circular nature of coronae, an alternative origin - impact - has been proposed. We compare the profiles across agreed-upon craters to several coronae that have been suggested as impact sites. For each feature, 36 profiles (taken every ten degrees) are aligned and then averaged together. For Mead, Cleopatra, Meitner, and Isabella craters, the profiles display the typical rim and basin structure expected for craters, but for Klenova crater the average is more domal, with only a few of the individual profiles looking crater-like. Among the "contested" coronae, the average profiles for Eurynome, Maya, and C21 appear crater-like, albeit with more variation among the individual profiles than seen in the agreed-upon craters. Anquet has a rim-and-basin structure, but unlike typical craters, the basin is elevated above the surrounding plains. Acrea appears to be a small hill in a large depression, again with a high degree of variability among the profiles. Ninhursag is clearly domal, and cannot be taken as a crater. A summary of the variability of the profiles - where 100% correlation would indicate perfect circular symmetry - indicates that, with the exception of Klenova, those features universally agreed-upon as craters have the highest correlation percentages - all at or above 80%. The disputed features are not as circular, although C21 is close. Based on this analysis, we conclude that Klenova has been mischaracterized as an impact crater, and that C21 and some other features previously classified as coronae may indeed be of impact origin. More careful analyses will be necessary to assess the origin of similar features.

Glycosyltransferases A and B: Four Critical Amino Acids Determine Blood Type

NASA Astrophysics Data System (ADS)

Rose, Natisha L.; Palcic, Monica M.; Evans, Stephen V.

2005-12-01

Human A, B, and O blood type is determined by the presence or absence of distinct carbohydrate structures on red blood cells. Type O individuals have α-fucose(1→2)galactose disaccharides [O(H) structures] on their cell surfaces while in type A or B individuals, the O antigen is capped by the addition of an α- N -acetylgalactosamine or α-galactose residue, respectively. The addition of these monosaccharides is catalyzed by glycosyltransferase A (GTA) or glycosyltransferase B (GTB). These are homologous enzymes differing by only 4 amino acids out of 354 that change the specificity from GTA to GTB. In this review the chemistry of the blood group ABO system and the role of GTA, GTB, and the four critical amino acids in determining blood group status are discussed. See JCE Featured Molecules .

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

Mandibulofacial Dysostosis with Microcephaly: Mutation and Database Update

PubMed Central

Huang, Lijia; Vanstone, Megan R.; Hartley, Taila; Osmond, Matthew; Barrowman, Nick; Allanson, Judith; Baker, Laura; Dabir, Tabib A.; Dipple, Katrina M.; Dobyns, William B.; Estrella, Jane; Faghfoury, Hanna; Favaro, Francine P.; Goel, Himanshu; Gregersen, Pernille A.; Gripp, Karen W.; Grix, Art; Guion-Almeida, Maria-Leine; Harr, Margaret H.; Hudson, Cindy; Hunter, Alasdair G.W.; Johnson, John; Joss, Shelagh K.; Kimball, Amy; Kini, Usha; Kline, Antonie D.; Lauzon, Julie; Lildballe, Dorte L.; López-González, Vanesa; Martinezmoles, Johanna; Meldrum, Cliff; Mirzaa, Ghayda M.; Morel, Chantal F.; Morton, Jenny E.V.; Pyle, Louise C.; Quintero-Rivera, Fabiola; Richer, Julie; Scheuerle, Angela E.; Schönewolf-Greulich, Bitten; Shears, Deborah J.; Silver, Josh; Smith, Amanda C.; Temple, I. Karen; van de Kamp, Jiddeke M.; van Dijk, Fleur S.; Vandersteen, Anthony M.; White, Sue M.; Zackai, Elaine H.; Zou, Ruobing; Bulman, Dennis E.; Boycott, Kym M.; Lines, Matthew A.

2017-01-01

Mandibulofacial dysostosis with microcephaly (MFDM) is a multiple malformation syndrome comprising microcephaly, craniofacial anomalies, hearing loss, dysmorphic features, and, in some cases, esophageal atresia. Haploinsufficiency of a spliceosomal GTPase, U5–116 kDa/EFTUD2, is responsible. Here, we review the molecular basis of MFDM in the 69 individuals described to date, and report mutations in 38 new individuals, bringing the total number of reported individuals to 107 individuals from 94 kindreds. Pathogenic EFTUD2 variants comprise 76 distinct mutations and seven microdeletions. Among point mutations, missense substitutions are infrequent (14 out of 76; 18%) relative to stop-gain (29 out of 76; 38%), and splicing (33 out of 76; 43%) mutations. Where known, mutation origin was de novo in 48 out of 64 individuals (75%), dominantly inherited in 12 out of 64 (19%), and due to proven germline mosaicism in four out of 64 (6%). Highly penetrant clinical features include, microcephaly, first and second arch craniofacial malformations, and hearing loss; esophageal atresia is present in an estimated ~27%. Microcephaly is virtually universal in childhood, with some adults exhibiting late “catch-up” growth and normocephaly at maturity. Occasionally reported anomalies, include vestibular and ossicular malformations, reduced mouth opening, atrophy of cerebral white matter, structural brain malformations, and epibulbar dermoid. All reported EFTUD2 mutations can be found in the EFTUD2 mutation database (http://databases.lovd.nl/shared/genes/EFTUD2). PMID:26507355

Mandibulofacial Dysostosis with Microcephaly: Mutation and Database Update.

PubMed

Huang, Lijia; Vanstone, Megan R; Hartley, Taila; Osmond, Matthew; Barrowman, Nick; Allanson, Judith; Baker, Laura; Dabir, Tabib A; Dipple, Katrina M; Dobyns, William B; Estrella, Jane; Faghfoury, Hanna; Favaro, Francine P; Goel, Himanshu; Gregersen, Pernille A; Gripp, Karen W; Grix, Art; Guion-Almeida, Maria-Leine; Harr, Margaret H; Hudson, Cindy; Hunter, Alasdair G W; Johnson, John; Joss, Shelagh K; Kimball, Amy; Kini, Usha; Kline, Antonie D; Lauzon, Julie; Lildballe, Dorte L; López-González, Vanesa; Martinezmoles, Johanna; Meldrum, Cliff; Mirzaa, Ghayda M; Morel, Chantal F; Morton, Jenny E V; Pyle, Louise C; Quintero-Rivera, Fabiola; Richer, Julie; Scheuerle, Angela E; Schönewolf-Greulich, Bitten; Shears, Deborah J; Silver, Josh; Smith, Amanda C; Temple, I Karen; van de Kamp, Jiddeke M; van Dijk, Fleur S; Vandersteen, Anthony M; White, Sue M; Zackai, Elaine H; Zou, Ruobing; Bulman, Dennis E; Boycott, Kym M; Lines, Matthew A

2016-02-01

Mandibulofacial dysostosis with microcephaly (MFDM) is a multiple malformation syndrome comprising microcephaly, craniofacial anomalies, hearing loss, dysmorphic features, and, in some cases, esophageal atresia. Haploinsufficiency of a spliceosomal GTPase, U5-116 kDa/EFTUD2, is responsible. Here, we review the molecular basis of MFDM in the 69 individuals described to date, and report mutations in 38 new individuals, bringing the total number of reported individuals to 107 individuals from 94 kindreds. Pathogenic EFTUD2 variants comprise 76 distinct mutations and seven microdeletions. Among point mutations, missense substitutions are infrequent (14 out of 76; 18%) relative to stop-gain (29 out of 76; 38%), and splicing (33 out of 76; 43%) mutations. Where known, mutation origin was de novo in 48 out of 64 individuals (75%), dominantly inherited in 12 out of 64 (19%), and due to proven germline mosaicism in four out of 64 (6%). Highly penetrant clinical features include, microcephaly, first and second arch craniofacial malformations, and hearing loss; esophageal atresia is present in an estimated ∼27%. Microcephaly is virtually universal in childhood, with some adults exhibiting late "catch-up" growth and normocephaly at maturity. Occasionally reported anomalies, include vestibular and ossicular malformations, reduced mouth opening, atrophy of cerebral white matter, structural brain malformations, and epibulbar dermoid. All reported EFTUD2 mutations can be found in the EFTUD2 mutation database (http://databases.lovd.nl/shared/genes/EFTUD2). © 2015 WILEY PERIODICALS, INC.

Modularising ontology and designing inference patterns to personalise health condition assessment: the case of obesity.

PubMed

Sojic, Aleksandra; Terkaj, Walter; Contini, Giorgia; Sacco, Marco

2016-05-04

The public health initiatives for obesity prevention are increasingly exploiting the advantages of smart technologies that can register various kinds of data related to physical, physiological, and behavioural conditions. Since individual features and habits vary among people, the design of appropriate intervention strategies for motivating changes in behavioural patterns towards a healthy lifestyle requires the interpretation and integration of collected information, while considering individual profiles in a personalised manner. The ontology-based modelling is recognised as a promising approach in facing the interoperability and integration of heterogeneous information related to characterisation of personal profiles. The presented ontology captures individual profiles across several obesity-related knowledge-domains structured into dedicated modules in order to support inference about health condition, physical features, behavioural habits associated with a person, and relevant changes over time. The modularisation strategy is designed to facilitate ontology development, maintenance, and reuse. The domain-specific modules formalised in the Web Ontology Language (OWL) integrate the domain-specific sets of rules formalised in the Semantic Web Rule Language (SWRL). The inference rules follow a modelling pattern designed to support personalised assessment of health condition as age- and gender-specific. The test cases exemplify a personalised assessment of the obesity-related health conditions for the population of teenagers. The paper addresses several issues concerning the modelling of normative concepts related to obesity and depicts how the public health concern impacts classification of teenagers according to their phenotypes. The modelling choices regarding the ontology-structure are explained in the context of the modelling goal to integrate multiple knowledge-domains and support reasoning about the individual changes over time. The presented modularisation pattern enhances reusability of the domain-specific modules across various health care domains.

Who gains clinical benefit from using insulin pump therapy? A qualitative study of the perceptions and views of health professionals involved in the Relative Effectiveness of Pumps over MDI and Structured Education (REPOSE) trial.

PubMed

Lawton, J; Kirkham, J; Rankin, D; White, D A; Elliott, J; Jaap, A; Smithson, W H; Heller, S

2016-02-01

To explore health professionals' views about insulin pump therapy [continuous subcutaneous insulin infusion (CSII)] and the types of individuals they thought would gain greatest clinical benefit from using this treatment. In-depth interviews with staff (n = 18) who delivered the Relative Effectiveness of Pumps Over MDI and Structured Education (REPOSE) trial. Data were analysed thematically. Staff perceived insulin pumps as offering a better self-management tool to some individuals due to the drip feed of insulin, the ability to alter basal rates and other advanced features. However, staff also noted that, because of the diversity of features on offer, CSII is a more technically complex therapy to execute than multiple daily injections. For this reason, staff described how, alongside clinical criteria, they had tended to select individuals for CSII in routine clinical practice based on their perceptions about whether they possessed the personal and psychological attributes needed to make optimal use of pump technology. Staff also described how their assumptions about personal and psychological suitability had been challenged by working on the REPOSE trial and observing individuals make effective use of CSII who they would not have recommended for this type of therapy in routine clinical practice. Our findings add to those studies that highlight the difficulties of using patient characteristics and variables to predict clinical success using CSII. To promote equitable access to CSII, attitudinal barriers and prejudicial assumptions amongst staff about who is able to make effective use of CSII may need to be addressed. © 2015 The Authors. Diabetic Medicine © 2015 Diabetes UK.

Influence of landscape structure on reef fish assemblages

USGS Publications Warehouse

Grober-Dunsmore, R.; Frazer, T.K.; Beets, J.P.; Lindberg, W.J.; Zwick, P.; Funicelli, N.A.

2008-01-01

Management of tropical marine environments calls for interdisciplinary studies and innovative methodologies that consider processes occurring over broad spatial scales. We investigated relationships between landscape structure and reef fish assemblage structure in the US Virgin Islands. Measures of landscape structure were transformed into a reduced set of composite indices using principal component analyses (PCA) to synthesize data on the spatial patterning of the landscape structure of the study reefs. However, composite indices (e.g., habitat diversity) were not particularly informative for predicting reef fish assemblage structure. Rather, relationships were interpreted more easily when functional groups of fishes were related to individual habitat features. In particular, multiple reef fish parameters were strongly associated with reef context. Fishes responded to benthic habitat structure at multiple spatial scales, with various groups of fishes each correlated to a unique suite of variables. Accordingly, future experiments should be designed to test functional relationships based on the ecology of the organisms of interest. Our study demonstrates that landscape-scale habitat features influence reef fish communities, illustrating promise in applying a landscape ecology approach to better understand factors that structure coral reef ecosystems. Furthermore, our findings may prove useful in design of spatially-based conservation approaches such as marine protected areas (MPAs), because landscape-scale metrics may serve as proxies for areas with high species diversity and abundance within the coral reef landscape. ?? 2007 Springer Science+Business Media B.V.

Characterizing polymorphic inversions in human genomes by single-cell sequencing

PubMed Central

Sanders, Ashley D.; Hills, Mark; Porubský, David; Guryev, Victor; Falconer, Ester; Lansdorp, Peter M.

2016-01-01

Identifying genomic features that differ between individuals and cells can help uncover the functional variants that drive phenotypes and disease susceptibilities. For this, single-cell studies are paramount, as it becomes increasingly clear that the contribution of rare but functional cellular subpopulations is important for disease prognosis, management, and progression. Until now, studying these associations has been challenged by our inability to map structural rearrangements accurately and comprehensively. To overcome this, we coupled single-cell sequencing of DNA template strands (Strand-seq) with custom analysis software to rapidly discover, map, and genotype genomic rearrangements at high resolution. This allowed us to explore the distribution and frequency of inversions in a heterogeneous cell population, identify several polymorphic domains in complex regions of the genome, and locate rare alleles in the reference assembly. We then mapped the entire genomic complement of inversions within two unrelated individuals to characterize their distinct inversion profiles and built a nonredundant global reference of structural rearrangements in the human genome. The work described here provides a powerful new framework to study structural variation and genomic heterogeneity in single-cell samples, whether from individuals for population studies or tissue types for biomarker discovery. PMID:27472961

The social determinants of oral health: new approaches to conceptualizing and researching complex causal networks.

PubMed

Newton, J Timothy; Bower, Elizabeth J

2005-02-01

Oral epidemiological research into the social determinants of oral health has been limited by the absence of a theoretical framework which reflects the complexity of real life social processes and the network of causal pathways between social structure and oral health and disease. In the absence of such a framework, social determinants are treated as isolated risk factors, attributable to the individual, having a direct impact on oral health. There is little sense of how such factors interrelate over time and place and the pathways between the factors and oral health. Features of social life which impact on individuals' oral health but are not reducible to the individual remain under-researched. A conceptual framework informing mainstream epidemiological research into the social determinants of health is applied to oral epidemiology. The framework suggests complex causal pathways between social structure and health via interlinking material, psychosocial and behavioural pathways. Methodological implications for oral epidemiological research informed by the framework, such as the use of multilevel modelling, path analysis and structural equation modelling, combining qualitative and quantitative research methods, and collaborative research, are discussed. Copyright Blackwell Munksgaard, 2005.

An analysis of the AVE-SESAME I period using statistical structure and correlation functions. [Atmospheric Variability Experiment-Severe Environmental Storm and Mesoscale Experiment

NASA Technical Reports Server (NTRS)

Fuelberg, H. E.; Meyer, P. J.

1984-01-01

Structure and correlation functions are used to describe atmospheric variability during the 10-11 April day of AVE-SESAME 1979 that coincided with the Red River Valley tornado outbreak. The special mesoscale rawinsonde data are employed in calculations involving temperature, geopotential height, horizontal wind speed and mixing ratio. Functional analyses are performed in both the lower and upper troposphere for the composite 24 h experiment period and at individual 3 h observation times. Results show that mesoscale features are prominent during the composite period. Fields of mixing ratio and horizontal wind speed exhibit the greatest amounts of small-scale variance, whereas temperature and geopotential height contain the least. Results for the nine individual times show that small-scale variance is greatest during the convective outbreak. The functions also are used to estimate random errors in the rawinsonde data. Finally, sensitivity analyses are presented to quantify confidence limits of the structure functions.

Quantitative Wood Anatomy-Practical Guidelines.

PubMed

von Arx, Georg; Crivellaro, Alan; Prendin, Angela L; Čufar, Katarina; Carrer, Marco

2016-01-01

Quantitative wood anatomy analyzes the variability of xylem anatomical features in trees, shrubs, and herbaceous species to address research questions related to plant functioning, growth, and environment. Among the more frequently considered anatomical features are lumen dimensions and wall thickness of conducting cells, fibers, and several ray properties. The structural properties of each xylem anatomical feature are mostly fixed once they are formed, and define to a large extent its functionality, including transport and storage of water, nutrients, sugars, and hormones, and providing mechanical support. The anatomical features can often be localized within an annual growth ring, which allows to establish intra-annual past and present structure-function relationships and its sensitivity to environmental variability. However, there are many methodological challenges to handle when aiming at producing (large) data sets of xylem anatomical data. Here we describe the different steps from wood sample collection to xylem anatomical data, provide guidance and identify pitfalls, and present different image-analysis tools for the quantification of anatomical features, in particular conducting cells. We show that each data production step from sample collection in the field, microslide preparation in the lab, image capturing through an optical microscope and image analysis with specific tools can readily introduce measurement errors between 5 and 30% and more, whereby the magnitude usually increases the smaller the anatomical features. Such measurement errors-if not avoided or corrected-may make it impossible to extract meaningful xylem anatomical data in light of the rather small range of variability in many anatomical features as observed, for example, within time series of individual plants. Following a rigid protocol and quality control as proposed in this paper is thus mandatory to use quantitative data of xylem anatomical features as a powerful source for many research topics.

Quantitative Wood Anatomy—Practical Guidelines

PubMed Central

von Arx, Georg; Crivellaro, Alan; Prendin, Angela L.; Čufar, Katarina; Carrer, Marco

2016-01-01

Quantitative wood anatomy analyzes the variability of xylem anatomical features in trees, shrubs, and herbaceous species to address research questions related to plant functioning, growth, and environment. Among the more frequently considered anatomical features are lumen dimensions and wall thickness of conducting cells, fibers, and several ray properties. The structural properties of each xylem anatomical feature are mostly fixed once they are formed, and define to a large extent its functionality, including transport and storage of water, nutrients, sugars, and hormones, and providing mechanical support. The anatomical features can often be localized within an annual growth ring, which allows to establish intra-annual past and present structure-function relationships and its sensitivity to environmental variability. However, there are many methodological challenges to handle when aiming at producing (large) data sets of xylem anatomical data. Here we describe the different steps from wood sample collection to xylem anatomical data, provide guidance and identify pitfalls, and present different image-analysis tools for the quantification of anatomical features, in particular conducting cells. We show that each data production step from sample collection in the field, microslide preparation in the lab, image capturing through an optical microscope and image analysis with specific tools can readily introduce measurement errors between 5 and 30% and more, whereby the magnitude usually increases the smaller the anatomical features. Such measurement errors—if not avoided or corrected—may make it impossible to extract meaningful xylem anatomical data in light of the rather small range of variability in many anatomical features as observed, for example, within time series of individual plants. Following a rigid protocol and quality control as proposed in this paper is thus mandatory to use quantitative data of xylem anatomical features as a powerful source for many research topics. PMID:27375641

The communicative potential of bat echolocation pulses.

PubMed

Jones, Gareth; Siemers, Björn M

2011-05-01

Ecological constraints often shape the echolocation pulses emitted by bat species. Consequently some (but not all) bats emit species-specific echolocation pulses. Because echolocation pulses are often intense and emitted at high rates, they are potential targets for eavesdropping by other bats. Echolocation pulses can also vary within species according to sex, body size, age, social group and geographic location. Whether these features can be recognised by other bats can only be determined reliably by playback experiments, which have shown that echolocation pulses do provide sufficient information for the identification of sex and individual in one species. Playbacks also show that bats can locate conspecifics and heterospecifics at foraging and roost sites by eavesdropping on echolocation pulses. Guilds of echolocating bat species often partition their use of pulse frequencies. Ecology, allometric scaling and phylogeny play roles here, but are not sufficient to explain this partitioning. Evidence is accumulating to support the hypothesis that frequency partitioning evolved to facilitate intraspecific communication. Acoustic character displacement occurs in at least one instance. Future research can relate genetic population structure to regional variation in echolocation pulse features and elucidate those acoustic features that most contribute to discrimination of individuals.

Opening the Black Box: Cognitive Strategies in Family Practice

PubMed Central

Christensen, Robert E.; Fetters, Michael D.; Green, Lee A.

2005-01-01

PURPOSE We wanted to describe the cognitive strategies used by family physicians when structuring the decision-making tasks of an outpatient visit. METHODS This qualitative study used cognitive task analysis, a structured interview method in which a trained interviewer works individually with expert decision makers to capture their stages and elements of information processing. RESULTS Eighteen family physicians of varying levels of experience participated. Three dominant themes emerged: time pressure, a high degree of variation in task structuring, and varying degrees of task automatization. Based on these data and previous research from the cognitive sciences, we developed a model of novice and expert approaches to decision making in primary care. The model illustrates differences in responses to unexpected opportunity in practice, particularly the expert’s use of attentional surplus (reserve capacity to handle problems) vs the novice’s choice between taking more time or displacing another task. CONCLUSIONS Family physicians have specific, highly individualized cognitive task-structuring approaches and show the decision behavior features typical of expert decision makers in other fields. This finding places constraints on and suggests useful approaches for improving practice. PMID:15798041

Obstacle avoidance in social groups: new insights from asynchronous models

PubMed Central

Croft, Simon; Budgey, Richard; Pitchford, Jonathan W.; Wood, A. Jamie

2015-01-01

For moving animals, the successful avoidance of hazardous obstacles is an important capability. Despite this, few models of collective motion have addressed the relationship between behavioural and social features and obstacle avoidance. We develop an asynchronous individual-based model for social movement which allows social structure within groups to be included. We assess the dynamics of group navigation and resulting collision risk in the context of information transfer through the system. In agreement with previous work, we find that group size has a nonlinear effect on collision risk. We implement examples of possible network structures to explore the impact social preferences have on collision risk. We show that any social heterogeneity induces greater obstacle avoidance with further improvements corresponding to groups containing fewer influential individuals. The model provides a platform for both further theoretical investigation and practical application. In particular, we argue that the role of social structures within bird flocks may have an important role to play in assessing the risk of collisions with wind turbines, but that new methods of data analysis are needed to identify these social structures. PMID:25833245

Statistical universals reveal the structures and functions of human music.

PubMed

Savage, Patrick E; Brown, Steven; Sakai, Emi; Currie, Thomas E

2015-07-21

Music has been called "the universal language of mankind." Although contemporary theories of music evolution often invoke various musical universals, the existence of such universals has been disputed for decades and has never been empirically demonstrated. Here we combine a music-classification scheme with statistical analyses, including phylogenetic comparative methods, to examine a well-sampled global set of 304 music recordings. Our analyses reveal no absolute universals but strong support for many statistical universals that are consistent across all nine geographic regions sampled. These universals include 18 musical features that are common individually as well as a network of 10 features that are commonly associated with one another. They span not only features related to pitch and rhythm that are often cited as putative universals but also rarely cited domains including performance style and social context. These cross-cultural structural regularities of human music may relate to roles in facilitating group coordination and cohesion, as exemplified by the universal tendency to sing, play percussion instruments, and dance to simple, repetitive music in groups. Our findings highlight the need for scientists studying music evolution to expand the range of musical cultures and musical features under consideration. The statistical universals we identified represent important candidates for future investigation.

Statistical universals reveal the structures and functions of human music

PubMed Central

Savage, Patrick E.; Brown, Steven; Sakai, Emi; Currie, Thomas E.

2015-01-01

Music has been called “the universal language of mankind.” Although contemporary theories of music evolution often invoke various musical universals, the existence of such universals has been disputed for decades and has never been empirically demonstrated. Here we combine a music-classification scheme with statistical analyses, including phylogenetic comparative methods, to examine a well-sampled global set of 304 music recordings. Our analyses reveal no absolute universals but strong support for many statistical universals that are consistent across all nine geographic regions sampled. These universals include 18 musical features that are common individually as well as a network of 10 features that are commonly associated with one another. They span not only features related to pitch and rhythm that are often cited as putative universals but also rarely cited domains including performance style and social context. These cross-cultural structural regularities of human music may relate to roles in facilitating group coordination and cohesion, as exemplified by the universal tendency to sing, play percussion instruments, and dance to simple, repetitive music in groups. Our findings highlight the need for scientists studying music evolution to expand the range of musical cultures and musical features under consideration. The statistical universals we identified represent important candidates for future investigation. PMID:26124105

Modelling the structure and kinematics of the Firework nebula: The nature of the GK Persei nova shell and its jet-like feature

NASA Astrophysics Data System (ADS)

Harvey, E.; Redman, M. P.; Boumis, P.; Akras, S.

2016-10-01

Aims: The shaping mechanisms of old nova remnants are probes for several important and unexplained processes, such as dust formation and the structure of evolved star nebulae. To gain a more complete understanding of the dynamics of the GK Per (1901) remnant, an examination of symmetry of the nova shell is explored, followed by a kinematical analysis of the previously detected jet-like feature in the context of the surrounding fossil planetary nebula. Methods: Faint-object high-resolution echelle spectroscopic observations and imaging were undertaken covering the knots which comprise the nova shell and the surrounding nebulosity. New imaging from the Aristarchos telescope in Greece and long-slit spectra from the Manchester Echelle Spectrometer instrument at the San Pedro Mártir observatory in Mexico were obtained, supplemented with archival observations from several other optical telescopes. Position-velocity arrays are produced of the shell, and also individual knots, and are then used for morpho-kinematic modelling with the shape code. The overall structure of the old knotty nova shell of GK Per and the planetary nebula in which it is embedded is then analysed. Results: Evidence is found for the interaction of knots with each other and with a wind component, most likely the periodic fast wind emanating from the central binary system. We find that a cylindrical shell with a lower velocity polar structure gives the best model fit to the spectroscopy and imaging. We show in this work that the previously seen jet-like feature is of low velocity. Conclusions: The individual knots have irregular tail shapes; we propose here that they emanate from episodic winds from ongoing dwarf nova outbursts by the central system. The nova shell is cylindrical, not spherical, and the symmetry axis relates to the inclination of the central binary system. Furthermore, the cylinder axis is aligned with the long axis of the bipolar planetary nebula in which it is embedded. Thus, the central binary system is responsible for the bipolarity of the planetary nebula and the cylindrical nova shell. The gradual planetary nebula ejecta versus sudden nova ejecta is the reason for the different degrees of bipolarity. We propose that the "jet" feature is an illuminated lobe of the fossil planetary nebula that surrounds the nova shell.

Jedi Public Health: Co-creating an Identity-Safe Culture to Promote Health Equity.

PubMed

Geronimus, Arline T; James, Sherman A; Destin, Mesmin; Graham, Louis A; Hatzenbuehler, Mark; Murphy, Mary; Pearson, Jay A; Omari, Amel; Thompson, James Phillip

2016-12-01

The extent to which socially-assigned and culturally mediated social identity affects health depends on contingencies of social identity that vary across and within populations in day-to-day life. These contingencies are structurally rooted and health damaging inasmuch as they activate physiological stress responses. They also have adverse effects on cognition and emotion, undermining self-confidence and diminishing academic performance. This impact reduces opportunities for social mobility, while ensuring those who "beat the odds" pay a physical price for their positive efforts. Recent applications of social identity theory toward closing racial, ethnic, and gender academic achievement gaps through changing features of educational settings, rather than individual students, have proved fruitful. We sought to integrate this evidence with growing social epidemiological evidence that structurally-rooted biopsychosocial processes have population health effects. We explicate an emergent framework, Jedi Public Health (JPH). JPH focuses on changing features of settings in everyday life, rather than individuals, to promote population health equity, a high priority, yet, elusive national public health objective. We call for an expansion and, in some ways, a re-orienting of efforts to eliminate population health inequity. Policies and interventions to remove and replace discrediting cues in everyday settings hold promise for disrupting the repeated physiological stress process activation that fuels population health inequities with potentially wide application.

Soil moisture in relation to geologic structure and lithology, northern California

NASA Technical Reports Server (NTRS)

Rich, E. I. (Principal Investigator)

1980-01-01

The author has identified the following significant results. Structural features in the Norther California Coast Ranges are clearly discernable on Nite-IR images and some of the structural linears may results in an extension of known faults within the region. The Late Mesozoic marine sedimentary rocks along the western margin of the Sacramento Valley are clearly defined on the Nite-IR images and in a gross way individual layers of sandstone can be differentiated from shale. Late Pleistocene alluvial fans are clearly differentiated from second generation Holocene fans on the basis of tonal characteristics. Although the tonal characteristics change with the seasons, the differentiation of the two sets of fans is still possible.

Static strain tuning of quantum dots embedded in a photonic wire

NASA Astrophysics Data System (ADS)

Tumanov, D.; Vaish, N.; Nguyen, H. A.; Curé, Y.; Gérard, J.-M.; Claudon, J.; Donatini, F.; Poizat, J.-Ph.

2018-03-01

We use strain to statically tune the semiconductor band gap of individual InAs quantum dots (QDs) embedded in a GaAs photonic wire featuring very efficient single photon collection. Thanks to the geometry of the structure, we are able to shift the QD excitonic transition by more than 25 meV by using nano-manipulators to apply the stress. Moreover, owing to the strong transverse strain gradient generated in the structure, we can relatively tune two QDs located in the wire waveguide and bring them in resonance, opening the way to the observation of collective effects such as superradiance.

Geomorphic mapping to support river restoration on the Trinity River downstream from Lewiston Dam, California, 1980-2011

USGS Publications Warehouse

Curtis, Jennifer A.; Guerrero, Timothy M.

2015-01-01

Historic land use, dam construction, water storage, and flow diversions in the Trinity River watershed have resulted in downstream geomorphic change, loss of salmonid habitat, and declines in salmonid populations. The USGS in cooperation with the Trinity River Restoration Program, a multi-agency partnership tasked with implementing federally mandated restoration, completed a geomorphic change assessment to inform the planning process for future restoration work. This report documents an ARCMAP geodatabase (v.10.0) containing geomorphic features digitized from a series of rectified orthophotographs (http://dx.doi.org/10.5066/F7TT4P04). Upland, riparian, and channel features were digitized from six available base images (1980, 1997, 2001, 2006, 2009, and 2011). This report describes the structure of the geodatabase and the methods used to delineate individual geomorphic features.

DYRK1A haploinsufficiency causes a new recognizable syndrome with microcephaly, intellectual disability, speech impairment, and distinct facies

PubMed Central

Ji, Jianling; Lee, Hane; Argiropoulos, Bob; Dorrani, Naghmeh; Mann, John; Martinez-Agosto, Julian A; Gomez-Ospina, Natalia; Gallant, Natalie; Bernstein, Jonathan A; Hudgins, Louanne; Slattery, Leah; Isidor, Bertrand; Le Caignec, Cédric; David, Albert; Obersztyn, Ewa; Wiśniowiecka-Kowalnik, Barbara; Fox, Michelle; Deignan, Joshua L; Vilain, Eric; Hendricks, Emily; Horton Harr, Margaret; Noon, Sarah E; Jackson, Jessi R; Wilkens, Alisha; Mirzaa, Ghayda; Salamon, Noriko; Abramson, Jeff; Zackai, Elaine H; Krantz, Ian; Innes, A Micheil; Nelson, Stanley F; Grody, Wayne W; Quintero-Rivera, Fabiola

2015-01-01

Dual-specificity tyrosine-(Y)-phosphorylation-regulated kinase 1 A (DYRK1A ) is a highly conserved gene located in the Down syndrome critical region. It has an important role in early development and regulation of neuronal proliferation. Microdeletions of chromosome 21q22.12q22.3 that include DYRK1A (21q22.13) are rare and only a few pathogenic single-nucleotide variants (SNVs) in the DYRK1A gene have been described, so as of yet, the landscape of DYRK1A disruptions and their associated phenotype has not been fully explored. We have identified 14 individuals with de novo heterozygous variants of DYRK1A; five with microdeletions, three with small insertions or deletions (INDELs) and six with deleterious SNVs. The analysis of our cohort and comparison with published cases reveals that phenotypes are consistent among individuals with the 21q22.12q22.3 microdeletion and those with translocation, SNVs, or INDELs within DYRK1A. All individuals shared congenital microcephaly at birth, intellectual disability, developmental delay, severe speech impairment, short stature, and distinct facial features. The severity of the microcephaly varied from −2 SD to −5 SD. Seizures, structural brain abnormalities, eye defects, ataxia/broad-based gait, intrauterine growth restriction, minor skeletal abnormalities, and feeding difficulties were present in two-thirds of all affected individuals. Our study demonstrates that haploinsufficiency of DYRK1A results in a new recognizable syndrome, which should be considered in individuals with Angelman syndrome-like features and distinct facial features. Our report represents the largest cohort of individuals with DYRK1A disruptions to date, and is the first attempt to define consistent genotype–phenotype correlations among subjects with 21q22.13 microdeletions and DYRK1A SNVs or small INDELs. PMID:25944381

The epileptology of Koolen-de Vries syndrome: Electro-clinico-radiologic findings in 31 patients.

PubMed

Myers, Kenneth A; Mandelstam, Simone A; Ramantani, Georgia; Rushing, Elisabeth J; de Vries, Bert B; Koolen, David A; Scheffer, Ingrid E

2017-06-01

This study was designed to describe the spectrum of epilepsy phenotypes in Koolen-de Vries syndrome (KdVS), a genetic syndrome involving dysmorphic features, intellectual disability, hypotonia, and congenital malformations, that occurs secondary to 17q21.31 microdeletions and heterozygous mutations in KANSL1. We were invited to attend a large gathering of individuals with KdVS and their families. While there, we recruited individuals with KdVS and seizures, and performed thorough phenotyping. Additional subjects were included who approached us after the family support group brought attention to our research via social media. Inclusion criteria were genetic testing results demonstrating 17q21.31 deletion or KANSL1 mutation, and at least one seizure. Thirty-one individuals were studied, aged 2-35 years. Median age at seizure onset was 3.5 years, and 9 of 22 had refractory seizures 2 years after onset. Focal impaired awareness seizures were the most frequent seizure type occurring in 20 of 31, usually with prominent autonomic features. Twenty-one patients had prolonged seizures and, at times, refractory status epilepticus. Electroencephalography (EEG) showed focal/multifocal epileptiform discharges in 20 of 26. MRI studies of 13 patients were reviewed, and all had structural anomalies. Corpus callosum dysgenesis, abnormal hippocampi, and dilated ventricles were the most common, although periventricular nodular heterotopia, focal cortical dysplasia, abnormal sulcation, and brainstem and cerebellum abnormalities were also observed. One patient underwent epilepsy surgery for a lesion that proved to be an angiocentric glioma. The typical epilepsy phenotype of KdVS involves childhood-onset focal seizures that are prolonged and have prominent autonomic features. Multifocal epileptiform discharges are the typical EEG pattern. Structural brain abnormalities may be universal, including signs of abnormal neuroblast migration and abnormal axonal guidance. Epilepsy surgery should be undertaken with care given the widespread neuroanatomic abnormalities; however, tumors are a rare, yet important, occurrence. Wiley Periodicals, Inc. © 2017 International League Against Epilepsy.

IMU-Based Gait Recognition Using Convolutional Neural Networks and Multi-Sensor Fusion.

PubMed

Dehzangi, Omid; Taherisadr, Mojtaba; ChangalVala, Raghvendar

2017-11-27

The wide spread usage of wearable sensors such as in smart watches has provided continuous access to valuable user generated data such as human motion that could be used to identify an individual based on his/her motion patterns such as, gait. Several methods have been suggested to extract various heuristic and high-level features from gait motion data to identify discriminative gait signatures and distinguish the target individual from others. However, the manual and hand crafted feature extraction is error prone and subjective. Furthermore, the motion data collected from inertial sensors have complex structure and the detachment between manual feature extraction module and the predictive learning models might limit the generalization capabilities. In this paper, we propose a novel approach for human gait identification using time-frequency (TF) expansion of human gait cycles in order to capture joint 2 dimensional (2D) spectral and temporal patterns of gait cycles. Then, we design a deep convolutional neural network (DCNN) learning to extract discriminative features from the 2D expanded gait cycles and jointly optimize the identification model and the spectro-temporal features in a discriminative fashion. We collect raw motion data from five inertial sensors placed at the chest, lower-back, right hand wrist, right knee, and right ankle of each human subject synchronously in order to investigate the impact of sensor location on the gait identification performance. We then present two methods for early (input level) and late (decision score level) multi-sensor fusion to improve the gait identification generalization performance. We specifically propose the minimum error score fusion (MESF) method that discriminatively learns the linear fusion weights of individual DCNN scores at the decision level by minimizing the error rate on the training data in an iterative manner. 10 subjects participated in this study and hence, the problem is a 10-class identification task. Based on our experimental results, 91% subject identification accuracy was achieved using the best individual IMU and 2DTF-DCNN. We then investigated our proposed early and late sensor fusion approaches, which improved the gait identification accuracy of the system to 93.36% and 97.06%, respectively.

Dynamical origins of the community structure of an online multi-layer society

NASA Astrophysics Data System (ADS)

Klimek, Peter; Diakonova, Marina; Eguíluz, Víctor M.; San Miguel, Maxi; Thurner, Stefan

2016-08-01

Social structures emerge as a result of individuals managing a variety of different social relationships. Societies can be represented as highly structured dynamic multiplex networks. Here we study the dynamical origins of the specific community structures of a large-scale social multiplex network of a human society that interacts in a virtual world of a massive multiplayer online game. There we find substantial differences in the community structures of different social actions, represented by the various layers in the multiplex network. Community sizes distributions are either fat-tailed or appear to be centered around a size of 50 individuals. To understand these observations we propose a voter model that is built around the principle of triadic closure. It explicitly models the co-evolution of node- and link-dynamics across different layers of the multiplex network. Depending on link and node fluctuation probabilities, the model exhibits an anomalous shattered fragmentation transition, where one layer fragments from one large component into many small components. The observed community size distributions are in good agreement with the predicted fragmentation in the model. This suggests that several detailed features of the fragmentation in societies can be traced back to the triadic closure processes.

Seismic, structural, and individual factors associated with earthquake related injury

PubMed Central

Peek-Asa, C; Ramirez, M; Seligson, H; Shoaf, K

2003-01-01

Background: Earthquakes cause thousands of deaths worldwide every year, and systematic study of the causes of these deaths can lead to their prevention. Few studies have examined how multiple types of risk factors are related to physical injury during an earthquake. Methods: A population based case-control study was conducted to examine how individual characteristics, building characteristics, and seismic features of the 1994 Northridge, California, earthquake contributed to physical injury. Cases included fatal and hospital-admitted injuries caused by the earthquake. Controls were drawn from a population based phone survey of county residents. Cases were individually matched to two sets of controls: one matched by age and gender and one matched by location at the time of the earthquake. Results: Individuals over age 65 had 2.9 times the risk of injury as younger people (95% confidence interval (CI) 1.2 to 7.4) and women had a 2.4 times greater risk than men (95% CI 1.2 to 5.1). Location in multiple unit residential and commercial structures each led to increased injury risk compared with single unit residential structures, but the exact estimate varied depending on the control group used. With every increase in ground motion of 10%g, injury risk increased 2.2 times (95% CI 1.6 to 3.3). Conclusions: Controlling for other factors, it was found that individual, building, and seismic characteristics were independently predictive of increased injury risk. Prevention and preparedness efforts should focus on each of these as potential points of intervention. PMID:12642562

Electrophoretic mobility shift in native gels indicates calcium-dependent structural changes of neuronal calcium sensor proteins.

PubMed

Viviano, Jeffrey; Krishnan, Anuradha; Wu, Hao; Venkataraman, Venkat

2016-02-01

In proteins of the neuronal calcium sensor (NCS) family, changes in structure as well as function are brought about by the binding of calcium. In this article, we demonstrate that these structural changes, solely due to calcium binding, can be assessed through electrophoresis in native gels. The results demonstrate that the NCS proteins undergo ligand-dependent conformational changes that are detectable in native gels as a gradual decrease in mobility with increasing calcium but not other tested divalent cations such as magnesium, strontium, and barium. Surprisingly, such a gradual change over the entire tested range is exhibited only by the NCS proteins but not by other tested calcium-binding proteins such as calmodulin and S100B, indicating that the change in mobility may be linked to a unique NCS family feature--the calcium-myristoyl switch. Even within the NCS family, the changes in mobility are characteristic of the protein, indicating that the technique is sensitive to the individual features of the protein. Thus, electrophoretic mobility on native gels provides a simple and elegant method to investigate calcium (small ligand)-induced structural changes at least in the superfamily of NCS proteins. Copyright © 2015 Elsevier Inc. All rights reserved.

[A family of short retroposons (Squaml) from squamate reptiles (Reptilia: Squamata): structure, evolution and correlation with phylogeny].

PubMed

Kosushkin, S A; Borodulina, O R; Solov'eva, E N; Grechko, V V

2008-01-01

We have isolated and characterised sequences of a SINE family specific for squamate reptiles from a genome of lacertid lizard that we called Squam1. Copies are 360-390 bp in length and share a significant similarity with tRNA gene sequence on its 5'-end. This family was also detected by us in DNA of representatives of varanids, iguanids (anolis), gekkonids, and snakes. No signs of it were found in DNA of mammals, birds, amphibians, and crocodiles. Detailed analysis of primary structure of the retroposons obtained by us from genomic libraries or GenBank sequences was carried out. Most taxa possess 2-3 subfamilies of the SINE in their genomes with specific diagnostic features in their primary structure. Individual variability of copies in different families is about 85% and is just slightly lower on the genera level. Comparison of consensus sequences on family level reveals a high degree of structural similarity with a number of specific apomorphic features which makes it a useful marker of phylogeny for this group of reptiles. Snakes do not show specific affinity to varanids when compared to other lizards, as it was suggested earlier.

Correlations in Scattered X-Ray Laser Pulses Reveal Nanoscale Structural Features of Viruses

DOE PAGES

Kurta, Ruslan P.; Donatelli, Jeffrey J.; Yoon, Chun Hong; ...

2017-10-12

We use extremely bright and ultrashort pulses from an x-ray free-electron laser (XFEL) to measure correlations in x rays scattered from individual bioparticles. This allows us to go beyond the traditional crystallography and single-particle imaging approaches for structure investigations. We employ angular correlations to recover the three-dimensional (3D) structure of nanoscale viruses from x-ray diffraction data measured at the Linac Coherent Light Source. Correlations provide us with a comprehensive structural fingerprint of a 3D virus, which we use both for model-based and ab initio structure recovery. The analyses reveal a clear indication that the structure of the viruses deviates frommore » the expected perfect icosahedral symmetry. Lastly, our results anticipate exciting opportunities for XFEL studies of the structure and dynamics of nanoscale objects by means of angular correlations.« less

Bananas, pesticides and health in southwestern Ecuador: A scalar narrative approach to targeting public health responses.

PubMed

Brisbois, Benjamin

2016-02-01

Public health responses to agricultural pesticide exposure are often informed by ethnographic or other qualitative studies of pesticide risk perception. In addition to highlighting the importance of structural determinants of exposure, such studies can identify the specific scales at which pesticide-exposed individuals locate responsibility for their health issues, with implications for study and intervention design. In this study, an ethnographic approach was employed to map scalar features within explanatory narratives of pesticides and health in Ecuador's banana-producing El Oro province. Unstructured observation, 14 key informant interviews and 15 in-depth semi-structured interviews were carried out during 8 months of fieldwork in 2011-2013. Analysis of interview data was informed by human geographic literature on the social construction of scale. Individual-focused narratives of some participants highlighted characteristics such as carelessness and ignorance, leading to suggestions for educational interventions. More structural explanations invoked farm-scale processes, such as uncontrolled aerial fumigations on plantations owned by elites. Organization into cooperatives helped to protect small-scale farmers from 'deadly' banana markets, which in turn were linked to the Ecuadorian nation-state and actors in the banana-consuming world. These scalar elements interacted in complex ways that appear linked to social class, as more well-off individuals frequently attributed the health problems of other (poorer) people to individual behaviours, while providing more structural explanations of their own difficulties. Such individualizing narratives may help to stabilize inequitable social structures. Research implications of this study include the possibility of using scale-focused qualitative research to generate theory and candidate levels for multi-level models. Equity implications include a need for public health researchers planning interventions to engage with scale-linked inequities, such as disparities within nation-states. Finally, the prominence of the global North in explanatory narratives is a useful reminder that 'structural factors' prominently include inequities related to the legacies of colonialism. Copyright © 2015 Elsevier Ltd. All rights reserved.

Auditory dysfunction in schizophrenia: integrating clinical and basic features

PubMed Central

Javitt, Daniel C.; Sweet, Robert A.

2015-01-01

Schizophrenia is a complex neuropsychiatric disorder that is associated with persistent psychosocial disability in affected individuals. Although studies of schizophrenia have traditionally focused on deficits in higher-order processes such as working memory and executive function, there is an increasing realization that, in this disorder, deficits can be found throughout the cortex and are manifest even at the level of early sensory processing. These deficits are highly amenable to translational investigation and represent potential novel targets for clinical intervention. Deficits, moreover, have been linked to specific structural abnormalities in post-mortem auditory cortex tissue from individuals with schizophrenia, providing unique insights into underlying pathophysiological mechanisms. PMID:26289573

Modeling the adoption of innovations in the presence of geographic and media influences.

PubMed

Toole, Jameson L; Cha, Meeyoung; González, Marta C

2012-01-01

While there is a large body of work examining the effects of social network structure on innovation adoption, models to date have lacked considerations of real geography or mass media. In this article, we show these features are crucial to making more accurate predictions of a social contagion and technology adoption at a city-to-city scale. Using data from the adoption of the popular micro-blogging platform, Twitter, we present a model of adoption on a network that places friendships in real geographic space and exposes individuals to mass media influence. We show that homophily both among individuals with similar propensities to adopt a technology and geographic location is critical to reproducing features of real spatiotemporal adoption. Furthermore, we estimate that mass media was responsible for increasing Twitter's user base two to four fold. To reflect this strength, we extend traditional contagion models to include an endogenous mass media agent that responds to those adopting an innovation as well as influencing agents to adopt themselves.

Song copying by humpback whales: themes and variations.

PubMed

Mercado, Eduardo; Herman, Louis M; Pack, Adam A

2005-04-01

Male humpback whales (Megaptera novaeangliae) produce long, structured sequences of sound underwater, commonly called "songs." Humpbacks progressively modify their songs over time in ways that suggest that individuals are copying song elements that they hear being used by other singers. Little is known about the factors that determine how whales learn from their auditory experiences. Song learning in birds is better understood and appears to be constrained by stable core attributes such as species-specific sound repertoires and song syntax. To clarify whether similar constraints exist for song learning by humpbacks, we analyzed changes over 14 years in the sounds used by humpback whales singing in Hawaiian waters. We found that although the properties of individual sounds within songs are quite variable over time, the overall distribution of certain acoustic features within the repertoire appears to be stable. In particular, our findings suggest that species-specific constraints on temporal features of song sounds determine song form, whereas spectral variability allows whales to flexibly adapt song elements.

Measurement of Electronic States of PbS Nanocrystal Quantum Dots Using Scanning Tunneling Spectroscopy: The Role of Parity Selection Rules in Optical Absorption

NASA Astrophysics Data System (ADS)

Diaconescu, Bogdan; Padilha, Lazaro A.; Nagpal, Prashant; Swartzentruber, Brian S.; Klimov, Victor I.

2013-03-01

We study the structure of electronic states in individual PbS nanocrystal quantum dots by scanning tunneling spectroscopy (STS) using one-to-two monolayer nanocrystal films treated with 1, 2-ethanedithiols (EDT). Up to six individual valence and conduction band states are resolved for a range of quantum dot sizes. The measured states’ energies are in good agreement with calculations using the k·p four-band envelope function formalism. A comparison of STS and optical absorption spectra indicates that some of the absorption features can only be explained by asymmetric transitions involving the states of different symmetries (e.g., S and P or P and D), which points towards the relaxation of the parity selection rules in these nanostructures. STS measurements also reveal a midgap feature, which is likely similar to one observed in previous charge transport studies of EDT-treated quantum dot films.

Brain properties predict proximity to symptom onset in sporadic Alzheimer’s disease

PubMed Central

Vogel, Jacob W; Vachon-Presseau, Etienne; Pichet Binette, Alexa; Tam, Angela; Orban, Pierre; La Joie, Renaud; Savard, Mélissa; Picard, Cynthia; Poirier, Judes; Bellec, Pierre; Breitner, John C S; Villeneuve, Sylvia

2018-01-01

Abstract See Tijms and Visser (doi:10.1093/brain/awy113) for a scientific commentary on this article. Alzheimer’s disease is preceded by a lengthy ‘preclinical’ stage spanning many years, during which subtle brain changes occur in the absence of overt cognitive symptoms. Predicting when the onset of disease symptoms will occur is an unsolved challenge in individuals with sporadic Alzheimer’s disease. In individuals with autosomal dominant genetic Alzheimer’s disease, the age of symptom onset is similar across generations, allowing the prediction of individual onset times with some accuracy. We extend this concept to persons with a parental history of sporadic Alzheimer’s disease to test whether an individual’s symptom onset age can be informed by the onset age of their affected parent, and whether this estimated onset age can be predicted using only MRI. Structural and functional MRIs were acquired from 255 ageing cognitively healthy subjects with a parental history of sporadic Alzheimer’s disease from the PREVENT-AD cohort. Years to estimated symptom onset was calculated as participant age minus age of parental symptom onset. Grey matter volume was extracted from T1-weighted images and whole-brain resting state functional connectivity was evaluated using degree count. Both modalities were summarized using a 444-region cortical-subcortical atlas. The entire sample was divided into training (n = 138) and testing (n = 68) sets. Within the training set, individuals closer to or beyond their parent’s symptom onset demonstrated reduced grey matter volume and altered functional connectivity, specifically in regions known to be vulnerable in Alzheimer’s disease. Machine learning was used to identify a weighted set of imaging features trained to predict years to estimated symptom onset. This feature set alone significantly predicted years to estimated symptom onset in the unseen testing data. This model, using only neuroimaging features, significantly outperformed a similar model instead trained with cognitive, genetic, imaging and demographic features used in a traditional clinical setting. We next tested if these brain properties could be generalized to predict time to clinical progression in a subgroup of 26 individuals from the Alzheimer’s Disease Neuroimaging Initiative, who eventually converted either to mild cognitive impairment or to Alzheimer’s dementia. The feature set trained on years to estimated symptom onset in the PREVENT-AD predicted variance in time to clinical conversion in this separate longitudinal dataset. Adjusting for participant age did not impact any of the results. These findings demonstrate that years to estimated symptom onset or similar measures can be predicted from brain features and may help estimate presymptomatic disease progression in at-risk individuals. PMID:29688388

Occurrence and structure of epipharyngeal pouches in bears (Ursidae)

PubMed Central

WEISSENGRUBER, G. E.; FORSTENPOINTNER, G.; KÜBBER-HEISS, A.; RIEDELBERGER, K.; SCHWAMMER, H.; GANZBERGER, K.

