Progressive Recruitment of Mesenchymal Progenitors Reveals a Time-Dependent Process of Cell Fate Acquisition in Mouse and Human Nephrogenesis.

PubMed

Lindström, Nils O; De Sena Brandine, Guilherme; Tran, Tracy; Ransick, Andrew; Suh, Gio; Guo, Jinjin; Kim, Albert D; Parvez, Riana K; Ruffins, Seth W; Rutledge, Elisabeth A; Thornton, Matthew E; Grubbs, Brendan; McMahon, Jill A; Smith, Andrew D; McMahon, Andrew P

2018-06-04

Mammalian nephrons arise from a limited nephron progenitor pool through a reiterative inductive process extending over days (mouse) or weeks (human) of kidney development. Here, we present evidence that human nephron patterning reflects a time-dependent process of recruitment of mesenchymal progenitors into an epithelial nephron precursor. Progressive recruitment predicted from high-resolution image analysis and three-dimensional reconstruction of human nephrogenesis was confirmed through direct visualization and cell fate analysis of mouse kidney organ cultures. Single-cell RNA sequencing of the human nephrogenic niche provided molecular insights into these early patterning processes and predicted developmental trajectories adopted by nephron progenitor cells in forming segment-specific domains of the human nephron. The temporal-recruitment model for nephron polarity and patterning suggested by direct analysis of human kidney development provides a framework for integrating signaling pathways driving mammalian nephrogenesis. Copyright © 2018 Elsevier Inc. All rights reserved.

Mistaking geography for biology: inferring processes from species distributions.

PubMed

Warren, Dan L; Cardillo, Marcel; Rosauer, Dan F; Bolnick, Daniel I

2014-10-01

Over the past few decades, there has been a rapid proliferation of statistical methods that infer evolutionary and ecological processes from data on species distributions. These methods have led to considerable new insights, but they often fail to account for the effects of historical biogeography on present-day species distributions. Because the geography of speciation can lead to patterns of spatial and temporal autocorrelation in the distributions of species within a clade, this can result in misleading inferences about the importance of deterministic processes in generating spatial patterns of biodiversity. In this opinion article, we discuss ways in which patterns of species distributions driven by historical biogeography are often interpreted as evidence of particular evolutionary or ecological processes. We focus on three areas that are especially prone to such misinterpretations: community phylogenetics, environmental niche modelling, and analyses of beta diversity (compositional turnover of biodiversity). Crown Copyright © 2014. Published by Elsevier Ltd. All rights reserved.

How self-reflection and self-certainty are related to neurocognitive functioning: an examination of cognitive insight in bipolar disorder.

PubMed

Van Camp, L S C; Oldenburg, J F E; Sabbe, B G C

2016-01-01

The pattern of associations between clinical insight, cognitive insight, and neurocognitive functioning was assessed in bipolar disorder patients. Data from 42 bipolar disorder patients were examined. Cognitive insight was measured using the Beck Cognitive Insight Scale (BCIS). The BCIS is a 15-item self-report instrument consisting of two subscales, self-reflectiveness and self-certainty. Clinical insight was measured by the use of the item G12 of the Positive and Negative Syndrome Scale. Neurocognitive functioning was assessed using the International Society for Bipolar Disorders-Battery for Assessment of Neurocognition. Correlation analyses revealed significant positive associations between self-reflectiveness and speed of processing, attention, working memory, visual learning, and reasoning and problem solving. The subscale self-certainty was negatively correlated to working memory, however, this correlation disappeared when we controlled for confounding variables. No correlations between clinical insight and neurocognition were found. In addition, there was no association between cognitive insight and clinical insight. Better neurocognitive functioning was more related to higher levels of self-reflectiveness than to diminished self-certainty.

Divergence with gene flow across a speciation continuum of Heliconius butterflies.

PubMed

Supple, Megan A; Papa, Riccardo; Hines, Heather M; McMillan, W Owen; Counterman, Brian A

2015-09-24

A key to understanding the origins of species is determining the evolutionary processes that drive the patterns of genomic divergence during speciation. New genomic technologies enable the study of high-resolution genomic patterns of divergence across natural speciation continua, where taxa pairs with different levels of reproductive isolation can be used as proxies for different stages of speciation. Empirical studies of these speciation continua can provide valuable insights into how genomes diverge during speciation. We examine variation across a handful of genomic regions in parapatric and allopatric populations of Heliconius butterflies with varying levels of reproductive isolation. Genome sequences were mapped to 2.2-Mb of the H. erato genome, including 1-Mb across the red color pattern locus and multiple regions unlinked to color pattern variation. Phylogenetic analyses reveal a speciation continuum of pairs of hybridizing races and incipient species in the Heliconius erato clade. Comparisons of hybridizing pairs of divergently colored races and incipient species reveal that genomic divergence increases with ecological and reproductive isolation, not only across the locus responsible for adaptive variation in red wing coloration, but also at genomic regions unlinked to color pattern. We observe high levels of divergence between the incipient species H. erato and H. himera, suggesting that divergence may accumulate early in the speciation process. Comparisons of genomic divergence between the incipient species and allopatric races suggest that limited gene flow cannot account for the observed high levels of divergence between the incipient species. Our results provide a reconstruction of the speciation continuum across the H. erato clade and provide insights into the processes that drive genomic divergence during speciation, establishing the H. erato clade as a powerful framework for the study of speciation.

Quantum Mechanics, Pattern Recognition, and the Mammalian Brain

NASA Astrophysics Data System (ADS)

Chapline, George

2008-10-01

Although the usual way of representing Markov processes is time asymmetric, there is a way of describing Markov processes, due to Schrodinger, which is time symmetric. This observation provides a link between quantum mechanics and the layered Bayesian networks that are often used in automated pattern recognition systems. In particular, there is a striking formal similarity between quantum mechanics and a particular type of Bayesian network, the Helmholtz machine, which provides a plausible model for how the mammalian brain recognizes important environmental situations. One interesting aspect of this relationship is that the "wake-sleep" algorithm for training a Helmholtz machine is very similar to the problem of finding the potential for the multi-channel Schrodinger equation. As a practical application of this insight it may be possible to use inverse scattering techniques to study the relationship between human brain wave patterns, pattern recognition, and learning. We also comment on whether there is a relationship between quantum measurements and consciousness.

Genetic and cellular mechanisms of the formation of Esophageal Atresia and Tracheoesophageal Fistula

PubMed Central

Jacobs, Ian J.; Que, Jianwen

2015-01-01

Foregut separation involves dynamic changes in the activities of signaling pathways and transcription factors. Recent mouse genetic studies demonstrate that some of these pathways interact with each other to form a complex network, leading to a unique dorsal-ventral patterning in the early foregut. In this review we will discuss how this unique dorsal-ventral patterning is set prior to the foregut separation and how disruption of this patterning affects the separation process. We will further discuss the roles of downstream targets of these pathways in regulating separation at cellular and molecular levels. Understanding the mechanism of normal separation process will provide us insights into the pathobiology of a relatively common birth defect Esophageal Atresia (EA) with/without Tracheo-esophageal Fistula (TEF). PMID:23679023

The Islamic State We Knew: Insights Before the Resurgence and Their Implications

DTIC Science & Technology

2015-01-01

smuggling process, such as the physical distribution process, and it can also broaden the fight against both oil and antiquities smuggling by...extortion, and create weapon shops . Observing a pattern of intimidation and assassinations against established government authorities can provide a...be targeted. This would degrade the Islamic State’s ability to sell oil and refined products. To broaden the fight against both oil and antiquities

Early childhood trauma in high-risk families: associations with caregiver emotional availability and insightfulness, and children's social information processing and social behavior.