2001-01-01

The infrequent mention of epipharyngeal pouches occurring in some species of bears indicates the scarcity of morphological and functional knowledge about these structures. In order to provide precise morphological data on the structure of these remarkable formations and to verify their taxonomic utility, the pharyngeal regions of 1 spectacled bear and 3 brown bears were examined. All these individuals possessed epipharyngeal pouches, which are tubular, blind-ending outpouchings of the caudodorsal pharyngeal wall equipped with respiratory epithelium and a thick layer of elastic fibres. While the spectacled bear and Ursus arctos syriacus possessed a single pouch on the caudodorsal wall of the nasopharynx, in Ursus arctos and Ursus arctos beringianus 2 unequally sized pouches were present. Two additional sacs of smaller size, representing outpouchings of the lateral pharyngeal wall, occurred in the spectacled bear. These findings prove epipharyngeal pouches to be constant and unique morphological features of the family Ursidae, the anatomical features suggesting involvement in the respiratory system most probably in important aspects of ursid phonation. This is the first description of epipharyngeal pouches in the spectacled bear. PMID:11322723

Mechanical Properties of the Upper Airway

PubMed Central

Strohl, Kingman P.; Butler, James P.; Malhotra, Atul

2013-01-01

The importance of the upper airway (nose, pharynx, and larynx) in health and in the pathogenesis of sleep apnea, asthma, and other airway diseases, discussed elsewhere in the Comprehensive Physiology series, prompts this review of the biomechanical properties and functional aspects of the upper airway. There is a literature based on anatomic or structural descriptions in static circumstances, albeit studied in limited numbers of individuals in both health and disease. As for dynamic features, the literature is limited to studies of pressure and flow through all or parts of the upper airway and to the effects of muscle activation on such features; however, the links between structure and function through airway size, shape, and compliance remain a topic that is completely open for investigation, particularly through analyses using concepts of fluid and structural mechanics. Throughout are included both historically seminal references, as well as those serving as signposts or updated reviews. This article should be considered a resource for concepts needed for the application of biomechanical models of upper airway physiology, applicable to understanding the pathophysiology of disease and anticipated results of treatment interventions. PMID:23723026

Optimized bio-inspired stiffening design for an engine nacelle.

PubMed

Lazo, Neil; Vodenitcharova, Tania; Hoffman, Mark

2015-11-04

Structural efficiency is a common engineering goal in which an ideal solution provides a structure with optimized performance at minimized weight, with consideration of material mechanical properties, structural geometry, and manufacturability. This study aims to address this goal in developing high performance lightweight, stiff mechanical components by creating an optimized design from a biologically-inspired template. The approach is implemented on the optimization of rib stiffeners along an aircraft engine nacelle. The helical and angled arrangements of cellulose fibres in plants were chosen as the bio-inspired template. Optimization of total displacement and weight was carried out using a genetic algorithm (GA) coupled with finite element analysis. Iterations showed a gradual convergence in normalized fitness. Displacement was given higher emphasis in optimization, thus the GA optimization tended towards individual designs with weights near the mass constraint. Dominant features of the resulting designs were helical ribs with rectangular cross-sections having large height-to-width ratio. Displacement reduction was at 73% as compared to an unreinforced nacelle, and is attributed to the geometric features and layout of the stiffeners, while mass is maintained within the constraint.

Recognition of the geologic framework of porphyry deposits on ERTS-1 imagery

NASA Technical Reports Server (NTRS)

Wilson, J. C. (Principal Investigator); Camp, L. W.

1973-01-01

The author has identified the following significant results. Preliminary analysis of a mosaic composing 20 individual ERTS-1 frames that covers most of Nevada and western Utah reveals both new and old structural features. Three separate provinces, the Basin and Range, the southern extension of the Columbia River Plateau volcanics, and the western edge of the Colorado Plateau are easily distinguishable. A west-northwest cross or transverse structural trend, the Las Vegas Shear zone, is present in the region running from the Sierra Nevada to Lake Mead. The Sevier, Hurricane and Grand Wash faults that define the Wasateh-Jerome structural zone, can be traced further on the ERTS-1 imagery than on existing tectonic maps. By use of a stereo viewer on the side-lap coverage of ERTS-1 imagery, it is possible in some instances to determine the direction of sedimentary beds, enabling anticlines and synclines to be mapped. Other geologic features, faults, direction of throw on faults, recent basalt flow contacts with older rhyolitic tuffs, volcanic cones, and subsidences can also be mapped.

Design, manufacturing and characterization of aero-elastically scaled wind turbine blades for testing active and passive load alleviation techniques within a ABL wind tunnel

NASA Astrophysics Data System (ADS)

Campagnolo, Filippo; Bottasso, Carlo L.; Bettini, Paolo

2014-06-01

In the research described in this paper, a scaled wind turbine model featuring individual pitch control (IPC) capabilities, and equipped with aero-elastically scaled blades featuring passive load reduction capabilities (bend-twist coupling, BTC), was constructed to investigate, by means of wind tunnel testing, the load alleviation potential of BTC and its synergy with active load reduction techniques. The paper mainly focus on the design of the aero-elastic blades and their dynamic and static structural characterization. The experimental results highlight that manufactured blades show desired bend-twist coupling behavior and are a first milestone toward their testing in the wind tunnel.

Quantum field theory and the linguistic Minimalist Program: a remarkable isomorphism

NASA Astrophysics Data System (ADS)

Piattelli-Palmarini, M.; Vitiello, G.

2017-08-01

By resorting to recent results, we show that an isomorphism exist between linguistic features of the Minimalist Program and the quantum field theory formalism of condensed matter physics. Specific linguistic features which admit a representation in terms of the many-body algebraic formalism are the unconstrained nature of recursive Merge, the operation of the Labeling Algorithm, the difference between pronounced and un-pronounced copies of elements in a sentence and the build-up of the Fibonacci sequence in the syntactic derivation of sentence structures. The collective dynamical nature of the formation process of Logical Forms leading to the individuation of the manifold of concepts and the computational self-consistency of languages are also discussed.

Untangling individual variation in natural populations: ecological, genetic and epigenetic correlates of long-term inequality in herbivory.

PubMed

Herrera, C M; Bazaga, P

2011-04-01

Individual variation in ecologically important features of organisms is a crucial element in ecology and evolution, yet disentangling its underlying causes is difficult in natural populations. We applied a genomic scan approach using amplified fragment length polymorphism (AFLP) markers to quantify the genetic basis of long-term individual differences in herbivory by mammals at a wild population of the violet Viola cazorlensis monitored for two decades. In addition, methylation-sensitive amplified polymorphism (MSAP) analyses were used to investigate the association between browsing damage and epigenetic characteristics of individuals, an aspect that has been not previously explored for any wild plant. Structural equation modelling was used to identify likely causal structures linking genotypes, epigenotypes and herbivory. Individuals of V. cazorlensis differed widely in the incidence of browsing mammals over the 20-year study period. Six AFLP markers (1.6% of total) were significantly related to herbivory, accounting altogether for 44% of population-wide variance in herbivory levels. MSAP analyses revealed considerable epigenetic variation among individuals, and differential browsing damage was significantly related to variation in multilocus epigenotypes. In addition, variation across plants in epigenetic characteristics was related to variation in several herbivory-related AFLP markers. Statistical comparison of alternative causal models suggested that individual differences in herbivory are the outcome of a complex causal structure where genotypes and epigenotypes are interconnected and have direct and indirect effects on herbivory. Insofar as methylation states of MSAP markers influential on herbivory are transgenerationally heritable, herbivore-driven evolutionary changes at the study population will involve correlated changes in genotypic and epigenotypic distributions. © 2011 Blackwell Publishing Ltd.

Modulation of a Pore in the Capsid of JC Polyomavirus Reduces Infectivity and Prevents Exposure of the Minor Capsid Proteins

PubMed Central

Nelson, Christian D. S.; Ströh, Luisa J.; Gee, Gretchen V.; O'Hara, Bethany A.; Stehle, Thilo

2015-01-01

ABSTRACT JC polyomavirus (JCPyV) infection of immunocompromised individuals results in the fatal demyelinating disease progressive multifocal leukoencephalopathy (PML). The viral capsid of JCPyV is composed primarily of the major capsid protein virus protein 1 (VP1), and pentameric arrangement of VP1 monomers results in the formation of a pore at the 5-fold axis of symmetry. While the presence of this pore is conserved among polyomaviruses, its functional role in infection or assembly is unknown. Here, we investigate the role of the 5-fold pore in assembly and infection of JCPyV by generating a panel of mutant viruses containing amino acid substitutions of the residues lining this pore. Multicycle growth assays demonstrated that the fitness of all mutants was reduced compared to that of the wild-type virus. Bacterial expression of VP1 pentamers containing substitutions to residues lining the 5-fold pore did not affect pentamer assembly or prevent association with the VP2 minor capsid protein. The X-ray crystal structures of selected pore mutants contained subtle changes to the 5-fold pore, and no other changes to VP1 were observed. Pore mutant pseudoviruses were not deficient in assembly, packaging of the minor capsid proteins, or binding to cells or in transport to the host cell endoplasmic reticulum. Instead, these mutant viruses were unable to expose VP2 upon arrival to the endoplasmic reticulum, a step that is critical for infection. This study demonstrated that the 5-fold pore is an important structural feature of JCPyV and that minor modifications to this structure have significant impacts on infectious entry. IMPORTANCE JCPyV is an important human pathogen that causes a severe neurological disease in immunocompromised individuals. While the high-resolution X-ray structure of the major capsid protein of JCPyV has been solved, the importance of a major structural feature of the capsid, the 5-fold pore, remains poorly understood. This pore is conserved across polyomaviruses and suggests either that these viruses have limited structural plasticity in this region or that this pore is important in infection or assembly. Using a structure-guided mutational approach, we showed that modulation of this pore severely inhibits JCPyV infection. These mutants do not appear deficient in assembly or early steps in infectious entry and are instead reduced in their ability to expose a minor capsid protein in the host cell endoplasmic reticulum. Our work demonstrates that the 5-fold pore is an important structural feature for JCPyV. PMID:25609820

Biomarkers of Eating Disorders Using Support Vector Machine Analysis of Structural Neuroimaging Data: Preliminary Results

PubMed Central

Cerasa, Antonio; Castiglioni, Isabella; Salvatore, Christian; Funaro, Angela; Martino, Iolanda; Alfano, Stefania; Donzuso, Giulia; Perrotta, Paolo; Gioia, Maria Cecilia; Gilardi, Maria Carla; Quattrone, Aldo

2015-01-01

Presently, there are no valid biomarkers to identify individuals with eating disorders (ED). The aim of this work was to assess the feasibility of a machine learning method for extracting reliable neuroimaging features allowing individual categorization of patients with ED. Support Vector Machine (SVM) technique, combined with a pattern recognition method, was employed utilizing structural magnetic resonance images. Seventeen females with ED (six with diagnosis of anorexia nervosa and 11 with bulimia nervosa) were compared against 17 body mass index-matched healthy controls (HC). Machine learning allowed individual diagnosis of ED versus HC with an Accuracy ≥ 0.80. Voxel-based pattern recognition analysis demonstrated that voxels influencing the classification Accuracy involved the occipital cortex, the posterior cerebellar lobule, precuneus, sensorimotor/premotor cortices, and the medial prefrontal cortex, all critical regions known to be strongly involved in the pathophysiological mechanisms of ED. Although these findings should be considered preliminary given the small size investigated, SVM analysis highlights the role of well-known brain regions as possible biomarkers to distinguish ED from HC at an individual level, thus encouraging the translational implementation of this new multivariate approach in the clinical practice. PMID:26648660

Multiscale pore structure and its effect on gas transport in organic-rich shale

NASA Astrophysics Data System (ADS)

Wu, Tianhao; Li, Xiang; Zhao, Junliang; Zhang, Dongxiao

2017-07-01

A systematic investigation of multiscale pore structure in organic-rich shale by means of the combination of various imaging techniques is presented, including the state-of-the-art Helium-Ion-Microscope (HIM). The study achieves insight into the major features at each scale and suggests the affordable techniques for specific objectives from the aspects of resolution, dimension, and cost. The pores, which appear to be isolated, are connected by smaller pores resolved by higher-resolution imaging. This observation provides valuable information, from the microscopic perspective of pore structure, for understanding how gas accumulates and transports from where it is generated. A comprehensive workflow is proposed based on the characteristics acquired from the multiscale pore structure analysis to simulate the gas transport process. The simulations are completed with three levels: the microscopic mechanisms should be taken into consideration at level I; the spatial distribution features of organic matter, inorganic matter, and macropores constitute the major issue at level II; and the microfracture orientation and topological structure are dominant factors at level III. The results of apparent permeability from simulations agree well with the values acquired from experiments. By means of the workflow, the impact of various gas transport mechanisms at different scales can be investigated more individually and precisely than conventional experiments.

MUFOLD-SS: New deep inception-inside-inception networks for protein secondary structure prediction.

PubMed

Fang, Chao; Shang, Yi; Xu, Dong

2018-05-01

Protein secondary structure prediction can provide important information for protein 3D structure prediction and protein functions. Deep learning offers a new opportunity to significantly improve prediction accuracy. In this article, a new deep neural network architecture, named the Deep inception-inside-inception (Deep3I) network, is proposed for protein secondary structure prediction and implemented as a software tool MUFOLD-SS. The input to MUFOLD-SS is a carefully designed feature matrix corresponding to the primary amino acid sequence of a protein, which consists of a rich set of information derived from individual amino acid, as well as the context of the protein sequence. Specifically, the feature matrix is a composition of physio-chemical properties of amino acids, PSI-BLAST profile, and HHBlits profile. MUFOLD-SS is composed of a sequence of nested inception modules and maps the input matrix to either eight states or three states of secondary structures. The architecture of MUFOLD-SS enables effective processing of local and global interactions between amino acids in making accurate prediction. In extensive experiments on multiple datasets, MUFOLD-SS outperformed the best existing methods and other deep neural networks significantly. MUFold-SS can be downloaded from http://dslsrv8.cs.missouri.edu/~cf797/MUFoldSS/download.html. © 2018 Wiley Periodicals, Inc.

Combination of lateral and PA view radiographs to study development of knee OA and associated pain

NASA Astrophysics Data System (ADS)

Minciullo, Luca; Thomson, Jessie; Cootes, Timothy F.

2017-03-01

Knee Osteoarthritis (OA) is the most common form of arthritis, affecting millions of people around the world. The effects of the disease have been studied using the shape and texture features of bones in PosteriorAnterior (PA) and Lateral radiographs separately. In this work we compare the utility of features from each view, and evaluate whether combining features from both is advantageous. We built a fully automated system to independently locate landmark points in both radiographic images using Random Forest Constrained Local Models. We extracted discriminative features from the two bony outlines using Appearance Models. The features were used to train Random Forest classifiers to solve three specific tasks: (i) OA classification, distinguishing patients with structural signs of OA from the others; (ii) predicting future onset of the disease and (iii) predicting which patients with no current pain will have a positive pain score later in a follow-up visit. Using a subset of the MOST dataset we show that the PA view has more discriminative features to classify and predict OA, while the lateral view contains features that achieve better performance in predicting pain, and that combining the features from both views gives a small improvement in accuracy of the classification compared to the individual views.

ANALYSIS OF CLINICAL AND DERMOSCOPIC FEATURES FOR BASAL CELL CARCINOMA NEURAL NETWORK CLASSIFICATION

PubMed Central

Cheng, Beibei; Stanley, R. Joe; Stoecker, William V; Stricklin, Sherea M.; Hinton, Kristen A.; Nguyen, Thanh K.; Rader, Ryan K.; Rabinovitz, Harold S.; Oliviero, Margaret; Moss, Randy H.

2012-01-01

Background Basal cell carcinoma (BCC) is the most commonly diagnosed cancer in the United States. In this research, we examine four different feature categories used for diagnostic decisions, including patient personal profile (patient age, gender, etc.), general exam (lesion size and location), common dermoscopic (blue-gray ovoids, leaf-structure dirt trails, etc.), and specific dermoscopic lesion (white/pink areas, semitranslucency, etc.). Specific dermoscopic features are more restricted versions of the common dermoscopic features. Methods Combinations of the four feature categories are analyzed over a data set of 700 lesions, with 350 BCCs and 350 benign lesions, for lesion discrimination using neural network-based techniques, including Evolving Artificial Neural Networks and Evolving Artificial Neural Network Ensembles. Results Experiment results based on ten-fold cross validation for training and testing the different neural network-based techniques yielded an area under the receiver operating characteristic curve as high as 0.981 when all features were combined. The common dermoscopic lesion features generally yielded higher discrimination results than other individual feature categories. Conclusions Experimental results show that combining clinical and image information provides enhanced lesion discrimination capability over either information source separately. This research highlights the potential of data fusion as a model for the diagnostic process. PMID:22724561

Comparison between flood prone areas' geomorphic features in the Abruzzo region

NASA Astrophysics Data System (ADS)

Orlando, D.; Giglioni, M.; Magnaldi, S.

2017-07-01

Flood risk maps are one of the main non-structural measures for risk mitigation, but, as the risk knowledge degree is directly proportional to the community interest and financial capability, many sites are devoid of flood inundation areas studies. Recently many authors have investigated the capability of flood prone areas individuation with geomorphological DIGITAL ELEVATION MODEL(DEM) based approaches. These approaches highlight the role of geomorphic features derived from DEM, in this case slope, curvature, elevation, and topographic wetness index, to preliminary inundated areas' identification, without using hydraulic simulations. The present studies aim to analyze the geomorphic features of different hazard levels that lie under the identified inundated areas that have been carried out by the Abruzzo Region Basin Authority. The Aterno-Pescara and Foro river basins have been investigated. The results show that the characteristics of the flooded areas can be clearly distinguished from those of the entire basin,however, the difficultly of geomorphic features in individuatingthe areas of different hazard classifications is obvious.

A feedback mechanism converts individual cell features into a supracellular ECM structure in Drosophila trachea

PubMed Central

Öztürk-Çolak, Arzu; Moussian, Bernard; Araújo, Sofia J; Casanova, Jordi

2016-01-01

The extracellular matrix (ECM), a structure contributed to and commonly shared by many cells in an organism, plays an active role during morphogenesis. Here, we used the Drosophila tracheal system to study the complex relationship between the ECM and epithelial cells during development. We show that there is an active feedback mechanism between the apical ECM (aECM) and the apical F-actin in tracheal cells. Furthermore, we reveal that cell-cell junctions are key players in this aECM patterning and organisation and that individual cells contribute autonomously to their aECM. Strikingly, changes in the aECM influence the levels of phosphorylated Src42A (pSrc) at cell junctions. Therefore, we propose that Src42A phosphorylation levels provide a link for the ECM environment to ensure proper cytoskeletal organisation. DOI: http://dx.doi.org/10.7554/eLife.09373.001 PMID:26836303

EEG-based Affect and Workload Recognition in a Virtual Driving Environment for ASD Intervention

PubMed Central

Wade, Joshua W.; Key, Alexandra P.; Warren, Zachary E.; Sarkar, Nilanjan

2017-01-01

objective To build group-level classification models capable of recognizing affective states and mental workload of individuals with autism spectrum disorder (ASD) during driving skill training. Methods Twenty adolescents with ASD participated in a six-session virtual reality driving simulator based experiment, during which their electroencephalogram (EEG) data were recorded alongside driving events and a therapist’s rating of their affective states and mental workload. Five feature generation approaches including statistical features, fractal dimension features, higher order crossings (HOC)-based features, power features from frequency bands, and power features from bins (Δf = 2 Hz) were applied to extract relevant features. Individual differences were removed with a two-step feature calibration method. Finally, binary classification results based on the k-nearest neighbors algorithm and univariate feature selection method were evaluated by leave-one-subject-out nested cross-validation to compare feature types and identify discriminative features. Results The best classification results were achieved using power features from bins for engagement (0.95) and boredom (0.78), and HOC-based features for enjoyment (0.90), frustration (0.88), and workload (0.86). Conclusion Offline EEG-based group-level classification models are feasible for recognizing binary low and high intensity of affect and workload of individuals with ASD in the context of driving. However, while promising the applicability of the models in an online adaptive driving task requires further development. Significance The developed models provide a basis for an EEG-based passive brain computer interface system that has the potential to benefit individuals with ASD with an affect- and workload-based individualized driving skill training intervention. PMID:28422647

A feature-based approach to modeling protein-protein interaction hot spots.

PubMed

Cho, Kyu-il; Kim, Dongsup; Lee, Doheon

2009-05-01

Identifying features that effectively represent the energetic contribution of an individual interface residue to the interactions between proteins remains problematic. Here, we present several new features and show that they are more effective than conventional features. By combining the proposed features with conventional features, we develop a predictive model for interaction hot spots. Initially, 54 multifaceted features, composed of different levels of information including structure, sequence and molecular interaction information, are quantified. Then, to identify the best subset of features for predicting hot spots, feature selection is performed using a decision tree. Based on the selected features, a predictive model for hot spots is created using support vector machine (SVM) and tested on an independent test set. Our model shows better overall predictive accuracy than previous methods such as the alanine scanning methods Robetta and FOLDEF, and the knowledge-based method KFC. Subsequent analysis yields several findings about hot spots. As expected, hot spots have a larger relative surface area burial and are more hydrophobic than other residues. Unexpectedly, however, residue conservation displays a rather complicated tendency depending on the types of protein complexes, indicating that this feature is not good for identifying hot spots. Of the selected features, the weighted atomic packing density, relative surface area burial and weighted hydrophobicity are the top 3, with the weighted atomic packing density proving to be the most effective feature for predicting hot spots. Notably, we find that hot spots are closely related to pi-related interactions, especially pi . . . pi interactions.

Prospective investigation of FOXP1 syndrome.

PubMed

Siper, Paige M; De Rubeis, Silvia; Trelles, Maria Del Pilar; Durkin, Allison; Di Marino, Daniele; Muratet, François; Frank, Yitzchak; Lozano, Reymundo; Eichler, Evan E; Kelly, Morgan; Beighley, Jennifer; Gerdts, Jennifer; Wallace, Arianne S; Mefford, Heather C; Bernier, Raphael A; Kolevzon, Alexander; Buxbaum, Joseph D

2017-01-01

Haploinsufficiency of the forkhead-box protein P1 ( FOXP1 ) gene leads to a neurodevelopmental disorder termed FOXP1 syndrome. Previous studies in individuals carrying FOXP1 mutations and deletions have described the presence of autism spectrum disorder (ASD) traits, intellectual disability, language impairment, and psychiatric features. The goal of the present study was to comprehensively characterize the genetic and clinical spectrum of FOXP1 syndrome. This is the first study to prospectively examine the genotype-phenotype relationship in multiple individuals with FOXP1 syndrome, using a battery of standardized clinical assessments. Genetic and clinical data was obtained and analyzed from nine children and adolescents between the ages of 5-17 with mutations in FOXP1 . Phenotypic characterization included gold standard ASD testing and norm-referenced measures of cognition, adaptive behavior, language, motor, and visual-motor integration skills. In addition, psychiatric, medical, neurological, and dysmorphology examinations were completed by a multidisciplinary team of clinicians. A comprehensive review of reported cases was also performed. All missense and in-frame mutations were mapped onto the three-dimensional structure of DNA-bound FOXP1. We have identified nine de novo mutations, including three frameshift, one nonsense, one mutation in an essential splice site resulting in frameshift and insertion of a premature stop codon, three missense, and one in-frame deletion. Reviewing prior literature, we found seven instances of recurrent mutations and another 34 private mutations. The majority of pathogenic missense and in-frame mutations, including all four missense mutations in our cohort, lie in the DNA-binding domain. Through structural analyses, we show that the mutations perturb amino acids necessary for binding to the DNA or interfere with the domain swapping that mediates FOXP1 dimerization. Individuals with FOXP1 syndrome presented with delays in early motor and language milestones, language impairment (expressive language > receptive language), ASD symptoms, visual-motor integration deficits, and complex psychiatric presentations characterized by anxiety, obsessive-compulsive traits, attention deficits, and externalizing symptoms. Medical features included non-specific structural brain abnormalities and dysmorphic features, endocrine and gastrointestinal problems, sleep disturbances, and sinopulmonary infections. This study identifies novel FOXP1 mutations associated with FOXP1 syndrome, identifies recurrent mutations, and demonstrates significant clustering of missense mutations in the DNA-binding domain. Clinical findings confirm the role FOXP1 plays in development across multiple domains of functioning. The genetic findings can be incorporated into clinical genetics practice to improve accurate genetic diagnosis of FOXP1 syndrome and the clinical findings can inform monitoring and treatment of individuals with FOXP1 syndrome.

Nuclear magnetic resonance detection and spectroscopy of single proteins using quantum logic

NASA Astrophysics Data System (ADS)

Lovchinsky, I.; Sushkov, A. O.; Urbach, E.; de Leon, N. P.; Choi, S.; De Greve, K.; Evans, R.; Gertner, R.; Bersin, E.; Müller, C.; McGuinness, L.; Jelezko, F.; Walsworth, R. L.; Park, H.; Lukin, M. D.

2016-02-01

Nuclear magnetic resonance spectroscopy is a powerful tool for the structural analysis of organic compounds and biomolecules but typically requires macroscopic sample quantities. We use a sensor, which consists of two quantum bits corresponding to an electronic spin and an ancillary nuclear spin, to demonstrate room temperature magnetic resonance detection and spectroscopy of multiple nuclear species within individual ubiquitin proteins attached to the diamond surface. Using quantum logic to improve readout fidelity and a surface-treatment technique to extend the spin coherence time of shallow nitrogen-vacancy centers, we demonstrate magnetic field sensitivity sufficient to detect individual proton spins within 1 second of integration. This gain in sensitivity enables high-confidence detection of individual proteins and allows us to observe spectral features that reveal information about their chemical composition.

Optimization of the structural configuration of ICBA/P3HT photovoltaic cells

NASA Astrophysics Data System (ADS)

Nemnes, G. A.; Iftimie, Sorina; Palici, Alexandra; Nicolaev, Adela; Mitran, T. L.; Radu, A.; Antohe, S.

2017-12-01

We investigate a possible route for optimization of organic P3HT:ICBA photovoltaic cells. In order to ensure a more efficient charge separation and collection at the electrodes, two- and three-layer structures are produced, where additional P3HT and ICBA single layers are placed adjacent to the mixed layer. The J-V characteristics are modeled using Monte-Carlo simulations in a flexible computational framework, reproducing the typical morphologies of the active layers. We discuss the implications of the structural modifications, in particular the enhancement of the open circuit voltage. Qualitative features of the theoretical simulations are validated by experiment. The proposed fabrication technique of using solvents with different boiling points for successive deposition of the individual layers may constitute an accessible route for producing optimized solar cell structures.

Discerning mild cognitive impairment and Alzheimer Disease from normal aging: morphologic characterization based on univariate and multivariate models.

PubMed

Liao, Weiqi; Long, Xiaojing; Jiang, Chunxiang; Diao, Yanjun; Liu, Xin; Zheng, Hairong; Zhang, Lijuan

2014-05-01

Differentiating mild cognitive impairment (MCI) and Alzheimer Disease (AD) from healthy aging remains challenging. This study aimed to explore the cerebral structural alterations of subjects with MCI or AD as compared to healthy elderly based on the individual and collective effects of cerebral morphologic indices using univariate and multivariate analyses. T1-weighted images (T1WIs) were retrieved from Alzheimer Disease Neuroimaging Initiative database for 116 subjects who were categorized into groups of healthy aging, MCI, and AD. Analysis of covariance (ANCOVA) and multivariate analysis of covariance (MANCOVA) were performed to explore the intergroup morphologic alterations indexed by surface area, curvature index, cortical thickness, and subjacent white matter volume with age and sex controlled as covariates, in 34 parcellated gyri regions of interest (ROIs) for both cerebral hemispheres based on the T1WI. Statistical parameters were mapped on the anatomic images to facilitate visual inspection. Global rather than region-specific structural alterations were revealed in groups of MCI and AD relative to healthy elderly using MANCOVA. ANCOVA revealed that the cortical thickness decreased more prominently in entorhinal, temporal, and cingulate cortices and was positively correlated with patients' cognitive performance in AD group but not in MCI. The temporal lobe features marked atrophy of white matter during the disease dynamics. Significant intercorrelations were observed among the morphologic indices with univariate analysis for given ROIs. Significant global structural alterations were identified in MCI and AD based on MANCOVA model with improved sensitivity. The intercorrelation among the morphologic indices may dampen the use of individual morphological parameter in featuring cerebral structural alterations. Decrease in cortical thickness is not reflective of the cognitive performance at the early stage of AD. Copyright © 2014 AUR. Published by Elsevier Inc. All rights reserved.

Semi-automatic mapping of cultural heritage from airborne laser scanning using deep learning

NASA Astrophysics Data System (ADS)

Due Trier, Øivind; Salberg, Arnt-Børre; Holger Pilø, Lars; Tonning, Christer; Marius Johansen, Hans; Aarsten, Dagrun

2016-04-01

This paper proposes to use deep learning to improve semi-automatic mapping of cultural heritage from airborne laser scanning (ALS) data. Automatic detection methods, based on traditional pattern recognition, have been applied in a number of cultural heritage mapping projects in Norway for the past five years. Automatic detection of pits and heaps have been combined with visual interpretation of the ALS data for the mapping of deer hunting systems, iron production sites, grave mounds and charcoal kilns. However, the performance of the automatic detection methods varies substantially between ALS datasets. For the mapping of deer hunting systems on flat gravel and sand sediment deposits, the automatic detection results were almost perfect. However, some false detections appeared in the terrain outside of the sediment deposits. These could be explained by other pit-like landscape features, like parts of river courses, spaces between boulders, and modern terrain modifications. However, these were easy to spot during visual interpretation, and the number of missed individual pitfall traps was still low. For the mapping of grave mounds, the automatic method produced a large number of false detections, reducing the usefulness of the semi-automatic approach. The mound structure is a very common natural terrain feature, and the grave mounds are less distinct in shape than the pitfall traps. Still, applying automatic mound detection on an entire municipality did lead to a new discovery of an Iron Age grave field with more than 15 individual mounds. Automatic mound detection also proved to be useful for a detailed re-mapping of Norway's largest Iron Age grave yard, which contains almost 1000 individual graves. Combined pit and mound detection has been applied to the mapping of more than 1000 charcoal kilns that were used by an iron work 350-200 years ago. The majority of charcoal kilns were indirectly detected as either pits on the circumference, a central mound, or both. However, kilns with a flat interior and a shallow ditch along the circumference were often missed by the automatic detection method. The successfulness of automatic detection seems to depend on two factors: (1) the density of ALS ground hits on the cultural heritage structures being sought, and (2) to what extent these structures stand out from natural terrain structures. The first factor may, to some extent, be improved by using a higher number of ALS pulses per square meter. The second factor is difficult to change, and also highlights another challenge: how to make a general automatic method that is applicable in all types of terrain within a country. The mixed experience with traditional pattern recognition for semi-automatic mapping of cultural heritage led us to consider deep learning as an alternative approach. The main principle is that a general feature detector has been trained on a large image database. The feature detector is then tailored to a specific task by using a modest number of images of true and false examples of the features being sought. Results of using deep learning are compared with previous results using traditional pattern recognition.

Tissue Feature-Based and Segmented Deformable Image Registration for Improved Modeling of the Shear Movement of the Lungs

PubMed Central

Xie, Yaoqin; Chao, Ming; Xing, Lei

2009-01-01

Purpose To report a tissue feature-based image registration strategy with explicit inclusion of the differential motions of thoracic structures. Methods and Materials The proposed technique started with auto-identification of a number of corresponding points with distinct tissue features. The tissue feature points were found by using the scale-invariant feature transform (SIFT) method. The control point pairs were then sorted into different “colors” according to the organs they reside and used to model the involved organs individually. A thin-plate spline (TPS) method was used to register a structure characterized by the control points with a given “color”. The proposed technique was applied to study a digital phantom case, three lung and three liver cancer patients. Results For the phantom case, a comparison with the conventional TPS method showed that the registration accuracy was markedly improved when the differential motions of the lung and chest wall were taken into account. On average, the registration error and the standard deviation (SD) of the 15 points against the known ground truth are reduced from 3.0 mm to 0.5 mm and from 1.5 mm to 0.2 mm, respectively, when the new method was used. Similar level of improvement was achieved for the clinical cases. Conclusions The segmented deformable approach provides a natural and logical solution to model the discontinuous organ motions and greatly improves the accuracy and robustness of deformable registration. PMID:19545792

Aromatic Structure in Simulates Titan Aerosol

NASA Technical Reports Server (NTRS)

Trainer, Melissa G.; Loeffler, M. J.; Anderson, C. M.; Hudson, R. L.; Samuelson, R. E.; Moore, M. A.

2011-01-01

Observations of Titan by the Cassini Composite Infrared Spectrometer (CIRS) between 560 and 20 per centimeter (approximately 18 to 500 micrometers) have been used to infer the vertical variations of Titan's ice abundances, as well as those of the aerosol from the surface to an altitude of 300 km [1]. The aerosol has a broad emission feature centered approximately at 140 per centimeter (71 micrometers). As seen in Figure 1, this feature cannot be reproduced using currently available optical constants from laboratory-generated Titan aerosol analogs [2]. The far-IR is uniquely qualified for investigating low-energy vibrational motions within the lattice structures of COITIDlex aerosol. The feature observed by CIRS is broad, and does not likely arise from individual molecules, but rather is representative of the skeletal movements of macromolecules. Since Cassini's arrival at Titan, benzene (C6H6) has been detected in the atmosphere at ppm levels as well as ions that may be polycyclic aromatic hydrocarbons (PAHs) [3]. We speculate that the feature may be a blended composite that can be identified with low-energy vibrations of two-dimensional lattice structures of large molecules, such as PAHs or nitrogenated aromatics. Such structures do not dominate the composition of analog materials generated from CH4 and N2 irradiation. We are performing studies forming aerosol analog via UV irradiation of aromatic precursors - specifically C6H6 - to understand how the unique chemical architecture of the products will influence the observable aerosol characteristics. The optical and chemical properties of the aromatic analog will be compared to those formed from CH4/N2 mixtures, with a focus on the as-yet unidentified far-IR absorbance feature. Preliminary results indicate that the photochemically-formed aromatic aerosol has distinct chemical composition, and may incorporate nitrogen either into the ring structure or adjoined chemical groups. These compositional differences are demonstrated in the aerosol mass spectra shown in Figure 2. The aromatic aerosol also demonstrates strong chemical reactivity when exposed to laboratory air, indicating substantial stored chemical potential. Oxidatoin and solubility studies wil be presented and implicatoins for prebiotic chemistry o nTitan will be discussed.

Genome accessibility is widely preserved and locally modulated during mitosis

PubMed Central

Hsiung, Chris C.-S.; Morrissey, Christapher S.; Udugama, Maheshi; Frank, Christopher L.; Keller, Cheryl A.; Baek, Songjoon; Giardine, Belinda; Crawford, Gregory E.; Sung, Myong-Hee; Hardison, Ross C.

2015-01-01

Mitosis entails global alterations to chromosome structure and nuclear architecture, concomitant with transient silencing of transcription. How cells transmit transcriptional states through mitosis remains incompletely understood. While many nuclear factors dissociate from mitotic chromosomes, the observation that certain nuclear factors and chromatin features remain associated with individual loci during mitosis originated the hypothesis that such mitotically retained molecular signatures could provide transcriptional memory through mitosis. To understand the role of chromatin structure in mitotic memory, we performed the first genome-wide comparison of DNase I sensitivity of chromatin in mitosis and interphase, using a murine erythroblast model. Despite chromosome condensation during mitosis visible by microscopy, the landscape of chromatin accessibility at the macromolecular level is largely unaltered. However, mitotic chromatin accessibility is locally dynamic, with individual loci maintaining none, some, or all of their interphase accessibility. Mitotic reduction in accessibility occurs primarily within narrow, highly DNase hypersensitive sites that frequently coincide with transcription factor binding sites, whereas broader domains of moderate accessibility tend to be more stable. In mitosis, proximal promoters generally maintain their accessibility more strongly, whereas distal regulatory elements tend to lose accessibility. Large domains of DNA hypomethylation mark a subset of promoters that retain accessibility during mitosis and across many cell types in interphase. Erythroid transcription factor GATA1 exerts site-specific changes in interphase accessibility that are most pronounced at distal regulatory elements, but has little influence on mitotic accessibility. We conclude that features of open chromatin are remarkably stable through mitosis, but are modulated at the level of individual genes and regulatory elements. PMID:25373146

Vibrational mode frequencies of silica species in SiO2-H2O liquids and glasses from ab initio molecular dynamics.

PubMed

Spiekermann, Georg; Steele-MacInnis, Matthew; Schmidt, Christian; Jahn, Sandro

2012-04-21

Vibrational spectroscopy techniques are commonly used to probe the atomic-scale structure of silica species in aqueous solution and hydrous silica glasses. However, unequivocal assignment of individual spectroscopic features to specific vibrational modes is challenging. In this contribution, we establish a connection between experimentally observed vibrational bands and ab initio molecular dynamics (MD) of silica species in solution and in hydrous silica glass. Using the mode-projection approach, we decompose the vibrations of silica species into subspectra resulting from several fundamental structural subunits: The SiO(4) tetrahedron of symmetry T(d), the bridging oxygen (BO) Si-O-Si of symmetry C(2v), the geminal oxygen O-Si-O of symmetry C(2v), the individual Si-OH stretching, and the specific ethane-like symmetric stretching contribution of the H(6)Si(2)O(7) dimer. This allows us to study relevant vibrations of these subunits in any degree of polymerization, from the Q(0) monomer up to the fully polymerized Q(4) tetrahedra. Demonstrating the potential of this approach for supplementing the interpretation of experimental spectra, we compare the calculated frequencies to those extracted from experimental Raman spectra of hydrous silica glasses and silica species in aqueous solution. We discuss observed features such as the double-peaked contribution of the Q(2) tetrahedral symmetric stretch, the individual Si-OH stretching vibrations, the origin of the experimentally observed band at 970 cm(-1) and the ethane-like vibrational contribution of the H(6)Si(2)O(7) dimer at 870 cm(-1).

Improving link prediction in complex networks by adaptively exploiting multiple structural features of networks

NASA Astrophysics Data System (ADS)

Ma, Chuang; Bao, Zhong-Kui; Zhang, Hai-Feng

2017-10-01

So far, many network-structure-based link prediction methods have been proposed. However, these methods only highlight one or two structural features of networks, and then use the methods to predict missing links in different networks. The performances of these existing methods are not always satisfied in all cases since each network has its unique underlying structural features. In this paper, by analyzing different real networks, we find that the structural features of different networks are remarkably different. In particular, even in the same network, their inner structural features are utterly different. Therefore, more structural features should be considered. However, owing to the remarkably different structural features, the contributions of different features are hard to be given in advance. Inspired by these facts, an adaptive fusion model regarding link prediction is proposed to incorporate multiple structural features. In the model, a logistic function combing multiple structural features is defined, then the weight of each feature in the logistic function is adaptively determined by exploiting the known structure information. Last, we use the "learnt" logistic function to predict the connection probabilities of missing links. According to our experimental results, we find that the performance of our adaptive fusion model is better than many similarity indices.

Dental Evidence in Forensic Identification - An Overview, Methodology and Present Status.

PubMed

Krishan, Kewal; Kanchan, Tanuj; Garg, Arun K

2015-01-01

Forensic odontology is primarily concerned with the use of teeth and oral structures for identification in a legal context. Various forensic odontology techniques help in the identification of the human remains in incidents such as terrorists' attacks, airplane, train and road accidents, fires, mass murders, and natural disasters such as tsunamis, earth quakes and floods, etc. (Disaster Victim Identification-DVI). Dental structures are the hardest and well protected structures in the body. These structures resist decomposition and high temperatures and are among the last ones to disintegrate after death. The principal basis of the dental identification lies in the fact that no two oral cavities are alike and the teeth are unique to an individual. The dental evidence of the deceased recovered from the scene of crime/occurrence is compared with the ante-mortem records for identification. Dental features such as tooth morphology, variations in shape and size, restorations, pathologies, missing tooth, wear patterns, crowding of the teeth, colour and position of the tooth, rotations and other peculiar dental anomalies give every individual a unique identity. In absence of ante-mortem dental records for comparison, the teeth can help in the determination of age, sex, race/ethnicity, habits, occupations, etc. which can give further clues regarding the identity of the individuals. This piece of writing gives an overview of dental evidence, its use in forensic identification and its limitations.

Dental Evidence in Forensic Identification – An Overview, Methodology and Present Status

PubMed Central

Krishan, Kewal; Kanchan, Tanuj; Garg, Arun K

2015-01-01

Forensic odontology is primarily concerned with the use of teeth and oral structures for identification in a legal context. Various forensic odontology techniques help in the identification of the human remains in incidents such as terrorists’ attacks, airplane, train and road accidents, fires, mass murders, and natural disasters such as tsunamis, earth quakes and floods, etc. (Disaster Victim Identification-DVI). Dental structures are the hardest and well protected structures in the body. These structures resist decomposition and high temperatures and are among the last ones to disintegrate after death. The principal basis of the dental identification lies in the fact that no two oral cavities are alike and the teeth are unique to an individual. The dental evidence of the deceased recovered from the scene of crime/occurrence is compared with the ante-mortem records for identification. Dental features such as tooth morphology, variations in shape and size, restorations, pathologies, missing tooth, wear patterns, crowding of the teeth, colour and position of the tooth, rotations and other peculiar dental anomalies give every individual a unique identity. In absence of ante-mortem dental records for comparison, the teeth can help in the determination of age, sex, race/ethnicity, habits, occupations, etc. which can give further clues regarding the identity of the individuals. This piece of writing gives an overview of dental evidence, its use in forensic identification and its limitations. PMID:26312096

Inferring Biological Structures from Super-Resolution Single Molecule Images Using Generative Models

PubMed Central

Maji, Suvrajit; Bruchez, Marcel P.

2012-01-01

Localization-based super resolution imaging is presently limited by sampling requirements for dynamic measurements of biological structures. Generating an image requires serial acquisition of individual molecular positions at sufficient density to define a biological structure, increasing the acquisition time. Efficient analysis of biological structures from sparse localization data could substantially improve the dynamic imaging capabilities of these methods. Using a feature extraction technique called the Hough Transform simple biological structures are identified from both simulated and real localization data. We demonstrate that these generative models can efficiently infer biological structures in the data from far fewer localizations than are required for complete spatial sampling. Analysis at partial data densities revealed efficient recovery of clathrin vesicle size distributions and microtubule orientation angles with as little as 10% of the localization data. This approach significantly increases the temporal resolution for dynamic imaging and provides quantitatively useful biological information. PMID:22629348

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

Levakhina, Y. M.; Mueller, J.; Buzug, T. M.

Purpose: This paper introduces a nonlinear weighting scheme into the backprojection operation within the simultaneous algebraic reconstruction technique (SART). It is designed for tomosynthesis imaging of objects with high-attenuation features in order to reduce limited angle artifacts. Methods: The algorithm estimates which projections potentially produce artifacts in a voxel. The contribution of those projections into the updating term is reduced. In order to identify those projections automatically, a four-dimensional backprojected space representation is used. Weighting coefficients are calculated based on a dissimilarity measure, evaluated in this space. For each combination of an angular view direction and a voxel position anmore » individual weighting coefficient for the updating term is calculated. Results: The feasibility of the proposed approach is shown based on reconstructions of the following real three-dimensional tomosynthesis datasets: a mammography quality phantom, an apple with metal needles, a dried finger bone in water, and a human hand. Datasets have been acquired with a Siemens Mammomat Inspiration tomosynthesis device and reconstructed using SART with and without suggested weighting. Out-of-focus artifacts are described using line profiles and measured using standard deviation (STD) in the plane and below the plane which contains artifact-causing features. Artifacts distribution in axial direction is measured using an artifact spread function (ASF). The volumes reconstructed with the weighting scheme demonstrate the reduction of out-of-focus artifacts, lower STD (meaning reduction of artifacts), and narrower ASF compared to nonweighted SART reconstruction. It is achieved successfully for different kinds of structures: point-like structures such as phantom features, long structures such as metal needles, and fine structures such as trabecular bone structures. Conclusions: Results indicate the feasibility of the proposed algorithm to reduce typical tomosynthesis artifacts produced by high-attenuation features. The proposed algorithm assigns weighting coefficients automatically and no segmentation or tissue-classification steps are required. The algorithm can be included into various iterative reconstruction algorithms with an additive updating strategy. It can also be extended to computed tomography case with the complete set of angular data.« less

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.

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.

Lex-SVM: exploring the potential of exon expression profiling for disease classification.

PubMed

Yuan, Xiongying; Zhao, Yi; Liu, Changning; Bu, Dongbo

2011-04-01

Exon expression profiling technologies, including exon arrays and RNA-Seq, measure the abundance of every exon in a gene. Compared with gene expression profiling technologies like 3' array, exon expression profiling technologies could detect alterations in both transcription and alternative splicing, therefore they are expected to be more sensitive in diagnosis. However, exon expression profiling also brings higher dimension, more redundancy, and significant correlation among features. Ignoring the correlation structure among exons of a gene, a popular classification method like L1-SVM selects exons individually from each gene and thus is vulnerable to noise. To overcome this limitation, we present in this paper a new variant of SVM named Lex-SVM to incorporate correlation structure among exons and known splicing patterns to promote classification performance. Specifically, we construct a new norm, ex-norm, including our prior knowledge on exon correlation structure to regularize the coefficients of a linear SVM. Lex-SVM can be solved efficiently using standard linear programming techniques. The advantage of Lex-SVM is that it can select features group-wisely, force features in a subgroup to take equal weihts and exclude the features that contradict the majority in the subgroup. Experimental results suggest that on exon expression profile, Lex-SVM is more accurate than existing methods. Lex-SVM also generates a more compact model and selects genes more consistently in cross-validation. Unlike L1-SVM selecting only one exon in a gene, Lex-SVM assigns equal weights to as many exons in a gene as possible, lending itself easier for further interpretation.

Retinal image quality assessment based on image clarity and content

NASA Astrophysics Data System (ADS)

Abdel-Hamid, Lamiaa; El-Rafei, Ahmed; El-Ramly, Salwa; Michelson, Georg; Hornegger, Joachim

2016-09-01

Retinal image quality assessment (RIQA) is an essential step in automated screening systems to avoid misdiagnosis caused by processing poor quality retinal images. A no-reference transform-based RIQA algorithm is introduced that assesses images based on five clarity and content quality issues: sharpness, illumination, homogeneity, field definition, and content. Transform-based RIQA algorithms have the advantage of considering retinal structures while being computationally inexpensive. Wavelet-based features are proposed to evaluate the sharpness and overall illumination of the images. A retinal saturation channel is designed and used along with wavelet-based features for homogeneity assessment. The presented sharpness and illumination features are utilized to assure adequate field definition, whereas color information is used to exclude nonretinal images. Several publicly available datasets of varying quality grades are utilized to evaluate the feature sets resulting in area under the receiver operating characteristic curve above 0.99 for each of the individual feature sets. The overall quality is assessed by a classifier that uses the collective features as an input vector. The classification results show superior performance of the algorithm in comparison to other methods from literature. Moreover, the algorithm addresses efficiently and comprehensively various quality issues and is suitable for automatic screening systems.

Implications of Sponge Biodiversity Patterns for the Management of a Marine Reserve in Northern Australia

PubMed Central

Przeslawski, Rachel; Alvarez, Belinda; Kool, Johnathan; Bridge, Tom; Caley, M. Julian; Nichol, Scott

2015-01-01

Marine reserves are becoming progressively more important as anthropogenic impacts continue to increase, but we have little baseline information for most marine environments. In this study, we focus on the Oceanic Shoals Commonwealth Marine Reserve (CMR) in northern Australia, particularly the carbonate banks and terraces of the Sahul Shelf and Van Diemen Rise which have been designated a Key Ecological Feature (KEF). We use a species-level inventory compiled from three marine surveys to the CMR to address several questions relevant to marine management: 1) Are carbonate banks and other raised geomorphic features associated with biodiversity hotspots? 2) Can environmental (depth, substrate hardness, slope) or biogeographic (east vs west) variables help explain local and regional differences in community structure? 3) Do sponge communities differ among individual raised geomorphic features? Approximately 750 sponge specimens were collected in the Oceanic Shoals CMR and assigned to 348 species, of which only 18% included taxonomically described species. Between eastern and western areas of the CMR, there was no difference between sponge species richness or assemblages on raised geomorphic features. Among individual raised geomorphic features, sponge assemblages were significantly different, but species richness was not. Species richness showed no linear relationships with measured environmental factors, but sponge assemblages were weakly associated with several environmental variables including mean depth and mean backscatter (east and west) and mean slope (east only). These patterns of sponge diversity are applied to support the future management and monitoring of this region, particularly noting the importance of spatial scale in biodiversity assessments and associated management strategies. PMID:26606745

Borderline Personality Features, Anger, and Intimate Partner Violence: An Experimental Manipulation of Rejection.

PubMed

Armenti, Nicholas A; Babcock, Julia C

2018-04-01

Individuals with borderline personality features may be susceptible to react to situational stressors with negative and interpersonally maladaptive emotionality (e.g., anger) and aggression. The current study attempted to test two moderated mediation models to investigate dispositional risk factors associated with borderline personality features and intimate partner violence (IPV). Results from an experimental rejection induction paradigm were examined using moderated regression to observe contextual reactions to imagined romantic rejection from a current romantic partner among individuals with borderline personality features. An ethnically diverse sample of 218 undergraduates at a large public university in the southwestern United States was recruited. Participants responded to demographic questions and self-report measures, and engaged in an experimental rejection induction paradigm. Borderline personality features was positively associated with rejection sensitivity, physical assault, and psychological aggression. Contrary to initial hypotheses, rejection sensitivity did not serve as a mediator of the relations between borderline personality features and physical assault and psychological aggression. However, trait anger mediated the relation between borderline personality features and psychological aggression. As such, trait anger may be an important explanatory variable in the relation between borderline personality features and psychological aggression specifically. Results of the rejection induction paradigm indicated that, for individuals who were asked to imagine an ambiguous rejection, the relation between borderline personality features and state anger post-rejection was strengthened. For individuals who imagined a critical rejection, there was no significant relation between borderline personality features and state anger post-rejection. Findings suggest that trait anger may be an important dispositional factor in the link between borderline personality features and IPV. In addition, contextual factors, such as ambiguous rejection by an intimate partner, may be especially relevant in activating anger or aggression in individuals with borderline personality features.

Numerical equilibrium analysis for structured consumer resource models.

PubMed

de Roos, A M; Diekmann, O; Getto, P; Kirkilionis, M A

2010-02-01

In this paper, we present methods for a numerical equilibrium and stability analysis for models of a size structured population competing for an unstructured resource. We concentrate on cases where two model parameters are free, and thus existence boundaries for equilibria and stability boundaries can be defined in the (two-parameter) plane. We numerically trace these implicitly defined curves using alternatingly tangent prediction and Newton correction. Evaluation of the maps defining the curves involves integration over individual size and individual survival probability (and their derivatives) as functions of individual age. Such ingredients are often defined as solutions of ODE, i.e., in general only implicitly. In our case, the right-hand sides of these ODE feature discontinuities that are caused by an abrupt change of behavior at the size where juveniles are assumed to turn adult. So, we combine the numerical solution of these ODE with curve tracing methods. We have implemented the algorithms for "Daphnia consuming algae" models in C-code. The results obtained by way of this implementation are shown in the form of graphs.

Craniofacial Anomalies And Biostereometrics

NASA Astrophysics Data System (ADS)

Christiansen, Richard L.

1980-07-01

Man's oral-facial structures are vital for the functions of breathing, mastication, swallowing, vision, and communication. When defective development of these tissues occurs, function becomes impaired and the anatomic features of the afflicted individual will frequently deviate from the norm. This error of form and function will classify the individual as being physically and psychosocially handicapped. The successful habilitation regimen of the handicapped person depends on the accurate analysis of both craniofacial anatomy and physiology of these individuals, as well as psychological implications of the disfigurement. Biostereometrics can contribute to the establishment of operationally valid measures for assessing the severity of the handicapping conditions. The heterogeneous nature of diverse disfigurement suggest that an improved classification of malformations would be beneficial. Three-dimensional analysis may also have significant influence on the accuracy of the diagnosis, and the establishment of a biologically sound treatment plan. Biostereometrics will contribute more fully if the three-dimensional surface analysis can be coordinated with a study of 1) the underlying skeletal structures, and 2) the operational musculature. Increased communication between the stereometric experts and the biological scientists should accelerate the application of this technique to the health problem.

Storage of features, conjunctions and objects in visual working memory.

PubMed

Vogel, E K; Woodman, G F; Luck, S J

2001-02-01

Working memory can be divided into separate subsystems for verbal and visual information. Although the verbal system has been well characterized, the storage capacity of visual working memory has not yet been established for simple features or for conjunctions of features. The authors demonstrate that it is possible to retain information about only 3-4 colors or orientations in visual working memory at one time. Observers are also able to retain both the color and the orientation of 3-4 objects, indicating that visual working memory stores integrated objects rather than individual features. Indeed, objects defined by a conjunction of four features can be retained in working memory just as well as single-feature objects, allowing many individual features to be retained when distributed across a small number of objects. Thus, the capacity of visual working memory must be understood in terms of integrated objects rather than individual features.

Prediction of beta-turns and beta-turn types by a novel bidirectional Elman-type recurrent neural network with multiple output layers (MOLEBRNN).

PubMed

Kirschner, Andreas; Frishman, Dmitrij

2008-10-01

Prediction of beta-turns from amino acid sequences has long been recognized as an important problem in structural bioinformatics due to their frequent occurrence as well as their structural and functional significance. Because various structural features of proteins are intercorrelated, secondary structure information has been often employed as an additional input for machine learning algorithms while predicting beta-turns. Here we present a novel bidirectional Elman-type recurrent neural network with multiple output layers (MOLEBRNN) capable of predicting multiple mutually dependent structural motifs and demonstrate its efficiency in recognizing three aspects of protein structure: beta-turns, beta-turn types, and secondary structure. The advantage of our method compared to other predictors is that it does not require any external input except for sequence profiles because interdependencies between different structural features are taken into account implicitly during the learning process. In a sevenfold cross-validation experiment on a standard test dataset our method exhibits the total prediction accuracy of 77.9% and the Mathew's Correlation Coefficient of 0.45, the highest performance reported so far. It also outperforms other known methods in delineating individual turn types. We demonstrate how simultaneous prediction of multiple targets influences prediction performance on single targets. The MOLEBRNN presented here is a generic method applicable in a variety of research fields where multiple mutually depending target classes need to be predicted. http://webclu.bio.wzw.tum.de/predator-web/.

The 3D morphology of the ejecta surrounding VY Canis Majoris

NASA Astrophysics Data System (ADS)

Jones, Terry Jay; Humphreys, Roberta M.; Helton, L. Andrew

2007-03-01

We use second epoch images taken with WFPC2 on the HST and imaging polarimetry taken with the HST/ACS/HRC to explore the three dimensional structure of the circumstellar dust distribution around the red supergiant VY Canis Majoris. Transverse motions, combined with radial velocities, provide a picture of the kinematics of the ejecta, including the total space motions. The fractional polarization and photometric colors provide an independent method of locating the physical position of the dust along the line-of-sight. Most of the individual arc-like features and clumps seen in the intensity image are also features in the fractional polarization map, and must be distinct geometric objects. The location of these features in the ejecta of VY CMa using kinematics and polarimetry agree well with each other, and strongly suggest they are the result of relatively massive ejections, probably associated with magnetic fields.

Observations and Analysis of the GK Persei Nova Shell and its "Jet-like" Feature

NASA Astrophysics Data System (ADS)

Harvey, E.; Redman, M. P.; Boumis, P.; Akras, S.

2015-12-01

GK Persei (1901, the "Firework Nebula") is an old but bright nova remnant that offers a chance to probe the physics and kinematics of nova shells. The kinematics in new and archival longslit optical echelle spectra were analysed using the SHAPE software. New imaging from the Aristarchos telescope continues to track the proper motion, extinction and structural evolution of the knots, which have been observed intermittently over several decades. We present for the first time, kinematical constraints on a large faint "jet" feature, that was previously detected beyond the shell boundary. These observational constraints allow for the generation of models for individual knots, interactions within knot complexes, and the "jet" feature. Put together, and taking into account dwarf-nova accelerated winds emanating from the central source, these data and models give a deeper insight into the GK Per nova remnant as a whole.

Self-organized structures in a superorganism: do ants “behave” like molecules?

NASA Astrophysics Data System (ADS)

Detrain, Claire; Deneubourg, Jean-Louis

2006-09-01

While the striking structures (e.g. nest architecture, trail networks) of insect societies may seem familiar to many of us, the understanding of pattern formation still constitutes a challenging problem. Over the last two decades, self-organization has dramatically changed our view on how collective decision-making and structures may emerge out of a population of ant workers having each their own individuality as well as a limited access to information. A variety of collective behaviour spontaneously outcome from multiple interactions between nestmates, even when there is no directing influence imposed by an external template, a pacemaker or a leader. By focussing this review on foraging structures, we show that ant societies display some properties which are usually considered in physico-chemical systems, as typical signatures of self-organization. We detail the key role played by feed-back loops, fluctuations, number of interacting units and sensitivity to environmental factors in the emergence of a structured collective behaviour. Nonetheless, going beyond simple analogies with non-living self-organized patterns, we stress on the specificities of social structures made of complex living units of which the biological features have been selected throughout the evolution depending on their adaptive value. In particular, we consider the ability of each ant individual to process information about environmental and social parameters, to accordingly tune its interactions with nestmates and ultimately to determine the final pattern emerging at the collective level. We emphasize on the parsimony and simplicity of behavioural rules at the individual level which allow an efficient processing of information, energy and matter within the whole colony.

HMPAS: Human Membrane Protein Analysis System

PubMed Central

2013-01-01

Background Membrane proteins perform essential roles in diverse cellular functions and are regarded as major pharmaceutical targets. The significance of membrane proteins has led to the developing dozens of resources related with membrane proteins. However, most of these resources are built for specific well-known membrane protein groups, making it difficult to find common and specific features of various membrane protein groups. Methods We collected human membrane proteins from the dispersed resources and predicted novel membrane protein candidates by using ortholog information and our membrane protein classifiers. The membrane proteins were classified according to the type of interaction with the membrane, subcellular localization, and molecular function. We also made new feature dataset to characterize the membrane proteins in various aspects including membrane protein topology, domain, biological process, disease, and drug. Moreover, protein structure and ICD-10-CM based integrated disease and drug information was newly included. To analyze the comprehensive information of membrane proteins, we implemented analysis tools to identify novel sequence and functional features of the classified membrane protein groups and to extract features from protein sequences. Results We constructed HMPAS with 28,509 collected known membrane proteins and 8,076 newly predicted candidates. This system provides integrated information of human membrane proteins individually and in groups organized by 45 subcellular locations and 1,401 molecular functions. As a case study, we identified associations between the membrane proteins and diseases and present that membrane proteins are promising targets for diseases related with nervous system and circulatory system. A web-based interface of this system was constructed to facilitate researchers not only to retrieve organized information of individual proteins but also to use the tools to analyze the membrane proteins. Conclusions HMPAS provides comprehensive information about human membrane proteins including specific features of certain membrane protein groups. In this system, user can acquire the information of individual proteins and specified groups focused on their conserved sequence features, involved cellular processes, and diseases. HMPAS may contribute as a valuable resource for the inference of novel cellular mechanisms and pharmaceutical targets associated with the human membrane proteins. HMPAS is freely available at http://fcode.kaist.ac.kr/hmpas. PMID:24564858

Exploring social structure effect on language evolution based on a computational model

NASA Astrophysics Data System (ADS)

Gong, Tao; Minett, James; Wang, William

2008-06-01

A compositionality-regularity coevolution model is adopted to explore the effect of social structure on language emergence and maintenance. Based on this model, we explore language evolution in three experiments, and discuss the role of a popular agent in language evolution, the relationship between mutual understanding and social hierarchy, and the effect of inter-community communications and that of simple linguistic features on convergence of communal languages in two communities. This work embodies several important interactions during social learning, and introduces a new approach that manipulates individuals' probabilities to participate in social interactions to study the effect of social structure. We hope it will stimulate further theoretical and empirical explorations on language evolution in a social environment.

Optimizing Radiometric Processing and Feature Extraction of Drone Based Hyperspectral Frame Format Imagery for Estimation of Yield Quantity and Quality of a Grass Sward

NASA Astrophysics Data System (ADS)

Näsi, R.; Viljanen, N.; Oliveira, R.; Kaivosoja, J.; Niemeläinen, O.; Hakala, T.; Markelin, L.; Nezami, S.; Suomalainen, J.; Honkavaara, E.

2018-04-01

Light-weight 2D format hyperspectral imagers operable from unmanned aerial vehicles (UAV) have become common in various remote sensing tasks in recent years. Using these technologies, the area of interest is covered by multiple overlapping hypercubes, in other words multiview hyperspectral photogrammetric imagery, and each object point appears in many, even tens of individual hypercubes. The common practice is to calculate hyperspectral orthomosaics utilizing only the most nadir areas of the images. However, the redundancy of the data gives potential for much more versatile and thorough feature extraction. We investigated various options of extracting spectral features in the grass sward quantity evaluation task. In addition to the various sets of spectral features, we used photogrammetry-based ultra-high density point clouds to extract features describing the canopy 3D structure. Machine learning technique based on the Random Forest algorithm was used to estimate the fresh biomass. Results showed high accuracies for all investigated features sets. The estimation results using multiview data provided approximately 10 % better results than the most nadir orthophotos. The utilization of the photogrammetric 3D features improved estimation accuracy by approximately 40 % compared to approaches where only spectral features were applied. The best estimation RMSE of 239 kg/ha (6.0 %) was obtained with multiview anisotropy corrected data set and the 3D features.

Vibrational Properties of Hydrogen-Bonded Systems Using the Multireference Generalization to the "On-the-Fly" Electronic Structure within Quantum Wavepacket ab Initio Molecular Dynamics (QWAIMD).

PubMed

Li, Junjie; Li, Xiaohu; Iyengar, Srinivasan S

2014-06-10

We discuss a multiconfigurational treatment of the "on-the-fly" electronic structure within the quantum wavepacket ab initio molecular dynamics (QWAIMD) method for coupled treatment of quantum nuclear effects with electronic structural effects. Here, multiple single-particle electronic density matrices are simultaneously propagated with a quantum nuclear wavepacket and other classical nuclear degrees of freedom. The multiple density matrices are coupled through a nonorthogonal configuration interaction (NOCI) procedure to construct the instantaneous potential surface. An adaptive-mesh-guided set of basis functions composed of Gaussian primitives are used to simplify the electronic structure calculations. Specifically, with the replacement of the atom-centered basis functions positioned on the centers of the quantum-mechanically treated nuclei by a mesh-guided band of basis functions, the two-electron integrals used to compute the electronic structure potential surface become independent of the quantum nuclear variable and hence reusable along the entire Cartesian grid representing the quantum nuclear coordinates. This reduces the computational complexity involved in obtaining a potential surface and facilitates the interpretation of the individual density matrices as representative diabatic states. The parametric nuclear position dependence of the diabatic states is evaluated at the initial time-step using a Shannon-entropy-based sampling function that depends on an approximation to the quantum nuclear wavepacket and the potential surface. This development is meant as a precursor to an on-the-fly fully multireference electronic structure procedure embedded, on-the-fly, within a quantum nuclear dynamics formalism. We benchmark the current development by computing structural, dynamic, and spectroscopic features for a series of bihalide hydrogen-bonded systems: FHF(-), ClHCl(-), BrHBr(-), and BrHCl(-). We find that the donor-acceptor structural features are in good agreement with experiments. Spectroscopic features are computed using a unified velocity/flux autocorrelation function and include vibrational fundamentals and combination bands. These agree well with experiments and other theories.

Exclusion of chromosome 1q21-q31 from linkage to three pedigrees affected by the pigment-dispersion syndrome

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

Paglinauan, C.; Haines, J.L.; Del Bono, E.A.

1995-05-01

The pigment-dispersion syndrome is a form of open-angle glaucoma that usually affects individuals in the first 3 decades of life. In addition to the typical optic-nerve degeneration seen in all types of glaucoma, the pigment-dispersion syndrome is characterized by distinctive clinical features including the deposition of pigment granules from the iris epithelium on a variety of ocular structures including the trabecular meshwork. Frequently this disorder affects young myopic individuals. In the early stages of the disease, affected individuals may have clinical evidence of dispersed pigment without an associated elevation of intraocular pressure and optic-nerve degeneration. However, as the disease processmore » progresses, many affected individuals ({approximately}50%) will develop elevated intraocular pressure and degeneration of the optic nerve, causing a permanent loss of sight. The pigment-dispersion syndrome shares several clinical features with the form of autosomal dominant juvenile open-angle glaucoma that recently has been mapped to the 1q21-q31 region of chromosome 1. Our results indicate that the pigment-dispersion syndrome, a form of glaucoma that may also affect the juvenile population, is genetically unrelated to the autosomal dominant form of juvenile glaucoma caused by a defect in a gene located in the 1q21-q31 region of chromosome 1. 15 refs., 2 figs., 1 tab.« less

Accurate prediction of hot spot residues through physicochemical characteristics of amino acid sequences.

PubMed

Chen, Peng; Li, Jinyan; Wong, Limsoon; Kuwahara, Hiroyuki; Huang, Jianhua Z; Gao, Xin

2013-08-01

Hot spot residues of proteins are fundamental interface residues that help proteins perform their functions. Detecting hot spots by experimental methods is costly and time-consuming. Sequential and structural information has been widely used in the computational prediction of hot spots. However, structural information is not always available. In this article, we investigated the problem of identifying hot spots using only physicochemical characteristics extracted from amino acid sequences. We first extracted 132 relatively independent physicochemical features from a set of the 544 properties in AAindex1, an amino acid index database. Each feature was utilized to train a classification model with a novel encoding schema for hot spot prediction by the IBk algorithm, an extension of the K-nearest neighbor algorithm. The combinations of the individual classifiers were explored and the classifiers that appeared frequently in the top performing combinations were selected. The hot spot predictor was built based on an ensemble of these classifiers and to work in a voting manner. Experimental results demonstrated that our method effectively exploited the feature space and allowed flexible weights of features for different queries. On the commonly used hot spot benchmark sets, our method significantly outperformed other machine learning algorithms and state-of-the-art hot spot predictors. The program is available at http://sfb.kaust.edu.sa/pages/software.aspx. Copyright © 2013 Wiley Periodicals, Inc.

Tectonics and kinematics of a foreland folded belt influenced by salt, arctic Canada

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

Harrison, J.C.

1996-12-31

The Ordovician (upper Arenig-Llanvirn) Bay Fiord Formation is one of three widespread evaporite units known to have profoundly influenced the style of contractional tectonics within the Innuitian orogen of Arctic Canada. In the western Arctic Islands, the salt-bearing Bay Fiord Formation has accommodated buckling and mostly subsurface thrusting in the west-trending Parry Islands foldbelt. A characteristic feature of this belt is a stratigraphic succession more than 10 km thick featuring three rigid and widespread sedimentary layers and two intervening ductile layers (lower salt and upper shale). The ductile strata have migrated to anticlinal welts during buckling. Other features of themore » foldbelt include (1) an extreme length of individual upright folds (up to 330 km), (2) extreme foldbelt width (up to 11%), (5) a shallow dipping salt decollement system (0.1{degrees}-0.6{degrees}) that has also been folded in the hinterland and later extended, and (6) a complete absence of halokinetic piercing diapirs. The progression from simple thrust-fold structure on the foldbelt periphery to complex in the interior provides a viable kinematic model for this and other contractional salt provinces. One feature of this model is a single massive triangle zone structure (passive roof duplex) that may envelop the entire 200-km width of the foldbelt and underlie an area exceeding 52,000 km{sup 2}.« less

Adult Vampire Bats Produce Contact Calls When Isolated: Acoustic Variation by Species, Population, Colony, and Individual

PubMed Central

Carter, Gerald G.; Logsdon, Ryane; Arnold, Bryan D.; Menchaca, Angelica; Medellin, Rodrigo A.

2012-01-01

Background Bat pups produce individually distinct isolation calls to facilitate maternal recognition. Increasing evidence suggests that, in group-living bat species, adults often use similar calls to maintain contact. We investigated if isolated adults from all three species of the highly cooperative vampire bats (Phyllostomidae: Desmodontinae) would produce vocally distinct contact calls when physically isolated. Methods/Principal Findings We assessed variation in contact calls recorded from isolated captive and wild-caught adult common vampire bats (Desmodus rotundus), white-winged vampire bats (Diaemus youngi) and hairy-legged vampire bats (Diphylla ecaudata). We compared species-typical contact call structure, and used information theory and permuted discriminate function analyses to examine call structure variation, and to determine if the individuality of contact calls is encoded by different call features across species and populations. We found that isolated adult vampire bats produce contact calls that vary by species, population, colony, and individual. However, much variation occurred within a single context and individual. We estimated signature information for captive Diaemus (same colony), captive Desmodus (same colony), and wild Desmodus (different colonies) at 3.21, 3.26, and 3.88 bits, respectively. Contact calls from a captive colony of Desmodus were less individually distinct than calls from wild-caught Desmodus from different colonies. Both the degree of individuality and parameters encoding individuality differed between the bats from a single captive colony and the wild-caught individuals from different groups. This result is consistent with, but not sufficient evidence of, vocal convergence in groups. Conclusion Our results show that adult vampire bats of all three species produce highly variable contact calls when isolated. Contact calls contain sufficient information for vocal discrimination, but also possess more intra-individual variation than is required for the sole purpose of identifying individuals. PMID:22719947

Volcanic structures and oral traditions of volcanism of Western Samoa (SW Pacific) and their implications for hazard education

NASA Astrophysics Data System (ADS)

Németh, Károly; Cronin, Shane J.

2009-10-01

The Samoan Islands have experienced > 2 million years of volcanism, culminating in historic eruptions at both the east and western ends of the chain including a major lava-producing episode on the island of Savai'i from AD 1905-1911. Upolu in Western Samoa has several areas mapped as early Holocene in age (> 5 ka), but here we present new evidence for fresh volcanic landforms and deposits, supported by a radiocarbon date of 1915 ± 65 yrs B.P., giving a maximum age to a phreatomagmatic tuff cone offshore of Cape Tapaga, east Upolu. In addition, we report on a parallel investigation of the oral traditions of communities surrounding fresh volcanic landforms that may reflect distant "volcanic memories" passed down over generations. To accommodate Samoan cultural structures, oral traditional knowledge was sought through semi-structured interviews with small groups (3-4) or individuals. Samoan facilitators focused on high-ranking and traditionally respected (particularly elderly) individuals for explanations of the origins of local features, including their genesis, use and any related geo-hazards. Areas targeted were those where young eruptions (< 3500 yr BP) were suspected from geological mapping. In stark contrast to communities in Vanuatu, Papua New Guinea or the Solomon Islands, the village communities show extremely limited knowledge of their volcanic heritage. Youthful volcanic landforms are often not recognised as such and appear to play little role in everyday life. Few, if any, legends are attached to any volcanic feature. Instead, oral traditions deal primarily with the origins of Samoans (overlain by strong Christian teachings), and past disputes/battles and wrongdoings between tribes/neighbours. The only exceptions to this were identified in legends from East Upolu, where offshore islands (tuff cones) are associated with late Holocene explosive phreatomagmatic volcanism. Maps drawn by individuals and groups interviewed, highlighted the resources and landscapes important in their lives. The majority of these were prepared as 3D oblique-view sketches, rather than plan-views, showing little in common with typical hazard maps used in the area. In addition, maps were commonly restricted strictly to boundaries of local communities, ignoring major features (such as fresh volcanic cones) that were in the territory of "next door" villages. These perspectives need to be focused upon in future iterations of hazard maps and hazard-education programmes for Samoa and similar Polynesian communities.

Unfakeable facial configurations affect strategic choices in trust games with or without information about past behavior.

PubMed

Rezlescu, Constantin; Duchaine, Brad; Olivola, Christopher Y; Chater, Nick

2012-01-01

Many human interactions are built on trust, so widespread confidence in first impressions generally favors individuals with trustworthy-looking appearances. However, few studies have explicitly examined: 1) the contribution of unfakeable facial features to trust-based decisions, and 2) how these cues are integrated with information about past behavior. Using highly controlled stimuli and an improved experimental procedure, we show that unfakeable facial features associated with the appearance of trustworthiness attract higher investments in trust games. The facial trustworthiness premium is large for decisions based solely on faces, with trustworthy identities attracting 42% more money (Study 1), and remains significant though reduced to 6% when reputational information is also available (Study 2). The face trustworthiness premium persists with real (rather than virtual) currency and when higher payoffs are at stake (Study 3). Our results demonstrate that cooperation may be affected not only by controllable appearance cues (e.g., clothing, facial expressions) as shown previously, but also by features that are impossible to mimic (e.g., individual facial structure). This unfakeable face trustworthiness effect is not limited to the rare situations where people lack any information about their partners, but survives in richer environments where relevant details about partner past behavior are available.

Unfakeable Facial Configurations Affect Strategic Choices in Trust Games with or without Information about Past Behavior

PubMed Central

Rezlescu, Constantin; Duchaine, Brad; Olivola, Christopher Y.; Chater, Nick

2012-01-01

Background Many human interactions are built on trust, so widespread confidence in first impressions generally favors individuals with trustworthy-looking appearances. However, few studies have explicitly examined: 1) the contribution of unfakeable facial features to trust-based decisions, and 2) how these cues are integrated with information about past behavior. Methodology/Principal Findings Using highly controlled stimuli and an improved experimental procedure, we show that unfakeable facial features associated with the appearance of trustworthiness attract higher investments in trust games. The facial trustworthiness premium is large for decisions based solely on faces, with trustworthy identities attracting 42% more money (Study 1), and remains significant though reduced to 6% when reputational information is also available (Study 2). The face trustworthiness premium persists with real (rather than virtual) currency and when higher payoffs are at stake (Study 3). Conclusions/Significance Our results demonstrate that cooperation may be affected not only by controllable appearance cues (e.g., clothing, facial expressions) as shown previously, but also by features that are impossible to mimic (e.g., individual facial structure). This unfakeable face trustworthiness effect is not limited to the rare situations where people lack any information about their partners, but survives in richer environments where relevant details about partner past behavior are available. PMID:22470553

Morphological alterations in the hippocampus of the Ts65Dn mouse model for Down Syndrome correlate with structural plasticity markers.

PubMed

Villarroya, Olga; Ballestín, Raúl; López-Hidalgo, Rosa; Mulet, Maria; Blasco-Ibáñez, José Miguel; Crespo, Carlos; Nacher, Juan; Gilabert-Juan, Javier; Varea, Emilio

2018-01-01

Down syndrome (DS) is the most common chromosomal aneuploidy. Although trisomy on chromosome 21 can display variable phenotypes, there is a common feature among all DS individuals: the presence of intellectual disability. This condition is partially attributed to abnormalities found in the hippocampus of individuals with DS and in the murine model for DS, Ts65Dn. To check if all hippocampal areas were equally affected in 4-5 month adult Ts65Dn mice, we analysed the morphology of dentate gyrus granule cells and cornu ammonis pyramidal neurons using Sholl method on Golgi-Cox impregnated neurons. Structural plasticity has been analysed using immunohistochemistry for plasticity molecules followed by densitometric analysis (Brain Derived Neurotrophic Factor (BDNF), Polysialylated form of the Neural Cell Adhesion Molecule (PSA-NCAM) and the Growth Associated Protein 43 (GAP43)). We observed an impairment in the dendritic arborisation of granule cells, but not in the pyramidal neurons in the Ts65Dn mice. When we analysed the expression of molecules related to structural plasticity in trisomic mouse hippocampus, we observed a reduction in the expression of BDNF and PSA-NCAM, and an increment in the expression of GAP43. These alterations were restricted to the regions related to dentate granule cells suggesting an interrelation. Therefore the impairment in dendritic arborisation and molecular plasticity is not a general feature of all Down syndrome principal neurons. Pharmacological manipulations of the levels of plasticity molecules could provide a way to restore granule cell morphology and function.

Physical modeling of geometrically confined disordered protein assemblies

NASA Astrophysics Data System (ADS)

Ando, David

2015-08-01

The transport of cargo across the nuclear membrane is highly selective and accomplished by a poorly understood mechanism involving hundreds of nucleoporins lining the inside of the nuclear pore complex (NPC). Currently, there is no clear picture of the overall structure formed by this collection of proteins within the pore, primarily due to their disordered nature and uncertainty regarding the properties of individual nucleoporins. We first study the defining characteristics of the amino acid sequences of nucleoporins through bioinformatics techniques, although bioinformatics of disordered proteins is especially challenging given high mutation rates for homologous proteins and that functionality may not be strongly related to sequence. Here we have performed a novel bioinformatic analysis, based on the spatial clustering of physically relevant features such as binding motifs and charges within disordered proteins, on thousands of FG motif containing nucleoporins (FG nups). The biophysical mechanism by which the critical FG nups regulate nucleocytoplasmic transport has remained elusive, yet our analysis revealed a set of highly conserved spatial features in the sequence structure of individual FG nups, such as the separation, localization, and ordering of FG motifs and charged residues along the protein chain. These sequence features are likely conserved due to a common functionality between species regarding how FG nups functionally regulate traffic, therefore these results constrain current models and eliminate proposed biophysical mechanisms responsible for regulation of nucleocytoplasmic traffic in the NPC which would not result in such a conserved amino acid sequence structure. Additionally, this method allows us to identify potentially functionally analogous disordered proteins across distantly related species. To understand the physical implications of the sequence features on structure and dynamics of the nucleoporins, we performed coarse-grained simulations of nucleoporins to understand their individual polymer properties. Our results indicate that different regions or blocks of an individual NPC protein can have distinctly different forms of disorder and that this property appears to be a conserved functional feature, consistent with the results of our physical bioinformatic analysis. Further simulations of grafted rings of FG nups mimicking the in vivo geometry of the NPC were performed and supplemented with polymer brush modeling to understand how aggregates of FG nups regulate transport in vivo. We found that the block structure at the individual protein level in terms of polymer properties is critical to the formation of a unique higher-order polymer brush architecture that can exist in distinct morphologies depending on the effective interaction energy between the phenylalanine glycine (FG) domains of different nups. Because the interactions between FG domains may be modulated by certain forms of transport factors, our results indicate that transitions between brush morphologies that correspond to open and closed states could play an important role in regulating transport across the NPC, suggesting novel forms of gated transport across membrane pores with wide biomimetic applicability in our Diblock Copolymer Brush Gate model. Previous experimental research has concluded that FG nups from S. cerevisiae are present in a bimodal distribution, with the "Forest Model" classifying FG nups as either diblock polymer like "trees" or single block polymer like "shrubs." Our simulation and polymer brush modeling results indicated that the function of the tree FG nups in the Diblock Copolymer Brush Gate (DCBG) model is to form a higher-order polymer brush architecture which can open and close to regulate transport across the NPC. Here we perform coarse grained simulations of the shrub FG nups which confirm that they have a single block polymer structure rather than the diblock structure of tree nups. Our molecular simulations also demonstrate that these single block FG nups are likely compact collapsed coil polymers, implying that shrubs are generally localized to their grafting location within the NPC. We find that adding a layer of shrub FG nups to the DCBG model increases the range of cargo sizes which are able to translocate the pore through a cooperative effect involving shrub and tree nups. This effect can explain the puzzling connection between shrub FG nup deletion mutants in S. cerevisiae and the resulting failure of certain large cargo transport through the NPC. Facilitation of large cargo transport via single block and diblock FG nup cooperativity in the nuclear pore could provide a model mechanism for designing future biomimetic pores of greater applicability. In summary, this dissertation presents a cohesive body of research that uses a combination of techniques including bioinformatics, coarse grained molecular modeling, and polymer brush theory to understand the properties of individual FG nups and how they behave in aggregate, strongly constraining possible biophysical mechanisms which may play a role in regulating traffic through the NPC. Our results are observed across different species and are consistent with many experimental observations which have been reported. Finally, our DCBG model for NPC function provides testable predictions for future experimental investigation and provides a foundation for the design and commercialization of biomimetic pores for filtering applications in vitro and industrial use.

Global features of the semiannual oscillation in stratospheric temperatures and comparison between seasons and hemispheres

NASA Technical Reports Server (NTRS)

Gao, Xin-Hai; Yu, Wen-Bi; Stanford, John L.

1987-01-01

Four years of satellite-derived microwave and infrared radiances are analyzed for the three-dimensional and seasonal variation of semiannual oscillations (SAO) in stratospheric temperatures, with particular focus on high latitudes, to investigate the effect of stratospheric warmings on SAO. Separate analyses of individual seasons in each hemisphere reveal that the strongest SAO in temperature occur in the Northern Hemisphere (NH) winter polar upper stratosphere. These results, together with the latitudinal structure of the temperature SAO and the fact that the NH polar SAO is nearly out of phase with the lower latitude SAO, are consistent with the existence of a global-scale, meridional circulation on the SAO time scale. The results suggest that polar stratospheric warmings are an important source of SAO in both high and low latitude stratospheric temperature fields. Interannual variations, three-dimensional phase structure, and zonal asymmetry of SAO are also detailed. The SH stratospheric SAO is dominated by a localized feature in the high-latitude, eastern hemisphere which tilts westward with height.

Foot Structure in Boys with Down Syndrome.

PubMed

Puszczałowska-Lizis, Ewa; Nowak, Krzysztof; Omorczyk, Jarosław; Ambroży, Tadeusz; Bujas, Przemysław; Nosiadek, Leszek

2017-01-01

Down syndrome (DS) is associated with numerous developmental abnormalities, some of which cause dysfunctions of the posture and the locomotor system. The analysis of selected features of the foot structure in boys with DS versus their peers without developmental disorders is done. The podoscopic examination was performed on 30 boys with DS aged 14-15 years. A control group consisted of 30 age- and gender-matched peers without DS. The feet of boys with DS are flatter compared to their healthy peers. The hallux valgus angle is not the most important feature differentiating the shape of the foot in the boys with DS and their healthy peers. In terms of the V toe setting, healthy boys had poorer results. Specialized therapeutic treatment in individuals with DS should involve exercises to increase the muscle strength around the foot joints, enhancing the stabilization in the joints and proprioception. Introducing orthotics and proper footwear is also important. It is also necessary to monitor the state of the foot in order to modify undertaken therapies.

Comparing solvophobic and multivalent induced collapse in polyelectrolyte brushes

DOE PAGES

Jackson, Nicholas E.; Brettmann, Blair K.; Vishwanath, Venkatram; ...

2017-02-03

Here, coarse-grained molecular dynamics enhanced by free-energy sampling methods is used to examine the roles of solvophobicity and multivalent salts on polyelectrolyte brush collapse. Specifically, we demonstrate that while ostensibly similar, solvophobic collapsed brushes and multivalent-ion collapsed brushes exhibit distinct mechanistic and structural features. Notably, multivalent-induced heterogeneous brush collapse is observed under good solvent polymer backbone conditions, demonstrating that the mechanism of multivalent collapse is not contingent upon a solvophobic backbone. Umbrella sampling of the potential of mean-force (PMF) between two individual brush strands confirms this analysis, revealing starkly different PMFs under solvophobic and multivalent conditions, suggesting the role ofmore » multivalent “bridging” as the discriminating feature in trivalent collapse. Structurally, multivalent ions show a propensity for nucleating order within collapsed brushes, whereas poor-solvent collapsed brushes are more disordered; this difference is traced to the existence of a metastable PMF minimum for poor solvent conditions, and a global PMF minimum for trivalent systems, under experimentally relevant conditions.« less

Comparing solvophobic and multivalent induced collapse in polyelectrolyte brushes

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

Jackson, Nicholas E.; Brettmann, Blair K.; Vishwanath, Venkatram

Here, coarse-grained molecular dynamics enhanced by free-energy sampling methods is used to examine the roles of solvophobicity and multivalent salts on polyelectrolyte brush collapse. Specifically, we demonstrate that while ostensibly similar, solvophobic collapsed brushes and multivalent-ion collapsed brushes exhibit distinct mechanistic and structural features. Notably, multivalent-induced heterogeneous brush collapse is observed under good solvent polymer backbone conditions, demonstrating that the mechanism of multivalent collapse is not contingent upon a solvophobic backbone. Umbrella sampling of the potential of mean-force (PMF) between two individual brush strands confirms this analysis, revealing starkly different PMFs under solvophobic and multivalent conditions, suggesting the role ofmore » multivalent “bridging” as the discriminating feature in trivalent collapse. Structurally, multivalent ions show a propensity for nucleating order within collapsed brushes, whereas poor-solvent collapsed brushes are more disordered; this difference is traced to the existence of a metastable PMF minimum for poor solvent conditions, and a global PMF minimum for trivalent systems, under experimentally relevant conditions.« less

Understanding multi-scale structural evolution in granular systems through gMEMS

NASA Astrophysics Data System (ADS)

Walker, David M.; Tordesillas, Antoinette

2013-06-01

We show how the rheological response of a material to applied loads can be systematically coded, analyzed and succinctly summarized, according to an individual grain's property (e.g. kinematics). Individual grains are considered as their own smart sensor akin to microelectromechanical systems (e.g. gyroscopes, accelerometers), each capable of recognizing their evolving role within self-organizing building block structures (e.g. contact cycles and force chains). A symbolic time series is used to represent their participation in such self-assembled building blocks and a complex network summarizing their interrelationship with other grains is constructed. In particular, relationships between grain time series are determined according to the information theory Hamming distance or the metric Euclidean distance. We then use topological distance to find network communities enabling groups of grains at remote physical metric distances in the material to share a classification. In essence grains with similar structural and functional roles at different scales are identified together. This taxonomy distills the dissipative structural rearrangements of grains down to its essential features and thus provides pointers for objective physics-based internal variable formalisms used in the construction of robust predictive continuum models.

Distinguishing molecular features and clinical characteristics of a putative new rhinovirus species, human rhinovirus C (HRV C).

PubMed

McErlean, Peter; Shackelton, Laura A; Andrews, Emily; Webster, Dale R; Lambert, Stephen B; Nissen, Michael D; Sloots, Theo P; Mackay, Ian M

2008-04-02

Human rhinoviruses (HRVs) are the most frequently detected pathogens in acute respiratory tract infections (ARTIs) and yet little is known about the prevalence, recurrence, structure and clinical impact of individual members. During 2007, the complete coding sequences of six previously unknown and highly divergent HRV strains were reported. To catalogue the molecular and clinical features distinguishing the divergent HRV strains, we undertook, for the first time, in silico analyses of all available polyprotein sequences and performed retrospective reviews of the medical records of cases in which variants of the prototype strain, HRV-QPM, had been detected. Genomic analyses revealed that the six divergent strains, residing within a clade we previously called HRV A2, had the shortest polyprotein of all picornaviruses investigated. Structure-based amino acid alignments identified conserved motifs shared among members of the genus Rhinovirus as well as substantive deletions and insertions unique to the divergent strains. Deletions mostly affected regions encoding proteins traditionally involved in antigenicity and serving as HRV and HEV receptor footprints. Because the HRV A2 strains cannot yet be cultured, we created homology models of predicted HRV-QPM structural proteins. In silico comparisons confirmed that HRV-QPM was most closely related to the major group HRVs. HRV-QPM was most frequently detected in infants with expiratory wheezing or persistent cough who had been admitted to hospital and required supplemental oxygen. It was the only virus detected in 65% of positive individuals. These observations contributed to an objective clinical impact ranging from mild to severe. The divergent strains did not meet classification requirements for any existing species of the genus Rhinovirus or Enterovirus. HRV A2 strains should be partitioned into at least one new species, putatively called Human rhinovirus C, populated by members detected with high frequency, from individuals with respiratory symptoms requiring hospital admission.

Modeling the Biodegradability of Chemical Compounds Using the Online CHEmical Modeling Environment (OCHEM)

PubMed Central

Vorberg, Susann

2013-01-01

Abstract Biodegradability describes the capacity of substances to be mineralized by free‐living bacteria. It is a crucial property in estimating a compound’s long‐term impact on the environment. The ability to reliably predict biodegradability would reduce the need for laborious experimental testing. However, this endpoint is difficult to model due to unavailability or inconsistency of experimental data. Our approach makes use of the Online Chemical Modeling Environment (OCHEM) and its rich supply of machine learning methods and descriptor sets to build classification models for ready biodegradability. These models were analyzed to determine the relationship between characteristic structural properties and biodegradation activity. The distinguishing feature of the developed models is their ability to estimate the accuracy of prediction for each individual compound. The models developed using seven individual descriptor sets were combined in a consensus model, which provided the highest accuracy. The identified overrepresented structural fragments can be used by chemists to improve the biodegradability of new chemical compounds. The consensus model, the datasets used, and the calculated structural fragments are publicly available at http://ochem.eu/article/31660. PMID:27485201

Coevolving agent strategies and network topology for the public goods games

NASA Astrophysics Data System (ADS)

Zhang, C. Y.; Zhang, J. L.; Xie, G. M.; Wang, L.

2011-03-01

Much of human cooperation remains an evolutionary riddle. Coevolutionary public goods games in structured populations are studied where players can change from an unproductive public goods game to a productive one, by evaluating the productivity of the public goods games. In our model, each individual participates in games organized by its neighborhood plus by itself. Coevolution here refers to an evolutionary process entailing both deletion of existing links and addition of new links between agents that accompanies the evolution of their strategies. Furthermore, we investigate the effects of time scale separation of strategy and structure on cooperation level. This study presents the following: Foremost, we observe that high cooperation levels in public goods interactions are attained by the entangled coevolution of strategy and structure. Presented results also confirm that the resulting networks show many features of real systems, such as cooperative behavior and hierarchical clustering. The heterogeneity of the interaction network is held responsible for the observed promotion of cooperation. We hope our work may offer an explanation for the origin of large-scale cooperative behavior among unrelated individuals.

Characterization of Polystyrene Soft Nanoparticles Using Small Angle Neutron Scattering

NASA Astrophysics Data System (ADS)

Martin, Halie; White, Tyler; Saito, Tomonori; Dadmun, Mark

Polymer nanocomposites have become a prominent area of research recently. With a growing variety of nanoparticles available, research probing the influence of particle morphology on the overall nanocomposite properties is also increasing. Nanoparticle dispersion is controlled by both the chemical nature and morphology of the nanoparticle where a crosslinked, fuzzy organic nanoparticle is anticipated to enhance the overall miscibility and create a homogenous dispersion within a like-polymer matrix. A semi-batch microemulsion polymerization forms organic, soft nanoparticles where the precise structure of the nanoparticle is controlled by monomer rate of addition and crosslinking density. We will report small angle neutron scattering results that correlate synthetic conditions to the structural characteristics of soft nanoparticles. This analysis provides characterization of the individual nanoparticle molecular weight, the radius of the crosslinked core, the thickness of the fuzzy interfacial layer, and provides insight into the overall topography of the soft nanoparticle. This research provides a pathway to investigate the effect of nanoscale structural features of the nanoparticle on their individual properties and those of nanocomposites that contain these soft nanoparticles. DOE-BES, Division of Materials Sciences and Engineering.

A rigid and thermally stable all ceramic optical support bench assembly for the LSST Camera

NASA Astrophysics Data System (ADS)

Kroedel, Matthias; Langton, J. Brian; Wahl, Bill

2017-09-01

This paper will present the ceramic design, fabrication and metrology results and assembly plan of the LSST camera optical bench structure which is using the unique manufacturing features of the HB-Cesic technology. The optical bench assembly consists of a rigid "Grid" fabrication supporting individual raft plates mounting sensor assemblies by way of a rigid kinematic support system to meet extreme stringent requirements for focal plane planarity and stability.

Speech reconstruction using a deep partially supervised neural network.

PubMed

McLoughlin, Ian; Li, Jingjie; Song, Yan; Sharifzadeh, Hamid R

2017-08-01

Statistical speech reconstruction for larynx-related dysphonia has achieved good performance using Gaussian mixture models and, more recently, restricted Boltzmann machine arrays; however, deep neural network (DNN)-based systems have been hampered by the limited amount of training data available from individual voice-loss patients. The authors propose a novel DNN structure that allows a partially supervised training approach on spectral features from smaller data sets, yielding very good results compared with the current state-of-the-art.

A Rejoinder.

PubMed

Nesselroade, John R; Molenaar, Peter C M

2016-01-01

Three commentaries on the Nesselroade and Molenaar target article in this issue are responded to in the interest of elaborating and defending the points of view expressed in our article. The commentaries feature philosophy of science, general structural modeling, and broad behavioral research perspectives. Responding to the commentaries afforded us the opportunity to clarify further matters that we deem critical to the fundamental matter of measurement in behavioral science, especially as it emphasizes (properly, we believe) the individual as the primary unit of analysis.

Group therapy techniques for sexually abused preteen girls.

PubMed

Berman, P

1990-01-01

This article describes an open-ended, structured, highly intensive therapy group for sexually abused preteen girls that was the primary mode of treatment for 11 girls from multiproblem, low-income, rural, white families. The active support of Child Protective Service workers was important in maintaining the girls in treatment in the face of strong parental opposition. Unique features of the group included simultaneous group goals and individualized goals. A case description illustrates the makeup and functioning of the program.

Random forest classification of large volume structures for visuo-haptic rendering in CT images

NASA Astrophysics Data System (ADS)

Mastmeyer, Andre; Fortmeier, Dirk; Handels, Heinz

2016-03-01

For patient-specific voxel-based visuo-haptic rendering of CT scans of the liver area, the fully automatic segmentation of large volume structures such as skin, soft tissue, lungs and intestine (risk structures) is important. Using a machine learning based approach, several existing segmentations from 10 segmented gold-standard patients are learned by random decision forests individually and collectively. The core of this paper is feature selection and the application of the learned classifiers to a new patient data set. In a leave-some-out cross-validation, the obtained full volume segmentations are compared to the gold-standard segmentations of the untrained patients. The proposed classifiers use a multi-dimensional feature space to estimate the hidden truth, instead of relying on clinical standard threshold and connectivity based methods. The result of our efficient whole-body section classification are multi-label maps with the considered tissues. For visuo-haptic simulation, other small volume structures would have to be segmented additionally. We also take a look into these structures (liver vessels). For an experimental leave-some-out study consisting of 10 patients, the proposed method performs much more efficiently compared to state of the art methods. In two variants of leave-some-out experiments we obtain best mean DICE ratios of 0.79, 0.97, 0.63 and 0.83 for skin, soft tissue, hard bone and risk structures. Liver structures are segmented with DICE 0.93 for the liver, 0.43 for blood vessels and 0.39 for bile vessels.

Genetic effects of landscape, habitat preference and demography on three co-occurring turtle species.

PubMed

Reid, Brendan N; Mladenoff, David J; Peery, M Zachariah

2017-02-01

Expanding the scope of landscape genetics beyond the level of single species can help to reveal how species traits influence responses to environmental change. Multispecies studies are particularly valuable in highly threatened taxa, such as turtles, in which the impacts of anthropogenic change are strongly influenced by interspecific differences in life history strategies, habitat preferences and mobility. We sampled approximately 1500 individuals of three co-occurring turtle species across a gradient of habitat change (including varying loss of wetlands and agricultural conversion of upland habitats) in the Midwestern USA. We used genetic clustering and multiple regression methods to identify associations between genetic structure and permanent landscape features, past landscape composition and landscape change in each species. Two aquatic generalists (the painted turtle, Chrysemys picta, and the snapping turtle Chelydra serpentina) both exhibited population genetic structure consistent with isolation by distance, modulated by aquatic landscape features. Genetic divergence for the more terrestrial Blanding's turtle (Emydoidea blandingii), on the other hand, was not strongly associated with geographic distance or aquatic features, and Bayesian clustering analysis indicated that many Emydoidea populations were genetically isolated. Despite long generation times, all three species exhibited associations between genetic structure and postsettlement habitat change, indicating that long generation times may not be sufficient to delay genetic drift resulting from recent habitat fragmentation. The concordances in genetic structure observed between aquatic species, as well as isolation in the endangered, long-lived Emydoidea, reinforce the need to consider both landscape composition and demographic factors in assessing differential responses to habitat change in co-occurring species. © 2016 John Wiley & Sons Ltd.

A feature-based approach to modeling protein–protein interaction hot spots

PubMed Central

Cho, Kyu-il; Kim, Dongsup; Lee, Doheon

2009-01-01

Identifying features that effectively represent the energetic contribution of an individual interface residue to the interactions between proteins remains problematic. Here, we present several new features and show that they are more effective than conventional features. By combining the proposed features with conventional features, we develop a predictive model for interaction hot spots. Initially, 54 multifaceted features, composed of different levels of information including structure, sequence and molecular interaction information, are quantified. Then, to identify the best subset of features for predicting hot spots, feature selection is performed using a decision tree. Based on the selected features, a predictive model for hot spots is created using support vector machine (SVM) and tested on an independent test set. Our model shows better overall predictive accuracy than previous methods such as the alanine scanning methods Robetta and FOLDEF, and the knowledge-based method KFC. Subsequent analysis yields several findings about hot spots. As expected, hot spots have a larger relative surface area burial and are more hydrophobic than other residues. Unexpectedly, however, residue conservation displays a rather complicated tendency depending on the types of protein complexes, indicating that this feature is not good for identifying hot spots. Of the selected features, the weighted atomic packing density, relative surface area burial and weighted hydrophobicity are the top 3, with the weighted atomic packing density proving to be the most effective feature for predicting hot spots. Notably, we find that hot spots are closely related to π–related interactions, especially π · · · π interactions. PMID:19273533

Nuclear magnetic resonance detection and spectroscopy of single proteins using quantum logic.

PubMed

Lovchinsky, I; Sushkov, A O; Urbach, E; de Leon, N P; Choi, S; De Greve, K; Evans, R; Gertner, R; Bersin, E; Müller, C; McGuinness, L; Jelezko, F; Walsworth, R L; Park, H; Lukin, M D

2016-02-19

Nuclear magnetic resonance spectroscopy is a powerful tool for the structural analysis of organic compounds and biomolecules but typically requires macroscopic sample quantities. We use a sensor, which consists of two quantum bits corresponding to an electronic spin and an ancillary nuclear spin, to demonstrate room temperature magnetic resonance detection and spectroscopy of multiple nuclear species within individual ubiquitin proteins attached to the diamond surface. Using quantum logic to improve readout fidelity and a surface-treatment technique to extend the spin coherence time of shallow nitrogen-vacancy centers, we demonstrate magnetic field sensitivity sufficient to detect individual proton spins within 1 second of integration. This gain in sensitivity enables high-confidence detection of individual proteins and allows us to observe spectral features that reveal information about their chemical composition. Copyright © 2016, American Association for the Advancement of Science.

Investigating the cognitive structure of stereotypes: Generic beliefs about groups predict social judgments better than statistical beliefs.

PubMed

Hammond, Matthew D; Cimpian, Andrei

2017-05-01

Stereotypes are typically defined as beliefs about groups, but this definition is underspecified. Beliefs about groups can be generic or statistical. Generic beliefs attribute features to entire groups (e.g., men are strong), whereas statistical beliefs encode the perceived prevalence of features (e.g., how common it is for men to be strong). In the present research, we sought to determine which beliefs-generic or statistical-are more central to the cognitive structure of stereotypes. Specifically, we tested whether generic or statistical beliefs are more influential in people's social judgments, on the assumption that greater functional importance indicates greater centrality in stereotype structure. Relative to statistical beliefs, generic beliefs about social groups were significantly stronger predictors of expectations (Studies 1-3) and explanations (Study 4) for unfamiliar individuals' traits. In addition, consistent with prior evidence that generic beliefs are cognitively simpler than statistical beliefs, generic beliefs were particularly predictive of social judgments for participants with more intuitive (vs. analytic) cognitive styles and for participants higher (vs. lower) in authoritarianism, who tend to view outgroups in simplistic, all-or-none terms. The present studies suggest that generic beliefs about groups are more central than statistical beliefs to the cognitive structure of stereotypes. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Uniform functional structure across spatial scales in an intertidal benthic assemblage.

PubMed

Barnes, R S K; Hamylton, Sarah

2015-05-01

To investigate the causes of the remarkable similarity of emergent assemblage properties that has been demonstrated across disparate intertidal seagrass sites and assemblages, this study examined whether their emergent functional-group metrics are scale related by testing the null hypothesis that functional diversity and the suite of dominant functional groups in seagrass-associated macrofauna are robust structural features of such assemblages and do not vary spatially across nested scales within a 0.4 ha area. This was carried out via a lattice of 64 spatially referenced stations. Although densities of individual components were patchily dispersed across the locality, rank orders of importance of the 14 functional groups present, their overall functional diversity and evenness, and the proportions of the total individuals contained within each showed, in contrast, statistically significant spatial uniformity, even at areal scales <2 m(2). Analysis of the proportional importance of the functional groups in their geospatial context also revealed weaker than expected levels of spatial autocorrelation, and then only at the smaller scales and amongst the most dominant groups, and only a small number of negative correlations occurred between the proportional importances of the individual groups. In effect, such patterning was a surface veneer overlying remarkable stability of assemblage functional composition across all spatial scales. Although assemblage species composition is known to be homogeneous in some soft-sediment marine systems over equivalent scales, this combination of patchy individual components yet basically constant functional-group structure seems as yet unreported. Copyright © 2015 Elsevier Ltd. All rights reserved.

Database for Rapid Dereplication of Known Natural Products Using Data from MS and Fast NMR Experiments.

PubMed

Zani, Carlos L; Carroll, Anthony R

2017-06-23

The discovery of novel and/or new bioactive natural products from biota sources is often confounded by the reisolation of known natural products. Dereplication strategies that involve the analysis of NMR and MS spectroscopic data to infer structural features present in purified natural products in combination with database searches of these substructures provide an efficient method to rapidly identify known natural products. Unfortunately this strategy has been hampered by the lack of publically available and comprehensive natural product databases and open source cheminformatics tools. A new platform, DEREP-NP, has been developed to help solve this problem. DEREP-NP uses the open source cheminformatics program DataWarrior to generate a database containing counts of 65 structural fragments present in 229 358 natural product structures derived from plants, animals, and microorganisms, published before 2013 and freely available in the nonproprietary Universal Natural Products Database (UNPD). By counting the number of times one or more of these structural features occurs in an unknown compound, as deduced from the analysis of its NMR ( 1 H, HSQC, and/or HMBC) and/or MS data, matching structures carrying the same numeric combination of searched structural features can be retrieved from the database. Confirmation that the matching structure is the same compound can then be verified through literature comparison of spectroscopic data. This methodology can be applied to both purified natural products and fractions containing a small number of individual compounds that are often generated as screening libraries. The utility of DEREP-NP has been verified through the analysis of spectra derived from compounds (and fractions containing two or three compounds) isolated from plant, marine invertebrate, and fungal sources. DEREP-NP is freely available at https://github.com/clzani/DEREP-NP and will help to streamline the natural product discovery process.

An emotional contagion model for heterogeneous social media with multiple behaviors

NASA Astrophysics Data System (ADS)

Xiong, Xi; Li, Yuanyuan; Qiao, Shaojie; Han, Nan; Wu, Yue; Peng, Jing; Li, Binyong

2018-01-01

The emotion varies and propagates with the spatial and temporal information of individuals through social media, which uncovers several interaction mechanisms and features the community structure in order to facilitate individuals' communication and emotional contagion in social networks. Aiming to show the detailed process and characteristics of emotional contagion within social media, we propose an emotional independent cascade model in which individual emotion can affect the subsequent emotion of his/her friends. The transmissibility is introduced to measure the capability of propagating emotion with respect to an individual in social networks. By analyzing the patterns of emotional contagion on Twitter data, we find that the value of transmissibility differs on different layers and on different community structures. Extensive experiments were conducted and the results reveal that, the polar emotion of hub users can lead to the disappearance of opposite emotion, and the transmissibility makes no sense. The final emotional distribution depends on the initial emotional distribution and the transmissibilities. Individuals from a small community are more likely to change their mood by the influence of community leaders. In addition, we compared the proposed model with two other models, the emotion-based spreader-ignorant-stifler model and the standard independent cascade model. The results demonstrate that the proposed model can reflect the real-world situation of emotional contagion for heterogeneous social media while the computational complexities of all these three models are similar.

Psychiatric Features in Neurotic Excoriation Patients: The Role of Childhood Trauma

PubMed Central

YALÇIN, Murat; TELLİOĞLU, Evrim; YILDIRIM, Deniz Uluhan; SAVRUN, B. Mert; ÖZMEN, Mine; AYDEMİR, Ertuğrul H.