PubMed

Ziv, Yair; Umphlet, Kristen L Capps; Olarte, Stephanie; Venza, Jimmy

2018-06-01

The links between exposure to adverse childhood experiences (ACEs), caregiver insightfulness and emotional availability, and the child's social information processing (SIP) and social behavior were examined in a sample of 15 preschool children enrolled in a Therapeutic Nursery Program (TNP). Children are typically referred to the TNP due to significant delays in their social emotional development that often result in difficulty functioning in typical childcare, home, and community settings. Caregiver insightfulness was measured via an interview with the caregiver. Emotional availability was coded based on observations of caregiver-child interactions. The child's SIP patterns were measured in an interview, and the child's behavior in preschool was assessed by teacher reports. Higher levels of exposure to ACE were hypothesized to be related to lower levels of caregiver emotional availability and insightfulness and to higher levels of the children's perceptual (i.e. SIP) and behavioral maladjustment. It was also hypothesized that caregiver emotional availability and insightfulness would be associated with one another and significantly associated with children's perceptions and behaviors. Caregivers reporting higher levels of exposure exhibited lower levels of insightfulness and emotional availability. No such associations were found between the child's exposure to ACE and the caregivers' perceptions and behaviors. In addition, more insightful caregivers showed higher levels of emotional availability. Finally, children with more emotionally available caregivers showed more competent SIP and social behavior.

Diffractive elements for generating microscale laser beam patterns: a Y2K problem

NASA Astrophysics Data System (ADS)

Teiwes, Stephan; Krueger, Sven; Wernicke, Guenther K.; Ferstl, Margit

2000-03-01

Lasers are widely used in industrial fabrication for engraving, cutting and many other purposes. However, material processing at very small scales is still a matter of concern. Advances in diffractive optics could provide for laser systems that could be used for engraving or cutting of micro-scale patterns at high speeds. In our paper we focus on the design of diffractive elements which can be used for this special application. It is a common desire in material processing to apply 'discrete' as well as 'continuous' beam patterns. Especially, the latter case is difficult to handle as typical micro-scale patterns are characterized by bad band-limitation properties, and as speckles can easily occur in beam patterns. It is shown in this paper that a standard iterative design method usually fails to obtain diffractive elements that generate diffraction patterns with acceptable quality. Insights gained from an analysis of the design problems are used to optimize the iterative design method. We demonstrate applicability and success of our approach by the design of diffractive phase elements that generate a discrete and a continuous 'Y2K' pattern.

New insight in magnetic saturation behavior of nickel hierarchical structures

NASA Astrophysics Data System (ADS)

Ma, Ji; Zhang, Jianxing; Liu, Chunting; Chen, Kezheng

2017-09-01

It is unanimously accepted that non-ferromagnetic inclusions in a ferromagnetic system will lower down total saturation magnetization in unit of emu/g. In this study, ;lattice strain; was found to be another key factor to have critical impact on magnetic saturation behavior of the system. The lattice strain determined assembling patterns of primary nanoparticles in hierarchical structures and was intimately related with the formation process of these architectures. Therefore, flower-necklace-like and cauliflower-like nickel hierarchical structures were used as prototype systems to evidence the relationship between assembling patterns of primary nanoparticles and magnetic saturation behaviors of these architectures. It was found that the influence of lattice strain on saturation magnetization outperformed that of non-ferromagnetic inclusions in these hierarchical structures. This will enable new insights into fundamental understanding of related magnetic effects.

Programming Pluralism: Using Learning Analytics to Detect Patterns in the Learning of Computer Programming

ERIC Educational Resources Information Center

Blikstein, Paulo; Worsley, Marcelo; Piech, Chris; Sahami, Mehran; Cooper, Steven; Koller, Daphne

2014-01-01

New high-frequency, automated data collection and analysis algorithms could offer new insights into complex learning processes, especially for tasks in which students have opportunities to generate unique open-ended artifacts such as computer programs. These approaches should be particularly useful because the need for scalable project-based and…

Dynamics of buckbrush populations under simulated forest restoration alternatives

Treesearch

David W. Huffman; Margaret M. Moore

2008-01-01

Plant population models are valuable tools for assessing ecological tradeoffs between forest management approaches. In addition, these models can provide insight on plant life history patterns and processes important for persistence and recovery of populations in changing environments. In this study, we evaluated a set of ecological restoration alternatives for their...

Dynamics of buckbrush populations under simulated forest restoration alternatives (P-53)

Treesearch

David W. Huffman; Margaret M. Moore

2008-01-01

Plant population models are valuable tools for assessing ecological tradeoffs between forest management approaches. In addition, these models can provide insight on plant life history patterns and processes important for persistence and recovery of populations in changing environments. In this study, we evaluated a set of ecological restoration alternatives for their...

Team Design Communication Patterns in e-Learning Design and Development

ERIC Educational Resources Information Center

Rapanta, Chrysi; Maina, Marcelo; Lotz, Nicole; Bacchelli, Alberto

2013-01-01

Prescriptive stage models have been found insufficient to describe the dynamic aspects of designing, especially in interdisciplinary e-learning design teams. There is a growing need for a systematic empirical analysis of team design processes that offer deeper and more detailed insights into instructional design (ID) than general models can offer.…

Concentration-discharge relationships to understand the interplay between hydrological and biogeochemical processes: insights from data analysis and numerical experiments in headwater catchments.

NASA Astrophysics Data System (ADS)

De Dreuzy, J. R.; Marçais, J.; Moatar, F.; Minaudo, C.; Courtois, Q.; Thomas, Z.; Longuevergne, L.; Pinay, G.

2017-12-01

Integration of hydrological and biogeochemical processes led to emerging patterns at the catchment scale. Monitoring in rivers reflects the aggregation of these effects. While discharge time series have been measured for decades, high frequency water quality monitoring in rivers now provides prominent measurements to characterize the interplay between hydrological and biogeochemical processes, especially to infer the processes that happen in the heterogeneous subsurface. However, we still lack frameworks to relate observed patterns to specific processes, because of the "organized complexity" of hydrological systems. Indeed, it is unclear what controls, for example, patterns in concentration-discharge (C/Q) relationships due to non-linear processes and hysteresis effects. Here we develop a non-intensive process-based model to test how the integration of different landforms (i.e. geological heterogeneities and structures, topographical features) with different biogeochemical reactivity assumptions (e.g. reactive zone locations) can shape the overall water quality time series. With numerical experiments, we investigate typical patterns in high frequency C/Q relationships. In headwater basins, we found that typical hysteretic patterns in C/Q relationships observed in data time series can be attributed to differences in water and solute locations stored across the hillslope. At the catchment scale though, these effects tend to average out by integrating contrasted hillslopes' landforms. Together these results suggest that information contained in headwater water quality monitoring can be used to understand how hydrochemical processes determine downstream conditions.

A neural network model for transference and repetition compulsion based on pattern completion.

PubMed

Javanbakht, Arash; Ragan, Charles L

2008-01-01

In recent years because of the fascinating growth of the body of neuroscientific knowledge, psychoanalytic scientists have worked on models for the neurological substrates of key psychoanalytic concepts. Transference is an important example. In this article, the psychological process of transference is described, employing the neurological function of pattern completion in hippocampal and thalamo-cortical pathways. Similarly, repetition compulsion is seen as another type of such neurological function; however, it is understood as an attempt for mastery of the unknown, rather than simply for mastery of past experiences and perceptions. Based on this suggested model of neurological function, the myth of the psychoanalyst as blank screen is seen as impossible and ineffective, based on neurofunctional understandings of neuropsychological process. The mutative effect of psychoanalytic therapy, correcting patterns of pathological relatedness, is described briefly from conscious and unconscious perspectives. While cognitive understanding (insight) helps to modify transferentially restored, maladaptive patterns of relatedness, the development of more adaptive patterns is also contingent upon an affective experience (working through), which alters the neurological substrates of unconscious, pathological affective patterns and their neurological functional correlates.