2015-01-01

Introduction Neurotic excoriation is a psychodermatological disease of primary psychological/psychiatric genesis, responsible for self-induced dermatological disorders. Childhood traumatic events are closely related with self-injurious behaviors. The aim of this study is to evaluate the psychiatric features of neurotic excoriation and to investigate the effect of childhood traumatic events on the disease. Methods Thirty-eight neurotic excoriation patients who did not receive any psychiatric treatment within the past year and 40 healthy individuals having similar sociodemographic features were included in the study. For clinical evaluation, the Structured Clinical Interview for DSM-IV Axis I Disorders, Beck Depression Inventory, Beck Anxiety Inventory, and Childhood Trauma Questionnaire-Short Form were applied to all the individuals. Results In this study, we observed that 78.9% of neurotic excoriation patients were diagnosed with at least one Axis I psychiatric disorder, the most frequent diagnoses of which were major depressive disorders and anxiety disorders. The anxiety and depression levels were significantly higher in the patient group than in the healthy individuals. Regarding the Childhood Trauma Questionnaire, emotional neglect, emotional abuse, and physical abuse subscales and weighted average total scores were found to be significantly higher in the patient group (p<.05). Conclusion Our study has shown a close relationship between neurotic excoriation and childhood traumatic events as well as the accompanying psychiatric problems. We suppose that early interventions by both dermatologists and psychiatrists and especially a detailed investigation of childhood traumatic events by establishing a therapeutic collaboration are highly important and that using psychotherapeutic interventions can result in better treatment outcomes in many patients. PMID:28360736

Describing the brain in autism in five dimensions--magnetic resonance imaging-assisted diagnosis of autism spectrum disorder using a multiparameter classification approach.

PubMed

Ecker, Christine; Marquand, Andre; Mourão-Miranda, Janaina; Johnston, Patrick; Daly, Eileen M; Brammer, Michael J; Maltezos, Stefanos; Murphy, Clodagh M; Robertson, Dene; Williams, Steven C; Murphy, Declan G M

2010-08-11

Autism spectrum disorder (ASD) is a neurodevelopmental condition with multiple causes, comorbid conditions, and a wide range in the type and severity of symptoms expressed by different individuals. This makes the neuroanatomy of autism inherently difficult to describe. Here, we demonstrate how a multiparameter classification approach can be used to characterize the complex and subtle structural pattern of gray matter anatomy implicated in adults with ASD, and to reveal spatially distributed patterns of discriminating regions for a variety of parameters describing brain anatomy. A set of five morphological parameters including volumetric and geometric features at each spatial location on the cortical surface was used to discriminate between people with ASD and controls using a support vector machine (SVM) analytic approach, and to find a spatially distributed pattern of regions with maximal classification weights. On the basis of these patterns, SVM was able to identify individuals with ASD at a sensitivity and specificity of up to 90% and 80%, respectively. However, the ability of individual cortical features to discriminate between groups was highly variable, and the discriminating patterns of regions varied across parameters. The classification was specific to ASD rather than neurodevelopmental conditions in general (e.g., attention deficit hyperactivity disorder). Our results confirm the hypothesis that the neuroanatomy of autism is truly multidimensional, and affects multiple and most likely independent cortical features. The spatial patterns detected using SVM may help further exploration of the specific genetic and neuropathological underpinnings of ASD, and provide new insights into the most likely multifactorial etiology of the condition.

Clinical characteristics and psychiatric comorbidity of pyromania.

PubMed

Grant, Jon E; Won Kim, Suck

2007-11-01

There have been few systematic studies of individuals with pyromania, and this paucity of research has hindered our understanding and treatment of this disorder. This study details the demographic and phenomenological features of individuals with DSM-IV lifetime pyromania. Twenty-one adult and adolescent subjects (recruited from inpatient and outpatient studies of impulse-control disorders) with lifetime DSM-IV pyromania were administered a semi-structured interview to elicit demographic data and information on the phenomenology, age at onset, and associated features of the disorder. Data were collected from October 2003 to September 2006. Twenty-one subjects (10 female [47.6%]) with lifetime pyromania (mean +/- SD age = 26.1 +/- 11.8 years; range, 15-49 years) were studied. The mean +/- SD age at onset for pyromania was 18.1 +/- 5.8 years. Eighteen subjects (85.7%) reported urges to set fires. Subjects reported a mean +/- SD frequency of setting 1 fire every 5.9 +/- 3.8 weeks. Much of the fire setting did not meet the legal definition of arson. Thirteen (61.9%) had a current comorbid Axis I mood disorder, and 10 (47.6%) met criteria for a current impulse-control disorder. Pyromania appears to be associated with high rates of psychiatric comorbidity. Research is needed to optimize patient care for individuals with this disorder.

Observations of fast-moving features in the debris disk of AU Mic on a three-year timescale: Confirmation and new discoveries

NASA Astrophysics Data System (ADS)

Boccaletti, A.; Sezestre, E.; Lagrange, A.-M.; Thébault, P.; Gratton, R.; Langlois, M.; Thalmann, C.; Janson, M.; Delorme, P.; Augereau, J.-C.; Schneider, G.; Milli, J.; Grady, C.; Debes, J.; Kral, Q.; Olofsson, J.; Carson, J.; Maire, A. L.; Henning, T.; Wisniewski, J.; Schlieder, J.; Dominik, C.; Desidera, S.; Ginski, C.; Hines, D.; Ménard, F.; Mouillet, D.; Pawellek, N.; Vigan, A.; Lagadec, E.; Avenhaus, H.; Beuzit, J.-L.; Biller, B.; Bonavita, M.; Bonnefoy, M.; Brandner, W.; Cantalloube, F.; Chauvin, G.; Cheetham, A.; Cudel, M.; Gry, C.; Daemgen, S.; Feldt, M.; Galicher, R.; Girard, J.; Hagelberg, J.; Janin-Potiron, P.; Kasper, M.; Coroller, H. Le; Mesa, D.; Peretti, S.; Perrot, C.; Samland, M.; Sissa, E.; Wildi, F.; Zurlo, A.; Rochat, S.; Stadler, E.; Gluck, L.; Origné, A.; Llored, M.; Baudoz, P.; Rousset, G.; Martinez, P.; Rigal, F.

2018-06-01

Context. The nearby and young M star AU Mic is surrounded by a debris disk in which we previously identified a series of large-scale arch-like structures that have never been seen before in any other debris disk and that move outward at high velocities. Aims: We initiated a monitoring program with the following objectives: (1) track the location of the structures and better constrain their projected speeds, (2) search for new features emerging closer in, and ultimately (3) understand the mechanism responsible for the motion and production of the disk features. Methods: AU Mic was observed at 11 different epochs between August 2014 and October 2017 with the IR camera and spectrograph of SPHERE. These high-contrast imaging data were processed with a variety of angular, spectral, and polarimetric differential imaging techniques to reveal the faintest structures in the disk. We measured the projected separations of the features in a systematic way for all epochs. We also applied the very same measurements to older observations from the Hubble Space Telescope (HST) with the visible cameras STIS and ACS. Results: The main outcomes of this work are (1) the recovery of the five southeastern broad arch-like structures we identified in our first study, and confirmation of their fast motion (projected speed in the range 4-12 km s-1); (2) the confirmation that the very first structures observed in 2004 with ACS are indeed connected to those observed later with STIS and now SPHERE; (3) the discovery of two new very compact structures at the northwest side of the disk (at 0.40'' and 0.55'' in May 2015) that move to the southeast at low speed; and (4) the identification of a new arch-like structure that might be emerging at the southeast side at about 0.4'' from the star (as of May 2016). Conclusions: Although the exquisite sensitivity of SPHERE allows one to follow the evolution not only of the projected separation, but also of the specific morphology of each individual feature, it remains difficult to distinguish between possible dynamical scenarios that may explain the observations. Understanding the exact origin of these features, the way they are generated, and their evolution over time is certainly a significant challenge in the context of planetary system formation around M stars. Based on data collected at the European Southern Observatory, Chile under programs 060.A-9249, 095.C-0298, 096.C-0625, 097.C-0865, 097.C-0813, 598.C-0359.A movie associated to Fig. 6 is available at http://https://www.aanda.org

Effective Moment Feature Vectors for Protein Domain Structures

PubMed Central

Shi, Jian-Yu; Yiu, Siu-Ming; Zhang, Yan-Ning; Chin, Francis Yuk-Lun

2013-01-01

Imaging processing techniques have been shown to be useful in studying protein domain structures. The idea is to represent the pairwise distances of any two residues of the structure in a 2D distance matrix (DM). Features and/or submatrices are extracted from this DM to represent a domain. Existing approaches, however, may involve a large number of features (100–400) or complicated mathematical operations. Finding fewer but more effective features is always desirable. In this paper, based on some key observations on DMs, we are able to decompose a DM image into four basic binary images, each representing the structural characteristics of a fundamental secondary structure element (SSE) or a motif in the domain. Using the concept of moments in image processing, we further derive 45 structural features based on the four binary images. Together with 4 features extracted from the basic images, we represent the structure of a domain using 49 features. We show that our feature vectors can represent domain structures effectively in terms of the following. (1) We show a higher accuracy for domain classification. (2) We show a clear and consistent distribution of domains using our proposed structural vector space. (3) We are able to cluster the domains according to our moment features and demonstrate a relationship between structural variation and functional diversity. PMID:24391828

Predicting human age using regional morphometry and inter-regional morphological similarity

NASA Astrophysics Data System (ADS)

Wang, Xun-Heng; Li, Lihua

2016-03-01

The goal of this study is predicting human age using neuro-metrics derived from structural MRI, as well as investigating the relationships between age and predictive neuro-metrics. To this end, a cohort of healthy subjects were recruited from 1000 Functional Connectomes Project. The ages of the participations were ranging from 7 to 83 (36.17+/-20.46). The structural MRI for each subject was preprocessed using FreeSurfer, resulting in regional cortical thickness, mean curvature, regional volume and regional surface area for 148 anatomical parcellations. The individual age was predicted from the combination of regional and inter-regional neuro-metrics. The prediction accuracy is r = 0.835, p < 0.00001, evaluated by Pearson correlation coefficient between predicted ages and actual ages. Moreover, the LASSO linear regression also found certain predictive features, most of which were inter-regional features. The turning-point of the developmental trajectories in human brain was around 40 years old based on regional cortical thickness. In conclusion, structural MRI could be potential biomarkers for the aging in human brain. The human age could be successfully predicted from the combination of regional morphometry and inter-regional morphological similarity. The inter-regional measures could be beneficial to investigating human brain connectome.

Genome accessibility is widely preserved and locally modulated during mitosis.

PubMed

Hsiung, Chris C-S; Morrissey, Christapher S; Udugama, Maheshi; Frank, Christopher L; Keller, Cheryl A; Baek, Songjoon; Giardine, Belinda; Crawford, Gregory E; Sung, Myong-Hee; Hardison, Ross C; Blobel, Gerd A

2015-02-01

Mitosis entails global alterations to chromosome structure and nuclear architecture, concomitant with transient silencing of transcription. How cells transmit transcriptional states through mitosis remains incompletely understood. While many nuclear factors dissociate from mitotic chromosomes, the observation that certain nuclear factors and chromatin features remain associated with individual loci during mitosis originated the hypothesis that such mitotically retained molecular signatures could provide transcriptional memory through mitosis. To understand the role of chromatin structure in mitotic memory, we performed the first genome-wide comparison of DNase I sensitivity of chromatin in mitosis and interphase, using a murine erythroblast model. Despite chromosome condensation during mitosis visible by microscopy, the landscape of chromatin accessibility at the macromolecular level is largely unaltered. However, mitotic chromatin accessibility is locally dynamic, with individual loci maintaining none, some, or all of their interphase accessibility. Mitotic reduction in accessibility occurs primarily within narrow, highly DNase hypersensitive sites that frequently coincide with transcription factor binding sites, whereas broader domains of moderate accessibility tend to be more stable. In mitosis, proximal promoters generally maintain their accessibility more strongly, whereas distal regulatory elements tend to lose accessibility. Large domains of DNA hypomethylation mark a subset of promoters that retain accessibility during mitosis and across many cell types in interphase. Erythroid transcription factor GATA1 exerts site-specific changes in interphase accessibility that are most pronounced at distal regulatory elements, but has little influence on mitotic accessibility. We conclude that features of open chromatin are remarkably stable through mitosis, but are modulated at the level of individual genes and regulatory elements. © 2015 Hsiung et al.; Published by Cold Spring Harbor Laboratory Press.

Comparative assessment of genetic and morphological variation at an extensive hybrid zone between two wild cats in southern Brazil.

PubMed

Trigo, Tatiane C; Tirelli, Flávia P; de Freitas, Thales R O; Eizirik, Eduardo

2014-01-01

Increased attention towards the Neotropical cats Leopardus guttulus and L. geoffroyi was prompted after genetic studies identified the occurrence of extensive hybridization between them at their geographic contact zone in southern Brazil. This is a region where two biomes intersect, each of which is associated with one of the hybridizing species (Atlantic Forest with L. guttulus and Pampas with L. geoffroyi). In this study, we conducted in-depth analyses of multiple molecular markers aiming to characterize the magnitude and spatial structure of this hybrid zone. We also performed a morphological assessment of these species, aiming to test their phenotypic differentiation at the contact zone, as well as the correlation between morphological features and the admixture status of the individuals. We found strong evidence for extensive and complex hybridization, with at least 40% of the individuals sampled in Rio Grande do Sul state (southernmost Brazil) identified as hybrids resulting from post-F1 generations. Despite such a high level of hybridization, samples collected in this state still comprised two recognizable clusters (genetically and morphologically). Genetically pure individuals were sampled mainly in regions farther from the contact zone, while hybrids concentrated in a central region (exactly at the interface between the two biomes). The morphological data set also revealed a strong spatial structure, which was correlated with the molecular results but displayed an even more marked separation between the clusters. Hybrids often did not present intermediate body sizes and could not be clearly distinguished morphologically from the parental forms. This observation suggests that some selective pressure may be acting on the hybrids, limiting their dispersal away from the hybrid zone and perhaps favoring genomic combinations that maintain adaptive phenotypic features of one or the other parental species.

Comparative Assessment of Genetic and Morphological Variation at an Extensive Hybrid Zone between Two Wild Cats in Southern Brazil

PubMed Central

Trigo, Tatiane C.; Tirelli, Flávia P.; de Freitas, Thales R. O.; Eizirik, Eduardo

2014-01-01

Increased attention towards the Neotropical cats Leopardus guttulus and L. geoffroyi was prompted after genetic studies identified the occurrence of extensive hybridization between them at their geographic contact zone in southern Brazil. This is a region where two biomes intersect, each of which is associated with one of the hybridizing species (Atlantic Forest with L. guttulus and Pampas with L. geoffroyi). In this study, we conducted in-depth analyses of multiple molecular markers aiming to characterize the magnitude and spatial structure of this hybrid zone. We also performed a morphological assessment of these species, aiming to test their phenotypic differentiation at the contact zone, as well as the correlation between morphological features and the admixture status of the individuals. We found strong evidence for extensive and complex hybridization, with at least 40% of the individuals sampled in Rio Grande do Sul state (southernmost Brazil) identified as hybrids resulting from post-F1 generations. Despite such a high level of hybridization, samples collected in this state still comprised two recognizable clusters (genetically and morphologically). Genetically pure individuals were sampled mainly in regions farther from the contact zone, while hybrids concentrated in a central region (exactly at the interface between the two biomes). The morphological data set also revealed a strong spatial structure, which was correlated with the molecular results but displayed an even more marked separation between the clusters. Hybrids often did not present intermediate body sizes and could not be clearly distinguished morphologically from the parental forms. This observation suggests that some selective pressure may be acting on the hybrids, limiting their dispersal away from the hybrid zone and perhaps favoring genomic combinations that maintain adaptive phenotypic features of one or the other parental species. PMID:25250657

Predictors of violence and depression: the case of adolescents in Turkey.

PubMed

Çiftçi, Ali; Kasapoglu, Aytul

2015-11-01

Violence is a leading problem that has a negative impact on daily living. Today, it continues to be an important topic owing to its widespread occurrence, especially among the youth. The main objective of this study is to specify the predictors that influence violence and depression observed among youth aged 15-18 years. While some of these factors are individual (age, gender, flirting, sports. etc.), the subjects' background, such as the family's education level, sibling number, etc., were investigated as social and environmental factors. In the survey, data were obtained from 109 high school students receiving education in a private teaching institution using a structured questionnaire technique. With regards the reliability of the survey, equal numbers of boys and girls were chosen from each year in high school lasting for 4 years. After asking questions that aim to obtain students' sociodemographic features, their depression level was surveyed using the Beck Depression Scale; meanwhile, the Violence Tendency Scale was used to survey their tendency to be violent. Findings revealed that some individual and domestic features of adolescents have significant impacts on their tendencies towards violence and depression.

Personality disorders among patients with panic disorder and individuals with high anxiety sensitivity.

PubMed

Osma, Jorge; García-Palacios, Azucena; Botella, Cristina; Barrada, Juan Ramón

2014-05-01

No studies have been found that compared the psychopathology features, including personality disorders, of Panic Disorder (PD) and Panic Disorder with Agoraphobia (PDA), and a nonclinical sample with anxiety vulnerability. The total sample included 152 participants, 52 in the PD/PDA, 45 in the high anxiety sensitivity (AS) sample, and 55 in the nonclinical sample. The participants in PD/PDA sample were evaluated with the structured interview ADIS-IV. The Brief Symptom Inventory and the MCMI-III were used in all three samples. Statistically significant differences were found between the PD/PDA and the nonclinical sample in all MCMI-III scales except for antisocial and compulsive. No significant differences were found between PD/PDA and the sample with high scores in AS. Phobic Anxiety and Paranoid Ideation were the only scales where there were significant differences between the PD/PDA sample and the high AS sample. Our findings showed that people who scored high on AS, despite not having a diagnosis of PD/PDA, were similar in regard to psychopathology features and personality to individuals with PD/PDA.

Developing Individualized IEP Goals in the Age of Technology: Quality Challenges and Solutions

ERIC Educational Resources Information Center

More, Cori M.; Hart Barnett, Juliet E.

2014-01-01

Many school districts have adopted commercially available software or templates for electronic Individualized Education Program (IEP) development. These programs have useful features that allow Individualized Education Programs to be electronically developed and reliably stored for each student. Although the program features are designed to…

The impact of jackpots on EGM gambling behavior: a review.

PubMed

Rockloff, Matthew J; Hing, Nerilee

2013-12-01

This paper reviews literature on how jackpots influence Electronic Gaming Machine (EGM) gambling behaviour. Most of the available evidence addresses the motivational effect of the mere presence of EGM jackpots on play, as actual wins are relatively rare for individual gamblers. The review identifies a distinction between rational, biased and irrational motivations that attract people to EGM jackpots. The evidence suggests that EGM jackpots should generate additional consumption on EGMs above machines that do not have such lottery-like features. Rational motivations are likely to lead to consumer surplus, whereas biased and irrational motivations are likely to contribute to excessive consumption. Moreover, there is evidence that excessive gambling consumption is strongly associated with gambling-related harm. Future research should identify how the structural features of different types of jackpots; such as progressive, deterministic, hidden, mystery, linked and wide-area jackpots; may differentially appeal to rational, biased and irrational gambling motivations. Jackpots are common feature of EGM games, and therefore it is important to have a better understanding of how jackpot features influence play on the machines.

Social Communication and Vocal Recognition in Free-Ranging Rhesus Monkeys

NASA Astrophysics Data System (ADS)

Rendall, Christopher Andrew

Kinship and individual identity are key determinants of primate sociality, and the capacity for vocal recognition of individuals and kin is hypothesized to be an important adaptation facilitating intra-group social communication. Research was conducted on adult female rhesus monkeys on Cayo Santiago, Puerto Rico to test this hypothesis for three acoustically distinct calls characterized by varying selective pressures on communicating identity: coos (contact calls), grunts (close range social calls), and noisy screams (agonistic recruitment calls). Vocalization playback experiments confirmed a capacity for both individual and kin recognition of coos, but not screams (grunts were not tested). Acoustic analyses, using traditional spectrographic methods as well as linear predictive coding techniques, indicated that coos (but not grunts or screams) were highly distinctive, and that the effects of vocal tract filtering--formants --contributed more to statistical discriminations of both individuals and kin groups than did temporal or laryngeal source features. Formants were identified from very short (23 ms.) segments of coos and were stable within calls, indicating that formant cues to individual and kin identity were available throughout a call. This aspect of formant cues is predicted to be an especially important design feature for signaling identity efficiently in complex acoustic environments. Results of playback experiments involving manipulated coo stimuli provided preliminary perceptual support for the statistical inference that formant cues take precedence in facilitating vocal recognition. The similarity of formants among female kin suggested a mechanism for the development of matrilineal vocal signatures from the genetic and environmental determinants of vocal tract morphology shared among relatives. The fact that screams --calls strongly expected to communicate identity--were not individually distinctive nor recognized suggested the possibility that their acoustic structure and role in signaling identity might be constrained by functional or morphological design requirements associated with their role in signaling submission.

Functional connectivity abnormalities and associated cognitive deficits in fetal alcohol Spectrum disorders (FASD).

PubMed

Wozniak, Jeffrey R; Mueller, Bryon A; Mattson, Sarah N; Coles, Claire D; Kable, Julie A; Jones, Kenneth L; Boys, Christopher J; Lim, Kelvin O; Riley, Edward P; Sowell, Elizabeth R

2017-10-01

Consistent with well-documented structural and microstructural abnormalities in prenatal alcohol exposure (PAE), recent studies suggest that functional connectivity (FC) may also be disrupted. We evaluated whole-brain FC in a large multi-site sample, examined its cognitive correlates, and explored its potential to objectively identify neurodevelopmental abnormality in individuals without definitive dysmorphic features. Included were 75 children with PAE and 68 controls from four sites. All participants had documented heavy prenatal alcohol exposure. All underwent a formal evaluation of physical anomalies and dysmorphic facial features. MRI data were collected using modified matched protocols on three platforms (Siemens, GE, and Philips). Resting-state FC was examined using whole-brain graph theory metrics to characterize each individual's connectivity. Although whole-brain FC metrics did not discriminate prenatally-exposed from unexposed overall, atypical FC (> 1 standard deviation from the grand mean) was significantly more common (2.7 times) in the PAE group vs. In a subset of 55 individuals (PAE and controls) whose dysmorphology examination could not definitively characterize them as either Fetal Alcohol Syndrome (FAS) or non-FAS, atypical FC was seen in 27 % of the PAE group, but 0 % of controls. Across participants, a 1 % difference in local network efficiency was associated with a 36 point difference in global cognitive functioning. Whole-brain FC metrics have potential to identify individuals with objective neurodevelopmental abnormalities from prenatal alcohol exposure. When applied to individuals unable to be classified as FAS or non-FAS from dysmorphology alone, these measures separate prenatally-exposed from non-exposed with high specificity.

Concurrency-based approaches to parallel programming

NASA Technical Reports Server (NTRS)

Kale, L.V.; Chrisochoides, N.; Kohl, J.; Yelick, K.

1995-01-01

The inevitable transition to parallel programming can be facilitated by appropriate tools, including languages and libraries. After describing the needs of applications developers, this paper presents three specific approaches aimed at development of efficient and reusable parallel software for irregular and dynamic-structured problems. A salient feature of all three approaches in their exploitation of concurrency within a processor. Benefits of individual approaches such as these can be leveraged by an interoperability environment which permits modules written using different approaches to co-exist in single applications.

Final Accumulative Results & Transfer of Knowledge of the Arizona Career Ladder Research & Evaluation Project: Impact on Student Achievement, Formulated Models, Network Anecdotes, & Recommendations to the Legislature for Policy Development, Program Continuation & State-Wide Expansion. Summative Report VIII.

ERIC Educational Resources Information Center

Packard, Richard D.; Dereshiwsky, Mary I.

This paper presents research findings concerning the Career Ladder pilot test program in Arizona. The program is designed to reward and motivate teachers based on performance. One of the program's key features is the flexibility and innovation allowed to participating districts in their individual development of program designs and structures. An…

Self-esteem and other-esteem in college students with borderline and avoidant personality disorder features: An experimental vignette study.

PubMed

Bowles, David P; Armitage, Chris J; Drabble, Jennifer; Meyer, Björn

2013-11-01

An experimental study investigated self-esteem and other-esteem responses to either fully supportive or less supportive interpersonal feedback in college students with avoidant and borderline personality disorder features (APD and BPD respectively). Disturbances in self-esteem and in evaluations of others are central to definitions of both APD and BPD, but the extent to which such interpersonal appraisals are responsive to contextual features, such as evaluative feedback from others, is not yet clear. In theory, we would expect that individuals with pronounced PD features would show more inflexible and more negative self-evaluations and others- evaluations than those without PD features. In this study with 169 undergraduates, APD but not BPD features were associated with other-contingent state self-esteem and other-esteem. A significant interaction indicated that highly avoidant respondents felt particularly negatively about themselves and their close others in situations that conveyed subtle criticism but not in situations signalling unequivocal support. This suggests that their self-esteem and other-esteem, rather than being rigidly negative, are instead highly contingent upon interpersonal feedback. Such context contingency has implications for the trait-like description of diagnostic characteristics within current taxonomies and is in line with contemporary dynamic models of personality structure and process. Copyright © 2013 John Wiley & Sons, Ltd.

The research on multi-projection correction based on color coding grid array

NASA Astrophysics Data System (ADS)

Yang, Fan; Han, Cheng; Bai, Baoxing; Zhang, Chao; Zhao, Yunxiu

2017-10-01

There are many disadvantages such as lower timeliness, greater manual intervention in multi-channel projection system, in order to solve the above problems, this paper proposes a multi-projector correction technology based on color coding grid array. Firstly, a color structured light stripe is generated by using the De Bruijn sequences, then meshing the feature information of the color structured light stripe image. We put the meshing colored grid intersection as the center of the circle, and build a white solid circle as the feature sample set of projected images. It makes the constructed feature sample set not only has the perceptual localization, but also has good noise immunity. Secondly, we establish the subpixel geometric mapping relationship between the projection screen and the individual projectors by using the structure of light encoding and decoding based on the color array, and the geometrical mapping relation is used to solve the homography matrix of each projector. Lastly the brightness inconsistency of the multi-channel projection overlap area is seriously interfered, it leads to the corrected image doesn't fit well with the observer's visual needs, and we obtain the projection display image of visual consistency by using the luminance fusion correction algorithm. The experimental results show that this method not only effectively solved the problem of distortion of multi-projection screen and the issue of luminance interference in overlapping region, but also improved the calibration efficient of multi-channel projective system and reduced the maintenance cost of intelligent multi-projection system.

Change of the image of the city in process of using traffic infrastructure

NASA Astrophysics Data System (ADS)

Alihodžić, Rifat; Vasiljević Tomić, Dragana; Iablonskii, Leonid

2017-10-01

Unique urban image cannot be experienced without moving within its structure. This paper deals with phenomenology considering changes of images of the city and influential factors closely related to it. Infrastructure gives basic structural scheme of every city, so its planning requires a high level proficiency. Some changes in these images can be observed during longer period of time. Sometimes it includes rapid changes of temporal layers, generated by building new urban elements on the exact same place where the old ones existed; while lighter change during the time passing is a regular occurrence. Creating completely new urban frames, caused by expanding the city, represents its dynamical variant. Topography is a significant factor, giving distinctive feature to the urbanity. This paper considers factors identified as generators of the change of the urban image, based on research so far. The structural elements are considered with the utmost attention. The importance of the city landmark, monumental complexes not possessing these features but having the importance in image of the city stability (as well as the inhabitants’ memory) are crucial elements of identifying its picture. Another significant factor is related to individual personal experience. However, there are also certain factors of significance features, but not considered within this paper. One such factor is change in coloring, being the special topic itself. The purpose of this work is to indicate that urban planning requires special attention in order to keep continuous nature of the urban image for the city to preserve its visual identity.

PredPPCrys: accurate prediction of sequence cloning, protein production, purification and crystallization propensity from protein sequences using multi-step heterogeneous feature fusion and selection.

PubMed

Wang, Huilin; Wang, Mingjun; Tan, Hao; Li, Yuan; Zhang, Ziding; Song, Jiangning

2014-01-01

X-ray crystallography is the primary approach to solve the three-dimensional structure of a protein. However, a major bottleneck of this method is the failure of multi-step experimental procedures to yield diffraction-quality crystals, including sequence cloning, protein material production, purification, crystallization and ultimately, structural determination. Accordingly, prediction of the propensity of a protein to successfully undergo these experimental procedures based on the protein sequence may help narrow down laborious experimental efforts and facilitate target selection. A number of bioinformatics methods based on protein sequence information have been developed for this purpose. However, our knowledge on the important determinants of propensity for a protein sequence to produce high diffraction-quality crystals remains largely incomplete. In practice, most of the existing methods display poorer performance when evaluated on larger and updated datasets. To address this problem, we constructed an up-to-date dataset as the benchmark, and subsequently developed a new approach termed 'PredPPCrys' using the support vector machine (SVM). Using a comprehensive set of multifaceted sequence-derived features in combination with a novel multi-step feature selection strategy, we identified and characterized the relative importance and contribution of each feature type to the prediction performance of five individual experimental steps required for successful crystallization. The resulting optimal candidate features were used as inputs to build the first-level SVM predictor (PredPPCrys I). Next, prediction outputs of PredPPCrys I were used as the input to build second-level SVM classifiers (PredPPCrys II), which led to significantly enhanced prediction performance. Benchmarking experiments indicated that our PredPPCrys method outperforms most existing procedures on both up-to-date and previous datasets. In addition, the predicted crystallization targets of currently non-crystallizable proteins were provided as compendium data, which are anticipated to facilitate target selection and design for the worldwide structural genomics consortium. PredPPCrys is freely available at http://www.structbioinfor.org/PredPPCrys.

Structural features based genome-wide characterization and prediction of nucleosome organization

PubMed Central

2012-01-01

Background Nucleosome distribution along chromatin dictates genomic DNA accessibility and thus profoundly influences gene expression. However, the underlying mechanism of nucleosome formation remains elusive. Here, taking a structural perspective, we systematically explored nucleosome formation potential of genomic sequences and the effect on chromatin organization and gene expression in S. cerevisiae. Results We analyzed twelve structural features related to flexibility, curvature and energy of DNA sequences. The results showed that some structural features such as DNA denaturation, DNA-bending stiffness, Stacking energy, Z-DNA, Propeller twist and free energy, were highly correlated with in vitro and in vivo nucleosome occupancy. Specifically, they can be classified into two classes, one positively and the other negatively correlated with nucleosome occupancy. These two kinds of structural features facilitated nucleosome binding in centromere regions and repressed nucleosome formation in the promoter regions of protein-coding genes to mediate transcriptional regulation. Based on these analyses, we integrated all twelve structural features in a model to predict more accurately nucleosome occupancy in vivo than the existing methods that mainly depend on sequence compositional features. Furthermore, we developed a novel approach, named DLaNe, that located nucleosomes by detecting peaks of structural profiles, and built a meta predictor to integrate information from different structural features. As a comparison, we also constructed a hidden Markov model (HMM) to locate nucleosomes based on the profiles of these structural features. The result showed that the meta DLaNe and HMM-based method performed better than the existing methods, demonstrating the power of these structural features in predicting nucleosome positions. Conclusions Our analysis revealed that DNA structures significantly contribute to nucleosome organization and influence chromatin structure and gene expression regulation. The results indicated that our proposed methods are effective in predicting nucleosome occupancy and positions and that these structural features are highly predictive of nucleosome organization. The implementation of our DLaNe method based on structural features is available online. PMID:22449207

Individual differences and time-varying features of modular brain architecture.

PubMed

Liao, Xuhong; Cao, Miao; Xia, Mingrui; He, Yong

2017-05-15

Recent studies have suggested that human brain functional networks are topologically organized into functionally specialized but inter-connected modules to facilitate efficient information processing and highly flexible cognitive function. However, these studies have mainly focused on group-level network modularity analyses using "static" functional connectivity approaches. How these extraordinary modular brain structures vary across individuals and spontaneously reconfigure over time remain largely unknown. Here, we employed multiband resting-state functional MRI data (N=105) from the Human Connectome Project and a graph-based modularity analysis to systematically investigate individual variability and dynamic properties in modular brain networks. We showed that the modular structures of brain networks dramatically vary across individuals, with higher modular variability primarily in the association cortex (e.g., fronto-parietal and attention systems) and lower variability in the primary systems. Moreover, brain regions spontaneously changed their module affiliations on a temporal scale of seconds, which cannot be simply attributable to head motion and sampling error. Interestingly, the spatial pattern of intra-subject dynamic modular variability largely overlapped with that of inter-subject modular variability, both of which were highly reproducible across repeated scanning sessions. Finally, the regions with remarkable individual/temporal modular variability were closely associated with network connectors and the number of cognitive components, suggesting a potential contribution to information integration and flexible cognitive function. Collectively, our findings highlight individual modular variability and the notable dynamic characteristics in large-scale brain networks, which enhance our understanding of the neural substrates underlying individual differences in a variety of cognition and behaviors. Copyright © 2017 Elsevier Inc. All rights reserved.

Classification of micro-CT images using 3D characterization of bone canal patterns in human osteogenesis imperfecta

NASA Astrophysics Data System (ADS)

Abidin, Anas Z.; Jameson, John; Molthen, Robert; Wismüller, Axel

2017-03-01

Few studies have analyzed the microstructural properties of bone in cases of Osteogenenis Imperfecta (OI), or `brittle bone disease'. Current approaches mainly focus on bone mineral density measurements as an indirect indicator of bone strength and quality. It has been shown that bone strength would depend not only on composition but also structural organization. This study aims to characterize 3D structure of the cortical bone in high-resolution micro CT images. A total of 40 bone fragments from 28 subjects (13 with OI and 15 healthy controls) were imaged using micro tomography using a synchrotron light source (SRµCT). Minkowski functionals - volume, surface, curvature, and Euler characteristics - describing the topological organization of the bone were computed from the images. The features were used in a machine learning task to classify between healthy and OI bone. The best classification performance (mean AUC - 0.96) was achieved with a combined 4-dimensional feature of all Minkowski functionals. Individually, the best feature performance was seen using curvature (mean AUC - 0.85), which characterizes the edges within a binary object. These results show that quantitative analysis of cortical bone microstructure, in a computer-aided diagnostics framework, can be used to distinguish between healthy and OI bone with high accuracy.

Feature-to-Feature Inference Under Conditions of Cue Restriction and Dimensional Correlation.

PubMed

Lancaster, Matthew E; Homa, Donald

2017-01-01

The present study explored feature-to-feature and label-to-feature inference in a category task for different category structures. In the correlated condition, each of the 4 dimensions comprising the category was positively correlated to each other and to the category label. In the uncorrelated condition, no correlation existed between the 4 dimensions comprising the category, although the dimension to category label correlation matched that of the correlated condition. After learning, participants made inference judgments of a missing feature, given 1, 2, or 3 feature cues; on half the trials, the category label was also included as a cue. The results showed superior inference of features following training on the correlated structure, with accurate inference when only a single feature was presented. In contrast, a single-feature cue resulted in chance levels of inference for the uncorrelated structure. Feature inference systematically improved with number of cues after training on the correlated structure. Surprisingly, a similar outcome was obtained for the uncorrelated structure, an outcome that must have reflected mediation via the category label. A descriptive model is briefly introduced to explain the results, with a suggestion that this paradigm might be profitably extended to hierarchical structures where the levels of feature-to-feature inference might vary with the depth of the hierarchy.

Novel chromatin texture features for the classification of pap smears

NASA Astrophysics Data System (ADS)

Bejnordi, Babak E.; Moshavegh, Ramin; Sujathan, K.; Malm, Patrik; Bengtsson, Ewert; Mehnert, Andrew

2013-03-01

This paper presents a set of novel structural texture features for quantifying nuclear chromatin patterns in cells on a conventional Pap smear. The features are derived from an initial segmentation of the chromatin into bloblike texture primitives. The results of a comprehensive feature selection experiment, including the set of proposed structural texture features and a range of different cytology features drawn from the literature, show that two of the four top ranking features are structural texture features. They also show that a combination of structural and conventional features yields a classification performance of 0.954±0.019 (AUC±SE) for the discrimination of normal (NILM) and abnormal (LSIL and HSIL) slides. The results of a second classification experiment, using only normal-appearing cells from both normal and abnormal slides, demonstrates that a single structural texture feature measuring chromatin margination yields a classification performance of 0.815±0.019. Overall the results demonstrate the efficacy of the proposed structural approach and that it is possible to detect malignancy associated changes (MACs) in Papanicoloau stain.

Platform technology for scalable assembly of instantaneously functional mosaic tissues

PubMed Central

Zhang, Boyang; Montgomery, Miles; Davenport-Huyer, Locke; Korolj, Anastasia; Radisic, Milica

2015-01-01

Engineering mature tissues requires a guided assembly of cells into organized three-dimensional (3D) structures with multiple cell types. Guidance is usually achieved by microtopographical scaffold cues or by cell-gel compaction. The assembly of individual units into functional 3D tissues is often time-consuming, relying on cell ingrowth and matrix remodeling, whereas disassembly requires an invasive method that includes either matrix dissolution or mechanical cutting. We invented Tissue-Velcro, a bio-scaffold with a microfabricated hook and loop system. The assembly of Tissue-Velcro preserved the guided cell alignment realized by the topographical features in the 2D scaffold mesh and allowed for the instant establishment of coculture conditions by spatially defined stacking of cardiac cell layers or through endothelial cell coating. The assembled cardiac 3D tissue constructs were immediately functional as measured by their ability to contract in response to electrical field stimulation. Facile, on-demand tissue disassembly was demonstrated while preserving the structure, physical integrity, and beating function of individual layers. PMID:26601234

Neuroimaging studies in people with gender incongruence.

PubMed

Kreukels, Baudewijntje P C; Guillamon, Antonio

2016-01-01

The current review gives an overview of brain studies in transgender people. First, we describe studies into the aetiology of feelings of gender incongruence, primarily addressing the sexual differentiation hypothesis: does the brain of transgender individuals resemble that of their natal sex, or that of their experienced gender? Findings from neuroimaging studies focusing on brain structure suggest that the brain phenotypes of trans women (MtF) and trans men (FtM) differ in various ways from control men and women with feminine, masculine, demasculinized and defeminized features. The brain phenotypes of people with feelings of gender incongruence may help us to figure out whether sex differentiation of the brain is atypical in these individuals, and shed light on gender identity development. Task-related imaging studies may show whether brain activation and task performance in transgender people is sex-atypical. Second, we review studies that evaluate the effects of cross-sex hormone treatment on the brain. This type of research provides knowledge on how changes in sex hormone levels may affect brain structure and function.

Quantum transport through single and multilayer icosahedral fullerenes

NASA Astrophysics Data System (ADS)

Lovey, Daniel A.; Romero, Rodolfo H.

2013-10-01

We use a tight-binding Hamiltonian and Green functions methods to calculate the quantum transmission through single-wall fullerenes and bilayered and trilayered onions of icosahedral symmetry attached to metallic leads. The electronic structure of the onion-like fullerenes takes into account the curvature and finite size of the fullerenes layers as well as the strength of the intershell interactions depending on to the number of interacting atom pairs belonging to adjacent shells. Misalignment of the symmetry axes of the concentric iscosahedral shells produces breaking of the level degeneracies of the individual shells, giving rise some narrow quasi-continuum bands instead of the localized discrete peaks of the individual fullerenes. As a result, the transmission function for non symmetrical onions is rapidly varying functions of the Fermi energy. Furthermore, we found that most of the features of the transmission through the onions are due to the electronic structure of the outer shell with additional Fano-like antiresonances arising from coupling with or between the inner shells.

[Features of the structure and parameters of the intra-alveolar septa in residents of Western Siberia].

PubMed

Shishkin, G S; Ustiuzhaninova, N V

1998-01-01

In inhabitants of Novosibirsk and Moscow district intraalveolar septum, the basic functional element of the lung consists of interstitial connective tissue and capillar network, limited with basement membranes, on which cells of epithelial lining are placed. There are no principal differences in septal structure between individuals from both regions. The majority of morphometric parameters are statistically similar, although certain peculiarities were noted in human subjects from Siberia, the most important of which is that air-blood barrier in them is 33% thinner than those in inhabitants of Moscow district. Majority of capillaries possess the air-blood barrier from both sides. This increases diffous capacity of the lungs and blood oxygenation level.

Potential of personal health record portals in the care of individuals with spinal cord injuries and disorders: Provider perspectives.

PubMed

Hill, Jennifer N; Smith, Bridget M; Weaver, Frances M; Nazi, Kim M; Thomas, Florian P; Goldstein, Barry; Hogan, Timothy P

2018-05-01

Although personal health record (PHR) portals are designed for patients, healthcare providers are a key influence in how patients use their features and realize benefits from them. A few studies have examined provider attitudes toward PHR portals, but none have focused on those who care for individuals with spinal cord injuries and disorders (SCI/D). We characterize SCI/D provider perspectives of PHR portals, including perceived advantages and disadvantages of PHR portal use in SCI/D care. Cross-sectional; semi-structured interviews. Spinal Cord Injury (SCI) Centers in the Veterans Health Administration. Twenty-six SCI/D healthcare providers. None. Perceived advantages and disadvantages of PHR portals. The complex situations of individuals with SCI/D shaped provider perspectives of PHR portals and their potential role in practice. Perceived advantages of PHR portal use in SCI/D care included the ability to coordinate information and care, monitor and respond to outpatient requests, support patient self-management activities, and provide reliable health information to patients. Perceived disadvantages of PHR portal use in SCI/D care included concerns about the quality of patient-generated health data, other potential liabilities for providers and workload burden, and the ability of individuals with SCI/D to understand clinical information accessed through a portal. Our study highlights advantages and disadvantages that should be considered when promoting engagement of SCI/D healthcare providers in use of PHR portals, and portal features that may have the most utility in SCI/D care.

Where East meets West: in the house of individuation.

PubMed

Stein, Murray

2017-02-01

The psychological process of individuation as experienced in Jungian work may lead to states of consciousness that resemble advanced spiritual developments across religious traditions and cultures. This is where Westerners may reach a common ground with the East. In the essentials and with respect to the final goal there is little difference among the many ways to the self, even if the cultural features in the landscape are disparate. In late stage Jungian analysis and individuation and in what Erich Neumann calls 'centroversion', the personal and the impersonal aspects of the personality accumulate around the ego-self axis to form a composite identity. In this complex structure the ego does not vanish but is joined to the impersonal archetypal levels of the psyche and identity thus becomes at once individual and archetypal. This is the third stage of conjunction as described by Jung in Mysterium Coniunctionis and it is identical to the type of consciousness depicted in the final scenes of Zen Buddhism's Ten Ox-Herding Pictures. © 2017, The Society of Analytical Psychology.

The sequential structure of brain activation predicts skill.

PubMed

Anderson, John R; Bothell, Daniel; Fincham, Jon M; Moon, Jungaa

2016-01-29

In an fMRI study, participants were trained to play a complex video game. They were scanned early and then again after substantial practice. While better players showed greater activation in one region (right dorsal striatum) their relative skill was better diagnosed by considering the sequential structure of whole brain activation. Using a cognitive model that played this game, we extracted a characterization of the mental states that are involved in playing a game and the statistical structure of the transitions among these states. There was a strong correspondence between this measure of sequential structure and the skill of different players. Using multi-voxel pattern analysis, it was possible to recognize, with relatively high accuracy, the cognitive states participants were in during particular scans. We used the sequential structure of these activation-recognized states to predict the skill of individual players. These findings indicate that important features about information-processing strategies can be identified from a model-based analysis of the sequential structure of brain activation. Copyright © 2015 Elsevier Ltd. All rights reserved.

The grammar of visual narrative: Neural evidence for constituent structure in sequential image comprehension.

PubMed

Cohn, Neil; Jackendoff, Ray; Holcomb, Phillip J; Kuperberg, Gina R

2014-11-01

Constituent structure has long been established as a central feature of human language. Analogous to how syntax organizes words in sentences, a narrative grammar organizes sequential images into hierarchic constituents. Here we show that the brain draws upon this constituent structure to comprehend wordless visual narratives. We recorded neural responses as participants viewed sequences of visual images (comics strips) in which blank images either disrupted individual narrative constituents or fell at natural constituent boundaries. A disruption of either the first or the second narrative constituent produced a left-lateralized anterior negativity effect between 500 and 700ms. Disruption of the second constituent also elicited a posteriorly-distributed positivity (P600) effect. These neural responses are similar to those associated with structural violations in language and music. These findings provide evidence that comprehenders use a narrative structure to comprehend visual sequences and that the brain engages similar neurocognitive mechanisms to build structure across multiple domains. Copyright © 2014 Elsevier Ltd. All rights reserved.

The grammar of visual narrative: Neural evidence for constituent structure in sequential image comprehension

PubMed Central

Cohn, Neil; Jackendoff, Ray; Holcomb, Phillip J.; Kuperberg, Gina R.

2014-01-01

Constituent structure has long been established as a central feature of human language. Analogous to how syntax organizes words in sentences, a narrative grammar organizes sequential images into hierarchic constituents. Here we show that the brain draws upon this constituent structure to comprehend wordless visual narratives. We recorded neural responses as participants viewed sequences of visual images (comics strips) in which blank images either disrupted individual narrative constituents or fell at natural constituent boundaries. A disruption of either the first or the second narrative constituent produced a left-lateralized anterior negativity effect between 500-700ms. Disruption of the second constituent also elicited a posteriorly-distributed positivity (P600) effect. These neural responses are similar to those associated with structural violations in language and music. These findings provide evidence that comprehenders use a narrative structure to comprehend visual sequences and that the brain engages similar neurocognitive mechanisms to build structure across multiple domains. PMID:25241329

The RCSB protein data bank: integrative view of protein, gene and 3D structural information

PubMed Central

Rose, Peter W.; Prlić, Andreas; Altunkaya, Ali; Bi, Chunxiao; Bradley, Anthony R.; Christie, Cole H.; Costanzo, Luigi Di; Duarte, Jose M.; Dutta, Shuchismita; Feng, Zukang; Green, Rachel Kramer; Goodsell, David S.; Hudson, Brian; Kalro, Tara; Lowe, Robert; Peisach, Ezra; Randle, Christopher; Rose, Alexander S.; Shao, Chenghua; Tao, Yi-Ping; Valasatava, Yana; Voigt, Maria; Westbrook, John D.; Woo, Jesse; Yang, Huangwang; Young, Jasmine Y.; Zardecki, Christine; Berman, Helen M.; Burley, Stephen K.

2017-01-01

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB, http://rcsb.org), the US data center for the global PDB archive, makes PDB data freely available to all users, from structural biologists to computational biologists and beyond. New tools and resources have been added to the RCSB PDB web portal in support of a ‘Structural View of Biology.’ Recent developments have improved the User experience, including the high-speed NGL Viewer that provides 3D molecular visualization in any web browser, improved support for data file download and enhanced organization of website pages for query, reporting and individual structure exploration. Structure validation information is now visible for all archival entries. PDB data have been integrated with external biological resources, including chromosomal position within the human genome; protein modifications; and metabolic pathways. PDB-101 educational materials have been reorganized into a searchable website and expanded to include new features such as the Geis Digital Archive. PMID:27794042

Revised simulation model does not predict rebound in gonorrhoea prevalence where core groups are treated in the presence of antimicrobial resistance.

PubMed

Trecker, Molly A; Hogan, Daniel J; Waldner, Cheryl L; Dillon, Jo-Anne R; Osgood, Nathaniel D

2015-06-01

To determine the effects of using discrete versus continuous quantities of people in a compartmental model examining the contribution of antimicrobial resistance (AMR) to rebound in the prevalence of gonorrhoea. A previously published transmission model was reconfigured to represent the occurrence of gonorrhoea in discrete persons, rather than allowing fractions of infected individuals during simulations. In the revised model, prevalence only rebounded under scenarios reproduced from the original paper when AMR occurrence was increased by 10(5) times. In such situations, treatment of high-risk individuals yielded outcomes very similar to those resulting from treatment of low-risk and intermediate-risk individuals. Otherwise, in contrast with the original model, prevalence was the lowest when the high-risk group was treated, supporting the current policy of targeting treatment to high-risk groups. Simulation models can be highly sensitive to structural features. Small differences in structure and parameters can substantially influence predicted outcomes and policy prescriptions, and must be carefully considered. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

The effect of a prudent adaptive behaviour on disease transmission

NASA Astrophysics Data System (ADS)

Scarpino, Samuel V.; Allard, Antoine; Hébert-Dufresne, Laurent

2016-11-01

The spread of disease can be slowed by certain aspects of real-world social networks, such as clustering and community structure, and of human behaviour, including social distancing and increased hygiene, many of which have already been studied. Here, we consider a model in which individuals with essential societal roles--be they teachers, first responders or health-care workers--fall ill, and are replaced with healthy individuals. We refer to this process as relational exchange, and incorporate it into a dynamic network model to demonstrate that replacing individuals can accelerate disease transmission. We find that the effects of this process are trivial in the context of a standard mass-action model, but dramatic when considering network structure, featuring accelerating spread, discontinuous transitions and hysteresis loops. This result highlights the inability of mass-action models to account for many behavioural processes. Using empirical data, we find that this mechanism parsimoniously explains observed patterns across 17 influenza outbreaks in the USA at a national level, 25 years of influenza data at the state level, and 19 years of dengue virus data from Puerto Rico. We anticipate that our findings will advance the emerging field of disease forecasting and better inform public health decision making during outbreaks.

Selfish genetic elements, genetic conflict, and evolutionary innovation.

PubMed

Werren, John H

2011-06-28

Genomes are vulnerable to selfish genetic elements (SGEs), which enhance their own transmission relative to the rest of an individual's genome but are neutral or harmful to the individual as a whole. As a result, genetic conflict occurs between SGEs and other genetic elements in the genome. There is growing evidence that SGEs, and the resulting genetic conflict, are an important motor for evolutionary change and innovation. In this review, the kinds of SGEs and their evolutionary consequences are described, including how these elements shape basic biological features, such as genome structure and gene regulation, evolution of new genes, origin of new species, and mechanisms of sex determination and development. The dynamics of SGEs are also considered, including possible "evolutionary functions" of SGEs.

Selfish genetic elements, genetic conflict, and evolutionary innovation

PubMed Central

Werren, John H.

2011-01-01

Genomes are vulnerable to selfish genetic elements (SGEs), which enhance their own transmission relative to the rest of an individual's genome but are neutral or harmful to the individual as a whole. As a result, genetic conflict occurs between SGEs and other genetic elements in the genome. There is growing evidence that SGEs, and the resulting genetic conflict, are an important motor for evolutionary change and innovation. In this review, the kinds of SGEs and their evolutionary consequences are described, including how these elements shape basic biological features, such as genome structure and gene regulation, evolution of new genes, origin of new species, and mechanisms of sex determination and development. The dynamics of SGEs are also considered, including possible “evolutionary functions” of SGEs. PMID:21690392

RNA helicase proteins as chaperones and remodelers

PubMed Central

Jarmoskaite, Inga; Russell, Rick

2014-01-01

Superfamily 2 helicase proteins are ubiquitous in RNA biology and have an extraordinarily broad set of functional roles. Central among these roles are to promote rearrangements of structured RNAs and to remodel RNA-protein complexes (RNPs), allowing formation of native RNA structure or progression through a functional cycle of structures. While all superfamily 2 helicases share a conserved helicase core, they are divided evolutionarily into several families, and it is principally proteins from three families, the DEAD-box, DEAH/RHA and Ski2-like families, that function to manipulate structured RNAs and RNPs. Strikingly, there are emerging differences in the mechanisms of these proteins, both between families and within the largest family (DEAD-box), and these differences appear to be tuned to their RNA or RNP substrates and their specific roles. This review outlines basic mechanistic features of the three families and surveys individual proteins and the current understanding of their biological substrates and mechanisms. PMID:24635478

[Structural plasticity associated with drugs addiction].

PubMed

Zhu, Jie; Cao, Guo-fen; Dang, Yong-hui; Chen, Teng

2011-12-01

An essential feature of drug addiction is that an individual continues to use drug despite the threat of severely adverse physical or psychosocial consequences. Persistent changes in behavior and psychological function that occur as a function of drugs of abuse are thought to be due to the reorganization of synaptic connections (structural plasticity) in relevant brain circuits (especially the brains reward circuits). In this paper we summarized evidence that, indeed, exposure to amphetamine, cocaine, nicotine or morphine produced persistent changes in the structure of dendrites and dendritic spines on cells in relevant brain regions. We also approached the potential molecular mechanisms of these changes. It is suggested that structural plasticity associated with exposure to drugs of abuse reflects a reorganization of patterns of synaptic connectivity in these neural systems, a reorganization that alters their operation, thus contributing to some of the persistent sequela associated with drug use-including addiction.