Using High Performance Computing to Examine the Processes of Neurogenesis Underlying Pattern Separation and Completion of Episodic Information.

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

Aimone, James Bradley; Bernard, Michael Lewis; Vineyard, Craig Michael

2014-10-01

Adult neurogenesis in the hippocampus region of the brain is a neurobiological process that is believed to contribute to the brain's advanced abilities in complex pattern recognition and cognition. Here, we describe how realistic scale simulations of the neurogenesis process can offer both a unique perspective on the biological relevance of this process and confer computational insights that are suggestive of novel machine learning techniques. First, supercomputer based scaling studies of the neurogenesis process demonstrate how a small fraction of adult-born neurons have a uniquely larger impact in biologically realistic scaled networks. Second, we describe a novel technical approach bymore » which the information content of ensembles of neurons can be estimated. Finally, we illustrate several examples of broader algorithmic impact of neurogenesis, including both extending existing machine learning approaches and novel approaches for intelligent sensing.« less

The notochord breaks bilateral symmetry by controlling cell shapes in the zebrafish laterality organ.

PubMed

Compagnon, Julien; Barone, Vanessa; Rajshekar, Srivarsha; Kottmeier, Rita; Pranjic-Ferscha, Kornelija; Behrndt, Martin; Heisenberg, Carl-Philipp

2014-12-22

Kupffer's vesicle (KV) is the zebrafish organ of laterality, patterning the embryo along its left-right (LR) axis. Regional differences in cell shape within the lumen-lining KV epithelium are essential for its LR patterning function. However, the processes by which KV cells acquire their characteristic shapes are largely unknown. Here, we show that the notochord induces regional differences in cell shape within KV by triggering extracellular matrix (ECM) accumulation adjacent to anterior-dorsal (AD) regions of KV. This localized ECM deposition restricts apical expansion of lumen-lining epithelial cells in AD regions of KV during lumen growth. Our study provides mechanistic insight into the processes by which KV translates global embryonic patterning into regional cell shape differences required for its LR symmetry-breaking function. Copyright © 2014 Elsevier Inc. All rights reserved.

Task Proficiency and L1 Private Speech

ERIC Educational Resources Information Center

Yamada, Minako

2005-01-01

There is a growing volume of research on task-based language use; however, the nature of "task proficiency" has not yet been clearly defined. In order to gain new insights, this study examines the relationship between the process of communication in an L2 and a task outcome by analysing lexical density, as obtained from the pattern of a…

Analyzing Public Discourse: Using Media Content Analysis to Understand the Policy Process

ERIC Educational Resources Information Center

Saraisky, Nancy Green

2016-01-01

One of the most basic and obvious sources of data for education policy analysis is text. This article discusses content analysis as an important part of the methodological toolbox for elucidating patterns and trends about education policy. Focusing specifically on media, I show how media content analysis can produce nuanced insights about the ways…

Patterns of taxonomic, phylogenetic diversity during a long-term succession of forest on the Loess Plateau, China: insights into assembly process

PubMed Central

Chai, Yongfu; Yue, Ming; Liu, Xiao; Guo, Yaoxin; Wang, Mao; Xu, Jinshi; Zhang, Chenguang; Chen, Yu; Zhang, Lixia; Zhang, Ruichang

2016-01-01

Quantifying the drivers underlying the distribution of biodiversity during succession is a critical issue in ecology and conservation, and also can provide insights into the mechanisms of community assembly. Ninety plots were established in the Loess Plateau region of northern Shaanxi in China. The taxonomic and phylogenetic (alpha and beta) diversity were quantified within six succession stages. Null models were used to test whether phylogenetic distance observed differed from random expectations. Taxonomic beta diversity did not show a regular pattern, while phylogenetic beta diversity decreased throughout succession. The shrub stage occurred as a transition from phylogenetic overdispersion to clustering either for NRI (Net Relatedness Index) or betaNRI. The betaNTI (Nearest Taxon Index) values for early stages were on average phylogenetically random, but for the betaNRI analyses, these stages were phylogenetically overdispersed. Assembly of woody plants differed from that of herbaceous plants during late community succession. We suggest that deterministic and stochastic processes respectively play a role in different aspects of community phylogenetic structure for early succession stage, and that community composition of late succession stage is governed by a deterministic process. In conclusion, the long-lasting evolutionary imprints on the present-day composition of communities arrayed along the succession gradient. PMID:27272407

Patterns of taxonomic, phylogenetic diversity during a long-term succession of forest on the Loess Plateau, China: insights into assembly process.

PubMed

Chai, Yongfu; Yue, Ming; Liu, Xiao; Guo, Yaoxin; Wang, Mao; Xu, Jinshi; Zhang, Chenguang; Chen, Yu; Zhang, Lixia; Zhang, Ruichang

2016-06-08

Quantifying the drivers underlying the distribution of biodiversity during succession is a critical issue in ecology and conservation, and also can provide insights into the mechanisms of community assembly. Ninety plots were established in the Loess Plateau region of northern Shaanxi in China. The taxonomic and phylogenetic (alpha and beta) diversity were quantified within six succession stages. Null models were used to test whether phylogenetic distance observed differed from random expectations. Taxonomic beta diversity did not show a regular pattern, while phylogenetic beta diversity decreased throughout succession. The shrub stage occurred as a transition from phylogenetic overdispersion to clustering either for NRI (Net Relatedness Index) or betaNRI. The betaNTI (Nearest Taxon Index) values for early stages were on average phylogenetically random, but for the betaNRI analyses, these stages were phylogenetically overdispersed. Assembly of woody plants differed from that of herbaceous plants during late community succession. We suggest that deterministic and stochastic processes respectively play a role in different aspects of community phylogenetic structure for early succession stage, and that community composition of late succession stage is governed by a deterministic process. In conclusion, the long-lasting evolutionary imprints on the present-day composition of communities arrayed along the succession gradient.

The combined impact of vineyard origin and processing winery on the elemental profile of red wines.

PubMed

Hopfer, Helene; Nelson, Jenny; Collins, Thomas S; Heymann, Hildegarde; Ebeler, Susan E

2015-04-01

The combined effects of vineyard origin and winery processing have been studied in 65 red wines samples. Grapes originating from five different vineyards within 40 miles of each other were processed in at least two different wineries. Sixty-three different elements were determined with inductively coupled-plasma mass spectrometry (ICP-MS), and wines were classified according to vineyard origin, processing winery, and the combination of both factors. Vineyard origin as well as winery processing have an impact on the elemental composition of wine, but each winery and each vineyard change the composition to a different degree. For some vineyards, wines showed a characteristic elemental pattern, independent of the processing winery, but the same was found for some wineries, with similar elemental pattern for all grapes processed in these wineries, independent of the vineyard origin. Studying the combined effects of grapegrowing and winemaking provides insight into the determination of geographical origin of red wines. Copyright © 2014 Elsevier Ltd. All rights reserved.

The role of Internal Solitary Waves on deep-water sedimentary processes: the case of up-slope migrating sediment waves off the Messina Strait

NASA Astrophysics Data System (ADS)

Droghei, Riccardo; Falcini, Federico; Martorelli, Eleonora; Salusti, Ettore; Sannino, Gianmaria; Santoleri, Rosalia; Chiocci, Francesco

2015-04-01

In the last decade joint marine geology and physical oceanography studies are demonstrating the inherited connection between deep-water sedimentary processes and dynamics of water masses in a fruitful exchange in which bedforms type and geometry highlight slow or periodic bottom current processes or event of and oceanography explains and predicts morphological and sedimentary pattern at the seafloor. We investigate the presence of an intriguing up-slope migrating and rotating sand waves observed off the north entrance of the Messina Strait by taking into account the main oceanographic process occurring in the Strait, namely the presence of tidal induced internal solitary waves (ISWs). We hypothesize that the observed deflected pattern of these sand waves is due to refraction of wave occurring at the LIW-MAW interface and that the motion of the grains is due to the increased particle velocity field during the passage of ISWs. We modeled their formations and compared the results with the observed geometries of the dune field. Our findings suggest an intrinsic relationship between the dune filed and the presence of internal solitary waves, and provide some insights about their dynamics and migration rate as in accordance with previous measurements and analysis. We believe that our work represents an innovative and promising link between the geological and oceanographic communities, and gives some insights on the role of ISWs on sedimentary process.

The Effects Of Urban Landscape Patterns On Rainfall-Runoff Processes At Small Scale

NASA Astrophysics Data System (ADS)

Chen, L.

2016-12-01

Many studies have indicated that urban landscape change may alter rainfall-runoff processes. However, how urban landscape pattern affect this process is little addressed. In this study, the hydrological effects of landscape pattern on rainfall-runoff processes at small-scale was explored. Twelve residential blocks with independent drainage systems in Beijing were selected as case study areas. Impervious metrics of these blocks, i.e., total impervious area (TIA) and directly connected impervious area (DCIA), were identified. A drainage index describing catchment general drainage load and the overland flow distance, Ad, was estimated and used as one of the landscape spatial metrics. Three scenarios were designed to test the potential influence of impervious surface pattern on runoff processes. Runoff variables including total and peak runoff depth (Qt and Qp) were simulated under different rainfall conditions by Storm Water Management Model (SWMM). The relationship between landscape patterns and runoff variables were analyzed, and further among the three scenarios. The results demonstrated that, in small urban blocks, spatial patterns have inherent influences on rainfall-runoff processes. Specifically, (1) Imperviousness acts as effective indicators in predicting both Qt and Qp. As rainfall intensity increases, the major affecting factor changes from DCIA to TIA for both Qt and Qp; (2) Increasing the size of drainage area dominated by each drainage inlet will benefit the block peak flow mitigation; (3) Different spatial concentrations of impervious surfaces have inherent influences on Qp, when impervious surfaces located away from the outlet can reduce the peak flow discharge. These findings may provide insights into the role of urban landscape patterns in driving rainfall-runoff responses in urbanization, which is essential for urban planning and stormwater management.

Thinking in clinical nursing practice: a study of critical care nurses' thinking applying the think-aloud, protocol analysis method.

PubMed

Han, Kyung-Ja; Kim, Hesook Suzie; Kim, Mae-Ja; Hong, Kyung-Ja; Park, Sungae; Yun, Soon-Nyoung; Song, Misoon; Jung, Yoenyi; Kim, Haewon; Kim, Dong-Oak Debbie; Choi, Heejung; Kim, Kyungae

2007-06-01

The purpose of the paper is to discover the patterns and processes of decision-making in clinical nursing practice. A set of think-aloud data from five critical care nurses during 40 to 50 minutes of caregiving in intensive care units were obtained and analyzed by applying the procedures recommended by Ericsson and Simon for protocol analysis. Four thinking processes before acting were identified to constitute various sorts of thoughts in which the nurses were engaged during patient care: reviewing, validation, consideration, rationalization, and action. In addition, three patterns of sequential streaming of thinking (short, intermediate, long) were identified to reveal various ways the nurses dealt with clinical situations involving nursing tasks and responsibilities. This study specifies the initial categories of thoughts for each of the processes and various patterns with which these processes are sequentially combined, providing insights into the ways nurses think about problems and address their concerns. The findings suggest that the thinking in clinical practice involves more than focused decision-making and reasoning, and needs to be examined from a broader perspective.

A regulatory governance perspective on health technology assessment (HTA) in France: the contextual mediation of common functional pressures.

PubMed

Barron, Anthony J G; Klinger, Corinna; Shah, Sara Mehmood Birchall; Wright, John S F

2015-02-01

The new regulatory governance perspective has introduced several insights to the study of health technology assessment (HTA): it has broadened the scope for the analysis of HTA; it has provided a more sophisticated account of national diversity and the potential for cross-border policy learning; and, it has dissolved the distinction between HTA assessment and appraisal processes. In this paper, we undertake a qualitative study of the French process for HTA with a view to introducing a fourth insight: that the emergence and continuing function of national agencies for HTA follows a broadly evolutionary pattern in which contextual factors play an important mediating role. We demonstrate that the French process for HTA is characterised by distinctive institutions, processes and evidential requirements. Consistent with the mediating role of this divergent policy context, we argue that even initiatives for the harmonisation of national approaches to HTA are likely to meet with divergent national policy responses. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Transition Characteristic Analysis of Traffic Evolution Process for Urban Traffic Network

PubMed Central

Chen, Hong; Li, Yang

2014-01-01

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

Spatial pattern and ecological process in the coffee agroforestry system.

PubMed

Perfecto, Ivette; Vandermeer, John

2008-04-01

The coffee agroforestry system provides an ideal platform for the study of spatial ecology. The uniform pattern of the coffee plants and shade trees allows for the study of pattern generation through intrinsic biological forces rather than extrinsic habitat patchiness. Detailed studies, focusing on a key mutualism between an ant (Azteca instabilis) and a scale insect (Coccus viridis), conducted in a 45-ha plot in a coffee agroforestry system have provided insights into (1) the quantitative evaluation of spatial pattern of the scale insect Coccus viridis on coffee bushes, (2) the mechanisms for the generation of patterns through the combination of local satellite ant nest formation and regional control from natural enemies, and (3) the consequences of the spatial pattern for the stability of predator-prey (host-parasitoid) systems, for a key coccinelid beetle preying on the scale insects and a phorid fly parasitoid parasitizing the ant.

Identifying typical patterns of vulnerability: A 5-step approach based on cluster analysis

NASA Astrophysics Data System (ADS)

Sietz, Diana; Lüdeke, Matthias; Kok, Marcel; Lucas, Paul; Carsten, Walther; Janssen, Peter

2013-04-01

Specific processes that shape the vulnerability of socio-ecological systems to climate, market and other stresses derive from diverse background conditions. Within the multitude of vulnerability-creating mechanisms, distinct processes recur in various regions inspiring research on typical patterns of vulnerability. The vulnerability patterns display typical combinations of the natural and socio-economic properties that shape a systems' vulnerability to particular stresses. Based on the identification of a limited number of vulnerability patterns, pattern analysis provides an efficient approach to improving our understanding of vulnerability and decision-making for vulnerability reduction. However, current pattern analyses often miss explicit descriptions of their methods and pay insufficient attention to the validity of their groupings. Therefore, the question arises as to how do we identify typical vulnerability patterns in order to enhance our understanding of a systems' vulnerability to stresses? A cluster-based pattern recognition applied at global and local levels is scrutinised with a focus on an applicable methodology and practicable insights. Taking the example of drylands, this presentation demonstrates the conditions necessary to identify typical vulnerability patterns. They are summarised in five methodological steps comprising the elicitation of relevant cause-effect hypotheses and the quantitative indication of mechanisms as well as an evaluation of robustness, a validation and a ranking of the identified patterns. Reflecting scale-dependent opportunities, a global study is able to support decision-making with insights into the up-scaling of interventions when available funds are limited. In contrast, local investigations encourage an outcome-based validation. This constitutes a crucial step in establishing the credibility of the patterns and hence their suitability for informing extension services and individual decisions. In this respect, working at the local level provides a clear advantage since, to a large extent, limitations in globally available observational data constrain such a validation on the global scale. Overall, the five steps are outlined in detail in order to facilitate and motivate the application of pattern recognition in other research studies concerned with vulnerability analysis, including future applications to different vulnerability frameworks. Such applications could promote the refinement of mechanisms in specific contexts and advance methodological adjustments. This would further increase the value of identifying typical patterns in the properties of socio-ecological systems for an improved understanding and management of the relation between these systems and particular stresses.