Analysis of forest structure using thematic mapper simulator data

NASA Technical Reports Server (NTRS)

Peterson, D. L.; Westman, W. E.; Brass, J. A.; Stephenson, N. J.; Ambrosia, V. G.; Spanner, M. A.

1986-01-01

The potential of Thematic Mapper Simulator (TMS) data for sensing forest structure information has been explored by principal components and feature selection techniques. In a survey of forest structural properties conducted for 123 field sites of the Sequoia National Park, the canopy closure could be well estimated (r = 0.62 to 0.69) by a variety of channel bands and band ratios, without reference to the forest type. Estimation of the basal area was less successful (r = 0.51 or less) on the average, but could be improved for certain forest types when data were stratified by floristic composition. To achieve such a stratification, individual sites were ordinated by a detrended correspondence analysis based on the canopy of dominant species. The analysis of forest structure in the Sequoia data suggests that total basal area can be best predicted in stands of lower density, and in younger even-aged managed stands.

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

Peterson, T. J.; Weisend, II, J. G.

The TESLA collaboration developed a unique variant of SRF cryomodule designs, the chief feature being use of the large, low pressure helium vapor return pipe as the structural support backbone of the cryomodule. Additional innovative features include all cryogenic piping within the cryomodule (no parallel external cryogenic transfer line), long strings of RF cavities within a single cryomodule, and cryomodules connected in series. Several projects, including FLASH and XFEL at DESY, LCLS-II at SLAC, and the ILC technical design have adopted this general design concept. Advantages include saving space by eliminating the external transfer line, relatively tight packing of RFmore » cavities along the beamline due to fewer warm-cold transitions, and potentially lower costs. However, a primary disadvantage is the relative lack of independence for warm-up, replacement, and cool-down of individual cryomodules.« less

Conductive Photo-Activated Porphyrin-ZnO Nanostructured Gas Sensor Array.

PubMed

Magna, Gabriele; Catini, Alexandro; Kumar, Raj; Palmacci, Massimo; Martinelli, Eugenio; Paolesse, Roberto; di Natale, Corrado

2017-04-01

Chemoresistors working at room temperature are attractive for low-consumption integrated sensors. Previous studies show that this feature can be obtained with photoconductive porphyrins-coated ZnO nanostructures. Furthermore, variations of the porphyrin molecular structure alter both the chemical sensitivity and the photoconductivity, and can be used to define the sensor characteristics. Based on these assumptions, we investigated the properties of an array of four sensors made of a layer of ZnO nanoparticles coated with porphyrins with the same molecular framework but different metal atoms. The array was tested with five volatile organic compounds (VOCs), each measured at different concentrations. Results confirm that the features of individual porphyrins influence the sensor behavior, and the differences among sensors are enough to enable the discrimination of volatile compounds disregarding their concentration.

Privacy Policy Enforcement for Ambient Ubiquitous Services

NASA Astrophysics Data System (ADS)

Oyomno, Were; Jäppinen, Pekka; Kerttula, Esa

Ubiquitous service providers leverage miniaturised computing terminals equipped with wireless capabilities to avail new service models. These models are pivoted on personal and inexpensive terminals to customise services to individual preferences. Portability, small sizes and compact keyboards are few features popularising mobile terminals. Features enable storing and carrying of ever increasing proportions of personal data and ability to use them in service adaptations. Ubiquitous services automate deeper soliciting of personal data transparently without the need for user interactions. Transparent solicitations, acquisitions and handling of personal data legitimises privacy concerns regarding disclosures, retention and re-use of the data. This study presents a policy enforcement for ubiquitous services that safeguards handling of users personal data and monitors adherence to stipulated privacy policies. Enforcement structures towards usability and scalability are presented.

Constraint-based stereo matching

NASA Technical Reports Server (NTRS)

Kuan, D. T.

1987-01-01

The major difficulty in stereo vision is the correspondence problem that requires matching features in two stereo images. Researchers describe a constraint-based stereo matching technique using local geometric constraints among edge segments to limit the search space and to resolve matching ambiguity. Edge segments are used as image features for stereo matching. Epipolar constraint and individual edge properties are used to determine possible initial matches between edge segments in a stereo image pair. Local edge geometric attributes such as continuity, junction structure, and edge neighborhood relations are used as constraints to guide the stereo matching process. The result is a locally consistent set of edge segment correspondences between stereo images. These locally consistent matches are used to generate higher-level hypotheses on extended edge segments and junctions to form more global contexts to achieve global consistency.

A knowledge based approach to matching human neurodegenerative disease and animal models

PubMed Central

Maynard, Sarah M.; Mungall, Christopher J.; Lewis, Suzanna E.; Imam, Fahim T.; Martone, Maryann E.

2013-01-01

Neurodegenerative diseases present a wide and complex range of biological and clinical features. Animal models are key to translational research, yet typically only exhibit a subset of disease features rather than being precise replicas of the disease. Consequently, connecting animal to human conditions using direct data-mining strategies has proven challenging, particularly for diseases of the nervous system, with its complicated anatomy and physiology. To address this challenge we have explored the use of ontologies to create formal descriptions of structural phenotypes across scales that are machine processable and amenable to logical inference. As proof of concept, we built a Neurodegenerative Disease Phenotype Ontology (NDPO) and an associated Phenotype Knowledge Base (PKB) using an entity-quality model that incorporates descriptions for both human disease phenotypes and those of animal models. Entities are drawn from community ontologies made available through the Neuroscience Information Framework (NIF) and qualities are drawn from the Phenotype and Trait Ontology (PATO). We generated ~1200 structured phenotype statements describing structural alterations at the subcellular, cellular and gross anatomical levels observed in 11 human neurodegenerative conditions and associated animal models. PhenoSim, an open source tool for comparing phenotypes, was used to issue a series of competency questions to compare individual phenotypes among organisms and to determine which animal models recapitulate phenotypic aspects of the human disease in aggregate. Overall, the system was able to use relationships within the ontology to bridge phenotypes across scales, returning non-trivial matches based on common subsumers that were meaningful to a neuroscientist with an advanced knowledge of neuroanatomy. The system can be used both to compare individual phenotypes and also phenotypes in aggregate. This proof of concept suggests that expressing complex phenotypes using formal ontologies provides considerable benefit for comparing phenotypes across scales and species. PMID:23717278

Long-Term Effects of Acute Stress on the Prefrontal-Limbic System in the Healthy Adult

PubMed Central

Wei, Dongtao; Du, Xue; Zhang, Qinglin; Liu, Guangyuan; Qiu, Jiang

2017-01-01

Most people are exposed to at least one traumatic event during the course of their lives, but large numbers of people do not develop posttraumatic stress disorders. Although previous studies have shown that repeated and chronic stress change the brain’s structure and function, few studies have focused on the long-term effects of acute stressful exposure in a nonclinical sample, especially the morphology and functional connectivity changes in brain regions implicated in emotional reactivity and emotion regulation. Forty-one months after the 5/12 Wenchuan earthquake, we investigated the effects of trauma exposure on the structure and functional connectivity of the brains of trauma-exposed healthy individuals compared with healthy controls matched for age, sex, and education. We then used machine-learning algorithms with the brain structural features to distinguish between the two groups at an individual level. In the trauma-exposed healthy individuals, our results showed greater gray matter density in prefrontal-limbic brain systems, including the dorsal anterior cingulate cortex, medial prefrontal cortex, amygdala and hippocampus, than in the controls. Further analysis showed stronger amygdala-hippocampus functional connectivity in the trauma-exposed healthy compared to the controls. Our findings revealed that survival of traumatic experiences, without developing PTSD, was associated with greater gray matter density in the prefrontal-limbic systems related to emotional regulation. PMID:28045980

Gray matter volume of the anterior insular cortex and social networking.

PubMed

Spagna, Alfredo; Dufford, Alexander J; Wu, Qiong; Wu, Tingting; Zheng, Weihao; Coons, Edgar E; Hof, Patrick R; Hu, Bin; Wu, Yanhong; Fan, Jin

2018-05-01

In human life, social context requires the engagement in complex interactions among individuals as the dynamics of social networks. The evolution of the brain as the neurological basis of the mind must be crucial in supporting social networking. Although the relationship between social networking and the amygdala, a small but core region for emotion processing, has been reported, other structures supporting sophisticated social interactions must be involved and need to be identified. In this study, we examined the relationship between morphology of the anterior insular cortex (AIC), a structure involved in basic and high-level cognition, and social networking. Two independent cohorts of individuals (New York group n = 50, Beijing group n = 100) were recruited. Structural magnetic resonance images were acquired and the social network index (SNI), a composite measure summarizing an individual's network diversity, size, and complexity, was measured. The association between morphological features of the AIC, in addition to amygdala, and the SNI was examined. Positive correlations between the measures of the volume as well as sulcal depth of the AIC and the SNI were found in both groups, while a significant positive correlation between the volume of the amygdala and the SNI was only found in the New York group. The converging results from the two groups suggest that the AIC supports network-level social interactions. © 2018 Wiley Periodicals, Inc.

An ICA-EBM-Based sEMG Classifier for Recognizing Lower Limb Movements in Individuals With and Without Knee Pathology.

PubMed

Naik, Ganesh R; Selvan, S Easter; Arjunan, Sridhar P; Acharyya, Amit; Kumar, Dinesh K; Ramanujam, Arvind; Nguyen, Hung T

2018-03-01

Surface electromyography (sEMG) data acquired during lower limb movements has the potential for investigating knee pathology. Nevertheless, a major challenge encountered with sEMG signals generated by lower limb movements is the intersubject variability, because the signals recorded from the leg or thigh muscles are contingent on the characteristics of a subject such as gait activity and muscle structure. In order to cope with this difficulty, we have designed a three-step classification scheme. First, the multichannel sEMG is decomposed into activities of the underlying sources by means of independent component analysis via entropy bound minimization. Next, a set of time-domain features, which would best discriminate various movements, are extracted from the source estimates. Finally, the feature selection is performed with the help of the Fisher score and a scree-plot-based statistical technique, prior to feeding the dimension-reduced features to the linear discriminant analysis. The investigation involves 11 healthy subjects and 11 individuals with knee pathology performing three different lower limb movements, namely, walking, sitting, and standing, which yielded an average classification accuracy of 96.1% and 86.2%, respectively. While the outcome of this study per se is very encouraging, with suitable improvement, the clinical application of such an sEMG-based pattern recognition system that distinguishes healthy and knee pathological subjects would be an attractive consequence.

Support Vector Machine-based classification of protein folds using the structural properties of amino acid residues and amino acid residue pairs.

PubMed

Shamim, Mohammad Tabrez Anwar; Anwaruddin, Mohammad; Nagarajaram, H A

2007-12-15

Fold recognition is a key step in the protein structure discovery process, especially when traditional sequence comparison methods fail to yield convincing structural homologies. Although many methods have been developed for protein fold recognition, their accuracies remain low. This can be attributed to insufficient exploitation of fold discriminatory features. We have developed a new method for protein fold recognition using structural information of amino acid residues and amino acid residue pairs. Since protein fold recognition can be treated as a protein fold classification problem, we have developed a Support Vector Machine (SVM) based classifier approach that uses secondary structural state and solvent accessibility state frequencies of amino acids and amino acid pairs as feature vectors. Among the individual properties examined secondary structural state frequencies of amino acids gave an overall accuracy of 65.2% for fold discrimination, which is better than the accuracy by any method reported so far in the literature. Combination of secondary structural state frequencies with solvent accessibility state frequencies of amino acids and amino acid pairs further improved the fold discrimination accuracy to more than 70%, which is approximately 8% higher than the best available method. In this study we have also tested, for the first time, an all-together multi-class method known as Crammer and Singer method for protein fold classification. Our studies reveal that the three multi-class classification methods, namely one versus all, one versus one and Crammer and Singer method, yield similar predictions. Dataset and stand-alone program are available upon request.

Lineaments of Texas - possible surface expressions of deep-seated phenomena. Final report

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

Woodruff, C.M. Jr.; Caran, S.C.

1984-04-01

Lineaments were identified on 51 Landsat images covering Texas and parts of adjacent states in Mexico and the United States. A method of identifying lineaments was designed so that the findings would be consistent, uncomplicated, objective, and reproducible. Lineaments denoted on the Landsat images were traced onto 1:250,000-scale work maps and then rendered cartographically on maps representing each of the 51 Landsat images at a scale of 1:500,000. At this stage more than 31,000 lineaments were identified. It included significant areas outside of Texas. In preparing the final lineament map of Texas at 1:1,000,000-scale from the 1:500,000-scale maps, all featuresmore » that lay outside Texas and repetition among features perceived by individual workers were eliminated. Cultural features were checked for before reducing and cartographically fitting the mosaic of 51 individual map sheets to a single map base. Lineaments that were partly colinear but with different end points were modified into a single lineament trace with the combined length of the two or more colinear lineaments. Each lineament was checked to determine its validity according to our definition. The features were edited again to eliminate processing artifacts within the image itself, as well as representations of cultural features (fencelines, roads, and the like) and geomorphic patterns unrelated to bedrock structure. Thus the more than 31,000 lineaments originally perceived were reduced to the approximately 15,000 presented on the 1:1,000,000 map. Interpretations of the lineaments are presented.« less

Illusory conjunctions in visual short-term memory: Individual differences in corpus callosum connectivity and splitting attention between the two hemifields.

PubMed

Qin, Shuo; Ray, Nicholas R; Ramakrishnan, Nithya; Nashiro, Kaoru; O'Connell, Margaret A; Basak, Chandramallika

2016-11-01

Overloading the capacity of visual attention can result in mistakenly combining the various features of an object, that is, illusory conjunctions. We hypothesize that if the two hemispheres separately process visual information by splitting attention, connectivity of corpus callosum-a brain structure integrating the two hemispheres-would predict the degree of illusory conjunctions. In the current study, we assessed two types of illusory conjunctions using a memory-scanning paradigm; the features were either presented across the two opposite hemifields or within the same hemifield. Four objects, each with two visual features, were briefly presented together followed by a probe-recognition and a confidence rating for the recognition accuracy. MRI scans were also obtained. Results indicated that successful recollection during probe recognition was better for across hemifields conjunctions compared to within hemifield conjunctions, lending support to the bilateral advantage of the two hemispheres in visual short-term memory. Age-related differences regarding the underlying mechanisms of the bilateral advantage indicated greater reliance on recollection-based processing in young and on familiarity-based processing in old. Moreover, the integrity of the posterior corpus callosum was more predictive of opposite hemifield illusory conjunctions compared to within hemifield illusory conjunctions, even after controlling for age. That is, individuals with lesser posterior corpus callosum connectivity had better recognition for objects when their features were recombined from the opposite hemifields than from the same hemifield. This study is the first to investigate the role of the corpus callosum in splitting attention between versus within hemifields. © 2016 Society for Psychophysiological Research.

Principal component analysis of three-dimensional face shape: Identifying shape features that change with age.

PubMed

Kurosumi, M; Mizukoshi, K

2018-05-01

The types of shape feature that constitutes a face have not been comprehensively established, and most previous studies of age-related changes in facial shape have focused on individual characteristics, such as wrinkle, sagging skin, etc. In this study, we quantitatively measured differences in face shape between individuals and investigated how shape features changed with age. We analyzed three-dimensionally the faces of 280 Japanese women aged 20-69 years and used principal component analysis to establish the shape features that characterized individual differences. We also evaluated the relationships between each feature and age, clarifying the shape features characteristic of different age groups. Changes in facial shape in middle age were a decreased volume of the upper face and increased volume of the whole cheeks and around the chin. Changes in older people were an increased volume of the lower cheeks and around the chin, sagging skin, and jaw distortion. Principal component analysis was effective for identifying facial shape features that represent individual and age-related differences. This method allowed straightforward measurements, such as the increase or decrease in cheeks caused by soft tissue changes or skeletal-based changes to the forehead or jaw, simply by acquiring three-dimensional facial images. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Predicting turns in proteins with a unified model.

PubMed

Song, Qi; Li, Tonghua; Cong, Peisheng; Sun, Jiangming; Li, Dapeng; Tang, Shengnan

2012-01-01

Turns are a critical element of the structure of a protein; turns play a crucial role in loops, folds, and interactions. Current prediction methods are well developed for the prediction of individual turn types, including α-turn, β-turn, and γ-turn, etc. However, for further protein structure and function prediction it is necessary to develop a uniform model that can accurately predict all types of turns simultaneously. In this study, we present a novel approach, TurnP, which offers the ability to investigate all the turns in a protein based on a unified model. The main characteristics of TurnP are: (i) using newly exploited features of structural evolution information (secondary structure and shape string of protein) based on structure homologies, (ii) considering all types of turns in a unified model, and (iii) practical capability of accurate prediction of all turns simultaneously for a query. TurnP utilizes predicted secondary structures and predicted shape strings, both of which have greater accuracy, based on innovative technologies which were both developed by our group. Then, sequence and structural evolution features, which are profile of sequence, profile of secondary structures and profile of shape strings are generated by sequence and structure alignment. When TurnP was validated on a non-redundant dataset (4,107 entries) by five-fold cross-validation, we achieved an accuracy of 88.8% and a sensitivity of 71.8%, which exceeded the most state-of-the-art predictors of certain type of turn. Newly determined sequences, the EVA and CASP9 datasets were used as independent tests and the results we achieved were outstanding for turn predictions and confirmed the good performance of TurnP for practical applications.

Predicting Turns in Proteins with a Unified Model

PubMed Central

Song, Qi; Li, Tonghua; Cong, Peisheng; Sun, Jiangming; Li, Dapeng; Tang, Shengnan

2012-01-01

Motivation Turns are a critical element of the structure of a protein; turns play a crucial role in loops, folds, and interactions. Current prediction methods are well developed for the prediction of individual turn types, including α-turn, β-turn, and γ-turn, etc. However, for further protein structure and function prediction it is necessary to develop a uniform model that can accurately predict all types of turns simultaneously. Results In this study, we present a novel approach, TurnP, which offers the ability to investigate all the turns in a protein based on a unified model. The main characteristics of TurnP are: (i) using newly exploited features of structural evolution information (secondary structure and shape string of protein) based on structure homologies, (ii) considering all types of turns in a unified model, and (iii) practical capability of accurate prediction of all turns simultaneously for a query. TurnP utilizes predicted secondary structures and predicted shape strings, both of which have greater accuracy, based on innovative technologies which were both developed by our group. Then, sequence and structural evolution features, which are profile of sequence, profile of secondary structures and profile of shape strings are generated by sequence and structure alignment. When TurnP was validated on a non-redundant dataset (4,107 entries) by five-fold cross-validation, we achieved an accuracy of 88.8% and a sensitivity of 71.8%, which exceeded the most state-of-the-art predictors of certain type of turn. Newly determined sequences, the EVA and CASP9 datasets were used as independent tests and the results we achieved were outstanding for turn predictions and confirmed the good performance of TurnP for practical applications. PMID:23144872

Big-data-based edge biomarkers: study on dynamical drug sensitivity and resistance in individuals.

PubMed

Zeng, Tao; Zhang, Wanwei; Yu, Xiangtian; Liu, Xiaoping; Li, Meiyi; Chen, Luonan

2016-07-01

Big-data-based edge biomarker is a new concept to characterize disease features based on biomedical big data in a dynamical and network manner, which also provides alternative strategies to indicate disease status in single samples. This article gives a comprehensive review on big-data-based edge biomarkers for complex diseases in an individual patient, which are defined as biomarkers based on network information and high-dimensional data. Specifically, we firstly introduce the sources and structures of biomedical big data accessible in public for edge biomarker and disease study. We show that biomedical big data are typically 'small-sample size in high-dimension space', i.e. small samples but with high dimensions on features (e.g. omics data) for each individual, in contrast to traditional big data in many other fields characterized as 'large-sample size in low-dimension space', i.e. big samples but with low dimensions on features. Then, we demonstrate the concept, model and algorithm for edge biomarkers and further big-data-based edge biomarkers. Dissimilar to conventional biomarkers, edge biomarkers, e.g. module biomarkers in module network rewiring-analysis, are able to predict the disease state by learning differential associations between molecules rather than differential expressions of molecules during disease progression or treatment in individual patients. In particular, in contrast to using the information of the common molecules or edges (i.e.molecule-pairs) across a population in traditional biomarkers including network and edge biomarkers, big-data-based edge biomarkers are specific for each individual and thus can accurately evaluate the disease state by considering the individual heterogeneity. Therefore, the measurement of big data in a high-dimensional space is required not only in the learning process but also in the diagnosing or predicting process of the tested individual. Finally, we provide a case study on analyzing the temporal expression data from a malaria vaccine trial by big-data-based edge biomarkers from module network rewiring-analysis. The illustrative results show that the identified module biomarkers can accurately distinguish vaccines with or without protection and outperformed previous reported gene signatures in terms of effectiveness and efficiency. © The Author 2015. Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

What determines direction of asymmetry: genes, environment or chance?

PubMed Central

2016-01-01

Conspicuous asymmetries seen in many animals and plants offer diverse opportunities to test how the development of a similar morphological feature has evolved in wildly different types of organisms. One key question is: do common rules govern how direction of asymmetry is determined (symmetry is broken) during ontogeny to yield an asymmetrical individual? Examples from numerous organisms illustrate how diverse this process is. These examples also provide some surprising answers to related questions. Is direction of asymmetry in an individual determined by genes, environment or chance? Is direction of asymmetry determined locally (structure by structure) or globally (at the level of the whole body)? Does direction of asymmetry persist when an asymmetrical structure regenerates following autotomy? The answers vary greatly for asymmetries as diverse as gastropod coiling direction, flatfish eye side, crossbill finch bill crossing, asymmetrical claws in shrimp, lobsters and crabs, katydid sound-producing structures, earwig penises and various plant asymmetries. Several examples also reveal how stochastic asymmetry in mollusc and crustacean early cleavage, in Drosophila oogenesis, and in Caenorhabditis elegans epidermal blast cell movement, is a normal component of deterministic development. Collectively, these examples shed light on the role of genes as leaders or followers in evolution. This article is part of the themed issue ‘Provocative questions in left–right asymmetry’. PMID:27821528

Structural Correlates of Reading the Mind in the Eyes in Autism Spectrum Disorder.

PubMed

Sato, Wataru; Uono, Shota; Kochiyama, Takanori; Yoshimura, Sayaka; Sawada, Reiko; Kubota, Yasutaka; Sakihama, Morimitsu; Toichi, Motomi

2017-01-01

Behavioral studies have shown that individuals with autism spectrum disorder (ASD) have impaired ability to read the mind in the eyes. Although this impairment is central to their social malfunctioning, its structural neural correlates remain unclear. To investigate this issue, we assessed Reading the Mind in the Eyes Test, revised version (Eyes Test) and acquired structural magnetic resonance images in adults with high-functioning ASD ( n = 19) and age-, sex- and intelligence quotient-matched typically developing (TD) controls ( n = 19). On the behavioral level, the Eyes Test scores were lower in the ASD group than in the control group. On the neural level, an interaction between group and Eyes Test score was found in the left temporoparietal junction (TPJ). A positive association between the Eyes Test score and gray matter volume of this region was evident in the control group, but not in the ASD group. This finding suggests that the failure to develop appropriate structural neural representations in the TPJ may underlie the impaired ability of individuals with ASD to read the mind in the eyes. These behavioral and neural findings provide support for the theories that impairments in processing eyes and the ability to infer others' mental states are the core symptoms of ASD, and that atypical features in the social brain network underlie such impairments.

GeoSciML version 3: A GML application for geologic information

NASA Astrophysics Data System (ADS)

International Union of Geological Sciences., I. C.; Richard, S. M.

2011-12-01

After 2 years of testing and development, XML schema for GeoSciML version 3 are now ready for application deployment. GeoSciML draws from many geoscience data modelling efforts to establish a common suite of feature types to represent information associated with geologic maps (materials, structures, and geologic units) and observations including structure data, samples, and chemical analyses. After extensive testing and use case analysis, in December 2008 the CGI Interoperability Working Group (IWG) released GeoSciML 2.0 as an application schema for basic geological information. GeoSciML 2.0 is in use to deliver geologic data by the OneGeology Europe portal, the Geological Survey of Canada Groundwater Information Network (wet GIN), and the Auscope Mineral Resources portal. GeoSciML to version 3.0 is updated to OGC Geography Markup Language v3.2, re-engineered patterns for association of element values with controlled vocabulary concepts, incorporation of ISO19156 Observation and Measurement constructs for representing numeric and categorical values and for representing analytical data, incorporation of EarthResourceML to represent mineral occurrences and mines, incorporation of the GeoTime model to represent GSSP and stratigraphic time scale, and refactoring of the GeoSciML namespace to follow emerging ISO practices for decoupling of dependencies between standardized namespaces. These changes will make it easier for data providers to link to standard vocabulary and registry services. The depth and breadth of GeoSciML remains largely unchanged, covering the representation of geologic units, earth materials and geologic structures. ISO19156 elements and patterns are used to represent sampling features such as boreholes and rock samples, as well as geochemical and geochronologic measurements. Geologic structures include shear displacement structures (brittle faults and ductile shears), contacts, folds, foliations, lineations and structures with no preferred orientation (e.g. 'miarolitic cavities'). The Earth material package allows for the description of both individual components, such as minerals, and compound materials, such as rocks or unconsolidated materials. Provision is made for alteration, weathering, metamorphism, particle geometry, fabric, and petrophysical descriptions. Mapped features describe the shape of the geological features using standard GML geometries, such as polygons, lines, points or 3D volumes. Geological events provide the age, process and environment of formation of geological features. The Earth Resource section includes features to represent mineral occurrences and mines and associated human activities independently. This addition allows description of resources and reserves that can comply with national and internationally accepted reporting codes. GeoSciML v3 is under consideration as the data model for INSPIRE annex 2 geologic reporting in Europe.

Mitosis detection using generic features and an ensemble of cascade adaboosts.

PubMed

Tek, F Boray

2013-01-01

Mitosis count is one of the factors that pathologists use to assess the risk of metastasis and survival of the patients, which are affected by the breast cancer. We investigate an application of a set of generic features and an ensemble of cascade adaboosts to the automated mitosis detection. Calculation of the features rely minimally on object-level descriptions and thus require minimal segmentation. The proposed work was developed and tested on International Conference on Pattern Recognition (ICPR) 2012 mitosis detection contest data. We plotted receiver operating characteristics curves of true positive versus false positive rates; calculated recall, precision, F-measure, and region overlap ratio measures. WE TESTED OUR FEATURES WITH TWO DIFFERENT CLASSIFIER CONFIGURATIONS: 1) An ensemble of single adaboosts, 2) an ensemble of cascade adaboosts. On the ICPR 2012 mitosis detection contest evaluation, the cascade ensemble scored 54, 62.7, and 58, whereas the non-cascade version scored 68, 28.1, and 39.7 for the recall, precision, and F-measure measures, respectively. Mostly used features in the adaboost classifier rules were a shape-based feature, which counted granularity and a color-based feature, which relied on Red, Green, and Blue channel statistics. The features, which express the granular structure and color variations, are found useful for mitosis detection. The ensemble of adaboosts performs better than the individual adaboost classifiers. Moreover, the ensemble of cascaded adaboosts was better than the ensemble of single adaboosts for mitosis detection.

Cortical hot spots and labyrinths: why cortical neuromodulation for episodic migraine with aura should be personalized

PubMed Central

Dahlem, Markus A.; Schmidt, Bernd; Bojak, Ingo; Boie, Sebastian; Kneer, Frederike; Hadjikhani, Nouchine; Kurths, Jürgen

2015-01-01

Stimulation protocols for medical devices should be rationally designed. For episodic migraine with aura we outline model-based design strategies toward preventive and acute therapies using stereotactic cortical neuromodulation. To this end, we regard a localized spreading depression (SD) wave segment as a central element in migraine pathophysiology. To describe nucleation and propagation features of the SD wave segment, we define the new concepts of cortical hot spots and labyrinths, respectively. In particular, we firstly focus exclusively on curvature-induced dynamical properties by studying a generic reaction-diffusion model of SD on the folded cortical surface. This surface is described with increasing level of details, including finally personalized simulations using patient's magnetic resonance imaging (MRI) scanner readings. At this stage, the only relevant factor that can modulate nucleation and propagation paths is the Gaussian curvature, which has the advantage of being rather readily accessible by MRI. We conclude with discussing further anatomical factors, such as areal, laminar, and cellular heterogeneity, that in addition to and in relation to Gaussian curvature determine the generalized concept of cortical hot spots and labyrinths as target structures for neuromodulation. Our numerical simulations suggest that these target structures are like fingerprints, they are individual features of each migraine sufferer. The goal in the future will be to provide individualized neural tissue simulations. These simulations should predict the clinical data and therefore can also serve as a test bed for exploring stereotactic cortical neuromodulation. PMID:25798103

The gravity of pollination: integrating at-site features into spatial analysis of contemporary pollen movement.

PubMed

DiLeo, Michelle F; Siu, Jenna C; Rhodes, Matthew K; López-Villalobos, Adriana; Redwine, Angela; Ksiazek, Kelly; Dyer, Rodney J

2014-08-01

Pollen-mediated gene flow is a major driver of spatial genetic structure in plant populations. Both individual plant characteristics and site-specific features of the landscape can modify the perceived attractiveness of plants to their pollinators and thus play an important role in shaping spatial genetic variation. Most studies of landscape-level genetic connectivity in plants have focused on the effects of interindividual distance using spatial and increasingly ecological separation, yet have not incorporated individual plant characteristics or other at-site ecological variables. Using spatially explicit simulations, we first tested the extent to which the inclusion of at-site variables influencing local pollination success improved the statistical characterization of genetic connectivity based upon examination of pollen pool genetic structure. The addition of at-site characteristics provided better models than those that only considered interindividual spatial distance (e.g. IBD). Models parameterized using conditional genetic covariance (e.g. population graphs) also outperformed those assuming panmixia. In a natural population of Cornus florida L. (Cornaceae), we showed that the addition of at-site characteristics (clumping of primary canopy opening above each maternal tree and maternal tree floral output) provided significantly better models describing gene flow than models including only between-site spatial (IBD) and ecological (isolation by resistance) variables. Overall, our results show that including interindividual and local ecological variation greatly aids in characterizing landscape-level measures of contemporary gene flow. © 2014 John Wiley & Sons Ltd.

Variable Use of Features Associated with African American English by Typically Developing Children

ERIC Educational Resources Information Center

Jackson, Janice E.; Pearson, Barbara Zurer

2010-01-01

Purpose: The well-known decline in the use of African American English (AAE) features by groups of school-aged AAE-speaking children was reexamined for patterns of overt-, zero-, and mixed-marking for individual features and individual speakers. Methods: Seven hundred twenty-nine typically developing children between the ages of 4 and 12--511…

Cross Flow Parameter Calculation for Aerodynamic Analysis

NASA Technical Reports Server (NTRS)

Norman, David, Jr. (Inventor)

2014-01-01

A system and method for determining a cross flow angle for a feature on a structure. A processor unit receives location information identifying a location of the feature on the structure, determines an angle of the feature, identifies flow information for the location, determines a flow angle using the flow information, and determines the cross flow angle for the feature using the flow angle and the angle of the feature. The flow information describes a flow of fluid across the structure. The flow angle comprises an angle of the flow of fluid across the structure for the location of the feature.

Novel Insights into DNA Methylation Features in Spermatozoa: Stability and Peculiarities

PubMed Central

Sayols, Sergi; Chianese, Chiara; Giachini, Claudia; Heyn, Holger; Esteller, Manel

2012-01-01

Data about the entire sperm DNA methylome are limited to two sperm donors whereas studies dealing with a greater number of subjects focused only on a few genes or were based on low resolution arrays. This implies that information about what we can consider as a normal sperm DNA methylome and whether it is stable among different normozoospermic individuals is still missing. The definition of the DNA methylation profile of normozoospermic men, the entity of inter-individual variability and the epigenetic characterization of quality-fractioned sperm subpopulations in the same subject (intra-individual variability) are relevant for a better understanding of pathological conditions. We addressed these questions by using the high resolution Infinium 450K methylation array and compared normal sperm DNA methylomes against somatic and cancer cells. Our study, based on the largest number of subjects (n = 8) ever considered for such a large number of CpGs (n = 487,517), provided clear evidence for i) a highly conserved DNA methylation profile among normozoospermic subjects; ii) a stable sperm DNA methylation pattern in different quality-fractioned sperm populations of the same individual. The latter finding is particularly relevant if we consider that different quality fractioned sperm subpopulations show differences in their structural features, metabolic and genomic profiles. We demonstrate, for the first time, that DNA methylation in normozoospermic men remains highly uniform regardless the quality of sperm subpopulations. In addition, our analysis provided both confirmatory and novel data concerning the sperm DNA methylome, including its peculiar features in respect to somatic and cancer cells. Our description about a highly polarized sperm DNA methylation profile, the clearly distinct genomic and functional organization of hypo- versus hypermethylated loci as well as the association of histone-enriched hypomethylated loci with embryonic development, which we now extended also to hypomethylated piRNAs-linked genes, provides solid basis for future basic and clinical research. PMID:23071498

A functional-structural kiwifruit vine model integrating architecture, carbon dynamics and effects of the environment.

PubMed

Cieslak, Mikolaj; Seleznyova, Alla N; Hanan, Jim

2011-04-01

Functional-structural modelling can be used to increase our understanding of how different aspects of plant structure and function interact, identify knowledge gaps and guide priorities for future experimentation. By integrating existing knowledge of the different aspects of the kiwifruit (Actinidia deliciosa) vine's architecture and physiology, our aim is to develop conceptual and mathematical hypotheses on several of the vine's features: (a) plasticity of the vine's architecture; (b) effects of organ position within the canopy on its size; (c) effects of environment and horticultural management on shoot growth, light distribution and organ size; and (d) role of carbon reserves in early shoot growth. Using the L-system modelling platform, a functional-structural plant model of a kiwifruit vine was created that integrates architectural development, mechanistic modelling of carbon transport and allocation, and environmental and management effects on vine and fruit growth. The branching pattern was captured at the individual shoot level by modelling axillary shoot development using a discrete-time Markov chain. An existing carbon transport resistance model was extended to account for several source/sink components of individual plant elements. A quasi-Monte Carlo path-tracing algorithm was used to estimate the absorbed irradiance of each leaf. Several simulations were performed to illustrate the model's potential to reproduce the major features of the vine's behaviour. The model simulated vine growth responses that were qualitatively similar to those observed in experiments, including the plastic response of shoot growth to local carbon supply, the branching patterns of two Actinidia species, the effect of carbon limitation and topological distance on fruit size and the complex behaviour of sink competition for carbon. The model is able to reproduce differences in vine and fruit growth arising from various experimental treatments. This implies it will be a valuable tool for refining our understanding of kiwifruit growth and for identifying strategies to improve production.

Bright-field electron tomography of individual inorganic fullerene-like structures.

PubMed

Bar Sadan, Maya; Wolf, Sharon G; Houben, Lothar

2010-03-01

Nanotubes and fullerene-like nanoparticles of various inorganic layered compounds have been studied extensively in recent years. Their characterisation on the atomic scale has proven essential for progress in synthesis as well as for the theoretical modelling of their physical properties. We show that with electron tomography it is possible to achieve a reliable reconstruction of the 3D structure of nested WS(2) or MoS(2) fullerene-like and nanotube structures with sub-nanometre resolution using electron microscopes that are not aberration-corrected. Model-based simulations were used to identify imaging parameters, under which structural features such as the shell structure can be retained in the tomogram reconstructed from bright-field micrographs. The isolation of a particle out of an agglomerate for the analysis of a single structure and its interconnection with other particles is facilitated through the tomograms. The internal structure of the layers within the particle alongside the shape and content of its internal void are reconstructed. The tomographic reconstruction yields insights regarding the growth process as well as structural defects, such as non-continuous layers, which relate to the lubrication properties.

Genetic variation in personality traits explains genetic overlap between borderline personality features and substance use disorders

PubMed Central

Few, Lauren R.; Grant, Julia D; Trull, Timothy J.; Statham, Dixie J.; Martin, Nicholas G.; Lynskey, Michael T.; Agrawal, Arpana

2014-01-01

Aims To examine the genetic overlap between borderline personality features (BPF) and substance use disorders (SUDs) and the extent to which variation in personality traits contributes to this covariance. Design Genetic structural equation modelling was used to partition the variance in and covariance between personality traits, BPF, and SUDs into additive genetic, shared, and individual-specific environmental factors. Setting All participants were registered with the Australian Twin Registry. Participants A total of 3,127 Australian adult twins participated in the study. Measurements Diagnoses of DSM-IV alcohol and cannabis abuse/dependence (AAD; CAD), and nicotine dependence (ND) were derived via computer-assisted telephone interview. BPF and five-factor model personality traits were derived via self-report questionnaires. Findings Genetic factors were responsible for 49% (95%CI: 42%–55%) of the variance in BPF, 38–42% (95%CI range: 32%–49%) for personality traits and 47% (95%CI: 17%–77%), 54% (95%CI: 43%–64%), and 78% (67%–86%) for ND, AAD and CAD, respectively. Genetic and individual-specific environmental correlations between BPF and SUDs ranged from .33–.56 (95%CI range: .19–.74) and .19–.32 (95%CI range: .06–.43), respectively. Overall, there was substantial support for genetic influences that were specific to AAD, ND and CAD (31%–69%). Finally, genetic variation in personality traits was responsible for 11% (Extraversion for CAD) to 59% (Neuroticism for AAD) of the correlation between BPF and SUDs. Conclusions Both genetic and individual-specific environmental factors contribute to comorbidity between borderline personality features and substance use disorders. A substantial proportion of this comorbidity can be attributed to variation in normal personality traits, particularly Neuroticism. PMID:25041562

Genetic variation in personality traits explains genetic overlap between borderline personality features and substance use disorders.

PubMed

Few, Lauren R; Grant, Julia D; Trull, Timothy J; Statham, Dixie J; Martin, Nicholas G; Lynskey, Michael T; Agrawal, Arpana

2014-12-01

To examine the genetic overlap between borderline personality features (BPF) and substance use disorders (SUDs) and the extent to which variation in personality traits contributes to this covariance. Genetic structural equation modelling was used to partition the variance in and covariance between personality traits, BPF and SUDs into additive genetic, shared and individual-specific environmental factors. All participants were registered with the Australian Twin Registry. A total of 3127 Australian adult twins participated in the study. Diagnoses of DSM-IV alcohol and cannabis abuse/dependence (AAD; CAD) and nicotine dependence (ND) were derived via computer-assisted telephone interview. BPF and five-factor model personality traits were derived via self-report questionnaires. Personality traits, BPF and substance use disorders were partially influenced by genetic factors with heritability estimates ranging from 0.38 (neuroticism; 95% confidence interval: 0.30-0.45) to 0.78 (CAD; 95% confidence interval: 0.67-0.86). Genetic and individual-specific environmental correlations between BPF and SUDs ranged from 0.33 to 0.56 (95% CI = 0.19-0.74) and 0.19-0.32 (95% CI = 0.06-0.43), respectively. Overall, there was substantial support for genetic influences that were specific to AAD, ND and CAD (30.76-68.60%). Finally, genetic variation in personality traits was responsible for 11.46% (extraversion for CAD) to 59.30% (neuroticism for AAD) of the correlation between BPF and SUDs. Both genetic and individual-specific environmental factors contribute to comorbidity between borderline personality features and substance use disorders. A substantial proportion of this comorbidity can be attributed to variation in normal personality traits, particularly neuroticism. © 2014 Society for the Study of Addiction.

Bayesian models for cost-effectiveness analysis in the presence of structural zero costs

PubMed Central

Baio, Gianluca

2014-01-01

Bayesian modelling for cost-effectiveness data has received much attention in both the health economics and the statistical literature, in recent years. Cost-effectiveness data are characterised by a relatively complex structure of relationships linking a suitable measure of clinical benefit (e.g. quality-adjusted life years) and the associated costs. Simplifying assumptions, such as (bivariate) normality of the underlying distributions, are usually not granted, particularly for the cost variable, which is characterised by markedly skewed distributions. In addition, individual-level data sets are often characterised by the presence of structural zeros in the cost variable. Hurdle models can be used to account for the presence of excess zeros in a distribution and have been applied in the context of cost data. We extend their application to cost-effectiveness data, defining a full Bayesian specification, which consists of a model for the individual probability of null costs, a marginal model for the costs and a conditional model for the measure of effectiveness (given the observed costs). We presented the model using a working example to describe its main features. © 2013 The Authors. Statistics in Medicine published by John Wiley & Sons, Ltd. PMID:24343868

Bayesian models for cost-effectiveness analysis in the presence of structural zero costs.

PubMed

Baio, Gianluca

2014-05-20

Bayesian modelling for cost-effectiveness data has received much attention in both the health economics and the statistical literature, in recent years. Cost-effectiveness data are characterised by a relatively complex structure of relationships linking a suitable measure of clinical benefit (e.g. quality-adjusted life years) and the associated costs. Simplifying assumptions, such as (bivariate) normality of the underlying distributions, are usually not granted, particularly for the cost variable, which is characterised by markedly skewed distributions. In addition, individual-level data sets are often characterised by the presence of structural zeros in the cost variable. Hurdle models can be used to account for the presence of excess zeros in a distribution and have been applied in the context of cost data. We extend their application to cost-effectiveness data, defining a full Bayesian specification, which consists of a model for the individual probability of null costs, a marginal model for the costs and a conditional model for the measure of effectiveness (given the observed costs). We presented the model using a working example to describe its main features. © 2013 The Authors. Statistics in Medicine published by John Wiley & Sons, Ltd.

Absence of auditory 'global interference' in autism.

PubMed

Foxton, Jessica M; Stewart, Mary E; Barnard, Louise; Rodgers, Jacqui; Young, Allan H; O'Brien, Gregory; Griffiths, Timothy D

2003-12-01

There has been considerable recent interest in the cognitive style of individuals with Autism Spectrum Disorder (ASD). One theory, that of weak central coherence, concerns an inability to combine stimulus details into a coherent whole. Here we test this theory in the case of sound patterns, using a new definition of the details (local structure) and the coherent whole (global structure). Thirteen individuals with a diagnosis of autism or Asperger's syndrome and 15 control participants were administered auditory tests, where they were required to match local pitch direction changes between two auditory sequences. When the other local features of the sequence pairs were altered (the actual pitches and relative time points of pitch direction change), the control participants obtained lower scores compared with when these details were left unchanged. This can be attributed to interference from the global structure, defined as the combination of the local auditory details. In contrast, the participants with ASD did not obtain lower scores in the presence of such mismatches. This was attributed to the absence of interference from an auditory coherent whole. The results are consistent with the presence of abnormal interactions between local and global auditory perception in ASD.

Length Variation in Mitochondrial DNA of the Minnow Cyprinella Spiloptera

PubMed Central

Broughton, R. E.; Dowling, T. E.

1994-01-01

Length differences in animal mitochondrial DNA (mtDNA) are common, frequently due to variation in copy number of direct tandem duplications. While such duplications appear to form without great difficulty in some taxonomic groups, they appear to be relatively short-lived, as typical duplication products are geographically restricted within species and infrequently shared among species. To better understand such length variation, we have studied a tandem and direct duplication of approximately 260 bp in the control region of the cyprinid fish, Cyprinella spiloptera. Restriction site analysis of 38 individuals was used to characterize population structure and the distribution of variation in repeat copy number. This revealed two length variants, including individuals with two or three copies of the repeat, and little geographic structure among populations. No standard length (single copy) genomes were found and heteroplasmy, a common feature of length variation in other taxa, was absent. Nucleotide sequence of tandem duplications and flanking regions localized duplication junctions in the phenylalanine tRNA and near the origin of replication. The locations of these junctions and the stability of folded repeat copies support the hypothesized importance of secondary structures in models of duplication formation. PMID:8001785

Cortical functional connectivity decodes subconscious, task-irrelevant threat-related emotion processing

PubMed Central

Pantazatos, Spiro P.; Talati, Ardesheer; Pavlidis, Paul; Hirsch, Joy

2012-01-01

It is currently unclear to what extent cortical structures are required for and engaged during subconscious processing of biologically salient affective stimuli (i.e. the ‘low-road’ vs. ‘many-roads’ hypotheses). Here we show that cortical-cortical and cortical-subcortical functional connectivity (FC) contain substantially more information, relative to subcortical-subcortical FC (i.e. ‘subcortical alarm’ and other limbic regions), that predicts subliminal fearful face processing within individuals using training data from separate subjects. A plot of classification accuracy vs. number of selected whole-brain FC features revealed 92% accuracy when learning was based on the top 8 features from each training set. The most informative FC was between right amygdala and precuneus, which increased during subliminal fear conditions, while left and right amygdala FC decreased, suggesting a bilateral decoupling of this key limbic region during processing of subliminal fear-related stimuli. Other informative FC included angular gyrus, middle temporal gyrus and cerebellum. These findings identify FC that decodes subliminally perceived, task-irrelevant affective stimuli, and suggest that cortical structures are actively engaged by and appear to be essential for subliminal fear processing. PMID:22484206

Cortical functional connectivity decodes subconscious, task-irrelevant threat-related emotion processing.

PubMed

Pantazatos, Spiro P; Talati, Ardesheer; Pavlidis, Paul; Hirsch, Joy

2012-07-16

It is currently unclear to what extent cortical structures are required for and engaged during subconscious processing of biologically salient affective stimuli (i.e. the 'low-road' vs. 'many-roads' hypotheses). Here we show that cortical-cortical and cortical-subcortical functional connectivity (FC) contain substantially more information, relative to subcortical-subcortical FC (i.e. 'subcortical alarm' and other limbic regions), that predicts subliminal fearful face processing within individuals using training data from separate subjects. A plot of classification accuracy vs. number of selected whole-brain FC features revealed 92% accuracy when learning was based on the top 8 features from each training set. The most informative FC was between right amygdala and precuneus, which increased during subliminal fear conditions, while left and right amygdala FC decreased, suggesting a bilateral decoupling of this key limbic region during processing of subliminal fear-related stimuli. Other informative FC included angular gyrus, middle temporal gyrus and cerebellum. These findings identify FC that decodes subliminally perceived, task-irrelevant affective stimuli, and suggest that cortical structures are actively engaged by and appear to be essential for subliminal fear processing. Published by Elsevier Inc.

Foot Structure in Boys with Down Syndrome

PubMed Central

Nowak, Krzysztof; Omorczyk, Jarosław; Ambroży, Tadeusz; Nosiadek, Leszek

2017-01-01

Introduction and Aim Down syndrome (DS) is associated with numerous developmental abnormalities, some of which cause dysfunctions of the posture and the locomotor system. The analysis of selected features of the foot structure in boys with DS versus their peers without developmental disorders is done. Materials and Methods The podoscopic examination was performed on 30 boys with DS aged 14-15 years. A control group consisted of 30 age- and gender-matched peers without DS. Results The feet of boys with DS are flatter compared to their healthy peers. The hallux valgus angle is not the most important feature differentiating the shape of the foot in the boys with DS and their healthy peers. In terms of the V toe setting, healthy boys had poorer results. Conclusions Specialized therapeutic treatment in individuals with DS should involve exercises to increase the muscle strength around the foot joints, enhancing the stabilization in the joints and proprioception. Introducing orthotics and proper footwear is also important. It is also necessary to monitor the state of the foot in order to modify undertaken therapies. PMID:28904967

Learning about the internal structure of categories through classification and feature inference.

PubMed

Jee, Benjamin D; Wiley, Jennifer

2014-01-01

Previous research on category learning has found that classification tasks produce representations that are skewed toward diagnostic feature dimensions, whereas feature inference tasks lead to richer representations of within-category structure. Yet, prior studies often measure category knowledge through tasks that involve identifying only the typical features of a category. This neglects an important aspect of a category's internal structure: how typical and atypical features are distributed within a category. The present experiments tested the hypothesis that inference learning results in richer knowledge of internal category structure than classification learning. We introduced several new measures to probe learners' representations of within-category structure. Experiment 1 found that participants in the inference condition learned and used a wider range of feature dimensions than classification learners. Classification learners, however, were more sensitive to the presence of atypical features within categories. Experiment 2 provided converging evidence that classification learners were more likely to incorporate atypical features into their representations. Inference learners were less likely to encode atypical category features, even in a "partial inference" condition that focused learners' attention on the feature dimensions relevant to classification. Overall, these results are contrary to the hypothesis that inference learning produces superior knowledge of within-category structure. Although inference learning promoted representations that included a broad range of category-typical features, classification learning promoted greater sensitivity to the distribution of typical and atypical features within categories.

Structural Behavioral Study on the General Aviation Network Based on Complex Network

NASA Astrophysics Data System (ADS)

Zhang, Liang; Lu, Na

2017-12-01

The general aviation system is an open and dissipative system with complex structures and behavioral features. This paper has established the system model and network model for general aviation. We have analyzed integral attributes and individual attributes by applying the complex network theory and concluded that the general aviation network has influential enterprise factors and node relations. We have checked whether the network has small world effect, scale-free property and network centrality property which a complex network should have by applying degree distribution of functions and proved that the general aviation network system is a complex network. Therefore, we propose to achieve the evolution process of the general aviation industrial chain to collaborative innovation cluster of advanced-form industries by strengthening network multiplication effect, stimulating innovation performance and spanning the structural hole path.

Magnetization transfer and adiabatic R 1ρ MRI in the brainstem of Parkinson's disease.

PubMed

Tuite, Paul J; Mangia, Silvia; Tyan, Andrew E; Lee, Michael K; Garwood, Michael; Michaeli, Shalom

2012-06-01

In addition to classic midbrain pathology, Parkinson's disease (PD) is accompanied by changes in pontine and medullary brainstem structures. These additional abnormalities may underlie non-motor features as well as play a role in motor disability. Using novel magnetic resonance imaging (MRI) methods based on rotating frame adiabatic R(1ρ) (i.e., measurements of longitudinal relaxation during adiabatic full passage pulses) and modified magnetization transfer (MT) MRI mapping, we sought to identify brainstem alterations in nine individuals with mild-moderate PD (off medication) and ten age-matched controls at 4 T. We discovered significant differences in MRI parameters between midbrain and medullary brainstem structures in control subjects as compared to PD patients. These findings support the presence of underlying functional/structural brainstem changes in mild-moderate PD. Copyright © 2012 Elsevier Ltd. All rights reserved.

Structure-Specific Statistical Mapping of White Matter Tracts

PubMed Central

Yushkevich, Paul A.; Zhang, Hui; Simon, Tony; Gee, James C.

2008-01-01

We present a new model-based framework for the statistical analysis of diffusion imaging data associated with specific white matter tracts. The framework takes advantage of the fact that several of the major white matter tracts are thin sheet-like structures that can be effectively modeled by medial representations. The approach involves segmenting major tracts and fitting them with deformable geometric medial models. The medial representation makes it possible to average and combine tensor-based features along directions locally perpendicular to the tracts, thus reducing data dimensionality and accounting for errors in normalization. The framework enables the analysis of individual white matter structures, and provides a range of possibilities for computing statistics and visualizing differences between cohorts. The framework is demonstrated in a study of white matter differences in pediatric chromosome 22q11.2 deletion syndrome. PMID:18407524

Structural and biophysical characterization of an antimicrobial peptide chimera comprised of lactoferricin and lactoferrampin.

PubMed

Haney, Evan F; Nazmi, Kamran; Bolscher, Jan G M; Vogel, Hans J

2012-03-01

Lactoferricin and lactoferrampin are two antimicrobial peptides found in the N-terminal lobe of bovine lactoferrin with broad spectrum antimicrobial activity against a range of Gram-positive and Gram-negative bacteria as well as Candida albicans. A heterodimer comprised of lactoferrampin joined to a fragment of lactoferricin was recently reported in which these two peptides were joined at their C-termini through the two amino groups of a single Lys residue (Bolscher et al., 2009, Biochimie 91(1):123-132). This hybrid peptide, termed LFchimera, has significantly higher antimicrobial activity compared to the individual peptides or an equimolar mixture of the two. In this work, the underlying mechanism behind the increased antibacterial activity of LFchimera was investigated. Differential scanning calorimetry studies demonstrated that all the peptides influenced the thermotropic phase behaviour of anionic phospholipid suspensions. Calcein leakage and vesicle fusion experiments with anionic liposomes revealed that LFchimera had enhanced membrane perturbing properties compared to the individual peptides. Peptide structures were evaluated using circular dichroism and NMR spectroscopy to gain insight into the structural features of LFchimera that contribute to the increased antimicrobial activity. The NMR solution structure, determined in a miscible co-solvent mixture of chloroform, methanol and water, revealed that the Lys linkage increased the helical content in LFchimera compared to the individual peptides, but it did not fix the relative orientations of lactoferricin and lactoferrampin with respect to each other. The structure of LFchimera provides insight into the conformation of this peptide in a membranous environment and improves our understanding of its antimicrobial mechanism of action. Copyright © 2011 Elsevier B.V. All rights reserved.

A pilot mixed-methods evaluation of MS INFoRm: a self-directed fatigue management resource for individuals with multiple sclerosis.

PubMed

Akbar, Nadine; Turpin, Karen; Petrin, Julie; Smyth, Penny; Finlayson, Marcia

2018-06-01

Fatigue management interventions for individuals with multiple sclerosis (MS) often feature structured programmes requiring repeated, in-person attendance that is not possible for all individuals. We sought to determine whether MS INFoRm, a self-directed fatigue management resource for individuals with MS, was worth further, more rigorous evaluation. Our indicators of worthiness were actual use of the resource by participants over 3 months, reductions in fatigue impact and increases in self-efficacy, and participant reports of changes in fatigue management knowledge and behaviours. This was a single-group, mixed-methods, before-after pilot study in individuals with MS reporting mild to moderate fatigue. Thirty-five participants were provided with MS INFoRm by a USB flash drive to use at home for 3 months, on their own volition. Twenty-three participants completed all standardized questionnaires, semi-structured interviews and study process measures. Participants reported actively using MS INFoRm over the 3-month study period (median total time spent using MS INFoRm=315 min) as well as significantly lower overall fatigue impact (Modified Fatigue Impact Scale: t=2.6, P=0.01), increased knowledge of MS fatigue (z=-2.8, P=0.01) and greater confidence in managing MS fatigue (z=-3.3, P=0.001). Individuals with significant reductions in fatigue impact also reported behavioural changes including tracking fatigue, better communication with others, greater awareness, improved quality of life and being more proactive. This study provides evidence that further rigorous evaluation of MS INFoRm, a self-directed resource for managing fatigue, is worth pursuing.

Structural and functional correlates for language efficiency in auditory word processing.

PubMed

Jung, JeYoung; Kim, Sunmi; Cho, Hyesuk; Nam, Kichun

2017-01-01

This study aims to provide convergent understanding of the neural basis of auditory word processing efficiency using a multimodal imaging. We investigated the structural and functional correlates of word processing efficiency in healthy individuals. We acquired two structural imaging (T1-weighted imaging and diffusion tensor imaging) and functional magnetic resonance imaging (fMRI) during auditory word processing (phonological and semantic tasks). Our results showed that better phonological performance was predicted by the greater thalamus activity. In contrary, better semantic performance was associated with the less activation in the left posterior middle temporal gyrus (pMTG), supporting the neural efficiency hypothesis that better task performance requires less brain activation. Furthermore, our network analysis revealed the semantic network including the left anterior temporal lobe (ATL), dorsolateral prefrontal cortex (DLPFC) and pMTG was correlated with the semantic efficiency. Especially, this network acted as a neural efficient manner during auditory word processing. Structurally, DLPFC and cingulum contributed to the word processing efficiency. Also, the parietal cortex showed a significate association with the word processing efficiency. Our results demonstrated that two features of word processing efficiency, phonology and semantics, can be supported in different brain regions and, importantly, the way serving it in each region was different according to the feature of word processing. Our findings suggest that word processing efficiency can be achieved by in collaboration of multiple brain regions involved in language and general cognitive function structurally and functionally.

Structure and function of APH(4)-Ia, a hygromycin B resistance enzyme.

PubMed

Stogios, Peter J; Shakya, Tushar; Evdokimova, Elena; Savchenko, Alexei; Wright, Gerard D

2011-01-21

The aminoglycoside phosphotransferase (APH) APH(4)-Ia is one of two enzymes responsible for bacterial resistance to the atypical aminoglycoside antibiotic hygromycin B (hygB). The crystal structure of APH(4)-Ia enzyme was solved in complex with hygB at 1.95 Å resolution. The APH(4)-Ia structure adapts a general two-lobe architecture shared by other APH enzymes and eukaryotic kinases, with the active site located at the interdomain cavity. The enzyme forms an extended hydrogen bond network with hygB primarily through polar and acidic side chain groups. Individual alanine substitutions of seven residues involved in hygB binding did not have significant effect on APH(4)-Ia enzymatic activity, indicating that the binding affinity is spread across a distributed network. hygB appeared as the only substrate recognized by APH(4)-Ia among the panel of 14 aminoglycoside compounds. Analysis of the active site architecture and the interaction with the hygB molecule demonstrated several unique features supporting such restricted substrate specificity. Primarily the APH(4)-Ia substrate-binding site contains a cluster of hydrophobic residues that provides a complementary surface to the twisted structure of the substrate. Similar to APH(2″) enzymes, the APH(4)-Ia is able to utilize either ATP or GTP for phosphoryl transfer. The defined structural features of APH(4)-Ia interactions with hygB and the promiscuity in regard to ATP or GTP binding could be exploited for the design of novel aminoglycoside antibiotics or inhibitors of this enzyme.

Structural and functional correlates for language efficiency in auditory word processing

PubMed Central

Kim, Sunmi; Cho, Hyesuk; Nam, Kichun

2017-01-01

This study aims to provide convergent understanding of the neural basis of auditory word processing efficiency using a multimodal imaging. We investigated the structural and functional correlates of word processing efficiency in healthy individuals. We acquired two structural imaging (T1-weighted imaging and diffusion tensor imaging) and functional magnetic resonance imaging (fMRI) during auditory word processing (phonological and semantic tasks). Our results showed that better phonological performance was predicted by the greater thalamus activity. In contrary, better semantic performance was associated with the less activation in the left posterior middle temporal gyrus (pMTG), supporting the neural efficiency hypothesis that better task performance requires less brain activation. Furthermore, our network analysis revealed the semantic network including the left anterior temporal lobe (ATL), dorsolateral prefrontal cortex (DLPFC) and pMTG was correlated with the semantic efficiency. Especially, this network acted as a neural efficient manner during auditory word processing. Structurally, DLPFC and cingulum contributed to the word processing efficiency. Also, the parietal cortex showed a significate association with the word processing efficiency. Our results demonstrated that two features of word processing efficiency, phonology and semantics, can be supported in different brain regions and, importantly, the way serving it in each region was different according to the feature of word processing. Our findings suggest that word processing efficiency can be achieved by in collaboration of multiple brain regions involved in language and general cognitive function structurally and functionally. PMID:28892503

Learning Microbial Community Structures with Supervised and Unsupervised Non-negative Matrix Factorization.

PubMed

Cai, Yun; Gu, Hong; Kenney, Toby

2017-08-31

Learning the structure of microbial communities is critical in understanding the different community structures and functions of microbes in distinct individuals. We view microbial communities as consisting of many subcommunities which are formed by certain groups of microbes functionally dependent on each other. The focus of this paper is on methods for extracting the subcommunities from the data, in particular Non-Negative Matrix Factorization (NMF). Our methods can be applied to both OTU data and functional metagenomic data. We apply the existing unsupervised NMF method and also develop a new supervised NMF method for extracting interpretable information from classification problems. The relevance of the subcommunities identified by NMF is demonstrated by their excellent performance for classification. Through three data examples, we demonstrate how to interpret the features identified by NMF to draw meaningful biological conclusions and discover hitherto unidentified patterns in the data. Comparing whole metagenomes of various mammals, (Muegge et al., Science 332:970-974, 2011), the biosynthesis of macrolides pathway is found in hindgut-fermenting herbivores, but not carnivores. This is consistent with results in veterinary science that macrolides should not be given to non-ruminant herbivores. For time series microbiome data from various body sites (Caporaso et al., Genome Biol 12:50, 2011), a shift in the microbial communities is identified for one individual. The shift occurs at around the same time in the tongue and gut microbiomes, indicating that the shift is a genuine biological trait, rather than an artefact of the method. For whole metagenome data from IBD patients and healthy controls (Qin et al., Nature 464:59-65, 2010), we identify differences in a number of pathways (some known, others new). NMF is a powerful tool for identifying the key features of microbial communities. These identified features can not only be used to perform difficult classification problems with a high degree of accuracy, they are also very interpretable and can lead to important biological insights into the structure of the communities. In addition, NMF is a dimension-reduction method (similar to PCA) in that it reduces the extremely complex microbial data into a low-dimensional representation, allowing a number of analyses to be performed more easily-for example, searching for temporal patterns in the microbiome. When we are interested in the differences between the structures of two groups of communities, supervised NMF provides a better way to do this, while retaining all the advantages of NMF-e.g. interpretability and a simple biological intuition.

The convergence of maturational change and structural covariance in human cortical networks.

PubMed

Alexander-Bloch, Aaron; Raznahan, Armin; Bullmore, Ed; Giedd, Jay

2013-02-13

Large-scale covariance of cortical thickness or volume in distributed brain regions has been consistently reported by human neuroimaging studies. The mechanism of this population covariance of regional cortical anatomy has been hypothetically related to synchronized maturational changes in anatomically connected neuronal populations. Brain regions that grow together, i.e., increase or decrease in volume at the same rate over the course of years in the same individual, are thus expected to demonstrate strong structural covariance or anatomical connectivity across individuals. To test this prediction, we used a structural MRI dataset on healthy young people (N = 108; aged 9-22 years at enrollment), comprising 3-6 longitudinal scans on each participant over 6-12 years of follow-up. At each of 360 regional nodes, and for each participant, we estimated the following: (1) the cortical thickness in the median scan and (2) the linear rate of change in cortical thickness over years of serial scanning. We constructed structural and maturational association matrices and networks from these measurements. Both structural and maturational networks shared similar global and nodal topological properties, as well as mesoscopic features including a modular community structure, a relatively small number of highly connected hub regions, and a bias toward short distance connections. Using resting-state functional magnetic resonance imaging data on a subset of the sample (N = 32), we also demonstrated that functional connectivity and network organization was somewhat predictable by structural/maturational networks but demonstrated a stronger bias toward short distance connections and greater topological segregation. Brain structural covariance networks are likely to reflect synchronized developmental change in distributed cortical regions.

Modeling error in assessment of mammographic image features for improved computer-aided mammography training: initial experience

NASA Astrophysics Data System (ADS)

Mazurowski, Maciej A.; Tourassi, Georgia D.

2011-03-01

In this study we investigate the hypothesis that there exist patterns in erroneous assessment of BI-RADS image features among radiology trainees when performing diagnostic interpretation of mammograms. We also investigate whether these error making patterns can be captured by individual user models. To test our hypothesis we propose a user modeling algorithm that uses the previous readings of a trainee to identify whether certain BI-RADS feature values (e.g. "spiculated" value for "margin" feature) are associated with higher than usual likelihood that the feature will be assessed incorrectly. In our experiments we used readings of 3 radiology residents and 7 breast imaging experts for 33 breast masses for the following BI-RADS features: parenchyma density, mass margin, mass shape and mass density. The expert readings were considered as the gold standard. Rule-based individual user models were developed and tested using the leave one-one-out crossvalidation scheme. Our experimental evaluation showed that the individual user models are accurate in identifying cases for which errors are more likely to be made. The user models captured regularities in error making for all 3 residents. This finding supports our hypothesis about existence of individual error making patterns in assessment of mammographic image features using the BI-RADS lexicon. Explicit user models identifying the weaknesses of each resident could be of great use when developing and adapting a personalized training plan to meet the resident's individual needs. Such approach fits well with the framework of adaptive computer-aided educational systems in mammography we have proposed before.

Differentiating Amino Acid Residues and Side Chain Orientations in Peptides Using Scanning Tunneling Microscopy

PubMed Central

Claridge, Shelley A.; Thomas, John C.; Silverman, Miles A.; Schwartz, Jeffrey J.; Yang, Yanlian; Wang, Chen; Weiss, Paul S.

2014-01-01

Single-molecule measurements of complex biological structures such as proteins are an attractive route for determining structures of the large number of important biomolecules that have proved refractory to analysis through standard techniques such as X-ray crystallography and nuclear magnetic resonance. We use a custom-built low-current scanning tunneling microscope to image peptide structure at the single-molecule scale in a model peptide that forms β sheets, a structural motif common in protein misfolding diseases. We successfully differentiate between histidine and alanine amino acid residues, and further differentiate side chain orientations in individual histidine residues, by correlating features in scanning tunneling microscope images with those in energy-optimized models. Beta sheets containing histidine residues are used as a model system due to the role histidine plays in transition metal binding associated with amyloid oligomerization in Alzheimer’s and other diseases. Such measurements are a first step toward analyzing peptide and protein structures at the single-molecule level. PMID:24219245

Structure-guided statistical textural distinctiveness for salient region detection in natural images.

PubMed

Scharfenberger, Christian; Wong, Alexander; Clausi, David A

2015-01-01

We propose a simple yet effective structure-guided statistical textural distinctiveness approach to salient region detection. Our method uses a multilayer approach to analyze the structural and textural characteristics of natural images as important features for salient region detection from a scale point of view. To represent the structural characteristics, we abstract the image using structured image elements and extract rotational-invariant neighborhood-based textural representations to characterize each element by an individual texture pattern. We then learn a set of representative texture atoms for sparse texture modeling and construct a statistical textural distinctiveness matrix to determine the distinctiveness between all representative texture atom pairs in each layer. Finally, we determine saliency maps for each layer based on the occurrence probability of the texture atoms and their respective statistical textural distinctiveness and fuse them to compute a final saliency map. Experimental results using four public data sets and a variety of performance evaluation metrics show that our approach provides promising results when compared with existing salient region detection approaches.

The (cost-)effectiveness of an individually tailored long-term worksite health promotion programme on physical activity and nutrition: design of a pragmatic cluster randomised controlled trial

PubMed Central

Robroek, Suzan JW; Bredt, Folef J; Burdorf, Alex

2007-01-01

Background Cardiovascular disease is the leading cause of disability and mortality in most Western countries. The prevalence of several risk factors, most notably low physical activity and poor nutrition, is very high. Therefore, lifestyle behaviour changes are of great importance. The worksite offers an efficient structure to reach large groups and to make use of a natural social network. This study investigates a worksite health promotion programme with individually tailored advice in physical activity and nutrition and individual counselling to increase compliance with lifestyle recommendations and sustainability of a healthy lifestyle. Methods/Design The study is a pragmatic cluster randomised controlled trial with the worksite as the unit of randomisation. All workers will receive a standard worksite health promotion program. Additionally, the intervention group will receive access to an individual Health Portal consisting of four critical features: a computer-tailored advice, a monitoring function, a personal coach, and opportunities to contact professionals at request. Participants are employees working for companies in the Netherlands, being literate enough to read and understand simple Internet-based messages in the Dutch language. A questionnaire to assess primary outcomes (compliance with national recommendations on physical activity and on fruit and vegetable intake) will take place at baseline and after 12 and 24 months. This questionnaire also assesses secondary outcomes including fat intake, self-efficacy and self-perceived barriers on physical activity and fruit and vegetable intake. Other secondary outcomes, including a cardiovascular risk profile and physical fitness, will be measured at baseline and after 24 months. Apart from the effect evaluation, a process evaluation will be carried out to gain insight into participation and adherence to the worksite health promotion programme. A cost-effectiveness analysis and sensitivity analysis will be carried out as well. Discussion The unique combination of features makes the individually tailored worksite health promotion programme a promising tool for health promotion. It is hypothesized that the Health Portal's features will counteract loss to follow-up, and will increase compliance with the lifestyle recommendations and sustainability of a healthy lifestyle. Trial registration Current Controlled Trials ISRCTN52854353. PMID:17888161

Correlative cellular ptychography with functionalized nanoparticles at the Fe L-edge

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

Gallagher-Jones, Marcus; Dias, Carlos Sato Baraldi; Pryor, Alan

Precise localization of nanoparticles within a cell is crucial to the understanding of cell-particle interactions and has broad applications in nanomedicine. Here in this paper, we report a proof-of-principle experiment for imaging individual functionalized nanoparticles within a mammalian cell by correlative microscopy. Using a chemically-fixed HeLa cell labeled with fluorescent core-shell nanoparticles as a model system, we implemented a graphene-oxide layer as a substrate to significantly reduce background scattering. We identified cellular features of interest by fluorescence microscopy, followed by scanning transmission X-ray tomography to localize the particles in 3D, and ptychographic coherent diffractive imaging of the fine features inmore » the region at high resolution. By tuning the X-ray energy to the Fe L-edge, we demonstrated sensitive detection of nanoparticles composed of a 22 nm magnetic Fe 3O 4 core encased by a 25-nm-thick fluorescent silica (SiO 2) shell. These fluorescent core-shell nanoparticles act as landmarks and offer clarity in a cellular context. Our correlative microscopy results confirmed a subset of particles to be fully internalized, and high-contrast ptychographic images showed two oxidation states of individual nanoparticles with a resolution of ~16.5 nm. The ability to precisely localize individual fluorescent nanoparticles within mammalian cells will expand our understanding of the structure/function relationships for functionalized nanoparticles.« less

Characterization of X-linked Hypohidrotic Ectodermal Dysplasia (XL-HED) Hair and Sweat Gland Phenotypes Using Phototrichogram Analysis and Live Confocal Imaging

PubMed Central

Jones, Kyle B.; Goodwin, Alice F.; Landan, Maya; Seidel, Kerstin; Tran, Dong-Kha; Hogue, Jacob; Chavez, Miquella; Fete, Mary; Yu, Wenli; Hussein, Tarek; Johnson, Ramsey; Huttner, Kenneth; Jheon, Andrew H.; Klein, Ophir D.

2015-01-01

Hypohidrotic ectodermal dysplasia (HED) is the most common type of ectodermal dysplasia (ED), which encompasses a large group of syndromes that share several phenotypic features such as missing or malformed ectodermal structures, including skin, hair, sweat glands, and teeth. X-linked hypohidrotic ectodermal dysplasia (XL-HED) is associated with mutations in ectodysplasin (EDA1). Hypohidrosis due to hypoplastic sweat glands and thin, sparse hair are phenotypic features that significantly affect the daily lives of XL-HED individuals and therefore require systematic analysis. We sought to determine the quality of life of individuals with XL-HED and to quantify sweat duct and hair phenotypes using confocal imaging, pilocarpine iontophoresis, and phototrichogram analysis. Using these highly sensitive and non-invasive techniques, we demonstrated that 11/12 XL-HED individuals presented with a complete absence of sweat ducts and that none produced sweat. We determined that the thin hair phenotype observed in XL-HED was due to multiple factors, such as fewer terminal hairs with decreased thickness and slower growth rate, as well as fewer follicular units and fewer hairs per unit. The precise characterization of XL-HED phenotypes using sensitive and non-invasive techniques presented in our study will improve upon larger genotype-phenotype studies and in the assessment of future therapies in XL-HED. PMID:23687000

The cultural evolution of emergent group-level traits.

PubMed

Smaldino, Paul E

2014-06-01

Many of the most important properties of human groups - including properties that may give one group an evolutionary advantage over another - are properly defined only at the level of group organization. Yet at present, most work on the evolution of culture has focused solely on the transmission of individual-level traits. I propose a conceptual extension of the theory of cultural evolution, particularly related to the evolutionary competition between cultural groups. The key concept in this extension is the emergent group-level trait. This type of trait is characterized by the structured organization of differentiated individuals and constitutes a unit of selection that is qualitatively different from selection on groups as defined by traditional multilevel selection (MLS) theory. As a corollary, I argue that the traditional focus on cooperation as the defining feature of human societies has missed an essential feature of cooperative groups. Traditional models of cooperation assume that interacting with one cooperator is equivalent to interacting with any other. However, human groups involve differential roles, meaning that receiving aid from one individual is often preferred to receiving aid from another. In this target article, I discuss the emergence and evolution of group-level traits and the implications for the theory of cultural evolution, including ramifications for the evolution of human cooperation, technology, and cultural institutions, and for the equivalency of multilevel selection and inclusive fitness approaches.

Correlative cellular ptychography with functionalized nanoparticles at the Fe L-edge

DOE PAGES

Gallagher-Jones, Marcus; Dias, Carlos Sato Baraldi; Pryor, Alan; ...

2017-07-06

Precise localization of nanoparticles within a cell is crucial to the understanding of cell-particle interactions and has broad applications in nanomedicine. Here in this paper, we report a proof-of-principle experiment for imaging individual functionalized nanoparticles within a mammalian cell by correlative microscopy. Using a chemically-fixed HeLa cell labeled with fluorescent core-shell nanoparticles as a model system, we implemented a graphene-oxide layer as a substrate to significantly reduce background scattering. We identified cellular features of interest by fluorescence microscopy, followed by scanning transmission X-ray tomography to localize the particles in 3D, and ptychographic coherent diffractive imaging of the fine features inmore » the region at high resolution. By tuning the X-ray energy to the Fe L-edge, we demonstrated sensitive detection of nanoparticles composed of a 22 nm magnetic Fe 3O 4 core encased by a 25-nm-thick fluorescent silica (SiO 2) shell. These fluorescent core-shell nanoparticles act as landmarks and offer clarity in a cellular context. Our correlative microscopy results confirmed a subset of particles to be fully internalized, and high-contrast ptychographic images showed two oxidation states of individual nanoparticles with a resolution of ~16.5 nm. The ability to precisely localize individual fluorescent nanoparticles within mammalian cells will expand our understanding of the structure/function relationships for functionalized nanoparticles.« less

Limited Documentation and Treatment Quality of Glycemic Inpatient Care in Relation to Structural Deficits of Heterogeneous Insulin Charts at a Large University Hospital.

PubMed

Kopanz, Julia; Lichtenegger, Katharina M; Sendlhofer, Gerald; Semlitsch, Barbara; Cuder, Gerald; Pak, Andreas; Pieber, Thomas R; Tax, Christa; Brunner, Gernot; Plank, Johannes

2018-02-09

Insulin charts represent a key component in the inpatient glycemic management process. The aim was to evaluate the quality of structure, documentation, and treatment of diabetic inpatient care to design a new standardized insulin chart for a large university hospital setting. Historically grown blank insulin charts in use at 39 general wards were collected and evaluated for quality structure features. Documentation and treatment quality were evaluated in a consecutive snapshot audit of filled-in charts. The primary end point was the percentage of charts with any medication error. Overall, 20 different blank insulin charts with variable designs and significant structural deficits were identified. A medication error occurred in 55% of the 102 audited filled-in insulin charts, consisting of prescription and management errors in 48% and 16%, respectively. Charts of insulin-treated patients had more medication errors relative to patients treated with oral medication (P < 0.01). Chart design did support neither clinical authorization of individual insulin prescription (10%), nor insulin administration confirmed by nurses' signature (25%), nor treatment of hypoglycemia (0%), which resulted in a reduced documentation and treatment quality in clinical practice 7%, 30%, 25%, respectively. A multitude of charts with variable design characteristics and structural deficits were in use across the inpatient wards. More than half of the inpatients had a chart displaying a medication error. Lack of structure quality features of the charts had an impact on documentation and treatment quality. Based on identified deficits and international standards, a new insulin chart was developed to overcome these quality hurdles.

Mechanism and energetics of dislocation cross-slip in hcp metals

NASA Astrophysics Data System (ADS)

Wu, Zhaoxuan; Curtin, W. A.

2016-10-01

Hexagonal close-packed (hcp) metals such as Mg, Ti, and Zr are lightweight and/or durable metals with critical structural applications in the automotive (Mg), aerospace (Ti), and nuclear (Zr) industries. The hcp structure, however, brings significant complications in the mechanisms of plastic deformation, strengthening, and ductility, and these complications pose significant challenges in advancing the science and engineering of these metals. In hcp metals, generalized plasticity requires the activation of slip on pyramidal planes, but the structure, motion, and cross-slip of the associated dislocations are not well established even though they determine ductility and influence strengthening. Here, atomistic simulations in Mg reveal the unusual mechanism of dislocation cross-slip between pyramidal I and II planes, which occurs by cross-slip of the individual partial dislocations. The energy barrier is controlled by a fundamental step/jog energy and the near-core energy difference between pyramidal dislocations. The near-core energy difference can be changed by nonglide stresses, leading to tension-compression asymmetry and even a switch in absolute stability from one glide plane to the other, both features observed experimentally in Mg, Ti, and their alloys. The unique cross-slip mechanism is governed by common features of the generalized stacking fault energy surfaces of hcp pyramidal planes and is thus expected to be generic to all hcp metals. An analytical model is developed to predict the cross-slip barrier as a function of the near-core energy difference and applied stresses and quantifies the controlling features of cross-slip and pyramidal I/II stability across the family of hcp metals.

URS DataBase: universe of RNA structures and their motifs.

PubMed

Baulin, Eugene; Yacovlev, Victor; Khachko, Denis; Spirin, Sergei; Roytberg, Mikhail

2016-01-01

The Universe of RNA Structures DataBase (URSDB) stores information obtained from all RNA-containing PDB entries (2935 entries in October 2015). The content of the database is updated regularly. The database consists of 51 tables containing indexed data on various elements of the RNA structures. The database provides a web interface allowing user to select a subset of structures with desired features and to obtain various statistical data for a selected subset of structures or for all structures. In particular, one can easily obtain statistics on geometric parameters of base pairs, on structural motifs (stems, loops, etc.) or on different types of pseudoknots. The user can also view and get information on an individual structure or its selected parts, e.g. RNA-protein hydrogen bonds. URSDB employs a new original definition of loops in RNA structures. That definition fits both pseudoknot-free and pseudoknotted secondary structures and coincides with the classical definition in case of pseudoknot-free structures. To our knowledge, URSDB is the first database supporting searches based on topological classification of pseudoknots and on extended loop classification.Database URL: http://server3.lpm.org.ru/urs/. © The Author(s) 2016. Published by Oxford University Press.

URS DataBase: universe of RNA structures and their motifs

PubMed Central

Baulin, Eugene; Yacovlev, Victor; Khachko, Denis; Spirin, Sergei; Roytberg, Mikhail

2016-01-01

The Universe of RNA Structures DataBase (URSDB) stores information obtained from all RNA-containing PDB entries (2935 entries in October 2015). The content of the database is updated regularly. The database consists of 51 tables containing indexed data on various elements of the RNA structures. The database provides a web interface allowing user to select a subset of structures with desired features and to obtain various statistical data for a selected subset of structures or for all structures. In particular, one can easily obtain statistics on geometric parameters of base pairs, on structural motifs (stems, loops, etc.) or on different types of pseudoknots. The user can also view and get information on an individual structure or its selected parts, e.g. RNA–protein hydrogen bonds. URSDB employs a new original definition of loops in RNA structures. That definition fits both pseudoknot-free and pseudoknotted secondary structures and coincides with the classical definition in case of pseudoknot-free structures. To our knowledge, URSDB is the first database supporting searches based on topological classification of pseudoknots and on extended loop classification. Database URL: http://server3.lpm.org.ru/urs/ PMID:27242032

ProQ3: Improved model quality assessments using Rosetta energy terms

PubMed Central

Uziela, Karolis; Shu, Nanjiang; Wallner, Björn; Elofsson, Arne

2016-01-01

Quality assessment of protein models using no other information than the structure of the model itself has been shown to be useful for structure prediction. Here, we introduce two novel methods, ProQRosFA and ProQRosCen, inspired by the state-of-art method ProQ2, but using a completely different description of a protein model. ProQ2 uses contacts and other features calculated from a model, while the new predictors are based on Rosetta energies: ProQRosFA uses the full-atom energy function that takes into account all atoms, while ProQRosCen uses the coarse-grained centroid energy function. The two new predictors also include residue conservation and terms corresponding to the agreement of a model with predicted secondary structure and surface area, as in ProQ2. We show that the performance of these predictors is on par with ProQ2 and significantly better than all other model quality assessment programs. Furthermore, we show that combining the input features from all three predictors, the resulting predictor ProQ3 performs better than any of the individual methods. ProQ3, ProQRosFA and ProQRosCen are freely available both as a webserver and stand-alone programs at http://proq3.bioinfo.se/. PMID:27698390

Profiling of the Tox21 Chemical Collection for Mitochondrial ...

EPA Pesticide Factsheets

Mitochondrial dysfunction has been implicated in the pathogenesis of a variety of disorders including cancer, diabetes, and neurodegenerative and cardiovascular diseases. Understanding how different environmental chemicals and drug-like molecules impact mitochondrial function represents an initial step in predicting exposure-related toxic effects and defining a possible role for such compounds in the onset of various diseases. OBJECTIVES: To identify individual chemicals and general structural features associated with the disruption of mitochondrial membrane potential (MMP). METHODS: We used a multiplexed quantitative high throughput screening (qHTS) approach combined with informatics tools to screen the Tox21 10,000 compound library (~8300 unique chemicals) at 15 concentrations in triplicate to identify chemicals and structural features that are associated with changes in MMP in HepG2 cells. RESULTS: In the primary screening, approximately 11% of the compounds (913 unique compounds) decreased the MMP after 1 h of treatment without affecting cell viability. Additionally, 309 compounds decreased MMP over a concentration range that also produced measurable cytotoxicity [half maximal inhibitory concentration (IC50) in MMP assay/IC50 in viability assay) ≤ 3, p<0.05]. Over 11% of the structural clusters that constitute the Tox21 library (76 of 651 clusters) were significantly enriched for compounds that decreased the MMP. CONCLUSIONS: Our multiplexed qHTS approach

[Risk and features of occupational diseases in nonferrous metallurgy workers of Kolsky Transpolar area].

PubMed

Siurin, S A; Chashchin, V P; Frolova, N M

2015-01-01

The study covered data on 977 cases of occupational diseases in 615 workers of nonferrous metallurgy in Kolsky Transpolar area. Findings are high risk of occupational diseases in workers engaged into electrolysis production of aluminium, all nickel reprocessing and pyrometallic copper reprocessing (GR 7.02-10.0). Electrolysis operators and anode operators of aluminium production are more prone to occupational diseases, with bone and muscular disorders (46.8%) prevalent in the morbidity structure. Respiratory diseases are more prevalent (68.2-100%) in the occupational morbidity structure of copper-nickelindustry workers. Conclusion is made on mandatory improvement of the work conditions and more effective individual protective means against occupational hazards in workers of nonferrous metallurgy in Kolsky Transpolar area.

Reduced chromium in olivine grains from lunar basalt 15555 - X-ray Absorption Near Edge Structure (XANES)

NASA Technical Reports Server (NTRS)

Sutton, S. R.; Jones, K. W.; Gordon, B.; Rivers, M. L.; Bajt, S.; Smith, J. V.

1993-01-01

The oxidation state of Cr in 200-micron regions within individual lunar olivine and pyroxene grains from lunar basalt 15555 was inferred using X-ray Absorption Near Edge Structure (XANES). Reference materials had previously been studied by optical absorption spectroscopy and included Cr-bearing borosilicate glasses synthesized under controlled oxygen fugacity and Cr-doped olivines. The energy dependence of XANES spectral features defined by these reference materials indicated that Cr is predominantly divalent in the lunar olivine and trivalent in the pyroxene. These results, coupled with the apparent f(02)-independence of partitioning coefficients for Cr into olivine, imply that the source magma was dominated by divalent Cr at the time of olivine crystallization.

Single-particle mapping of nonequilibrium nanocrystal transformations

DOE PAGES

Ye, Xingchen; Jones, Matthew R.; Frechette, Layne B.; ...

2016-11-18

Chemists have developed mechanistic insight into numerous chemical reactions by thoroughly characterizing nonequilibrium species. Although methods to probe these processes are well established for molecules, analogous techniques for understanding intermediate structures in nanomaterials have been lacking. For this study, we monitor the shape evolution of individual anisotropic gold nanostructures as they are oxidatively etched in a graphene liquid cell with a controlled redox environment. Short-lived, nonequilibrium nanocrystals are observed, structurally analyzed, and rationalized through Monte Carlo simulations. Understanding these reaction trajectories provides important fundamental insight connecting high-energy nanocrystal morphologies to the development of kinetically stabilized surface features and demonstrates themore » importance of developing tools capable of probing short-lived nanoscale species at the single-particle level.« less

Polarization and angle independent magneto-electric Fano resonance in multilayer hetero-nanoshells

NASA Astrophysics Data System (ADS)

Wang, Wudeng; Xiong, Li; Zheng, Li; Li, Wei; Shi, Ying; Qi, Jianguang

2018-05-01

In this work, we have demonstrated that the Si-SiO2 -Au multilayer hetero-nanoshells can support the polarization and angle independent magneto-electric Fano resonance. Such Fano resonance arises from the direct destructive interference between the orthogonal electric dipole mode of Au core and magnetic dipole mode of the Si shell and is independent of the angle due to the high structural symmetry. In contrast to metal particle arrays, here is a possibility to generate controllable interaction between the electric and magnetic dipole resonances of individual nanoshell with the structural features. The discrete magnetic responses provided directly by the Si shell pave the groundwork for designing the magnetic responses at optical frequencies and enable many fascinating applications in nanophotonics.

Scale invariance in natural and artificial collective systems: a review

PubMed Central

Huepe, Cristián

2017-01-01

Self-organized collective coordinated behaviour is an impressive phenomenon, observed in a variety of natural and artificial systems, in which coherent global structures or dynamics emerge from local interactions between individual parts. If the degree of collective integration of a system does not depend on size, its level of robustness and adaptivity is typically increased and we refer to it as scale-invariant. In this review, we first identify three main types of self-organized scale-invariant systems: scale-invariant spatial structures, scale-invariant topologies and scale-invariant dynamics. We then provide examples of scale invariance from different domains in science, describe their origins and main features and discuss potential challenges and approaches for designing and engineering artificial systems with scale-invariant properties. PMID:29093130

On decentralized control of large-scale systems

NASA Technical Reports Server (NTRS)

Siljak, D. D.

1978-01-01

A scheme is presented for decentralized control of large-scale linear systems which are composed of a number of interconnected subsystems. By ignoring the interconnections, local feedback controls are chosen to optimize each decoupled subsystem. Conditions are provided to establish compatibility of the individual local controllers and achieve stability of the overall system. Besides computational simplifications, the scheme is attractive because of its structural features and the fact that it produces a robust decentralized regulator for large dynamic systems, which can tolerate a wide range of nonlinearities and perturbations among the subsystems.

Spatial and temporal analysis of DIII-D 3D magnetic diagnostic data

DOE PAGES

Strait, E. J.; King, J. D.; Hanson, J. M.; ...

2016-08-11

An extensive set of magnetic diagnostics in DIII-D is aimed at measuring non-axisymmetric "3D" features of tokamak plasmas, with typical amplitudes ~10 -3 to 10 -5 of the total magnetic field. We describe hardware and software techniques used at DIII-D to condition the individual signals and analysis to estimate the spatial structure from an ensemble of discrete measurements. Lastly, applications of the analysis include detection of non-rotating MHD instabilities, plasma control, and validation of MHD stability and 3D equilibrium models.

Vortex line topology during vortex tube reconnection

NASA Astrophysics Data System (ADS)

McGavin, P.; Pontin, D. I.

2018-05-01

This paper addresses reconnection of vortex tubes, with particular focus on the topology of the vortex lines (field lines of the vorticity). This analysis of vortex line topology reveals key features of the reconnection process, such as the generation of many small flux rings, formed when reconnection occurs in multiple locations in the vortex sheet between the tubes. Consideration of three-dimensional reconnection principles leads to a robust measurement of the reconnection rate, even once instabilities break the symmetry. It also allows us to identify internal reconnection of vortex lines within the individual vortex tubes. Finally, the introduction of a third vortex tube is shown to render the vortex reconnection process fully three-dimensional, leading to a fundamental change in the topological structure of the process. An additional interesting feature is the generation of vorticity null points.

Building superlattices from individual nanoparticles via template-confined DNA-mediated assembly

NASA Astrophysics Data System (ADS)

Lin, Qing-Yuan; Mason, Jarad A.; Li, Zhongyang; Zhou, Wenjie; O’Brien, Matthew N.; Brown, Keith A.; Jones, Matthew R.; Butun, Serkan; Lee, Byeongdu; Dravid, Vinayak P.; Aydin, Koray; Mirkin, Chad A.

2018-02-01

DNA programmable assembly has been combined with top-down lithography to construct superlattices of discrete, reconfigurable nanoparticle architectures on a gold surface over large areas. Specifically, the assembly of individual colloidal plasmonic nanoparticles with different shapes and sizes is controlled by oligonucleotides containing “locked” nucleic acids and confined environments provided by polymer pores to yield oriented architectures that feature tunable arrangements and independently controllable distances at both nanometer- and micrometer-length scales. These structures, which would be difficult to construct by other common assembly methods, provide a platform to systematically study and control light-matter interactions in nanoparticle-based optical materials. The generality and potential of this approach are explored by identifying a broadband absorber with a solvent polarity response that allows dynamic tuning of visible light absorption.

Building superlattices from individual nanoparticles via template-confined DNA-mediated assembly

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

Lin, Qing-Yuan; Mason, Jarad A.; Li, Zhongyang

DNA programmable assembly has been combined with top-down lithography to construct superlattices of discrete, reconfigurable nanoparticle architectures on a gold surface over large areas. Specifically, individual colloidal plasmonic nanoparticles with different shapes and sizes are assembled with ‘locked” nucleic acids in polymer pores into oriented architectures that feature tunable arrangements and independently controllable distances at both nanometer and micrometer length scales. These structures, which would be difficult to construct via other common assembly methods, provide a platform to systematically study and control light-matter interactions in nanoparticle-based optical materials. The generality and potential of this approach is explored by identifying amore » broadband absorber with a solvent polarity response that allows dynamic tuning of the wavelength response and amplitude of visible light absorption.« less

Is autism partly a consolidation disorder?

PubMed

Femia, Lisa A; Hasselmo, Michael E

2002-12-01

Computational modeling has been useful for understanding processes of encoding and consolidation in cortical structures. In particular, this work suggests a role of neuromodulators in setting dynamics for consolidation processes during different stages of waking and sleep. Because autistic individuals show symptoms of a cognitive nature coupled with a high prevalence of comorbid conditions such as epileptiform discharge during sleep and sleep disorders, it is possible that autism could involve a breakdown in consolidation processes, which are essential to build effective cognitive representations of the environment on the basis of individual experiences. In this article, theories of consolidation during different stages of waking and sleep and the role of different neuromodulators in these consolidation processes are reviewed in conjunction with different features of autism, which may be understood in the context of these theories.

Classifying MCI Subtypes in Community-Dwelling Elderly Using Cross-Sectional and Longitudinal MRI-Based Biomarkers

PubMed Central

Guan, Hao; Liu, Tao; Jiang, Jiyang; Tao, Dacheng; Zhang, Jicong; Niu, Haijun; Zhu, Wanlin; Wang, Yilong; Cheng, Jian; Kochan, Nicole A.; Brodaty, Henry; Sachdev, Perminder; Wen, Wei

2017-01-01

Amnestic MCI (aMCI) and non-amnestic MCI (naMCI) are considered to differ in etiology and outcome. Accurately classifying MCI into meaningful subtypes would enable early intervention with targeted treatment. In this study, we employed structural magnetic resonance imaging (MRI) for MCI subtype classification. This was carried out in a sample of 184 community-dwelling individuals (aged 73–85 years). Cortical surface based measurements were computed from longitudinal and cross-sectional scans. By introducing a feature selection algorithm, we identified a set of discriminative features, and further investigated the temporal patterns of these features. A voting classifier was trained and evaluated via 10 iterations of cross-validation. The best classification accuracies achieved were: 77% (naMCI vs. aMCI), 81% (aMCI vs. cognitively normal (CN)) and 70% (naMCI vs. CN). The best results for differentiating aMCI from naMCI were achieved with baseline features. Hippocampus, amygdala and frontal pole were found to be most discriminative for classifying MCI subtypes. Additionally, we observed the dynamics of classification of several MRI biomarkers. Learning the dynamics of atrophy may aid in the development of better biomarkers, as it may track the progression of cognitive impairment. PMID:29085292

Automatic change detection: does the auditory system use representations of individual stimulus features or gestalts?

PubMed

Deacon, D; Nousak, J M; Pilotti, M; Ritter, W; Yang, C M

1998-07-01

The effects of global and feature-specific probabilities of auditory stimuli were manipulated to determine their effects on the mismatch negativity (MMN) of the human event-related potential. The question of interest was whether the automatic comparison of stimuli indexed by the MMN was performed on representations of individual stimulus features or on gestalt representations of their combined attributes. The design of the study was such that both feature and gestalt representations could have been available to the comparator mechanism generating the MMN. The data were consistent with the interpretation that the MMN was generated following an analysis of stimulus features.

IR spectroscopic characteristics of cell cycle and cell death probed by synchrotron radiation based Fourier transform IR spectromicroscopy

NASA Technical Reports Server (NTRS)

Holman, H. Y.; Martin, M. C.; Blakely, E. A.; Bjornstad, K.; McKinney, W. R.

2000-01-01

Synchrotron radiation based Fourier transform IR (SR-FTIR) spectromicroscopy allows the study of individual living cells with a high signal to noise ratio. Here we report the use of the SR-FTIR technique to investigate changes in IR spectral features from individual human lung fibroblast (IMR-90) cells in vitro at different points in their cell cycle. Clear changes are observed in the spectral regions corresponding to proteins, DNA, and RNA as a cell changes from the G(1)-phase to the S-phase and finally into mitosis. These spectral changes include markers for the changing secondary structure of proteins in the cell, as well as variations in DNA/RNA content and packing as the cell cycle progresses. We also observe spectral features that indicate that occasional cells are undergoing various steps in the process of cell death. The dying or dead cell has a shift in the protein amide I and II bands corresponding to changing protein morphologies, and a significant increase in the intensity of an ester carbonyl C===O peak at 1743 cm(-1) is observed. Copyright John Wiley & Sons, Inc. Biopolymers (Biospectroscopy) 57: 329-335, 2000.

[Urbanization mechanisms in bird species: population systems transformations or adaptations at the individual level?].

PubMed

Fridman, V S; Eremkin, G S; Zakharova-Kubareva, N Iu

2008-01-01

The present research deals with urbanization of wild bird and mammal species. Forms and mechanisms of population steadiness in the urban landscape have been examined. The urbanization process turned out to be a directed change of the population system forming de novo in the urbolandscape leading to a sustainable organization peculiar for the particular environment. The population organization of different types in urbolandscape is found to provide its stability under conditions of directed and fast changes accompanied with instability and heterogenous structure of habitats. It is shown that the same type of population organization meets the corresponding demands among different species settling in the urban environment. Its features are "openness" and "flowage" of the groups, far order of settlement levels and other units of population system, constant movements of the individuals between the groups as a respond to the signals of urboenvironment significant changes. The "urban" variant of the population system organization turns out to be opposite to that of the same species in the non-urban habitats. After formation of the urban types by the species and successful developing of the town, the urban population becomes separated from the maternal local population and begins to exist independently in the urban landscape. The variety of adaptation aberrations in ecology, behavior, and mode of life of urban birds is the population system stability function in the urban landscape and is not a results of individual selection. It is shown that the urbanization process of the species goes firstly on the population level being the system structure transformation developed by the species towards the most stable state in the town (city) territory. Only after the appearance of stable urban population, the urban individuals show the rapid growth of different changes in ecology, behavior, mode of life that was traditionally described by naturalists as species adaptation to the city conditions. The key features of urban population stability/instability are described. Their application to closely related species allows us to distinguish potential urbanists from instable and vulnerable species that could be soon pushed out of the city. The application of corresponding criteria to the urban populations of such species constituting one guild allows us to predict if their developing in the given town would be successful or unsuccessful. The latter is very important since close species are, as a rule, ecologically indistinguishable in the urbanized landscapes. So one can not predict successful/unsuccessful urbanization taking into account the differences in the range of habitats, breeding success, and other external features.

Temporal Processing Instability with Millisecond Accuracy Is a Cardinal Feature of Sensorimotor Impairments in Autism Spectrum Disorder: Analysis Using the Synchronized Finger-Tapping Task

ERIC Educational Resources Information Center

Morimoto, Chie; Hida, Eisuke; Shima, Keisuke; Okamura, Hitoshi

2018-01-01

To identify a specific sensorimotor impairment feature of autism spectrum disorder (ASD), we focused on temporal processing with millisecond accuracy. A synchronized finger-tapping task was used to characterize temporal processing in individuals with ASD as compared to typically developing (TD) individuals. We found that individuals with ASD…

Self-esteem as a mediator of the relationship between role functioning and symptoms for individuals with severe mental illness: a prospective analysis of Modified Labeling theory.

PubMed

Davis, Lisa; Kurzban, Seth; Brekke, John

2012-05-01

Despite a growing body of evidence supporting the efficacy of psychosocial rehabilitation for individuals with severe mental illness (SMI), a large proportion of these individuals remain unable to maintain basic social roles such as employee, parent, or spouse. This study investigated whether changes in role functioning over time impact symptom severity indirectly through the mechanism of changes in self-esteem as posited by Modified Labeling theory. The study sample was composed of 148 individuals diagnosed with schizophrenia, schizoaffective disorder, bipolar disorder with psychotic features, and major depression with psychotic features who elected to participate in community-based psychosocial rehabilitation services. Measures of role functioning, self-esteem, and psychiatric symptoms were gathered at baseline and six months through a combination of structured clinical interviews and self-report surveys. SEM results at baseline provided support for a model in which self-esteem fully mediated the relationship between role functioning and psychiatric symptoms. The final model explained 20% of the variance in psychiatric symptoms. Analyses at six months post-baseline (time 2) indicate that changes in self-esteem fully mediated the relationship between changes in role functioning and changes in psychiatric symptoms. The final change model explained 23% of the variance in changes in psychiatric symptoms. Results provide empirical support for the principles underlying Modified Labeling theory. Implications include the need for interventions that focus on social participation as a means of improving self-esteem, thereby decreasing symptom exacerbation and future relapse for people with SMI. Copyright © 2012 Elsevier B.V. All rights reserved.

On the Perception of Religious Group Membership from Faces

PubMed Central

Rule, Nicholas O.; Garrett, James V.; Ambady, Nalini

2010-01-01

Background The study of social categorization has largely been confined to examining groups distinguished by perceptually obvious cues. Yet many ecologically important group distinctions are less clear, permitting insights into the general processes involved in person perception. Although religious group membership is thought to be perceptually ambiguous, folk beliefs suggest that Mormons and non-Mormons can be categorized from their appearance. We tested whether Mormons could be distinguished from non-Mormons and investigated the basis for this effect to gain insight to how subtle perceptual cues can support complex social categorizations. Methodology/Principal Findings Participants categorized Mormons' and non-Mormons' faces or facial features according to their group membership. Individuals could distinguish between the two groups significantly better than chance guessing from their full faces and faces without hair, with eyes and mouth covered, without outer face shape, and inverted 180°; but not from isolated features (i.e., eyes, nose, or mouth). Perceivers' estimations of their accuracy did not match their actual accuracy. Exploration of the remaining features showed that Mormons and non-Mormons significantly differed in perceived health and that these perceptions were related to perceptions of skin quality, as demonstrated in a structural equation model representing the contributions of skin color and skin texture. Other judgments related to health (facial attractiveness, facial symmetry, and structural aspects related to body weight) did not differ between the two groups. Perceptions of health were also responsible for differences in perceived spirituality, explaining folk hypotheses that Mormons are distinct because they appear more spiritual than non-Mormons. Conclusions/Significance Subtle markers of group membership can influence how others are perceived and categorized. Perceptions of health from non-obvious and minimal cues distinguished individuals according to their religious group membership. These data illustrate how the non-conscious detection of very subtle differences in others' appearances supports cognitively complex judgments such as social categorization. PMID:21151864

Reporting of methodological features in observational studies of pre-harvest food safety.

PubMed

Sargeant, Jan M; O'Connor, Annette M; Renter, David G; Kelton, David F; Snedeker, Kate; Wisener, Lee V; Leonard, Erin K; Guthrie, Alessia D; Faires, Meredith

2011-02-01

Observational studies in pre-harvest food safety may be useful for identifying risk factors and for evaluating potential mitigation strategies to reduce foodborne pathogens. However, there are no structured reporting guidelines for these types of study designs in livestock species. Our objective was to evaluate the reporting of observational studies in the pre-harvest food safety literature using guidelines modified from the human healthcare literature. We identified 100 pre-harvest food safety studies published between 1999 and 2009. Each study was evaluated independently by two reviewers using a structured checklist. Of the 38 studies that explicitly stated the observational study design, 27 were described as cross-sectional studies, eight as case-control studies, and three as cohort studies. Study features reported in over 75% of the selected studies included: description of the geographic location of the studies, definitions and sources of data for outcomes, organizational level and source of data for independent variables, description of statistical methods and results, number of herds enrolled in the study and included in the analysis, and sources of study funding. However, other features were not consistently reported, including details related to eligibility criteria for groups (such as barn, room, or pen) and individuals, numbers of groups and individuals included in various stages of the study, identification of primary outcomes, the distinction between putative risk factors and confounding variables, the identification of a primary exposure variable, the referent level for evaluation of categorical variable associations, methods of controlling confounding variables and missing variables, model fit, details of subset analysis, demographic information at the sampling unit level, and generalizability of the study results. Improvement in reporting of observational studies of pre-harvest food safety will aid research readers and reviewers in interpreting and evaluating the results of such studies. Copyright © 2010 Elsevier B.V. All rights reserved.

In search of a unifying theory of complex brain evolution.

PubMed

Krubitzer, Leah

2009-03-01

The neocortex is the part of the brain that is involved in perception, cognition, and volitional motor control. In mammals it is a highly dynamic structure that has been dramatically altered in different lineages, and these alterations account for the remarkable variations in behavior that species exhibit. When we consider how this structure changes and becomes more complex in some mammals such as humans, we must also consider how the alterations that occur at macro levels of organization, such as the level of the individual and social system, as well as micro levels of organization, such as the level of neurons, synapses and molecules, impact the neocortex. It is also important to consider the constraints imposed on the evolution of the neocortex. Observations of highly conserved features of cortical organization that all mammals share, as well as the convergent evolution of similar features of organization, indicate that the constraints imposed on the neocortex are pervasive and restrict the avenues along which evolution can proceed. Although both genes and the laws of physics place formidable constraints on the evolution of all animals, humans have evolved a number of mechanisms that allow them to loosen these constraints and often alter the course of their own evolution. While this cortical plasticity is a defining feature of mammalian neocortex, it appears to be exaggerated in humans and could be considered a unique derivation of our species.

Digital microfabrication of user-defined 3D microstructures in cell-laden hydrogels.

PubMed

Soman, Pranav; Chung, Peter H; Zhang, A Ping; Chen, Shaochen

2013-11-01

Complex 3D interfacial arrangements of cells are found in several in vivo biosystems such as blood vasculature, renal glomeruli, and intestinal villi. Current tissue engineering techniques fail to develop suitable 3D microenvironments to evaluate the concurrent effects of complex topography and cell encapsulation. There is a need to develop new fabrication approaches that control cell density and distribution within complex 3D features. In this work, we present a dynamic projection printing process that allows rapid construction of complex 3D structures using custom-defined computer-aided-design (CAD) files. Gelatin-methacrylate (GelMA) constructs featuring user-defined spiral, pyramid, flower, and dome micro-geometries were fabricated with and without encapsulated cells. Encapsulated cells demonstrate good cell viability across all geometries both on the scaffold surface and internal to the structures. Cells respond to geometric cues individually as well as collectively throughout the larger-scale patterns. Time-lapse observations also reveal the dynamic nature of mechanical interactions between cells and micro-geometry. When compared to conventional cell-seeding, cell encapsulation within complex 3D patterned scaffolds provides long-term control over proliferation, cell morphology, and geometric guidance. Overall, this biofabrication technique offers a flexible platform to evaluate cell interactions with complex 3D micro-features, with the ability to scale-up towards high-throughput screening platforms. © 2013 Wiley Periodicals, Inc.