Contextual and perceptual brain processes underlying moral cognition: a quantitative meta-analysis of moral reasoning and moral emotions.

PubMed

Sevinc, Gunes; Spreng, R Nathan

2014-01-01

Human morality has been investigated using a variety of tasks ranging from judgments of hypothetical dilemmas to viewing morally salient stimuli. These experiments have provided insight into neural correlates of moral judgments and emotions, yet these approaches reveal important differences in moral cognition. Moral reasoning tasks require active deliberation while moral emotion tasks involve the perception of stimuli with moral implications. We examined convergent and divergent brain activity associated with these experimental paradigms taking a quantitative meta-analytic approach. A systematic search of the literature yielded 40 studies. Studies involving explicit decisions in a moral situation were categorized as active (n = 22); studies evoking moral emotions were categorized as passive (n = 18). We conducted a coordinate-based meta-analysis using the Activation Likelihood Estimation to determine reliable patterns of brain activity. Results revealed a convergent pattern of reliable brain activity for both task categories in regions of the default network, consistent with the social and contextual information processes supported by this brain network. Active tasks revealed more reliable activity in the temporoparietal junction, angular gyrus and temporal pole. Active tasks demand deliberative reasoning and may disproportionately involve the retrieval of social knowledge from memory, mental state attribution, and construction of the context through associative processes. In contrast, passive tasks reliably engaged regions associated with visual and emotional information processing, including lingual gyrus and the amygdala. A laterality effect was observed in dorsomedial prefrontal cortex, with active tasks engaging the left, and passive tasks engaging the right. While overlapping activity patterns suggest a shared neural network for both tasks, differential activity suggests that processing of moral input is affected by task demands. The results provide novel insight into distinct features of moral cognition, including the generation of moral context through associative processes and the perceptual detection of moral salience.

Contextual and Perceptual Brain Processes Underlying Moral Cognition: A Quantitative Meta-Analysis of Moral Reasoning and Moral Emotions

PubMed Central

Sevinc, Gunes; Spreng, R. Nathan

2014-01-01

Background and Objectives Human morality has been investigated using a variety of tasks ranging from judgments of hypothetical dilemmas to viewing morally salient stimuli. These experiments have provided insight into neural correlates of moral judgments and emotions, yet these approaches reveal important differences in moral cognition. Moral reasoning tasks require active deliberation while moral emotion tasks involve the perception of stimuli with moral implications. We examined convergent and divergent brain activity associated with these experimental paradigms taking a quantitative meta-analytic approach. Data Source A systematic search of the literature yielded 40 studies. Studies involving explicit decisions in a moral situation were categorized as active (n = 22); studies evoking moral emotions were categorized as passive (n = 18). We conducted a coordinate-based meta-analysis using the Activation Likelihood Estimation to determine reliable patterns of brain activity. Results & Conclusions Results revealed a convergent pattern of reliable brain activity for both task categories in regions of the default network, consistent with the social and contextual information processes supported by this brain network. Active tasks revealed more reliable activity in the temporoparietal junction, angular gyrus and temporal pole. Active tasks demand deliberative reasoning and may disproportionately involve the retrieval of social knowledge from memory, mental state attribution, and construction of the context through associative processes. In contrast, passive tasks reliably engaged regions associated with visual and emotional information processing, including lingual gyrus and the amygdala. A laterality effect was observed in dorsomedial prefrontal cortex, with active tasks engaging the left, and passive tasks engaging the right. While overlapping activity patterns suggest a shared neural network for both tasks, differential activity suggests that processing of moral input is affected by task demands. The results provide novel insight into distinct features of moral cognition, including the generation of moral context through associative processes and the perceptual detection of moral salience. PMID:24503959

Inferring biodiversity maintenance mechanisms from ecological pattern

NASA Astrophysics Data System (ADS)

Ostling, Annette

Among a set of competitors for a single common resource, the best will simply exclude the others. Yet in nature we can see astounding diversity of competing species. Do close similarities in species' response to the local environment primarily explain their coexistence? Or is this diversity possible because of differences between species that stabilize their coexistence? And if so, what particular differences between species are important in particular communities? Some ecological communities lend themselves to experimental manipulation to begin to answer these questions. Yet for many other communities, such as tree species in forests, the logistical hurdles to this approach are daunting. Faster progress could be made in ecology if insight into biodiversity maintenance mechanisms could be gained from patterns exhibited in local ecological communities, such as how coexisting species are distributed in their ecological traits and relative abundance. Hurdles that we need to overcome to be able to gain such insight include: 1) further developing neutral theory, a quantitative process-based null model of community pattern resulting when species similarities are what allow their coexistence, and 2) better understanding what patterns to expect when species differences dominate instead, particularly in the context of stochasticity and immigration. I will describe our ongoing research to overcome these hurdles, to provide better tools for analyzing observed pattern. National Science Foundation Advancing Theory in Biology Grant 1038678, Danish National Research Foundation Grant DNRF 96 for the Center of Macroecology, Evolution and Climate.

Insights from long-term research on the Fernow Experimental Forest

Treesearch

Mary Beth Adams

2016-01-01

In 1951, five weirs were constructed in the mixed hardwood forests of the Fernow Experimental Forest and watershed research began. Specializing in long-term watershed scale manipulations, researchers at the Fernow have evaluated effects of various silvicultural practices on water yield, seasonal flow patterns, water quality and on ecosystem processes and ecosystem...

Analyzing Pauses in Computer-Assisted EFL Writing--A Computer-Keystroke-Log Perspective

ERIC Educational Resources Information Center

Xu, Cuiqin; Qi, Yan

2017-01-01

Using computer keystroke logs, this study investigated how writing skill affected L2 writers' pausing patterns to gain insights into their management of the cognitive writing processes. The 59 participants, 29 in the more-skilled group and 30 in the less-skilled group, were recruited from a college English course at a key Chinese university. The…

Wind-driven circulation patterns in a shallow estuarine lake: St Lucia, South Africa

NASA Astrophysics Data System (ADS)

Schoen, Julia H.; Stretch, Derek D.; Tirok, Katrin

2014-06-01

The spatiotemporal structure of wind-driven circulation patterns and associated water exchanges or residence times can drive important bio-hydrodynamic interactions in shallow lakes and estuaries. The St Lucia estuarine lake in South Africa is an example of such a system. It is a UNESCO World Heritage Site and RAMSAR wetland of international importance but no detailed research on its circulation patterns has previously been undertaken. In this study, a hydrodynamic model was used to investigate the structure of these circulations to provide insights into their role in transport and water exchange processes. A strong diurnal temporal pattern of wind speeds, together with directional switching between two dominant directions, drives intermittent water exchanges and mixing between the lake basins. “High speed flows in shallow nearshore areas with slower upwind counter-flows in deeper areas, linked by circulatory gyres, are key features of the circulation”. These patterns are strongly influenced by the complex geometry of St Lucia and constrictions in the system. Water exchange time scales are non-homogeneous with some basin extremities having relatively long residence times. The influence of the circulation patterns on biological processes is discussed.

Evolutionary and demographic processes shaping geographic patterns of genetic diversity in a keystone species, the African forest elephant (Loxodonta cyclotis).

PubMed

Ishida, Yasuko; Gugala, Natalie A; Georgiadis, Nicholas J; Roca, Alfred L

2018-05-01

The past processes that have shaped geographic patterns of genetic diversity may be difficult to infer from current patterns. However, in species with sex differences in dispersal, differing phylogeographic patterns between mitochondrial (mt) and nuclear (nu) DNA may provide contrasting insights into past events. Forest elephants ( Loxodonta cyclotis ) were impacted by climate and habitat change during the Pleistocene, which likely shaped phylogeographic patterns in mitochondrial (mt) DNA that have persisted due to limited female dispersal. By contrast, the nuclear (nu) DNA phylogeography of forest elephants in Central Africa has not been determined. We therefore examined the population structure of Central African forest elephants by genotyping 94 individuals from six localities at 21 microsatellite loci. Between forest elephants in western and eastern Congolian forests, there was only modest genetic differentiation, a pattern highly discordant with that of mtDNA. Nuclear genetic patterns are consistent with isolation by distance. Alternatively, male-mediated gene flow may have reduced the previous regional differentiation in Central Africa suggested by mtDNA patterns, which likely reflect forest fragmentation during the Pleistocene. In species like elephants, male-mediated gene flow erases the nuclear genetic signatures of past climate and habitat changes, but these continue to persist as patterns in mtDNA because females do not disperse. Conservation implications of these results are discussed.

Insights into drying of non-circular sessile nanofluid droplet towards multi-scale surface patterning using a wall-less confinement architecture.

PubMed

Kabi, Prasenjit; Chaudhuri, Swetaprovo; Basu, Saptarshi

2016-10-04

Surface patterning with functional colloids is an important research area due to its widespread applicability in domains ranging from nano-electronics, pharmaceutics, semi-conductors, photovoltaics among others. To this endeavour, we propose a low-cost patterning technique that aspires to eliminate the more expensive methodologies presently in practise. Using a simple document stamp on which patterns of any geometry can be embossed, we are able to print two-dimensional mm-scale "wall-less confinement" using ink based hydrophobic fence on any plasma treated superhydrophilic surface. The confinement is subsequently filled with nanocolloidal liquid(s). Using the confinement geometry, we are able to control the 3D shape of the droplet to exhibit multiple interfacial curvatures. The droplet in the "wall-less confinements" evaporates naturally exhibiting unique geometry (curvature) induced flow structures which induce the nanoparticles to self-assemble into functional patterns. We have also shown that by modifying the geometry of the pattern, evaporation, flow and particle deposition dynamics get altered leading to precipitate topologies from macro to microscales. We, present two such geometrical designs which demonstrate the capability of modifying both the macroscopic as well as the microscopic features of the final precipitate. We have also provided a description of the physical mechanisms of the drying process by resolving the unique flow pattern using a combination of imaging and μPIV (micro particle image velocimetry). These provide insights into the coupled dynamics of evaporation and flow responsible for the evolution of particle deposition pattern. Precipitate characterization using SEM and dark-field microscopy highlight the transformation in the deposit morphology.

Between-Word Processes in Children with Speech Difficulties: Insights from a Usage-Based Approach to Phonology

ERIC Educational Resources Information Center

Newton, Caroline

2012-01-01

There are some children with speech and/or language difficulties who are significantly more difficult to understand in connected speech than in single words. The study reported here explores the between-word behaviours of three such children, aged 11;8, 12;2 and 12;10. It focuses on whether these patterns could be accounted for by lenition, as…

IgG4 hypophysitis - a rare and underdiagnosed cause of pituitary gland and stalk mass-like thickening.

PubMed

Murphy, Alexandra N; Hannon, Anne Marie; Brett, Francesca M; Agha, Amar; Javadpour, Mohsen; Looby, Seamus

2018-01-01

Our aim is to present a typical case of IgG4-related hypophysitis, which will offer insight into the aetiology and pathogenesis of this relatively newly described disease. IgG4 Related Disease is a protean systemic condition that mimics inflammatory, infectious, and malignant processes. Biopsy of affected organs will show a typical histopathological pattern.

Fact vs fiction--how paratextual information shapes our reading processes.

PubMed

Altmann, Ulrike; Bohrn, Isabel C; Lubrich, Oliver; Menninghaus, Winfried; Jacobs, Arthur M

2014-01-01

Our life is full of stories: some of them depict real-life events and were reported, e.g. in the daily news or in autobiographies, whereas other stories, as often presented to us in movies and novels, are fictional. However, we have only little insights in the neurocognitive processes underlying the reading of factual as compared to fictional contents. We investigated the neurocognitive effects of reading short narratives, labeled to be either factual or fictional. Reading in a factual mode engaged an activation pattern suggesting an action-based reconstruction of the events depicted in a story. This process seems to be past-oriented and leads to shorter reaction times at the behavioral level. In contrast, the brain activation patterns corresponding to reading fiction seem to reflect a constructive simulation of what might have happened. This is in line with studies on imagination of possible past or future events.

Fact vs fiction—how paratextual information shapes our reading processes

PubMed Central

Altmann, Ulrike; Bohrn, Isabel C.; Lubrich, Oliver; Menninghaus, Winfried; Jacobs, Arthur M.

2014-01-01

Our life is full of stories: some of them depict real-life events and were reported, e.g. in the daily news or in autobiographies, whereas other stories, as often presented to us in movies and novels, are fictional. However, we have only little insights in the neurocognitive processes underlying the reading of factual as compared to fictional contents. We investigated the neurocognitive effects of reading short narratives, labeled to be either factual or fictional. Reading in a factual mode engaged an activation pattern suggesting an action-based reconstruction of the events depicted in a story. This process seems to be past-oriented and leads to shorter reaction times at the behavioral level. In contrast, the brain activation patterns corresponding to reading fiction seem to reflect a constructive simulation of what might have happened. This is in line with studies on imagination of possible past or future events. PMID:22956671

Morphological priming by itself: a study of Portuguese conjugations.

PubMed

Veríssimo, João; Clahsen, Harald

2009-07-01

Does the language processing system make use of abstract grammatical categories and representations that are not directly visible from the surface form of a linguistic expression? This study examines stem-formation processes and conjugation classes, a case of 'pure' morphology that provides insight into the role of grammatical structure in language processing. We report results from a cross-modal priming experiment examining 1st and 3rd conjugation verb forms in Portuguese. Although items were closely matched with respect to a range of non-morphological factors, distinct priming patterns were found for 1st and 3rd conjugation stems. We attribute the observed priming patterns to different representations of conjugational stems, combinatorial morphologically structured ones for 1st conjugation and un-analyzed morphologically unstructured ones for 3rd conjugation stems. Our findings underline the importance of morphology for language comprehension indicating that morphological analysis goes beyond the identification of grammatical morphemes.

Implications of recurrent disturbance for genetic diversity.

PubMed

Davies, Ian D; Cary, Geoffrey J; Landguth, Erin L; Lindenmayer, David B; Banks, Sam C

2016-02-01

Exploring interactions between ecological disturbance, species' abundances and community composition provides critical insights for ecological dynamics. While disturbance is also potentially an important driver of landscape genetic patterns, the mechanisms by which these patterns may arise by selective and neutral processes are not well-understood. We used simulation to evaluate the relative importance of disturbance regime components, and their interaction with demographic and dispersal processes, on the distribution of genetic diversity across landscapes. We investigated genetic impacts of variation in key components of disturbance regimes and spatial patterns that are likely to respond to climate change and land management, including disturbance size, frequency, and severity. The influence of disturbance was mediated by dispersal distance and, to a limited extent, by birth rate. Nevertheless, all three disturbance regime components strongly influenced spatial and temporal patterns of genetic diversity within subpopulations, and were associated with changes in genetic structure. Furthermore, disturbance-induced changes in temporal population dynamics and the spatial distribution of populations across the landscape resulted in disrupted isolation by distance patterns among populations. Our results show that forecast changes in disturbance regimes have the potential to cause major changes to the distribution of genetic diversity within and among populations. We highlight likely scenarios under which future changes to disturbance size, severity, or frequency will have the strongest impacts on population genetic patterns. In addition, our results have implications for the inference of biological processes from genetic data, because the effects of dispersal on genetic patterns were strongly mediated by disturbance regimes.

DEVELOPMENTAL DIVERSITY OF AMPHIBIANS

PubMed Central

Elinson, Richard P.; del Pino, Eugenia M.