Salutogenic service user involvement in nursing research: a case study.

PubMed

Mjøsund, Nina Helen; Vinje, Hege Forbech; Eriksson, Monica; Haaland-Øverby, Mette; Jensen, Sven Liang; Kjus, Solveig; Norheim, Irene; Portaasen, Inger-Lill; Espnes, Geir Arild

2018-05-12

The aim was to explore the process of involving mental healthcare service users in a mental health promotion research project as research advisors and to articulate features of the collaboration which encouraged and empowered the advisors to make significant contributions to the research process and outcome. There is an increasing interest in evaluating aspects of service user involvement in nursing research. Few descriptions exist of features that enable meaningful service user involvement. We draw on experiences from conducting research which used the methodology interpretative phenomenological analysis to explore how persons with mental disorders perceived mental health. Aside from the participants in the project, five research advisors with service user experience were involved in the entire research process. We applied a case study design to explore the ongoing processes of service user involvement. Documents and texts produced while conducting the project (2012-2016), as well as transcripts from multistage focus group discussions with the research advisors, were analysed. The level of involvement was dynamic and varied throughout the different stages of the research process. Six features: leadership, meeting structure, role clarification, being members of a team, a focus on possibilities and being seen and treated as holistic individuals, were guiding principles for a salutogenic service user involvement. These features strengthened the advisors' perception of themselves as valuable and competent contributors. Significant contributions from research advisors were promoted by facilitating the process of involvement. A supporting structure and atmosphere were consistent with a salutogenic service user involvement. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Quantifying site-specific physical heterogeneity within an estuarine seascape

USGS Publications Warehouse

Kennedy, Cristina G.; Mather, Martha E.; Smith, Joseph M.

2017-01-01

Quantifying physical heterogeneity is essential for meaningful ecological research and effective resource management. Spatial patterns of multiple, co-occurring physical features are rarely quantified across a seascape because of methodological challenges. Here, we identified approaches that measured total site-specific heterogeneity, an often overlooked aspect of estuarine ecosystems. Specifically, we examined 23 metrics that quantified four types of common physical features: (1) river and creek confluences, (2) bathymetric variation including underwater drop-offs, (3) land features such as islands/sandbars, and (4) major underwater channel networks. Our research at 40 sites throughout Plum Island Estuary (PIE) provided solutions to two problems. The first problem was that individual metrics that measured heterogeneity of a single physical feature showed different regional patterns. We solved this first problem by combining multiple metrics for a single feature using a within-physical feature cluster analysis. With this approach, we identified sites with four different types of confluences and three different types of underwater drop-offs. The second problem was that when multiple physical features co-occurred, new patterns of total site-specific heterogeneity were created across the seascape. This pattern of total heterogeneity has potential ecological relevance to structure-oriented predators. To address this second problem, we identified sites with similar types of total physical heterogeneity using an across-physical feature cluster analysis. Then, we calculated an additive heterogeneity index, which integrated all physical features at a site. Finally, we tested if site-specific additive heterogeneity index values differed for across-physical feature clusters. In PIE, the sites with the highest additive heterogeneity index values were clustered together and corresponded to sites where a fish predator, adult striped bass (Morone saxatilis), aggregated in a related acoustic tracking study. In summary, we have shown general approaches to quantifying site-specific heterogeneity.

Coordination of Leaf Photosynthesis, Transpiration, and Structural Traits in Rice and Wild Relatives (Genus Oryza)1[W][OA

PubMed Central

Giuliani, Rita; Koteyeva, Nuria; Voznesenskaya, Elena; Evans, Marc A.; Cousins, Asaph B.; Edwards, Gerald E.

2013-01-01

The genus Oryza, which includes rice (Oryza sativa and Oryza glaberrima) and wild relatives, is a useful genus to study leaf properties in order to identify structural features that control CO2 access to chloroplasts, photosynthesis, water use efficiency, and drought tolerance. Traits, 26 structural and 17 functional, associated with photosynthesis and transpiration were quantified on 24 accessions (representatives of 17 species and eight genomes). Hypotheses of associations within, and between, structure, photosynthesis, and transpiration were tested. Two main clusters of positively interrelated leaf traits were identified: in the first cluster were structural features, leaf thickness (Thickleaf), mesophyll (M) cell surface area exposed to intercellular air space per unit of leaf surface area (Smes), and M cell size; a second group included functional traits, net photosynthetic rate, transpiration rate, M conductance to CO2 diffusion (gm), stomatal conductance to gas diffusion (gs), and the gm/gs ratio. While net photosynthetic rate was positively correlated with gm, neither was significantly linked with any individual structural traits. The results suggest that changes in gm depend on covariations of multiple leaf (Smes) and M cell (including cell wall thickness) structural traits. There was an inverse relationship between Thickleaf and transpiration rate and a significant positive association between Thickleaf and leaf transpiration efficiency. Interestingly, high gm together with high gm/gs and a low Smes/gm ratio (M resistance to CO2 diffusion per unit of cell surface area exposed to intercellular air space) appear to be ideal for supporting leaf photosynthesis while preserving water; in addition, thick M cell walls may be beneficial for plant drought tolerance. PMID:23669746

Coordination of Leaf Photosynthesis, Transpiration, and Structural Traits in Rice and Wild Relatives (Genus Oryza).

PubMed

Giuliani, Rita; Koteyeva, Nuria; Voznesenskaya, Elena; Evans, Marc A; Cousins, Asaph B; Edwards, Gerald E

2013-07-01

The genus Oryza, which includes rice (Oryza sativa and Oryza glaberrima) and wild relatives, is a useful genus to study leaf properties in order to identify structural features that control CO(2) access to chloroplasts, photosynthesis, water use efficiency, and drought tolerance. Traits, 26 structural and 17 functional, associated with photosynthesis and transpiration were quantified on 24 accessions (representatives of 17 species and eight genomes). Hypotheses of associations within, and between, structure, photosynthesis, and transpiration were tested. Two main clusters of positively interrelated leaf traits were identified: in the first cluster were structural features, leaf thickness (Thick(leaf)), mesophyll (M) cell surface area exposed to intercellular air space per unit of leaf surface area (S(mes)), and M cell size; a second group included functional traits, net photosynthetic rate, transpiration rate, M conductance to CO(2) diffusion (g(m)), stomatal conductance to gas diffusion (g(s)), and the g(m)/g(s) ratio.While net photosynthetic rate was positively correlated with gm, neither was significantly linked with any individual structural traits. The results suggest that changes in gm depend on covariations of multiple leaf (S(mes)) and M cell (including cell wall thickness) structural traits. There was an inverse relationship between Thick(leaf) and transpiration rate and a significant positive association between Thick(leaf) and leaf transpiration efficiency. Interestingly, high g(m) together with high g(m)/g(s) and a low S(mes)/g(m) ratio (M resistance to CO(2) diffusion per unit of cell surface area exposed to intercellular air space) appear to be ideal for supporting leaf photosynthesis while preserving water; in addition, thick M cell walls may be beneficial for plant drought tolerance.

Contributions of individual face features to face discrimination.

PubMed

Logan, Andrew J; Gordon, Gael E; Loffler, Gunter

2017-08-01

Faces are highly complex stimuli that contain a host of information. Such complexity poses the following questions: (a) do observers exhibit preferences for specific information? (b) how does sensitivity to individual face parts compare? These questions were addressed by quantifying sensitivity to different face features. Discrimination thresholds were determined for synthetic faces under the following conditions: (i) 'full face': all face features visible; (ii) 'isolated feature': single feature presented in isolation; (iii) 'embedded feature': all features visible, but only one feature modified. Mean threshold elevations for isolated features, relative to full-faces, were 0.84x, 1.08, 2.12, 3.34, 4.07 and 4.47 for head-shape, hairline, nose, mouth, eyes and eyebrows respectively. Hence, when two full faces can be discriminated at threshold, the difference between the eyes is about four times less than what is required when discriminating between isolated eyes. In all cases, sensitivity was higher when features were presented in isolation than when they were embedded within a face context (threshold elevations of 0.94x, 1.74, 2.67, 2.90, 5.94 and 9.94). This reveals a specific pattern of sensitivity to face information. Observers are between two and four times more sensitive to external than internal features. The pattern for internal features (higher sensitivity for the nose, compared to mouth, eyes and eyebrows) is consistent with lower sensitivity for those parts affected by facial dynamics (e.g. facial expressions). That isolated features are easier to discriminate than embedded features supports a holistic face processing mechanism which impedes extraction of information about individual features from full faces. Copyright © 2017 Elsevier Ltd. All rights reserved.

Evolutionary model with genetics, aging, and knowledge

NASA Astrophysics Data System (ADS)

Bustillos, Armando Ticona; de Oliveira, Paulo Murilo

2004-02-01

We represent a process of learning by using bit strings, where 1 bits represent the knowledge acquired by individuals. Two ways of learning are considered: individual learning by trial and error, and social learning by copying knowledge from other individuals or from parents in the case of species with parental care. The age-structured bit string allows us to study how knowledge is accumulated during life and its influence over the genetic pool of a population after many generations. We use the Penna model to represent the genetic inheritance of each individual. In order to study how the accumulated knowledge influences the survival process, we include it to help individuals to avoid the various death situations. Modifications in the Verhulst factor do not show any special feature due to its random nature. However, by adding years to life as a function of the accumulated knowledge, we observe an improvement of the survival rates while the genetic fitness of the population becomes worse. In this latter case, knowledge becomes more important in the last years of life where individuals are threatened by diseases. Effects of offspring overprotection and differences between individual and social learning can also be observed. Sexual selection as a function of knowledge shows some effects when fidelity is imposed.

Chinese wine classification system based on micrograph using combination of shape and structure features

NASA Astrophysics Data System (ADS)

Wan, Yi

2011-06-01

Chinese wines can be classification or graded by the micrographs. Micrographs of Chinese wines show floccules, stick and granule of variant shape and size. Different wines have variant microstructure and micrographs, we study the classification of Chinese wines based on the micrographs. Shape and structure of wines' particles in microstructure is the most important feature for recognition and classification of wines. So we introduce a feature extraction method which can describe the structure and region shape of micrograph efficiently. First, the micrographs are enhanced using total variation denoising, and segmented using a modified Otsu's method based on the Rayleigh Distribution. Then features are extracted using proposed method in the paper based on area, perimeter and traditional shape feature. Eight kinds total 26 features are selected. Finally, Chinese wine classification system based on micrograph using combination of shape and structure features and BP neural network have been presented. We compare the recognition results for different choices of features (traditional shape features or proposed features). The experimental results show that the better classification rate have been achieved using the combinational features proposed in this paper.

Stigmergic construction and topochemical information shape ant nest architecture

PubMed Central

Khuong, Anaïs; Gautrais, Jacques; Perna, Andrea; Sbaï, Chaker; Combe, Maud; Kuntz, Pascale; Jost, Christian; Theraulaz, Guy

2016-01-01

The nests of social insects are not only impressive because of their sheer complexity but also because they are built from individuals whose work is not centrally coordinated. A key question is how groups of insects coordinate their building actions. Here, we use a combination of experimental and modeling approaches to investigate nest construction in the ant Lasius niger. We quantify the construction dynamics and the 3D structures built by ants. Then, we characterize individual behaviors and the interactions of ants with the structures they build. We show that two main interactions are involved in the coordination of building actions: (i) a stigmergic-based interaction that controls the amplification of depositions at some locations and is attributable to a pheromone added by ants to the building material; and (ii) a template-based interaction in which ants use their body size as a cue to control the height at which they start to build a roof from existing pillars. We then develop a 3D stochastic model based on these individual behaviors to analyze the effect of pheromone presence and strength on construction dynamics. We show that the model can quantitatively reproduce key features of construction dynamics, including a large-scale pattern of regularly spaced pillars, the formation and merging of caps over the pillars, and the remodeling of built structures. Finally, our model suggests that the lifetime of the pheromone is a highly influential parameter that controls the growth and form of nest architecture. PMID:26787857

Stigmergic construction and topochemical information shape ant nest architecture.

PubMed

Khuong, Anaïs; Gautrais, Jacques; Perna, Andrea; Sbaï, Chaker; Combe, Maud; Kuntz, Pascale; Jost, Christian; Theraulaz, Guy

2016-02-02

The nests of social insects are not only impressive because of their sheer complexity but also because they are built from individuals whose work is not centrally coordinated. A key question is how groups of insects coordinate their building actions. Here, we use a combination of experimental and modeling approaches to investigate nest construction in the ant Lasius niger. We quantify the construction dynamics and the 3D structures built by ants. Then, we characterize individual behaviors and the interactions of ants with the structures they build. We show that two main interactions are involved in the coordination of building actions: (i) a stigmergic-based interaction that controls the amplification of depositions at some locations and is attributable to a pheromone added by ants to the building material; and (ii) a template-based interaction in which ants use their body size as a cue to control the height at which they start to build a roof from existing pillars. We then develop a 3D stochastic model based on these individual behaviors to analyze the effect of pheromone presence and strength on construction dynamics. We show that the model can quantitatively reproduce key features of construction dynamics, including a large-scale pattern of regularly spaced pillars, the formation and merging of caps over the pillars, and the remodeling of built structures. Finally, our model suggests that the lifetime of the pheromone is a highly influential parameter that controls the growth and form of nest architecture.

Resting State EEG-based biometrics for individual identification using convolutional neural networks.

PubMed

Lan Ma; Minett, James W; Blu, Thierry; Wang, William S-Y

2015-08-01

Biometrics is a growing field, which permits identification of individuals by means of unique physical features. Electroencephalography (EEG)-based biometrics utilizes the small intra-personal differences and large inter-personal differences between individuals' brainwave patterns. In the past, such methods have used features derived from manually-designed procedures for this purpose. Another possibility is to use convolutional neural networks (CNN) to automatically extract an individual's best and most unique neural features and conduct classification, using EEG data derived from both Resting State with Open Eyes (REO) and Resting State with Closed Eyes (REC). Results indicate that this CNN-based joint-optimized EEG-based Biometric System yields a high degree of accuracy of identification (88%) for 10-class classification. Furthermore, rich inter-personal difference can be found using a very low frequency band (0-2Hz). Additionally, results suggest that the temporal portions over which subjects can be individualized is less than 200 ms.

Association Between Borderline Personality Features and Temporal Summation of Second Pain: A Cross-Sectional Study.

PubMed

You, Dokyoung S; Meagher, Mary W

2017-01-01

Individuals with greater borderline personality features may be vulnerable to chronic pain. Because pain is an unpleasant sensory and emotional experience, affect dysregulation as the core personality feature may be linked to pain hypersensitivity. Studies have found that greater borderline features are associated with increased intensity in clinical and experimental pain, and that depression mediates this increase. The current study further examined the association between borderline features and heat pain sensitivity, the contribution of affect dysregulation and the other borderline personality factors (identity problems, negative relationships, self-harming/impulsivity) to the association, and depression as a mediator. Additionally, we examined whether blunted sympathetic responses mediate the association between borderline features and temporal summation of second pain (TSSP). Thermal pain threshold, thermal TSSP and aftersensations pain were assessed in 79 healthy individuals with varying degrees of borderline features. TSSP is a proxy measure for central sensitization and refers to the gradual increase in pain to repeated nociceptive stimuli. A regression analysis showed that greater borderline features predicted greater TSSP (β = .22, p = .050, R 2 = .05). Borderline features were unrelated to pain threshold and TSSP decay. A stepwise regression showed greater TSSP in individuals with greater borderline features was accounted for by the negative relationships factor rather than the affect dysregulation factor. The results of mediational analyses showed depression and blunted sympathetic skin conductance responses mediated the positive association between TSSP and borderline features.

Enhancing facial features by using clear facial features

NASA Astrophysics Data System (ADS)

Rofoo, Fanar Fareed Hanna

2017-09-01

The similarity of features between individuals of same ethnicity motivated the idea of this project. The idea of this project is to extract features of clear facial image and impose them on blurred facial image of same ethnic origin as an approach to enhance a blurred facial image. A database of clear images containing 30 individuals equally divided to five different ethnicities which were Arab, African, Chines, European and Indian. Software was built to perform pre-processing on images in order to align the features of clear and blurred images. And the idea was to extract features of clear facial image or template built from clear facial images using wavelet transformation to impose them on blurred image by using reverse wavelet. The results of this approach did not come well as all the features did not align together as in most cases the eyes were aligned but the nose or mouth were not aligned. Then we decided in the next approach to deal with features separately but in the result in some cases a blocky effect was present on features due to not having close matching features. In general the available small database did not help to achieve the goal results, because of the number of available individuals. The color information and features similarity could be more investigated to achieve better results by having larger database as well as improving the process of enhancement by the availability of closer matches in each ethnicity.

A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning

PubMed Central

Valouev, Anton; Ichikawa, Jeffrey; Tonthat, Thaisan; Stuart, Jeremy; Ranade, Swati; Peckham, Heather; Zeng, Kathy; Malek, Joel A.; Costa, Gina; McKernan, Kevin; Sidow, Arend; Fire, Andrew; Johnson, Steven M.

2008-01-01

Using the massively parallel technique of sequencing by oligonucleotide ligation and detection (SOLiD; Applied Biosystems), we have assessed the in vivo positions of more than 44 million putative nucleosome cores in the multicellular genetic model organism Caenorhabditis elegans. These analyses provide a global view of the chromatin architecture of a multicellular animal at extremely high density and resolution. While we observe some degree of reproducible positioning throughout the genome in our mixed stage population of animals, we note that the major chromatin feature in the worm is a diversity of allowed nucleosome positions at the vast majority of individual loci. While absolute positioning of nucleosomes can vary substantially, relative positioning of nucleosomes (in a repeated array structure likely to be maintained at least in part by steric constraints) appears to be a significant property of chromatin structure. The high density of nucleosomal reads enabled a substantial extension of previous analysis describing the usage of individual oligonucleotide sequences along the span of the nucleosome core and linker. We release this data set, via the UCSC Genome Browser, as a resource for the high-resolution analysis of chromatin conformation and DNA accessibility at individual loci within the C. elegans genome. PMID:18477713

Individual Morphological Brain Network Construction Based on Multivariate Euclidean Distances Between Brain Regions.

PubMed

Yu, Kaixin; Wang, Xuetong; Li, Qiongling; Zhang, Xiaohui; Li, Xinwei; Li, Shuyu

2018-01-01

Morphological brain network plays a key role in investigating abnormalities in neurological diseases such as mild cognitive impairment (MCI) and Alzheimer's disease (AD). However, most of the morphological brain network construction methods only considered a single morphological feature. Each type of morphological feature has specific neurological and genetic underpinnings. A combination of morphological features has been proven to have better diagnostic performance compared with a single feature, which suggests that an individual morphological brain network based on multiple morphological features would be beneficial in disease diagnosis. Here, we proposed a novel method to construct individual morphological brain networks for two datasets by calculating the exponential function of multivariate Euclidean distance as the evaluation of similarity between two regions. The first dataset included 24 healthy subjects who were scanned twice within a 3-month period. The topological properties of these brain networks were analyzed and compared with previous studies that used different methods and modalities. Small world property was observed in all of the subjects, and the high reproducibility indicated the robustness of our method. The second dataset included 170 patients with MCI (86 stable MCI and 84 progressive MCI cases) and 169 normal controls (NC). The edge features extracted from the individual morphological brain networks were used to distinguish MCI from NC and separate MCI subgroups (progressive vs. stable) through the support vector machine in order to validate our method. The results showed that our method achieved an accuracy of 79.65% (MCI vs. NC) and 70.59% (stable MCI vs. progressive MCI) in a one-dimension situation. In a multiple-dimension situation, our method improved the classification performance with an accuracy of 80.53% (MCI vs. NC) and 77.06% (stable MCI vs. progressive MCI) compared with the method using a single feature. The results indicated that our method could effectively construct an individual morphological brain network based on multiple morphological features and could accurately discriminate MCI from NC and stable MCI from progressive MCI, and may provide a valuable tool for the investigation of individual morphological brain networks.

Further delineation of cardio-facio-cutaneous syndrome: clinical features of 38 individuals with proven mutations.

PubMed

Armour, C M; Allanson, J E

2008-04-01

Cardio-facio-cutaneous syndrome (CFC) is a multiple congenital anomaly/mental retardation syndrome named because of a characteristic facies, cardiac anomalies, and ectodermal abnormalities. While considerable literature describes the main features, few studies have documented the frequencies of less common features allowing a greater appreciation of the full phenotype. We have analysed clinical data on 38 individuals with CFC and a confirmed mutation in one of the genes known to cause the condition. We provide data on well-established features, and those that are less often described. Polyhydramnios (77%) and prematurity (49%) were common perinatal issues. 71% of individuals had a cardiac anomaly, the most common being pulmonary valve stenosis (42%), hypertrophic cardiomyopathy (39%), and atrial septal defect (28%). Hair anomalies were also typical: 92% had curly hair, 84% sparse hair, and 86% absent or sparse eyebrows. The most frequent cutaneous features were keratosis pilaris (73%), hyperkeratosis (61%) and nevi (76%). Significant and long lived gastrointestinal dysmotility (71%), seizures (49%), optic nerve hypoplasia (30%) and renal anomalies, chiefly hydronephrosis (20%), were among the less well known issues reported. This study reports a broad range of clinical issues in a large cohort of individuals with molecular confirmation of CFC.

Systematic individualized narrative language intervention on the personal narratives of children with autism.

PubMed

Petersen, Douglas B; Brown, Catherine L; Ukrainetz, Teresa A; Wise, Christine; Spencer, Trina D; Zebre, Jennifer

2014-01-01

The purpose of this study was to investigate the effect of an individualized, systematic language intervention on the personal narratives of children with autism. A single-subject, multiple-baseline design across participants and behaviors was used to examine the effect of the intervention on language features of personal narratives. Three 6- to 8-year-old boys with autism participated in 12 individual intervention sessions that targeted 2-3 story grammar elements (e.g., problem, plan) and 3-4 linguistic complexity elements (e.g., causal subordination, adverbs) selected from each participant's baseline performance. Intervention involved repeated retellings of customized model narratives and the generation of personal narratives with a systematic reduction of visual and verbal scaffolding. Independent personal narratives generated at the end of each baseline, intervention, and maintenance session were analyzed for presence and sophistication of targeted features. Graphical and statistical results showed immediate improvement in targeted language features as a function of intervention. There was mixed evidence of maintenance 2 and 7 weeks after intervention. Children with autism can benefit from an individualized, systematic intervention targeting specific narrative language features. Greater intensity of intervention may be needed to gain enduring effects for some language features.

Bioinspired Cellular Structures: Additive Manufacturing and Mechanical Properties

NASA Astrophysics Data System (ADS)

Stampfl, J.; Pettermann, H. E.; Liska, R.

Biological materials (e.g., wood, trabecular bone, marine skeletons) rely heavily on the use of cellular architecture, which provides several advantages. (1) The resulting structures can bear the variety of "real life" load spectra using a minimum of a given bulk material, featuring engineering lightweight design principles. (2) The inside of the structures is accessible to body fluids which deliver the required nutrients. (3) Furthermore, cellular architectures can grow organically by adding or removing individual struts or by changing the shape of the constituting elements. All these facts make the use of cellular architectures a reasonable choice for nature. Using additive manufacturing technologies (AMT), it is now possible to fabricate such structures for applications in engineering and biomedicine. In this chapter, we present methods that allow the 3D computational analysis of the mechanical properties of cellular structures with open porosity. Various different cellular architectures including disorder are studied. In order to quantify the influence of architecture, the apparent density is always kept constant. Furthermore, it is shown that how new advanced photopolymers can be used to tailor the mechanical and functional properties of the fabricated structures.

Design principles of hair-like structures as biological machines

PubMed Central

2018-01-01

Hair-like structures are prevalent throughout biology and frequently act to sense or alter interactions with an organism's environment. The overall shape of a hair is simple: a long, filamentous object that protrudes from the surface of an organism. This basic design, however, can confer a wide range of functions, owing largely to the flexibility and large surface area that it usually possesses. From this simple structural basis, small changes in geometry, such as diameter, curvature and inter-hair spacing, can have considerable effects on mechanical properties, allowing functions such as mechanosensing, attachment, movement and protection. Here, we explore how passive features of hair-like structures, both individually and within arrays, enable diverse functions across biology. Understanding the relationships between form and function can provide biologists with an appreciation for the constraints and possibilities on hair-like structures. Additionally, such structures have already been used in biomimetic engineering with applications in sensing, water capture and adhesion. By examining hairs as a functional mechanical unit, geometry and arrangement can be rationally designed to generate new engineering devices and ideas. PMID:29848593

Analysis of the Cytomorphological Features in Atypical Urine Specimens following Application of The Paris System for Reporting Urinary Cytology.

PubMed

Glass, Ryan; Rosen, Lisa; Chau, Karen; Sheikh-Fayyaz, Sylvat; Farmer, Peter; Coutsouvelis, Constantinos; Slim, Farah; Brenkert, Ryan; Das, Kasturi; Raab, Stephen; Cocker, Rubina

2018-01-01

This study investigates the use of The Paris System (TPS) for Reporting Urinary Cytopathology and examines the performance of individual and combined morphological features in atypical urine cytologies. We reviewed 118 atypical cytologies with subsequent bladder biopsies for the presence of several morphological features and reclassified them into Paris System categories. The sensitivity and specificity of individual and combined features were calculated along with the risk of malignancy. An elevated nuclear-to-cytoplasmic ratio was only predictive of malignancy if seen in single cells, while irregular nuclear borders, hyperchromasia, and coarse granular chromatin were predictive in single cells and in groups. Identification of coarse chromatin alone yielded a malignancy risk comparable to 2-feature combinations. The use of TPS criteria identified the specimens at a higher risk of malignancy. Our findings support the use of TPS criteria, suggesting that the presence of coarse chromatin is more specific than other individual features, and confirming that cytologic atypia is more worrisome in single cells than in groups. © 2017 S. Karger AG, Basel.

Spontaneous formation of structurally diverse membrane channel architectures from a single antimicrobial peptide

NASA Astrophysics Data System (ADS)

Wang, Yukun; Chen, Charles H.; Hu, Dan; Ulmschneider, Martin B.; Ulmschneider, Jakob P.

2016-11-01

Many antimicrobial peptides (AMPs) selectively target and form pores in microbial membranes. However, the mechanisms of membrane targeting, pore formation and function remain elusive. Here we report an experimentally guided unbiased simulation methodology that yields the mechanism of spontaneous pore assembly for the AMP maculatin at atomic resolution. Rather than a single pore, maculatin forms an ensemble of structurally diverse temporarily functional low-oligomeric pores, which mimic integral membrane protein channels in structure. These pores continuously form and dissociate in the membrane. Membrane permeabilization is dominated by hexa-, hepta- and octamers, which conduct water, ions and small dyes. Pores form by consecutive addition of individual helices to a transmembrane helix or helix bundle, in contrast to current poration models. The diversity of the pore architectures--formed by a single sequence--may be a key feature in preventing bacterial resistance and could explain why sequence-function relationships in AMPs remain elusive.

Growth Structure and Properties of Gradient Nanocrystalline Coatings of the Ti-Al-Si-Cu-N System

NASA Astrophysics Data System (ADS)

Ovchinnikov, S. V.; Pinzhin, Yu. P.

2016-10-01

Methods of electron microprobe analysis, X-ray structure analysis and electron microscopy were used to study the element composition and features of the structure-phase, elastic stress state of nanocrystalline coatings of the Ti- Al- Si- Cu- N system with gradient of copper concentration across their thickness. The authors established the effects of element composition modification, non-monotonous behavior of the lattice constant of alloyed nitride and rise in the bending-torsion value of the crystalline lattice in individual nanocrystals to values of around 400 degrees/μm with increase in copper concentration, whereas the sizes of alloyed nitride crystals remained practically unchanged. Mechanical (hardness), adhesion and tribological properties of coatings were examined. Comparative analysis demonstrates higher values of adhesion characteristics in the case of gradient coatings of the Ti- Al- Si- Cu- N system than in the case of single-layer (with constant element concentration) analogues.

Genetic variability, individuality and the evolution of the mammalian brain.

PubMed

Lipp, H P

1995-12-01

The neo-Darwinian theory of evolution has difficulty in explaining the rapid evolution of mammalian brain and behavior. I shall argue that the plasticity mechanisms of the brain (i.e., system homeostasis, developmental reorganization, structural adult plasticity, and cognition and learning) have evolved primarily as genetic buffer systems which protect subtle mutations influencing brain structures from natural selection. These buffer systems permit accumulation of genetic variation in the higher system levels of the brain (simply defined as structures with late differentiation), while low-level systems are kept constant by natural selection. The organization of this intrinsic genetic buffering system provides several features facilitating neo-Darwinian evolution: In conclusion, the evolutionary appearance of cognition and intelligence is an ordinary biological mechanism compensating evolutionary drags such as long lifespans and fewer offspring. The concept has heuristic value for identifying gene-brain-behavior relationships and for explaining behavioral consequences of artifical gene deletions.

Single Molecule Stepping and Structural Dynamics of Myosin X

PubMed Central

Sun, Yujie; Sato, Osamu; Ruhnow, Felix; Arsenault, Mark E.; Ikebe, Mitsuo; Goldman, Yale E.

2010-01-01

Myosin X is an unconventional myosin with puzzling motility properties. We studied the motility of dimerized myosin X using single molecule fluorescence techniques – polTIRF, FIONA, and Parallax to measure rotation angles and 3-dimensional position of the molecule during its walk. It was found that Myosin X steps processively in a hand-over-hand manner following a left-handed helical path along both single actin filaments and bundles. Its step size and velocity are smaller on actin bundles than individual filaments, suggesting myosin X often steps onto neighboring filaments in a bundle. The data suggest that a previously postulated single α-helical domain mechanically extends the 3-IQ motif lever arm and either the neck-tail hinge or the tail is flexible. These structural features, in conjunction with the membrane and microtubule binding domains, enable myosin X to perform multiple functions on varied actin structures in cells. PMID:20364131

Mineral exploration potential of ERTS-1 data

NASA Technical Reports Server (NTRS)

Brewer, W. A. (Principal Investigator); Erskine, M. C., Jr.; Prindle, R. O.

1972-01-01

The author has identified the following significant results. Preliminary analysis of a mosaic composing eight individual ERTS frames (1:1,000,000) extending well beyond the test site has revealed a number of tectonic structural trends that are controlled by regional lineations. So far most of the regional lineations fall into three general directions: east by northeast, northwest, and north-south. From preliminary examination, it appears that the older Precambrian basement predominates in the NE-bearing structural trends, whereas the predominate NW trend is most likely associated with the Texas Structural Zone, and the north-south trend being the Utah-Arizona belt and/or part of the southern Basin and Range Province. One major lineation, made up of many parallel lineations, is noticeable just north of Lake Pleasant which extends for approximately 100 miles in a northern direction out of the target area. This feature corresponds to a Precambrian schist formation shown on the USGS geologic map of Arizona.

Natural products as an inspiration in the diversity-oriented synthesis of bioactive compound libraries

PubMed Central

Cordier, Christopher; Morton, Daniel; Murrison, Sarah; O'Leary-Steele, Catherine

2008-01-01

The purpose of diversity-oriented synthesis is to drive the discovery of small molecules with previously unknown biological functions. Natural products necessarily populate biologically relevant chemical space, since they bind both their biosynthetic enzymes and their target macromolecules. Natural product families are, therefore, libraries of pre-validated, functionally diverse structures in which individual compounds selectively modulate unrelated macromolecular targets. This review describes examples of diversity-oriented syntheses which have, to some extent, been inspired by the structures of natural products. Particular emphasis is placed on innovations that allow the synthesis of compound libraries that, like natural products, are skeletally diverse. Mimicking the broad structural features of natural products may allow the discovery of compounds that modulate the functions of macromolecules for which ligands are not known. The ability of innovations in diversity-oriented synthesis to deliver such compounds is critically assessed. PMID:18663392

Hippocampal dentation: Structural variation and its association with episodic memory in healthy adults.

PubMed

Fleming Beattie, Julia; Martin, Roy C; Kana, Rajesh K; Deshpande, Hrishikesh; Lee, Seongtaek; Curé, Joel; Ver Hoef, Lawrence

2017-07-01

While the hippocampus has long been identified as a structure integral to memory, the relationship between morphology and function has yet to be fully explained. We present an analysis of hippocampal dentation, a morphological feature previously unexplored in regard to its relationship with episodic memory. "Hippocampal dentation" in this case refers to surface convolutions, primarily present in the CA1/subiculum on the inferior aspect of the hippocampus. Hippocampal dentation was visualized using ultra-high resolution structural MRI and evaluated using a novel visual rating scale. The degree of hippocampal dentation was found to vary considerably across individuals, and was positively associated with verbal memory recall and visual memory recognition in a sample of 22 healthy adults. This study is the first to characterize the variation in hippocampal dentation in a healthy cohort and to demonstrate its association with aspects of episodic memory. Copyright © 2017 Elsevier Ltd. All rights reserved.

Aluminum nanostructures with strong visible-range SERS activity for versatile micropatterning of molecular security labels.

PubMed

Lay, Chee Leng; Koh, Charlynn Sher Lin; Wang, Jing; Lee, Yih Hong; Jiang, Ruibin; Yang, Yijie; Yang, Zhe; Phang, In Yee; Ling, Xing Yi

2018-01-03

The application of aluminum (Al)-based nanostructures for visible-range plasmonics, especially for surface-enhanced Raman scattering (SERS), currently suffers from inconsistent local electromagnetic field distributions and/or inhomogeneous distribution of probe molecules. Herein, we lithographically fabricate structurally uniform Al nanostructures which enable homogeneous adsorption of various probe molecules. Individual Al nanostructures exhibit strong local electromagnetic field enhancements, in turn leading to intense SERS activity. The average SERS enhancement factor (EF) for individual nanostructures exceeds 10 4 for non-resonant probe molecules in the visible spectrum. These Al nanostructures also retain more than 70% of their original SERS intensities after one-month storage, displaying superb stability under ambient conditions. We further achieve tunable polarization-dependent SERS responses using anisotropic Al nanostructures, facilitating the design of sophisticated SERS-based security labels. Our micron-sized security label comprises two-tier security features, including a machine-readable hybrid quick-response (QR) code overlaid with a set of ciphertexts. Our work demonstrates the versatility of Al-based structures in low-cost modern chemical nano-analytics and forgery protection.

Body structure and composition of canoeists and kayakers: analysis of junior and teenage polish national canoeing team.

PubMed

Hagner-Derengowska, M; Hagner, W; Zubrzycki, Iz; Krakowiak, H; Słomko, W; Dzierżanowski, M; Rakowski, A; Wiącek-Zubrzycka, M

2014-12-01

The somatic build, biological age, general state of health, mental predisposition and physical fitness are the criteria for selection of individuals in competitive sport. The present study aims to analys the differences in body structure and composition of canoeists and kayakers and derive conclusions regarding the criteria for selection of individuals incompetitive sport. The research was conducted on a group of 32 men aged between 17 and 22: 16 kayakers and 16 Canadian canoeists of the junior and teenage Polish national canoeing team. Body composition was examined by means of bioelectrical segmental impedance. Body build type was determined using the anthropometric Heath-Carter method. Statistical analysis was performed using the Welch t-test. The examination of morphological features reveals significant differences in the studied parameters between the canoeists and kayakers. There are also significant differences between competitors of the Sydney 2000 Olympic Games and the studied group. We found that competitive kayakers should be taller than canoeists. The lower part of the body in kayakers is more developed than in canoeists and canoeists are more dehydrated than kayakers.

Analysis and modeling of heat-labile enterotoxins of Escherichia coli suggests a novel space with insights into receptor preference.

PubMed

Krishna Raja, M; Ghosh, Asit Ranjan; Vino, S; Sajitha Lulu, S

2015-01-01

Features of heat-labile enterotoxins of Escherichia coli which make them fit to use as novel receptors for antidiarrheals are not completely explored. Data-set of 14 different serovars of enterotoxigenic Escherichia coli producing heat-labile toxins were taken from NCBI Genbank database and used in the study. Sequence analysis showed mutations in different subunits and also at their interface residues. As these toxins lack crystallography structures, homology modeling using Modeller 9.11 led to the structural approximation for the E. coli producing heat-labile toxins. Interaction of modeled toxin subunits with proanthocyanidin, an antidiarrheal showed several strong hydrogen bonding interactions at the cost of minimized energy. The hits were subsequently characterized by molecular dynamics simulation studies to monitor their binding stabilities. This study looks into novel space where the ligand can choose the receptor preference not as a whole but as an individual subunit. Mutation at interface residues and interaction among subunits along with the binding of ligand to individual subunits would help to design a non-toxic labile toxin and also to improve the therapeutics.

Resolving the Spatial Structures of Bound Hole States in Black Phosphorus.

PubMed

Qiu, Zhizhan; Fang, Hanyan; Carvalho, Alexandra; Rodin, A S; Liu, Yanpeng; Tan, Sherman J R; Telychko, Mykola; Lv, Pin; Su, Jie; Wang, Yewu; Castro Neto, A H; Lu, Jiong

2017-11-08

Understanding the local electronic properties of individual defects and dopants in black phosphorus (BP) is of great importance for both fundamental research and technological applications. Here, we employ low-temperature scanning tunnelling microscope (LT-STM) to probe the local electronic structures of single acceptors in BP. We demonstrate that the charge state of individual acceptors can be reversibly switched by controlling the tip-induced band bending. In addition, acceptor-related resonance features in the tunnelling spectra can be attributed to the formation of Rydberg-like bound hole states. The spatial mapping of the quantum bound states shows two distinct shapes evolving from an extended ellipse shape for the 1s ground state to a dumbbell shape for the 2p x excited state. The wave functions of bound hole states can be well-described using the hydrogen-like model with anisotropic effective mass, corroborated by our theoretical calculations. Our findings not only provide new insight into the many-body interactions around single dopants in this anisotropic two-dimensional material but also pave the way to the design of novel quantum devices.

Wrinkle ridges on Venusian plains: Indicators of shallow crustal stress orientations at local and regional scales

NASA Technical Reports Server (NTRS)

Mcgill, George E.

1992-01-01

The plains regions of Venus exhibit a complex array of structural features, including deformation belts of various types, wrinkle ridges, grabens, and enigmatic radar-bright linears. Probably the most pervasive of these structures are the wrinkle ridges, which appear to be morphologically identical to their counterparts on the Moon and Mars. Almost all workers agree that wrinkle ridges result from horizontal compressive stresses in the crust; they either are explained as flexural fold structures, or alternatively as scarps or folds related to reverse faults. Wrinkle ridges generally are narrow, have small amplitudes, and commonly are closely spaced as well, characteristics that imply a shallow crustal origin. If wrinkle ridges are due to horizontally directed compressive stresses in the shallow crust, as generally has been inferred, then the trends of these features provide a means to map both local and regional orientations of principal stresses in the uppermost part of the venusian crust: maximum compressive stress is normal to the ridges, minimum compressive stress is normal to the topographic surface, and thus the wrinkle ridge trends trace the orientation of the intermediate principal stress. Because there are few plains areas on Venus totally devoid of wrinkle ridges, it should be possible to establish a number of interesting relationships on a near-global scale by mapping the trends of wrinkle ridges wherever they occur. The present study is addressing three questions: (1) Do the trends of wrinkle ridges define domains that are large relative to the sizes of individual plains regions? If so, can these domains be related to large-scale topographic or geologic features? (2) Are regional trends of wrinkle ridges affected by local features such as coronae? If so, is it possible to determine the relative ages of the far-field and local stresses from detailed study of trend inheritance or superposition relationships? (3) What is the relationship between wrinkle ridges and the larger ridges that make up ridge belts?

PredPPCrys: Accurate Prediction of Sequence Cloning, Protein Production, Purification and Crystallization Propensity from Protein Sequences Using Multi-Step Heterogeneous Feature Fusion and Selection

PubMed Central

Wang, Huilin; Wang, Mingjun; Tan, Hao; Li, Yuan; Zhang, Ziding; Song, Jiangning

2014-01-01

X-ray crystallography is the primary approach to solve the three-dimensional structure of a protein. However, a major bottleneck of this method is the failure of multi-step experimental procedures to yield diffraction-quality crystals, including sequence cloning, protein material production, purification, crystallization and ultimately, structural determination. Accordingly, prediction of the propensity of a protein to successfully undergo these experimental procedures based on the protein sequence may help narrow down laborious experimental efforts and facilitate target selection. A number of bioinformatics methods based on protein sequence information have been developed for this purpose. However, our knowledge on the important determinants of propensity for a protein sequence to produce high diffraction-quality crystals remains largely incomplete. In practice, most of the existing methods display poorer performance when evaluated on larger and updated datasets. To address this problem, we constructed an up-to-date dataset as the benchmark, and subsequently developed a new approach termed ‘PredPPCrys’ using the support vector machine (SVM). Using a comprehensive set of multifaceted sequence-derived features in combination with a novel multi-step feature selection strategy, we identified and characterized the relative importance and contribution of each feature type to the prediction performance of five individual experimental steps required for successful crystallization. The resulting optimal candidate features were used as inputs to build the first-level SVM predictor (PredPPCrys I). Next, prediction outputs of PredPPCrys I were used as the input to build second-level SVM classifiers (PredPPCrys II), which led to significantly enhanced prediction performance. Benchmarking experiments indicated that our PredPPCrys method outperforms most existing procedures on both up-to-date and previous datasets. In addition, the predicted crystallization targets of currently non-crystallizable proteins were provided as compendium data, which are anticipated to facilitate target selection and design for the worldwide structural genomics consortium. PredPPCrys is freely available at http://www.structbioinfor.org/PredPPCrys. PMID:25148528

Lipidomic profiling reveals distinct differences in plasma lipid composition in healthy, prediabetic, and type 2 diabetic individuals

PubMed Central

Zhong, Huanzi; Fang, Chao; Fan, Yanqun; Lu, Yan; Wen, Bo; Ren, Huahui; Hou, Guixue; Yang, Fangming; Xie, Hailiang; Jie, Zhuye; Peng, Ye; Ye, Zhiqiang; Wu, Jiegen; Zi, Jin; Zhao, Guoqing; Chen, Jiayu; Bao, Xiao; Hu, Yihe; Gao, Yan; Zhang, Jun; Yang, Huanming; Wang, Jian; Madsen, Lise; Kristiansen, Karsten

2017-01-01

Abstract The relationship between dyslipidemia and type 2 diabetes mellitus (T2D) has been extensively reported, but the global lipid profiles, especially in the East Asia population, associated with the development of T2D remain to be characterized. Liquid chromatography coupled to tandem mass spectrometry was applied to detect the global lipidome in the fasting plasma of 293 Chinese individuals, including 114 T2D patients, 81 prediabetic subjects, and 98 individuals with normal glucose tolerance (NGT). Both qualitative and quantitative analyses revealed a gradual change in plasma lipid features with T2D patients exhibiting characteristics close to those of prediabetic individuals, whereas they differed significantly from individuals with NGT. We constructed and validated a random forest classifier with 28 lipidomic features that effectively discriminated T2D from NGT or prediabetes. Most of the selected features significantly correlated with diabetic clinical indices. Hydroxybutyrylcarnitine was positively correlated with fasting plasma glucose, 2-hour postprandial glucose, glycated hemoglobin, and insulin resistance index (HOMA-IR). Lysophosphatidylcholines such as lysophosphatidylcholine (18:0), lysophosphatidylcholine (18:1), and lysophosphatidylcholine (18:2) were all negatively correlated with HOMA-IR. The altered plasma lipidome in Chinese T2D and prediabetic subjects suggests that lipid features may play a role in the pathogenesis of T2D and that such features may provide a basis for evaluating risk and monitoring disease development. PMID:28505362

Cerebellum and personality traits.

PubMed

Petrosini, Laura; Cutuli, Debora; Picerni, Eleonora; Laricchiuta, Daniela

2015-02-01

Personality traits are multidimensional traits comprising cognitive, emotional, and behavioral characteristics, and a wide array of cerebral structures mediate individual variability. Differences in personality traits covary with brain morphometry in specific brain regions. A cerebellar role in emotional and affective processing and on personality characteristics has been suggested. In a large sample of healthy subjects of both sexes and differently aged, the macro- and micro-structural variations of the cerebellum were correlated with the scores obtained in the Temperament and Character Inventory (TCI) by Cloninger. Cerebellar volumes were associated positively with Novelty Seeking scores and negatively with Harm Avoidance scores. Given the cerebellar contribution in personality traits and emotional processing, we investigated the cerebellar involvement even in alexithymia, construct of personality characterized by impairment in cognitive, emotional, and affective processing. Interestingly, the subjects with high alexithymic traits had larger volumes in the bilateral Crus 1. The cerebellar substrate for some personality dimensions extends the relationship between personality and brain areas to a structure up to now thought to be involved mainly in motor and cognitive functions, much less in emotional processes and even less in personality individual differences. The enlarged volumes of Crus 1 in novelty seekers and alexithymics support the tendency to action featuring both personality constructs. In fact, Novelty Seeking and alexithymia are rooted in behavior and inescapably have a strong action component, resulting in stronger responses in the structures more focused on action and embodiment, as the cerebellum is.

Structure and origin of Australian ring and dome features with reference to the search for asteroid impact events

NASA Astrophysics Data System (ADS)

Glikson, Andrew

2018-01-01

Ring, dome and crater features on the Australian continent and shelf include (A) 38 structures of confirmed or probable asteroid and meteorite impact origin and (B) numerous buried and exposed ring, dome and crater features of undefined origin. A large number of the latter include structural and geophysical elements consistent with impact structures, pending test by field investigations and/or drilling. This paper documents and briefly describes 43 ring and dome features with the aim of appraising their similarities and differences from those of impact structures. Discrimination between impact structures and igneous plugs, volcanic caldera and salt domes require field work and/or drilling. Where crater-like morphological patterns intersect pre-existing linear structural features and contain central morphological highs and unique thrust and fault patterns an impact connection needs to tested in the field. Hints of potential buried impact structures may be furnished by single or multi-ring TMI patterns, circular TMI quiet zones, corresponding gravity patterns, low velocity and non-reflective seismic zones.

Asymmetries in visual search for conjunctive targets.

PubMed

Cohen, A

1993-08-01

Asymmetry is demonstrated between conjunctive targets in visual search with no detectable asymmetries between the individual features that compose these targets. Experiment 1 demonstrated this phenomenon for targets composed of color and shape. Experiment 2 and 4 demonstrate this asymmetry for targets composed of size and orientation and for targets composed of contrast level and orientation, respectively. Experiment 3 demonstrates that search rate of individual features cannot predict search rate for conjunctive targets. These results demonstrate the need for 2 levels of representations: one of features and one of conjunction of features. A model related to the modified feature integration theory is proposed to account for these results. The proposed model and other models of visual search are discussed.

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

Heredia-Langner, Alejandro; Amidan, Brett G.; Matzner, Shari

We present results from the optimization of a re-identification process using two sets of biometric data obtained from the Civilian American and European Surface Anthropometry Resource Project (CAESAR) database. The datasets contain real measurements of features for 2378 individuals in a standing (43 features) and seated (16 features) position. A genetic algorithm (GA) was used to search a large combinatorial space where different features are available between the probe (seated) and gallery (standing) datasets. Results show that optimized model predictions obtained using less than half of the 43 gallery features and data from roughly 16% of the individuals available producemore » better re-identification rates than two other approaches that use all the information available.« less

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.

Schooling Increases Risk Exposure for Fish Navigating Past Artificial Barriers

PubMed Central

Lemasson, Bertrand H.; Haefner, James W.; Bowen, Mark D.

2014-01-01

Artificial barriers have become ubiquitous features in freshwater ecosystems and they can significantly impact a region's biodiversity. Assessing the risk faced by fish forced to navigate their way around artificial barriers is largely based on assays of individual swimming behavior. However, social interactions can significantly influence fish movement patterns and alter their risk exposure. Using an experimental flume, we assessed the effects of social interactions on the amount of time required for juvenile palmetto bass (Morone chrysops × M. saxatilis) to navigate downstream past an artificial barrier. Fish were released either individually or in groups into the flume using flow conditions that approached the limit of their expected swimming stamina. We compared fish swimming behaviors under solitary and schooling conditions and measured risk as the time individuals spent exposed to the barrier. Solitary fish generally turned with the current and moved quickly downstream past the barrier, while fish in groups swam against the current and displayed a 23-fold increase in exposure time. Solitary individuals also showed greater signs of skittish behavior than those released in groups, which was reflected by larger changes in their accelerations and turning profiles. While groups displayed fission-fusion dynamics, inter-individual positions were highly structured and remained steady over time. These spatial patterns align with theoretical positions necessary to reduce swimming exertion through either wake capturing or velocity sheltering, but diverge from any potential gains from channeling effects between adjacent neighbors. We conclude that isolated performance trials and projections based on individual behaviors can lead to erroneous predictions of risk exposure along engineered structures. Our results also suggest that risk perception and behavior may be more important than a fish's swimming stamina in artificially modified systems. PMID:25268736

Schooling increases risk exposure for fish navigating past artificial barriers.

PubMed

Lemasson, Bertrand H; Haefner, James W; Bowen, Mark D

2014-01-01

Artificial barriers have become ubiquitous features in freshwater ecosystems and they can significantly impact a region's biodiversity. Assessing the risk faced by fish forced to navigate their way around artificial barriers is largely based on assays of individual swimming behavior. However, social interactions can significantly influence fish movement patterns and alter their risk exposure. Using an experimental flume, we assessed the effects of social interactions on the amount of time required for juvenile palmetto bass (Morone chrysops × M. saxatilis) to navigate downstream past an artificial barrier. Fish were released either individually or in groups into the flume using flow conditions that approached the limit of their expected swimming stamina. We compared fish swimming behaviors under solitary and schooling conditions and measured risk as the time individuals spent exposed to the barrier. Solitary fish generally turned with the current and moved quickly downstream past the barrier, while fish in groups swam against the current and displayed a 23-fold increase in exposure time. Solitary individuals also showed greater signs of skittish behavior than those released in groups, which was reflected by larger changes in their accelerations and turning profiles. While groups displayed fission-fusion dynamics, inter-individual positions were highly structured and remained steady over time. These spatial patterns align with theoretical positions necessary to reduce swimming exertion through either wake capturing or velocity sheltering, but diverge from any potential gains from channeling effects between adjacent neighbors. We conclude that isolated performance trials and projections based on individual behaviors can lead to erroneous predictions of risk exposure along engineered structures. Our results also suggest that risk perception and behavior may be more important than a fish's swimming stamina in artificially modified systems.

Preferential selection based on degree difference in the spatial prisoner's dilemma games

NASA Astrophysics Data System (ADS)

Huang, Changwei; Dai, Qionglin; Cheng, Hongyan; Li, Haihong

2017-10-01

Strategy evolution in spatial evolutionary games is generally implemented through imitation processes between individuals. In most previous studies, it is assumed that individuals pick up one of their neighbors randomly to learn from. However, by considering the heterogeneity of individuals' influence in the real society, preferential selection is more realistic. Here, we introduce a preferential selection mechanism based on degree difference into spatial prisoner's dilemma games on Erdös-Rényi networks and Barabási-Albert scale-free networks and investigate the effects of the preferential selection on cooperation. The results show that, when the individuals prefer to choose the neighbors who have small degree difference with themselves to imitate, cooperation is hurt by the preferential selection. In contrast, when the individuals prefer to choose those large degree difference neighbors to learn from, there exists optimal preference strength resulting in the maximal cooperation level no matter what the network structure is. In addition, we investigate the robustness of the results against variations of the noise, the average degree and the size of network in the model, and find that the qualitative features of the results are unchanged.

Perceiving goals and actions in individuals with autism spectrum disorders.

PubMed

Zalla, Tiziana; Labruyère, Nelly; Georgieff, Nicolas

2013-10-01

In the present study, we investigated the ability to parse familiar sequences of action into meaningful events in young individuals with autism spectrum disorders (ASDs), as compared to young individuals with typical development (TD) and young individuals with moderate mental retardation or learning disabilities (MLDs). While viewing two videotaped movies, participants were requested to detect the boundary transitions between component events at both fine and coarse levels of the action hierarchical structure. Overall, reduced accuracy for event detection was found in participants with ASDs, relative to participants with TD, at both levels of action segmentation. The performance was, however, equally diminished in participants with ASDs and MLDs under the course-grained segmentation suggesting that difficulties to detect fine-grained events in ASDs cannot be explained by a general intellectual dysfunction. Reduced accuracy for event detection was related to diminished event recall, memory for event sequence and Theory of Mind abilities. We hypothesized that difficulties with event detection result from a deficit disrupting the on-line processing of kinematic features and physical changes of dynamic human actions. An impairment at the earlier stages of the event encoding process might contribute to deficits in episodic memory and social functioning in individuals with ASDs.