2011-01-01

The current model amphibian, Xenopus laevis, develops rapidly in water to a tadpole which metamorphoses into a frog. Many amphibians deviate from the X. laevis developmental pattern. Among other adaptations, their embryos develop in foam nests on land or in pouches on their mother’s back or on a leaf guarded by a parent. The diversity of developmental patterns includes multinucleated oogenesis, lack of RNA localization, huge non-pigmented eggs, and asynchronous, irregular early cleavages. Variations in patterns of gastrulation highlight the modularity of this critical developmental period. Many species have eliminated the larva or tadpole and directly develop to the adult. The wealth of developmental diversity among amphibians coupled with the wealth of mechanistic information from X. laevis permit comparisons that provide deeper insights into developmental processes. PMID:22662314

Adaptive Classification of Landscape Process and Function: An Integration of Geoinformatics and Self-Organizing Maps

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

Coleman, Andre M.

2009-07-17

The advanced geospatial information extraction and analysis capabilities of a Geographic Information System (GISs) and Artificial Neural Networks (ANNs), particularly Self-Organizing Maps (SOMs), provide a topology-preserving means for reducing and understanding complex data relationships in the landscape. The Adaptive Landscape Classification Procedure (ALCP) is presented as an adaptive and evolutionary capability where varying types of data can be assimilated to address different management needs such as hydrologic response, erosion potential, habitat structure, instrumentation placement, and various forecast or what-if scenarios. This paper defines how the evaluation and analysis of spatial and/or temporal patterns in the landscape can provide insight intomore » complex ecological, hydrological, climatic, and other natural and anthropogenic-influenced processes. Establishing relationships among high-dimensional datasets through neurocomputing based pattern recognition methods can help 1) resolve large volumes of data into a structured and meaningful form; 2) provide an approach for inferring landscape processes in areas that have limited data available but exhibit similar landscape characteristics; and 3) discover the value of individual variables or groups of variables that contribute to specific processes in the landscape. Classification of hydrologic patterns in the landscape is demonstrated.« less

Dietary patterns in the Avon Longitudinal Study of Parents and Children

PubMed Central

Jones, Louise R.; Northstone, Kate

2015-01-01

Publications from the Avon Longitudinal Study of Parents and Children that used empirically derived dietary patterns were reviewed. The relationships of dietary patterns with socioeconomic background and childhood development were examined. Diet was assessed using food frequency questionnaires and food records. Three statistical methods were used: principal components analysis, cluster analysis, and reduced rank regression. Throughout childhood, children and parents have similar dietary patterns. The “health-conscious” and “traditional” patterns were associated with high intakes of fruits and/or vegetables and better nutrient profiles than the “processed” patterns. There was evidence of tracking in childhood diet, with the “health-conscious” patterns tracking most strongly, followed by the “processed” pattern. An “energy-dense, low-fiber, high-fat” dietary pattern was extracted using reduced rank regression; high scores on this pattern were associated with increasing adiposity. Maternal education was a strong determinant of pattern score or cluster membership; low educational attainment was associated with higher scores on processed, energy-dense patterns in both parents and children. The Avon Longitudinal Study of Parents and Children has provided unique insights into the value of empirically derived dietary patterns and has demonstrated that they are a useful tool in nutritional epidemiology. PMID:26395343

How to design a horizontal patient-focused hospital.

PubMed

Murphy, E C; Ruflin, P

1993-05-01

Work Imaging is an executive information system for analyzing the cost effectiveness and efficiency of work processes and structures in health care. Advanced Work Imaging relational database technology allows managers and employees to take a sample work activities profile organization-wide. This is married to financial and organizational data to produce images of work within and across all functions, departments, and levels. The images are benchmarked against best practice data to provide insight on the quality and cost efficiency of work practice patterns, from individual roles to departmental skill mix to organization-wide service processes.

Novel applications of Tablet PCs to investigate expert cognition in the geosciences

NASA Astrophysics Data System (ADS)

Turner, Sheldon; Libarkin, Julie

2012-05-01

In this paper, we present new methodologies developed to investigate cognitive processes related to perceiving and interpreting Earth phenomena. This area of study, known as geocognition, is an emerging and vital aspect of geoscience. Geocognition gives geoscientists an understanding of how people conceptualize earth processes. For example, geocognition research can be used to generate effective strategies for increasing public scientific literacy in this new era of climate change and energy crisis. We collected spatial visualization and working memory data using a Camtasia add-on for PowerPoint to generate a unique set of static drawings and videos of the drawing process. Analyzing these data provides unique insight into the underlying cognitive processes. For example, quantitative patterns that emerge within a subpopulation of novices or experts show us the common errors and patterns in how objects are drawn, including drawing order and time spent drawing. We believe that these unique data will contribute to the ongoing efforts to generate new understanding of the nature of geoscientific expertise.

Role of mechanical factors in cortical folding development

NASA Astrophysics Data System (ADS)

Razavi, Mir Jalil; Zhang, Tuo; Li, Xiao; Liu, Tianming; Wang, Xianqiao

2015-09-01

Deciphering mysteries of the structure-function relationship in cortical folding has emerged as the cynosure of recent research on brain. Understanding the mechanism of convolution patterns can provide useful insight into the normal and pathological brain function. However, despite decades of speculation and endeavors the underlying mechanism of the brain folding process remains poorly understood. This paper focuses on the three-dimensional morphological patterns of a developing brain under different tissue specification assumptions via theoretical analyses, computational modeling, and experiment verifications. The living human brain is modeled with a soft structure having outer cortex and inner core to investigate the brain development. Analytical interpretations of differential growth of the brain model provide preliminary insight into the critical growth ratio for instability and crease formation of the developing brain followed by computational modeling as a way to offer clues for brain's postbuckling morphology. Especially, tissue geometry, growth ratio, and material properties of the cortex are explored as the most determinant parameters to control the morphogenesis of a growing brain model. As indicated in results, compressive residual stresses caused by the sufficient growth trigger instability and the brain forms highly convoluted patterns wherein its gyrification degree is specified with the cortex thickness. Morphological patterns of the developing brain predicted from the computational modeling are consistent with our neuroimaging observations, thereby clarifying, in part, the reason of some classical malformation in a developing brain.

Anatomical insights into the interaction of emotion and cognition in the prefrontal cortex

PubMed Central

Ray, Rebecca; Zald, David H.

2011-01-01

Ray, R. and D. Zald. Anatomical insights into the interaction of emotion and cognition in the prefrontal cortex. NEUROSCI BIOBEHAV REV 36(X) XXX-XXX, 2011. -Psychological research increasingly indicates that emotional processes interact with other aspects of cognition. Studies have demonstrated both the ability of emotional stimuli to influence a broad range of cognitive operations, and the ability of humans to use top-down cognitive control mechanisms to regulate emotional responses. Portions of the prefrontal cortex appear to play a significant role in these interactions. However, the manner in which these interactions are implemented remains only partially elucidated. In the present review we describe the anatomical connections between ventral and dorsal prefrontal areas as well as their connections with limbic regions. Only a subset of prefrontal areas are likely to directly influence amygdalar processing, and as such models of prefrontal control of emotions and models of emotional regulation should be constrained to plausible pathways of influence. We also focus on how the specific pattern of feedforward and feedback connections between these regions may dictate the nature of information flow between ventral and dorsal prefrontal areas and the amygdala. These patterns of connections are inconsistent with several commonly expressed assumptions about the nature of communications between emotion and cognition. PMID:21889953

Neural Correlates of Learning from Induced Insight: A Case for Reward-Based Episodic Encoding

PubMed Central

Kizilirmak, Jasmin M.; Thuerich, Hannes; Folta-Schoofs, Kristian; Schott, Björn H.; Richardson-Klavehn, Alan