Modeling process-structure-property relationships for additive manufacturing

NASA Astrophysics Data System (ADS)

Yan, Wentao; Lin, Stephen; Kafka, Orion L.; Yu, Cheng; Liu, Zeliang; Lian, Yanping; Wolff, Sarah; Cao, Jian; Wagner, Gregory J.; Liu, Wing Kam

2018-02-01

This paper presents our latest work on comprehensive modeling of process-structure-property relationships for additive manufacturing (AM) materials, including using data-mining techniques to close the cycle of design-predict-optimize. To illustrate the processstructure relationship, the multi-scale multi-physics process modeling starts from the micro-scale to establish a mechanistic heat source model, to the meso-scale models of individual powder particle evolution, and finally to the macro-scale model to simulate the fabrication process of a complex product. To link structure and properties, a highefficiency mechanistic model, self-consistent clustering analyses, is developed to capture a variety of material response. The model incorporates factors such as voids, phase composition, inclusions, and grain structures, which are the differentiating features of AM metals. Furthermore, we propose data-mining as an effective solution for novel rapid design and optimization, which is motivated by the numerous influencing factors in the AM process. We believe this paper will provide a roadmap to advance AM fundamental understanding and guide the monitoring and advanced diagnostics of AM processing.

Unravelling surface and interfacial structures of a metal-organic framework by transmission electron microscopy.

PubMed

Zhu, Yihan; Ciston, Jim; Zheng, Bin; Miao, Xiaohe; Czarnik, Cory; Pan, Yichang; Sougrat, Rachid; Lai, Zhiping; Hsiung, Chia-En; Yao, Kexin; Pinnau, Ingo; Pan, Ming; Han, Yu

2017-05-01

Metal-organic frameworks (MOFs) are crystalline porous materials with designable topology, porosity and functionality, having promising applications in gas storage and separation, ion conduction and catalysis. It is challenging to observe MOFs with transmission electron microscopy (TEM) due to the extreme instability of MOFs upon electron beam irradiation. Here, we use a direct-detection electron-counting camera to acquire TEM images of the MOF ZIF-8 with an ultralow dose of 4.1 electrons per square ångström to retain the structural integrity. The obtained image involves structural information transferred up to 2.1 Å, allowing the resolution of individual atomic columns of Zn and organic linkers in the framework. Furthermore, TEM reveals important local structural features of ZIF-8 crystals that cannot be identified by diffraction techniques, including armchair-type surface terminations and coherent interfaces between assembled crystals. These observations allow us to understand how ZIF-8 crystals self-assemble and the subsequent influence of interfacial cavities on mass transport of guest molecules.

Unravelling surface and interfacial structures of a metal-organic framework by transmission electron microscopy

NASA Astrophysics Data System (ADS)

Zhu, Yihan; Ciston, Jim; Zheng, Bin; Miao, Xiaohe; Czarnik, Cory; Pan, Yichang; Sougrat, Rachid; Lai, Zhiping; Hsiung, Chia-En; Yao, Kexin; Pinnau, Ingo; Pan, Ming; Han, Yu

2017-05-01

Metal-organic frameworks (MOFs) are crystalline porous materials with designable topology, porosity and functionality, having promising applications in gas storage and separation, ion conduction and catalysis. It is challenging to observe MOFs with transmission electron microscopy (TEM) due to the extreme instability of MOFs upon electron beam irradiation. Here, we use a direct-detection electron-counting camera to acquire TEM images of the MOF ZIF-8 with an ultralow dose of 4.1 electrons per square ångström to retain the structural integrity. The obtained image involves structural information transferred up to 2.1 Å, allowing the resolution of individual atomic columns of Zn and organic linkers in the framework. Furthermore, TEM reveals important local structural features of ZIF-8 crystals that cannot be identified by diffraction techniques, including armchair-type surface terminations and coherent interfaces between assembled crystals. These observations allow us to understand how ZIF-8 crystals self-assemble and the subsequent influence of interfacial cavities on mass transport of guest molecules.

[Personality Traits Screening in a Colombian Adult Population Sample - Colombian National Survey of Mental Health-2015].

PubMed

Oviedo, Gabriel Fernando; Gómez-Restrepo, Carlos; Rondón, Martín; Borda Bohigas, Juan Pablo; Tamayo Martínez, Nathalie

2016-12-01

Personality refers to the individual style in characteristic patterns of thinking, feeling and behaving. Traits may configure a personality disorder when there is a long-lasting rigid pattern of inner experience that deviates from the expectations of the individual's culture, are inflexible and form maladaptative schemes in different interpersonal scenarios. Given the pervasiveness of this structure, they cause impairment of functioning in the affected person. To establish the prevalence of personality traits in all selected adults, using the module-structured interview WHO WHM-CIDI-CAPI for clusters A, B and C of personality traits. Colombian National Survey on Mental Health with persons older than 18 years of age. Personality traits that are the most frequently described: Cluster A 46% (95%CI, 45.2-48.1) of people believe they are convinced that there are conspiracies behind many things in the world. Regarding the features of cluster B, 35.6% (95%CI, 34.2-37.0) of the population reports that generally they do not feel bad when offending or upsetting someone and 35.4% (95%CI, 33.9-36.8) refer to show feelings to anyone. The highest proportion of traits were found to the probable borderline personality disorder, as 4.6% (95%CI, 4.1-5.2) of the Colombian population aged 18 and older has 6 or more features of this type, and is the widely reported as an individual entity with similar rates in men and women. The high prevalence of disruptive personality traits requires more research. The high prevalence reported for borderline personality traits suggests the need to implement measures to improve and integrate a collaborative model of care for people afflicted with a possible borderline personality disorder. Copyright © 2016 Asociación Colombiana de Psiquiatría. Publicado por Elsevier España. All rights reserved.

Local topography shapes fine-scale spatial genetic structure in the Arkansas Valley evening primrose, Oenothera harringtonii (Onagraceae).

PubMed

Rhodes, Matthew K; Fant, Jeremie B; Skogen, Krissa A

2014-01-01

Identifying factors that shape the spatial distribution of genetic variation is crucial to understanding many population- and landscape-level processes. In this study, we explore fine-scale spatial genetic structure in Oenothera harringtonii (Onagraceae), an insect-pollinated, gravity-dispersed herb endemic to the grasslands of south-central and southeastern Colorado, USA. We genotyped 315 individuals with 11 microsatellite markers and utilized a combination of spatial autocorrelation analyses and landscape genetic models to relate life history traits and landscape features to dispersal processes. Spatial genetic structure was consistent with theoretical expectations of isolation by distance, but this pattern was weak (Sp = 0.00374). Anisotropic analyses indicated that spatial genetic structure was markedly directional, in this case consistent with increased dispersal along prominent slopes. Landscape genetic models subsequently confirmed that spatial genetic variation was significantly influenced by local topographic heterogeneity, specifically that geographic distance, elevation and aspect were important predictors of spatial genetic structure. Among these variables, geographic distance was ~68% more important than elevation in describing spatial genetic variation, and elevation was ~42% more important than aspect after removing the effect of geographic distance. From these results, we infer a mechanism of hydrochorous seed dispersal along major drainages aided by seasonal monsoon rains. Our findings suggest that landscape features may shape microevolutionary processes at much finer spatial scales than typically considered, and stress the importance of considering how particular dispersal vectors are influenced by their environmental context. © The American Genetic Association 2014. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Social network cohesion in school classes promotes prosocial behavior

PubMed Central

Crone, Eveline A.; Meuwese, Rosa; Güroğlu, Berna

2018-01-01

Adolescence is a key period of social development at the end of which individuals are expected to take on adult social roles. The school class, as the most salient peer group, becomes the prime environment that impacts social development during adolescence. Using social network analyses, we investigated how individual and group level features are related to prosocial behavior and social capital (generalized trust). We mapped the social networks within 22 classrooms of adolescents aged between 12 and 18 years (N = 611), and collected data on social behaviors towards peers. Our results indicate that individuals with high centrality show both higher levels of prosocial behavior and relational aggression. Importantly, greater social cohesion in the classroom was associated with (1) reduced levels of antisocial behavior towards peers and (2) increased generalized trust. These results provide novel insights in the relationship between social structure and social behavior, and stress the importance of the school environment in the development of not only intellectual but also social capital. PMID:29617405

Social network cohesion in school classes promotes prosocial behavior.

PubMed

van den Bos, Wouter; Crone, Eveline A; Meuwese, Rosa; Güroğlu, Berna

2018-01-01

Adolescence is a key period of social development at the end of which individuals are expected to take on adult social roles. The school class, as the most salient peer group, becomes the prime environment that impacts social development during adolescence. Using social network analyses, we investigated how individual and group level features are related to prosocial behavior and social capital (generalized trust). We mapped the social networks within 22 classrooms of adolescents aged between 12 and 18 years (N = 611), and collected data on social behaviors towards peers. Our results indicate that individuals with high centrality show both higher levels of prosocial behavior and relational aggression. Importantly, greater social cohesion in the classroom was associated with (1) reduced levels of antisocial behavior towards peers and (2) increased generalized trust. These results provide novel insights in the relationship between social structure and social behavior, and stress the importance of the school environment in the development of not only intellectual but also social capital.

Tracking employment shocks using mobile phone data

PubMed Central

Toole, Jameson L.; Lin, Yu-Ru; Muehlegger, Erich; Shoag, Daniel; González, Marta C.; Lazer, David

2015-01-01

Can data from mobile phones be used to observe economic shocks and their consequences at multiple scales? Here we present novel methods to detect mass layoffs, identify individuals affected by them and predict changes in aggregate unemployment rates using call detail records (CDRs) from mobile phones. Using the closure of a large manufacturing plant as a case study, we first describe a structural break model to correctly detect the date of a mass layoff and estimate its size. We then use a Bayesian classification model to identify affected individuals by observing changes in calling behaviour following the plant's closure. For these affected individuals, we observe significant declines in social behaviour and mobility following job loss. Using the features identified at the micro level, we show that the same changes in these calling behaviours, aggregated at the regional level, can improve forecasts of macro unemployment rates. These methods and results highlight promise of new data resources to measure microeconomic behaviour and improve estimates of critical economic indicators. PMID:26018965

Automated discovery of structural features of the optic nerve head on the basis of image and genetic data

NASA Astrophysics Data System (ADS)

Christopher, Mark; Tang, Li; Fingert, John H.; Scheetz, Todd E.; Abramoff, Michael D.

2014-03-01

Evaluation of optic nerve head (ONH) structure is a commonly used clinical technique for both diagnosis and monitoring of glaucoma. Glaucoma is associated with characteristic changes in the structure of the ONH. We present a method for computationally identifying ONH structural features using both imaging and genetic data from a large cohort of participants at risk for primary open angle glaucoma (POAG). Using 1054 participants from the Ocular Hypertension Treatment Study, ONH structure was measured by application of a stereo correspondence algorithm to stereo fundus images. In addition, the genotypes of several known POAG genetic risk factors were considered for each participant. ONH structural features were discovered using both a principal component analysis approach to identify the major modes of variance within structural measurements and a linear discriminant analysis approach to capture the relationship between genetic risk factors and ONH structure. The identified ONH structural features were evaluated based on the strength of their associations with genotype and development of POAG by the end of the OHTS study. ONH structural features with strong associations with genotype were identified for each of the genetic loci considered. Several identified ONH structural features were significantly associated (p < 0.05) with the development of POAG after Bonferroni correction. Further, incorporation of genetic risk status was found to substantially increase performance of early POAG prediction. These results suggest incorporating both imaging and genetic data into ONH structural modeling significantly improves the ability to explain POAG-related changes to ONH structure.

Visualization of HIV T Cell Virological Synapses and Virus-Containing Compartments by Three-Dimensional Correlative Light and Electron Microscopy

PubMed Central

Wang, Lili; Eng, Edward T.; Law, Kenneth; Gordon, Ronald E.; Rice, William J.

2016-01-01

ABSTRACT Virological synapses (VS) are adhesive structures that form between infected and uninfected cells to enhance the spread of HIV-1. During T cell VS formation, viral proteins are actively recruited to the site of cell-cell contact where the viral material is efficiently translocated to target cells into heterogeneous, protease-resistant, antibody-inaccessible compartments. Using correlative light and electron microscopy (CLEM), we define the membrane topography of the virus-containing compartments (VCC) where HIV is found following VS-mediated transfer. Focused ion beam scanning electron microscopy (FIB-SEM) and serial sectioning transmission electron microscopy (SS-TEM) were used to better resolve the fluorescent Gag-containing structures within the VCC. We found that small punctate fluorescent signals correlated with single viral particles in enclosed vesicular compartments or surface-localized virus particles and that large fluorescent signals correlated with membranous Gag-containing structures with unknown pathological function. CLEM imaging revealed distinct pools of newly deposited viral proteins within endocytic and nonendocytic compartments in VS target T cells. IMPORTANCE This study directly correlates individual virus-associated objects observed in light microscopy with ultrastructural features seen by electron microscopy in the HIV-1 virological synapse. This approach elucidates which infection-associated ultrastructural features represent bona fide HIV protein complexes. We define the morphology of some HIV cell-to-cell transfer intermediates as true endocytic compartments and resolve unique synapse-associated viral structures created by transfer across virological synapses. PMID:27847357

Crystal structure of the Rous sarcoma virus intasome

DOE PAGES

Yin, Zhiqi; Shi, Ke; Banerjee, Surajit; ...

2016-02-17

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

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

Stogios, Peter J.; Shakya, Tushar; Evdokimova, Elena

The aminoglycoside phosphotransferase (APH) APH(4)-Ia is one of two enzymes responsible for bacterial resistance to the atypical aminoglycoside antibiotic hygromycin B (hygB). The crystal structure of APH(4)-Ia enzyme was solved in complex with hygB at 1.95 {angstrom} resolution. The APH(4)-Ia structure adapts a general two-lobe architecture shared by other APH enzymes and eukaryotic kinases, with the active site located at the interdomain cavity. The enzyme forms an extended hydrogen bond network with hygB primarily through polar and acidic side chain groups. Individual alanine substitutions of seven residues involved in hygB binding did not have significant effect on APH(4)-Ia enzymatic activity,more » indicating that the binding affinity is spread across a distributed network. hygB appeared as the only substrate recognized by APH(4)-Ia among the panel of 14 aminoglycoside compounds. Analysis of the active site architecture and the interaction with the hygB molecule demonstrated several unique features supporting such restricted substrate specificity. Primarily the APH(4)-Ia substrate-binding site contains a cluster of hydrophobic residues that provides a complementary surface to the twisted structure of the substrate. Similar to APH(2{double_prime}) enzymes, the APH(4)-Ia is able to utilize either ATP or GTP for phosphoryl transfer. The defined structural features of APH(4)-Ia interactions with hygB and the promiscuity in regard to ATP or GTP binding could be exploited for the design of novel aminoglycoside antibiotics or inhibitors of this enzyme.« less

Prevalence and correlates of binge eating disorder related features in the community.

PubMed

Mustelin, Linda; Bulik, Cynthia M; Kaprio, Jaakko; Keski-Rahkonen, Anna

2017-02-01

Binge eating disorder (BED) is associated with high levels of obesity and psychological suffering, but little is known about 1) the distribution of features of BED in the general population and 2) their consequences for weight development and psychological distress in young adulthood. We investigated the prevalence of features of BED and their association with body mass index (BMI) and psychological distress among men (n = 2423) and women (n = 2825) from the longitudinal community-based FinnTwin16 cohort (born 1975-1979). Seven eating-related cognitions and behaviors similar to the defining features of BED were extracted from the Eating Disorder Inventory-2 and were assessed at a mean age of 24. BMI and psychological distress, measured with the General Health Questionnaire, were assessed at ages 24 and 34. We assessed prevalence of the features and their association with BMI and psychological distress cross-sectionally and prospectively. More than half of our participants reported at least one feature of BED; clustering of several features in one individual was less common, particularly among men. The most frequently reported feature was 'stuffing oneself with food', whereas the least common was 'eating or drinking in secrecy'. All individual features of BED and their clustering particularly were associated with higher BMI and more psychological distress cross-sectionally. Prospectively, the clustering of features of BED predicted increase in psychological distress but not additional weight gain when baseline BMI was accounted for. In summary, although some features of BED were common, the clustering of several features in one individual was not. The features were cumulatively associated with BMI and psychological distress and predicted further increase in psychological distress over ten years of follow-up. Copyright © 2016. Published by Elsevier Ltd.

The external morphology of adult female Egrasilus labracis as shown using hexamethyldisilazane treated, uncoated specimens for scanning electron microscopy.

PubMed

Murray, Harry M; Hill, Stephen J; Ang, Keng P

2016-07-01

The description and application of a modified Scanning Electron Microscope preparation technique using hexamethyldisilazane for small parasitic copepods was demonstrated though a high resolution depiction of individuals of Ergasilus labracis sampled from three spined stickleback (Gasterosteus aculeatus) in Bay D'Espoir, Newfoundland during summer 2015 and from archival samples retrieved from Atlantic salmon par (Salmo salar) stored at the Atlantic reference centre, St. Andrews, New Brunswick. The specimens were very well preserved showing high quality detail of important features and verifying those previously described using light microscopy by Hogans. Additionally the technique allowed excellent in situ demonstrations of mouth parts, swimming legs, and unusual and previously undescribed features of the second antenna including prominent striations and pore-like structures found to define the claw. It is thought that this technique will become a quick and efficient tool for describing important taxonomic features of small parasitic copepods like E. labracis or other similar small aquatic organisms. Microsc. Res. Tech. 79:657-663, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Physical characteristics and evolutionary trends of continental rifts

NASA Technical Reports Server (NTRS)

Ramberg, I. B.; Morgan, P.

1984-01-01

Rifts may be defined as zones beneath which the entire lithosphere has ruptured in extension. They are widespread and occur in a variety of tectonic settings, and range up to 2,600 m.y. in age. The object of this review is to highlight characteristic features of modern and ancient rifts, to emphasize differences and similarities in order to help characterize evolutionary trends, to identify physical conditions favorable for initiation as well as termination of rifting, and to provide constraints for future modeling studies of rifting. Rifts are characterized on the basis of their structural, geomorphic, magmatic and geophysical features and the diverse character of these features and their evolutionary trends through time are discussed. Mechanisms of rifting are critically examined in terms of the physical characteristics and evolutionary trends of rifts, and it is concluded that while simple models can give valuable insight into specific processes of rifting, individual rifts can rarely, if ever, be characterized by well defined trends predicted by these models. More data are required to clearly define evolutionary trends, and the models require development to incorporate the effects of lithospheric heterogeneities and complex geologic histories.

Psychopathological and clinical features of remitted anorexia nervosa patients: a six-year follow-up study.

PubMed

Lo Sauro, Carolina; Castellini, Giovanni; Lelli, Lorenzo; Faravelli, Carlo; Ricca, Valdo

2013-01-01

Remission from anorexia nervosa (AN) is a controversial issue, as remitted individuals have been found to show residual anorectic attitudes and concerns about weight and shape. The aims of this study were to evaluate the psychopathological features of remitted AN subjects 6 years after the end of a cognitive behavioural therapy and the predictors of reduction in psychopathology. The sample was composed of 134 AN subjects, evaluated at baseline, at the end of treatment, 3 and 6 years after the end of treatment, by means of the Structured Clinical Interview for Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition and several self-reported questionnaires. Remitted patients at 6 years of follow-up still showed higher eating and shape concerns, compared with healthy controls. Duration of illness, obsessive-compulsive and depressive symptoms were moderators of change in psychopathology across time. Psychopathological features represent an enduring trait for AN patients. General psychopathology showed different effects on symptoms reduction across time. Copyright © 2012 John Wiley & Sons, Ltd and Eating Disorders Association.

Verb deficits in Alzheimer’s disease and agrammatism: Implications for lexical organization☆

PubMed Central

Kim, Mikyong; Thompson, Cynthia K.

2011-01-01

This study examined the nature of verb deficits in 14 individuals with probable Alzheimer’s Disease (PrAD) and nine with agrammatic aphasia. Production was tested, controlling both semantic and syntactic features of verbs, using noun and verb naming, sentence completion, and narrative tasks. Noun and verb comprehension and a grammaticality judgment task also were administered. Results showed that while both PrAD and agrammatic subjects showed impaired verb naming, the syntactic features of verbs (i.e., argument structure) influenced agrammatic, but not Alzheimer’s disease patients’ verb production ability. That is, agrammatic patients showed progressively greater difficulty with verbs associated with more arguments, as has been shown in previous studies (e.g., Kim & Thompson, 2000; Thompson, 2003; Thompson, Lange, Schneider, & Shapiro, 1997), and suggest a syntactic basis for verb production deficits in agrammatism. Conversely, the semantic complexity of verbs affected PrAD, but not agrammatic, patients’ performance, suggesting “bottom-up” breakdown in their verb lexicon, paralleling that of nouns, resulting from the degradation or loss of semantic features of verbs. PMID:14698726

Forests of opportunities and mischief: disentangling the interactions between forests, parasites and immune responses.

PubMed

Renner, Swen C; Lüdtke, Bruntje; Kaiser, Sonja; Kienle, Julia; Schaefer, H Martin; Segelbacher, Gernot; Tschapka, Marco; Santiago-Alarcon, Diego

2016-08-01

Habitat characteristics determine the presence of individuals through resource availability, but at the same time, such features also influence the occurrence of parasites. We analyzed how birds respond to changes in interior forest structures, to forest management regimes, and to the risk of haemosporidian infections. We captured and took blood samples from blackcaps (Sylvia atricapilla) and chaffinches (Fringilla coelebs) in three different forest types (beech, mixed deciduous, spruce). We measured birds' body asymmetries, detected avian haemosporidians, and counted white blood cells as an immune measure of each individual per forest type. We used, to our knowledge for the first time, continuous forest structural parameters to quantify habitat structure, and found significant effects of habitat structure on parasite prevalence that previously have been undetected. We found three times higher prevalence for blackcaps compared with chaffinches. Parasite intensity varied significantly within host species depending on forest type, being lowest in beech forests for both host species. Structurally complex habitats with a high degree of entropy had a positive effect on the likelihood of acquiring an infection, but the effect on prevalence was negative for forest sections with a south facing aspect. For blackcaps, forest gaps also had a positive effect on prevalence, but canopy height had a negative one. Our results suggest that forest types and variations in forest structure influence the likelihood of acquiring an infection, which subsequently has an influence on host health status and body condition; however, responses to some environmental factors are host-specific. Copyright © 2016 Australian Society for Parasitology. Published by Elsevier Ltd. All rights reserved.

Interpersonal Development, Stability, and Change in Early Adulthood

PubMed Central

Wright, Aidan G. C.; Pincus, Aaron L.; Lenzenweger, Mark F.

2011-01-01

Objective This goal of this research was to explore the development of the interpersonal system mapped by the interpersonal circumplex in early adulthood (Ages 18-22). Method This study uses the Longitudinal Study of Personality Disorders sample (N = 250; 53% Female). Participants completed the Revised Interpersonal Adjective Scales (Wiggins, Trapnell, & Phillips, 1988) in their freshman, sophomore, and senior years of college. Estimates of structural, rank-order, mean, individual, and ipsative stability were calculated for the broad interpersonal dimensions of Dominance and Affiliation, and also the lower-order octant scales. Additionally, the interpersonal profile parameters of differentiation and prototypicality were calculated at each wave and explored longitudinally, and also used as predictors of interpersonal stability. Results We found excellent structural and high rank-order and ipsative stability in the interpersonal scales over this time period. Mean increases on the Affiliation axis, but not on the Dominance axis, were found to mask differential rates of change among the octant scales, along with significant individual variation in the rates of change. Interpersonal differentiation and prototypicality were related to higher stability in overall interpersonal style. Conclusions Results point to evidence of both stability and nuanced change, illuminating some of the features of the structural variables that can be derived from interpersonal circumplex profiles. PMID:22224462

Cortical Thickness Predicts the First Onset of Major Depression in Adolescence

PubMed Central

Foland-Ross, Lara C.; Sacchet, Matthew D.; Prasad, Gautam; Gilbert, Brooke; Thompson, Paul M.; Gotlib, Ian H.

2015-01-01

Given the increasing prevalence of Major Depressive Disorder and recent advances in preventative treatments for this disorder, an important challenge in pediatric neuroimaging is the early identification of individuals at risk for depression. We examined whether machine learning can be used to predict the onset of depression at the individual level. Thirty-three never-disordered adolescents (10–15 years old) underwent structural MRI. Participants were followed for 5 years to monitor the emergence of clinically significant depressive symptoms. We used support vector machines (SVMs) to test whether baseline cortical thickness could reliably distinguish adolescents who develop depression from adolescents who remained free of any Axis I disorder. Accuracies from subsampled cross-validated classification were used to assess classifier performance. Baseline cortical thickness correctly predicted the future onset of depression with an overall accuracy of 70% (69% sensitivity, 70% specificity; p = 0.021). Examination of SVM feature weights indicated that the right medial orbitofrontal, right precentral, left anterior cingulate, and bilateral insular cortex contributed most strongly to this classification. These findings indicate that cortical gray matter structure can predict the subsequent onset of depression. An important direction for future research is to elucidate mechanisms by which these anomalies in gray matter structure increase risk for developing this disorder. PMID:26315399

Cortical thickness predicts the first onset of major depression in adolescence.

PubMed

Foland-Ross, Lara C; Sacchet, Matthew D; Prasad, Gautam; Gilbert, Brooke; Thompson, Paul M; Gotlib, Ian H

2015-11-01

Given the increasing prevalence of Major Depressive Disorder and recent advances in preventative treatments for this disorder, an important challenge in pediatric neuroimaging is the early identification of individuals at risk for depression. We examined whether machine learning can be used to predict the onset of depression at the individual level. Thirty-three never-disordered adolescents (10-15 years old) underwent structural MRI. Participants were followed for 5 years to monitor the emergence of clinically significant depressive symptoms. We used support vector machines (SVMs) to test whether baseline cortical thickness could reliably distinguish adolescents who develop depression from adolescents who remained free of any Axis I disorder. Accuracies from subsampled cross-validated classification were used to assess classifier performance. Baseline cortical thickness correctly predicted the future onset of depression with an overall accuracy of 70% (69% sensitivity, 70% specificity; p=0.021). Examination of SVM feature weights indicated that the right medial orbitofrontal, right precentral, left anterior cingulate, and bilateral insular cortex contributed most strongly to this classification. These findings indicate that cortical gray matter structure can predict the subsequent onset of depression. An important direction for future research is to elucidate mechanisms by which these anomalies in gray matter structure increase risk for developing this disorder. Copyright © 2015 Elsevier Ltd. All rights reserved.

Influence of Nutrient Availability and Quorum Sensing on the Formation of Metabolically Inactive Microcolonies Within Structurally Heterogeneous Bacterial Biofilms: An Individual-Based 3D Cellular Automata Model.

PubMed

Machineni, Lakshmi; Rajapantul, Anil; Nandamuri, Vandana; Pawar, Parag D

2017-03-01

The resistance of bacterial biofilms to antibiotic treatment has been attributed to the emergence of structurally heterogeneous microenvironments containing metabolically inactive cell populations. In this study, we use a three-dimensional individual-based cellular automata model to investigate the influence of nutrient availability and quorum sensing on microbial heterogeneity in growing biofilms. Mature biofilms exhibited at least three structurally distinct strata: a high-volume, homogeneous region sandwiched between two compact sections of high heterogeneity. Cell death occurred preferentially in layers in close proximity to the substratum, resulting in increased heterogeneity in this section of the biofilm; the thickness and heterogeneity of this lowermost layer increased with time, ultimately leading to sloughing. The model predicted the formation of metabolically dormant cellular microniches embedded within faster-growing cell clusters. Biofilms utilizing quorum sensing were more heterogeneous compared to their non-quorum sensing counterparts, and resisted sloughing, featuring a cell-devoid layer of EPS atop the substratum upon which the remainder of the biofilm developed. Overall, our study provides a computational framework to analyze metabolic diversity and heterogeneity of biofilm-associated microorganisms and may pave the way toward gaining further insights into the biophysical mechanisms of antibiotic resistance.

Disease Burden and Symptom Structure of Autism in Neurofibromatosis Type 1: A Study of the International NF1-ASD Consortium Team (INFACT).

PubMed

Morris, Stephanie M; Acosta, Maria T; Garg, Shruti; Green, Jonathan; Huson, Susan; Legius, Eric; North, Kathryn N; Payne, Jonathan M; Plasschaert, Ellen; Frazier, Thomas W; Weiss, Lauren A; Zhang, Yi; Gutmann, David H; Constantino, John N

2016-12-01

Recent reports have demonstrated a higher incidence of autism spectrum disorder (ASD) and substantially elevated autistic trait burden in individuals with neurofibromatosis type 1 (NF1). However, important discrepancies regarding the distribution of autistic traits, sex predominance, and association between ASD symptoms and attentional problems have emerged, and critical features of the ASD phenotype within NF1 have never been adequately explored. Establishing NF1 as a monogenic cause for ASD has important implications for affected patients and for future research focused on establishing convergent pathogenic mechanisms relevant to the potential treatment targets for ASD. To characterize the quantitative autistic trait (QAT) burden in a pooled NF1 data set. Anonymized, individual-level primary data were accumulated from 6 tertiary referral centers in the United States, Belgium, United Kingdom, and Australia. A total of 531 individuals recruited from NF1 clinical centers were included in the study. Distribution of ASD traits (Social Responsiveness Scale, second edition [SRS-2], with T scores of ≥75 associated with a categorical ASD diagnosis); attention-deficit/hyperactivity disorder (ADHD) traits (4 versions of Conners Rating Scale, with T scores of ≥65 indicating clinically significant ADHD symptoms); ASD symptom structure, latent structure, base rate derived from mixture modeling; and familiality. Of the 531 patients included in the analysis, 247 were male (46.5%); median age was 11 years (range, 2.5-83.9 years). QAT scores were continuously distributed and pathologically shifted; 13.2% (95% CI, 10.3%-16.1%) of individuals scored within the most severe range (ie, above the first percentile of the general population distribution) in which the male to female ratio was markedly attenuated (1.6:1) relative to idiopathic ASD. Autistic symptoms in this NF1 cohort demonstrated a robust unitary factor structure, with the first principal component explaining 30.9% of the variance in SRS-2 scores, and a strong association with ADHD symptoms (r = 0.61). Within-family correlation for QAT burden (intraclass correlation coefficient, 0.73 in NF1-affected first-degree relatives) exceeded that observed in the general population and ASD family samples. This study provides confirmation that the diversity of mutations that give rise to NF1 function as quantitative trait loci for ASD. Moreover, the within-family correlation implicates a high degree of mutational specificity for this associated phenotype. Clinicians should be alerted to the increased frequency of this disabling comorbidity, and the scientific community should be aware of the potential for this monogenic disorder to help elucidate the biological features of idiopathic autism.

Disease Burden and Symptom Structure of Autism in Neurofibromatosis Type 1

PubMed Central

Morris, Stephanie M.; Acosta, Maria T.; Garg, Shruti; Green, Jonathan; Huson, Susan; Legius, Eric; North, Kathryn N.; Payne, Jonathan M.; Plasschaert, Ellen; Frazier, Thomas W.; Weiss, Lauren A.; Zhang, Yi; Gutmann, David H.; Constantino, John N.

2017-01-01

IMPORTANCE Recent reports have demonstrated a higher incidence of autism spectrum disorder (ASD) and substantially elevated autistic trait burden in individuals with neurofibromatosis type 1 (NF1). However, important discrepancies regarding the distribution of autistic traits, sex predominance, and association between ASD symptoms and attentional problems have emerged, and critical features of the ASD phenotype within NF1 have never been adequately explored. Establishing NF1 as a monogenic cause for ASD has important implications for affected patients and for future research focused on establishing convergent pathogenic mechanisms relevant to the potential treatment targets for ASD. OBJECTIVE To characterize the quantitative autistic trait (QAT) burden in a pooled NF1 data set. DESIGN, SETTING, AND PARTICIPANTS Anonymized, individual-level primary data were accumulated from 6 tertiary referral centers in the United States, Belgium, United Kingdom, and Australia. A total of 531 individuals recruited from NF1 clinical centers were included in the study. MAIN OUTCOMES AND MEASURES Distribution of ASD traits (Social Responsiveness Scale, second edition [SRS-2], with T scores of ≥75 associated with a categorical ASD diagnosis); attention-deficit/hyperactivity disorder (ADHD) traits (4 versions of Conners Rating Scale, with T scores of ≥65 indicating clinically significant ADHD symptoms); ASD symptom structure, latent structure, base rate derived from mixture modeling; and familiality. RESULTS Of the 531 patients included in the analysis, 247 were male (46.5%); median age was 11 years (range, 2.5–83.9 years). QAT scores were continuously distributed and pathologically shifted; 13.2%(95%CI, 10.3%–16.1%) of individuals scored within the most severe range (ie, above the first percentile of the general population distribution) in which the male to female ratio was markedly attenuated (1.6:1) relative to idiopathic ASD. Autistic symptoms in this NF1 cohort demonstrated a robust unitary factor structure, with the first principal component explaining 30.9%of the variance in SRS-2 scores, and a strong association with ADHD symptoms (r = 0.61). Within-family correlation for QAT burden (intraclass correlation coefficient, 0.73 in NF1-affected first-degree relatives) exceeded that observed in the general population and ASD family samples. CONCLUSIONS AND RELEVANCE This study provides confirmation that the diversity of mutations that give rise to NF1 function as quantitative trait loci for ASD. Moreover, the within-family correlation implicates a high degree of mutational specificity for this associated phenotype. Clinicians should be alerted to the increased frequency of this disabling comorbidity, and the scientific community should be aware of the potential for this monogenic disorder to help elucidate the biological features of idiopathic autism. PMID:27760236

Analysis of cosmetic residues on a single human hair by ATR FT-IR microspectroscopy

NASA Astrophysics Data System (ADS)

Pienpinijtham, Prompong; Thammacharoen, Chuchaat; Naranitad, Suwimol; Ekgasit, Sanong

2018-05-01

In this work, ATR FT-IR spectra of single human hair and cosmetic residues on hair surface are successfully collected using a homemade dome-shaped Ge μIRE accessary installed on an infrared microscope. By collecting ATR spectra of hairs from the same person, the spectral patterns are identical and superimposed while different spectral features are observed from ATR spectra of hairs collected from different persons. The spectral differences depend on individual hair characteristics, chemical treatments, and cosmetics on hair surface. The "Contact-and-Collect" technique that transfers remarkable materials on the hair surface to the tip of the Ge μIRE enables an identification of cosmetics on a single hair. Moreover, the differences between un-split and split hairs are also studied in this report. These highly specific spectral features can be employed for unique identification or for differentiation of hairs based on the molecular structures of hairs and cosmetics on hairs.

Human behavior. Sex equality can explain the unique social structure of hunter-gatherer bands.

PubMed

Dyble, M; Salali, G D; Chaudhary, N; Page, A; Smith, D; Thompson, J; Vinicius, L; Mace, R; Migliano, A B

2015-05-15

The social organization of mobile hunter-gatherers has several derived features, including low within-camp relatedness and fluid meta-groups. Although these features have been proposed to have provided the selective context for the evolution of human hypercooperation and cumulative culture, how such a distinctive social system may have emerged remains unclear. We present an agent-based model suggesting that, even if all individuals in a community seek to live with as many kin as possible, within-camp relatedness is reduced if men and women have equal influence in selecting camp members. Our model closely approximates observed patterns of co-residence among Agta and Mbendjele BaYaka hunter-gatherers. Our results suggest that pair-bonding and increased sex egalitarianism in human evolutionary history may have had a transformative effect on human social organization. Copyright © 2015, American Association for the Advancement of Science.

The perception of regularity in an isochronous stimulus in zebra finches (Taeniopygia guttata) and humans.

PubMed

van der Aa, Jeroen; Honing, Henkjan; ten Cate, Carel

2015-06-01

Perceiving temporal regularity in an auditory stimulus is considered one of the basic features of musicality. Here we examine whether zebra finches can detect regularity in an isochronous stimulus. Using a go/no go paradigm we show that zebra finches are able to distinguish between an isochronous and an irregular stimulus. However, when the tempo of the isochronous stimulus is changed, it is no longer treated as similar to the training stimulus. Training with three isochronous and three irregular stimuli did not result in improvement of the generalization. In contrast, humans, exposed to the same stimuli, readily generalized across tempo changes. Our results suggest that zebra finches distinguish the different stimuli by learning specific local temporal features of each individual stimulus rather than attending to the global structure of the stimuli, i.e., to the temporal regularity. Copyright © 2015 Elsevier B.V. All rights reserved.

Discovery of multi-ring basins - Gestalt perception in planetary science

NASA Technical Reports Server (NTRS)

Hartmann, W. K.

1981-01-01

Early selenographers resolved individual structural components of multi-ring basin systems but missed the underlying large-scale multi-ring basin patterns. The recognition of multi-ring basins as a general class of planetary features can be divided into five steps. Gilbert (1893) took a first step in recognizing radial 'sculpture' around the Imbrium basin system. Several writers through the 1940's rediscovered the radial sculpture and extended this concept by describing concentric rings around several circular maria. Some reminiscences are given about the fourth step - discovery of the Orientale basin and other basin systems by rectified lunar photography at the University of Arizona in 1961-62. Multi-ring basins remained a lunar phenomenon until the fifth step - discovery of similar systems of features on other planets, such as Mars (1972), Mercury (1974), and possibly Callisto and Ganymede (1979). This sequence is an example of gestalt recognition whose implications for scientific research are discussed.

[Gerontodietology].

PubMed

Baranovskiĭ, A Iu; Protopopova, O B

2012-01-01

Gerontodietology is one of the most important parts of dietetics studying problems of nutrition of elderly and old persons and persons with high risk of early and pathological aging, developing principles of rational nutrition, prophylactic and curative nutrition and methods of its organization. Functional structure of modern gerontodietology, its scientific-methodical bases, terminological features are presented. Composition and features of healthy nutrition of elderly people is described in details, methods of its optimization and individualization are given. Notions of geriatric dietotherapy, its principal difference from curative nutrition of patients of other ages are described. Large section of the article is devoted to the modern problems of prophylactic gerontodietology, intended more for persons with high risk of early aging than for elderly persons. Theoretic basis and methodological contents of prophylactic gerontodietology are presented; practical recommendations on dietetic means to prevent intensive development of involution processes and organic pathology in the body are described.

[The age-specific features of palm dermatoglyphics in the adults subjects].

PubMed

Teplov, K V; Bozhchenko, A P; Tolmachev, I A; Moiseenko, S A

2016-01-01

This article was designed to consider the congenital age-specific features of palm dermatoglyphics in the adults subjects (including the type of the papillary patterns, axial tri-radii, the termini of palmar main lines, the rudiments of palmar lines, the dermatoglyphic ridge count between the stable anatomical structures). The objective of the study was to look for the new diagnostic markers of the biological age. It included the identification of the palm prints obtained from 180 Caucasoid men and 120 women at the age varying from 16 to 80 years. The results of the mathematical and statistical analysis provided the basis for drawing up the list of 18 attributes of palm dermatoglyphics significantly (p<0.05) differing in the frequency of occurrence between the representatives of individual age groups. The methods are proposed allowing to use these findings for the expert evaluation of the age of unknown subjects.

The GOAL-to-HAL/S translator specification. [for space shuttle

NASA Technical Reports Server (NTRS)

Stanten, S. F.; Flanders, J. H.

1973-01-01

The specification sets forth a technical framework within which to deal with the transfer of specific GOAL features to HAL/S. Key technical features of the translator are described which communicate with the data bank, handle repeat statements, and deal with software interrupts. GOAL programs, databank information, and GOAL system subroutines are integrated into one GOAL in HAL/S. This output is fully compatible HAL/S source ready for insertion into the HAL/S compiler. The Translator uses a PASS1 to establish all the global data needed for the HAL/S output program. Individual GOAL statements are translated in PASS2. The specification document makes extensive use of flowcharts to specify exactly how each variation of each GOAL statement is to be translated. The specification also deals with definitions and assumptions, executive support structure and implementation. An appendix, entitled GOAL-to-HAL Mapping, provides examples of translated GOAL statements.

Evaluation of 3D-Jury on CASP7 models.

PubMed

Kaján, László; Rychlewski, Leszek

2007-08-21

3D-Jury, the structure prediction consensus method publicly available in the Meta Server http://meta.bioinfo.pl/, was evaluated using models gathered in the 7th round of the Critical Assessment of Techniques for Protein Structure Prediction (CASP7). 3D-Jury is an automated expert process that generates protein structure meta-predictions from sets of models obtained from partner servers. The performance of 3D-Jury was analysed for three aspects. First, we examined the correlation between the 3D-Jury score and a model quality measure: the number of correctly predicted residues. The 3D-Jury score was shown to correlate significantly with the number of correctly predicted residues, the correlation is good enough to be used for prediction. 3D-Jury was also found to improve upon the competing servers' choice of the best structure model in most cases. The value of the 3D-Jury score as a generic reliability measure was also examined. We found that the 3D-Jury score separates bad models from good models better than the reliability score of the original server in 27 cases and falls short of it in only 5 cases out of a total of 38. We report the release of a new Meta Server feature: instant 3D-Jury scoring of uploaded user models. The 3D-Jury score continues to be a good indicator of structural model quality. It also provides a generic reliability score, especially important for models that were not assigned such by the original server. Individual structure modellers can also benefit from the 3D-Jury scoring system by testing their models in the new instant scoring feature http://meta.bioinfo.pl/compare_your_model_example.pl available in the Meta Server.

Evaluation of 3D-Jury on CASP7 models

PubMed Central

Kaján, László; Rychlewski, Leszek

2007-01-01

Background 3D-Jury, the structure prediction consensus method publicly available in the Meta Server , was evaluated using models gathered in the 7th round of the Critical Assessment of Techniques for Protein Structure Prediction (CASP7). 3D-Jury is an automated expert process that generates protein structure meta-predictions from sets of models obtained from partner servers. Results The performance of 3D-Jury was analysed for three aspects. First, we examined the correlation between the 3D-Jury score and a model quality measure: the number of correctly predicted residues. The 3D-Jury score was shown to correlate significantly with the number of correctly predicted residues, the correlation is good enough to be used for prediction. 3D-Jury was also found to improve upon the competing servers' choice of the best structure model in most cases. The value of the 3D-Jury score as a generic reliability measure was also examined. We found that the 3D-Jury score separates bad models from good models better than the reliability score of the original server in 27 cases and falls short of it in only 5 cases out of a total of 38. We report the release of a new Meta Server feature: instant 3D-Jury scoring of uploaded user models. Conclusion The 3D-Jury score continues to be a good indicator of structural model quality. It also provides a generic reliability score, especially important for models that were not assigned such by the original server. Individual structure modellers can also benefit from the 3D-Jury scoring system by testing their models in the new instant scoring feature available in the Meta Server. PMID:17711571

A computer model for the 30S ribosome subunit.

PubMed Central

Kuntz, I D; Crippen, G M

1980-01-01

We describe a computer-generated model for the locations of the 21 proteins of the 30S subunit of the E. coli ribosome. The model uses a new method of incorporating experimental measurements based on a mathematical technique called distance geometry. In this paper, we use data from two sources: immunoelectron microscopy and neutron-scattering studies. The data are generally self-consistent and lead to a set of relatively well-defined structures in which individual protein coordinates differ by approximately 20 A from one structure to another. Two important features of this calculation are the use of extended proteins rather than just the centers of mass, and the ability to confine the protein locations within an arbitrary boundary surface so that only solutions with an approximate 30S "shape" are permitted. PMID:7020786

[Max Weber's illness--sociologic aspects of the depressive structure].

PubMed

Frommer, J; Frommer, S

1993-05-01

Between 1897 and 1902 the economist and sociologist Max Weber from Heidelberg suffered from a severe depressive crisis with multiple recurrences of its symptomatology in the following years. The biographic background of the disease process is examined. Questions regarding the specific diagnosis are discussed. Furthermore, his work shows that Weber was indirectly deeply concerned with the cultural, historical and social background conditions of depressive experience and behavior in the context of his study on Protestantic Ethics and the Spirit of Capitalism. Weber's definition of modern society as an iron cage, determined by Occidental Rationalism, shows that this cultural background demands a great amount of role conformity from the individual. Weber's theoretical approach should spark interest in the current psychopathological discussion of the characteristic structural features of a depressed personality.

Mechanism and energetics of 〈c + a〉 dislocation cross-slip in hcp metals.

PubMed

Wu, Zhaoxuan; Curtin, W A

2016-10-04

Hexagonal close-packed (hcp) metals such as Mg, Ti, and Zr are lightweight and/or durable metals with critical structural applications in the automotive (Mg), aerospace (Ti), and nuclear (Zr) industries. The hcp structure, however, brings significant complications in the mechanisms of plastic deformation, strengthening, and ductility, and these complications pose significant challenges in advancing the science and engineering of these metals. In hcp metals, generalized plasticity requires the activation of slip on pyramidal planes, but the structure, motion, and cross-slip of the associated [Formula: see text] dislocations are not well established even though they determine ductility and influence strengthening. Here, atomistic simulations in Mg reveal the unusual mechanism of [Formula: see text] dislocation cross-slip between pyramidal I and II planes, which occurs by cross-slip of the individual partial dislocations. The energy barrier is controlled by a fundamental step/jog energy and the near-core energy difference between pyramidal [Formula: see text] dislocations. The near-core energy difference can be changed by nonglide stresses, leading to tension-compression asymmetry and even a switch in absolute stability from one glide plane to the other, both features observed experimentally in Mg, Ti, and their alloys. The unique cross-slip mechanism is governed by common features of the generalized stacking fault energy surfaces of hcp pyramidal planes and is thus expected to be generic to all hcp metals. An analytical model is developed to predict the cross-slip barrier as a function of the near-core energy difference and applied stresses and quantifies the controlling features of cross-slip and pyramidal I/II stability across the family of hcp metals.

Mechanism and energetics of 〈c + a〉 dislocation cross-slip in hcp metals

PubMed Central

Wu, Zhaoxuan; Curtin, W. A.

2016-01-01

Hexagonal close-packed (hcp) metals such as Mg, Ti, and Zr are lightweight and/or durable metals with critical structural applications in the automotive (Mg), aerospace (Ti), and nuclear (Zr) industries. The hcp structure, however, brings significant complications in the mechanisms of plastic deformation, strengthening, and ductility, and these complications pose significant challenges in advancing the science and engineering of these metals. In hcp metals, generalized plasticity requires the activation of slip on pyramidal planes, but the structure, motion, and cross-slip of the associated 〈c+a〉 dislocations are not well established even though they determine ductility and influence strengthening. Here, atomistic simulations in Mg reveal the unusual mechanism of 〈c+a〉 dislocation cross-slip between pyramidal I and II planes, which occurs by cross-slip of the individual partial dislocations. The energy barrier is controlled by a fundamental step/jog energy and the near-core energy difference between pyramidal 〈c+a〉 dislocations. The near-core energy difference can be changed by nonglide stresses, leading to tension–compression asymmetry and even a switch in absolute stability from one glide plane to the other, both features observed experimentally in Mg, Ti, and their alloys. The unique cross-slip mechanism is governed by common features of the generalized stacking fault energy surfaces of hcp pyramidal planes and is thus expected to be generic to all hcp metals. An analytical model is developed to predict the cross-slip barrier as a function of the near-core energy difference and applied stresses and quantifies the controlling features of cross-slip and pyramidal I/II stability across the family of hcp metals. PMID:27647908

The First Global Geological Map of Mercury

NASA Astrophysics Data System (ADS)

Prockter, L. M.; Head, J. W., III; Byrne, P. K.; Denevi, B. W.; Kinczyk, M. J.; Fassett, C.; Whitten, J. L.; Thomas, R.; Ernst, C. M.

2015-12-01

Geological maps are tools with which to understand the distribution and age relationships of surface geological units and structural features on planetary surfaces. Regional and limited global mapping of Mercury has already yielded valuable science results, elucidating the history and distribution of several types of units and features, such as regional plains, tectonic structures, and pyroclastic deposits. To date, however, no global geological map of Mercury exists, and there is currently no commonly accepted set of standardized unit descriptions and nomenclature. With MESSENGER monochrome image data, we are undertaking the global geological mapping of Mercury at the 1:15M scale applying standard U.S. Geological Survey mapping guidelines. This map will enable the development of the first global stratigraphic column of Mercury, will facilitate comparisons among surface units distributed discontinuously across the planet, and will provide guidelines for mappers so that future mapping efforts will be consistent and broadly interpretable by the scientific community. To date we have incorporated three major datasets into the global geological map: smooth plains units, tectonic structures, and impact craters and basins >20 km in diameter. We have classified most of these craters by relative age on the basis of the state of preservation of morphological features and standard classification schemes first applied to Mercury by the Mariner 10 imaging team. Additional datasets to be incorporated include intercrater plains units and crater ejecta deposits. In some regions MESSENGER color data is used to supplement the monochrome data, to help elucidate different plains units. The final map will be published online, together with a peer-reviewed publication. Further, a digital version of the map, containing individual map layers, will be made publicly available for use within geographic information systems (GISs).

Characterization of computer network events through simultaneous feature selection and clustering of intrusion alerts

NASA Astrophysics Data System (ADS)

Chen, Siyue; Leung, Henry; Dondo, Maxwell

2014-05-01

As computer network security threats increase, many organizations implement multiple Network Intrusion Detection Systems (NIDS) to maximize the likelihood of intrusion detection and provide a comprehensive understanding of intrusion activities. However, NIDS trigger a massive number of alerts on a daily basis. This can be overwhelming for computer network security analysts since it is a slow and tedious process to manually analyse each alert produced. Thus, automated and intelligent clustering of alerts is important to reveal the structural correlation of events by grouping alerts with common features. As the nature of computer network attacks, and therefore alerts, is not known in advance, unsupervised alert clustering is a promising approach to achieve this goal. We propose a joint optimization technique for feature selection and clustering to aggregate similar alerts and to reduce the number of alerts that analysts have to handle individually. More precisely, each identified feature is assigned a binary value, which reflects the feature's saliency. This value is treated as a hidden variable and incorporated into a likelihood function for clustering. Since computing the optimal solution of the likelihood function directly is analytically intractable, we use the Expectation-Maximisation (EM) algorithm to iteratively update the hidden variable and use it to maximize the expected likelihood. Our empirical results, using a labelled Defense Advanced Research Projects Agency (DARPA) 2000 reference dataset, show that the proposed method gives better results than the EM clustering without feature selection in terms of the clustering accuracy.

Experiments on automatic classification of tissue malignancy in the field of digital pathology

NASA Astrophysics Data System (ADS)

Pereira, J.; Barata, R.; Furtado, Pedro

2017-06-01

Automated analysis of histological images helps diagnose and further classify breast cancer. Totally automated approaches can be used to pinpoint images for further analysis by the medical doctor. But tissue images are especially challenging for either manual or automated approaches, due to mixed patterns and textures, where malignant regions are sometimes difficult to detect unless they are in very advanced stages. Some of the major challenges are related to irregular and very diffuse patterns, as well as difficulty to define winning features and classifier models. Although it is also hard to segment correctly into regions, due to the diffuse nature, it is still crucial to take low-level features over individualized regions instead of the whole image, and to select those with the best outcomes. In this paper we report on our experiments building a region classifier with a simple subspace division and a feature selection model that improves results over image-wide and/or limited feature sets. Experimental results show modest accuracy for a set of classifiers applied over the whole image, while the conjunction of image division, per-region low-level extraction of features and selection of features, together with the use of a neural network classifier achieved the best levels of accuracy for the dataset and settings we used in the experiments. Future work involves deep learning techniques, adding structures semantics and embedding the approach as a tumor finding helper in a practical Medical Imaging Application.