2016-01-01

Experiencing insight when solving problems can improve memory formation for both the problem and its solution. The underlying neural processes involved in this kind of learning are, however, thus far insufficiently understood. Here, we conceptualized insight as the sudden understanding of a novel relationship between known stimuli that fits into existing knowledge and is accompanied by a positive emotional response. Hence, insight is thought to comprise associative novelty, schema congruency, and intrinsic reward, all of which are separately known to enhance memory performance. We examined the neural correlates of learning from induced insight with functional magnetic resonance imaging (fMRI) using our own version of the compound-remote-associates-task (CRAT) in which each item consists of three clue words and a solution word. (Pseudo-)Solution words were presented after a brief period of problem-solving attempts to induce either sudden comprehension (CRA items) or continued incomprehension (control items) at a specific time point. By comparing processing of the solution words of CRA with control items, we found induced insight to elicit activation of the rostral anterior cingulate cortex/medial prefrontal cortex (rACC/mPFC) and left hippocampus. This pattern of results lends support to the role of schema congruency (rACC/mPFC) and associative novelty (hippocampus) in the processing of induced insight. We propose that (1) the mPFC not only responds to schema-congruent information, but also to the detection of novel schemata, and (2) that the hippocampus responds to a form of associative novelty that is not just a novel constellation of familiar items, but rather comprises a novel meaningful relationship between the items—which was the only difference between our insight and no insight conditions. To investigate episodic long-term memory encoding, we compared CRA items whose solution word was recognized 24 h after encoding to those with forgotten solutions. We found activation in the left striatum and parts of the left amygdala, pointing to a potential role of brain reward circuitry in the encoding of the solution words. We propose that learning from induced insight mainly relies on the amygdala evaluating the internal value (as an affective evaluation) of the suddenly comprehended information, and striatum-dependent reward-based learning. PMID:27847490

Neural Correlates of Learning from Induced Insight: A Case for Reward-Based Episodic Encoding.

PubMed

Kizilirmak, Jasmin M; Thuerich, Hannes; Folta-Schoofs, Kristian; Schott, Björn H; Richardson-Klavehn, Alan

2016-01-01

Experiencing insight when solving problems can improve memory formation for both the problem and its solution. The underlying neural processes involved in this kind of learning are, however, thus far insufficiently understood. Here, we conceptualized insight as the sudden understanding of a novel relationship between known stimuli that fits into existing knowledge and is accompanied by a positive emotional response. Hence, insight is thought to comprise associative novelty, schema congruency, and intrinsic reward, all of which are separately known to enhance memory performance. We examined the neural correlates of learning from induced insight with functional magnetic resonance imaging (fMRI) using our own version of the compound-remote-associates-task (CRAT) in which each item consists of three clue words and a solution word. (Pseudo-)Solution words were presented after a brief period of problem-solving attempts to induce either sudden comprehension (CRA items) or continued incomprehension (control items) at a specific time point. By comparing processing of the solution words of CRA with control items, we found induced insight to elicit activation of the rostral anterior cingulate cortex/medial prefrontal cortex (rACC/mPFC) and left hippocampus. This pattern of results lends support to the role of schema congruency (rACC/mPFC) and associative novelty (hippocampus) in the processing of induced insight. We propose that (1) the mPFC not only responds to schema-congruent information, but also to the detection of novel schemata, and (2) that the hippocampus responds to a form of associative novelty that is not just a novel constellation of familiar items, but rather comprises a novel meaningful relationship between the items-which was the only difference between our insight and no insight conditions. To investigate episodic long-term memory encoding, we compared CRA items whose solution word was recognized 24 h after encoding to those with forgotten solutions. We found activation in the left striatum and parts of the left amygdala, pointing to a potential role of brain reward circuitry in the encoding of the solution words. We propose that learning from induced insight mainly relies on the amygdala evaluating the internal value (as an affective evaluation) of the suddenly comprehended information, and striatum-dependent reward-based learning.

Probabilistic Analysis of Pattern Formation in Monotonic Self-Assembly

PubMed Central

Moore, Tyler G.; Garzon, Max H.; Deaton, Russell J.

2015-01-01

Inspired by biological systems, self-assembly aims to construct complex structures. It functions through piece-wise, local interactions among component parts and has the potential to produce novel materials and devices at the nanoscale. Algorithmic self-assembly models the product of self-assembly as the output of some computational process, and attempts to control the process of assembly algorithmically. Though providing fundamental insights, these computational models have yet to fully account for the randomness that is inherent in experimental realizations, which tend to be based on trial and error methods. In order to develop a method of analysis that addresses experimental parameters, such as error and yield, this work focuses on the capability of assembly systems to produce a pre-determined set of target patterns, either accurately or perhaps only approximately. Self-assembly systems that assemble patterns that are similar to the targets in a significant percentage are “strong” assemblers. In addition, assemblers should predominantly produce target patterns, with a small percentage of errors or junk. These definitions approximate notions of yield and purity in chemistry and manufacturing. By combining these definitions, a criterion for efficient assembly is developed that can be used to compare the ability of different assembly systems to produce a given target set. Efficiency is a composite measure of the accuracy and purity of an assembler. Typical examples in algorithmic assembly are assessed in the context of these metrics. In addition to validating the method, they also provide some insight that might be used to guide experimentation. Finally, some general results are established that, for efficient assembly, imply that every target pattern is guaranteed to be assembled with a minimum common positive probability, regardless of its size, and that a trichotomy exists to characterize the global behavior of typical efficient, monotonic self-assembly systems in the literature. PMID:26421616

Proteomic analysis of Bombyx mori molting fluid: Insights into the molting process.

PubMed

Liu, Hua-Wei; Wang, Luo-Ling; Tang, Xin; Dong, Zhao-Ming; Guo, Peng-Chao; Zhao, Dong-Chao; Xia, Qing-You; Zhao, Ping

2018-02-20

Molting is an essential biological process occurring multiple times throughout the life cycle of most Ecdysozoa. Molting fluids accumulate and function in the exuvial space during the molting process. In this study, we used liquid chromatography-tandem mass spectrometry to investigate the molting fluids to analyze the molecular mechanisms of molting in the silkworm, Bombyx mori. In total, 375 proteins were identified in molting fluids from the silkworm at 14-16h before pupation and eclosion, including 12 chitin metabolism-related enzymes, 35 serine proteases, 15 peptidases, and 38 protease inhibitors. Gene ontology analysis indicated that "catalytic" constitutes the most enriched function in the molting fluid. Gene expression patterns and bioinformatic analyses suggested that numerous enzymes are involved in the degradation of cuticle proteins and chitin. Protein-protein interaction network and activity analyses showed that protease inhibitors are involved in the regulation of multiple pathways in molting fluid. Additionally, many immune-related proteins may be involved in the immune defense during molting. These results provide a comprehensive proteomic insight into proteolytic enzymes and protease inhibitors in molting fluid, and will likely improve the current understanding of physiological processes in insect molting. Insect molting constitutes a dynamic physiological process. To better understand this process, we used LC-MS/MS to investigate the proteome of silkworm molting fluids and identified key proteins involved in silkworm molting. The biological processes of the old cuticle degradation pathway and immune defense response were analyzed in the proteome of silkworm molting fluid. We report that protease inhibitors serve as key factors in the regulation of the molting process. The proteomic results provide new insight into biological molting processes in insects. Copyright © 2017 Elsevier B.V. All rights reserved.

Network analysis reveals multiscale controls on streamwater chemistry

USGS Publications Warehouse

McGuire, Kevin J.; Torgersen, Christian E.; Likens, Gene E.; Buso, Donald C.; Lowe, Winsor H.; Bailey, Scott W.

2014-01-01

By coupling synoptic data from a basin-wide assessment of streamwater chemistry with network-based geostatistical analysis, we show that spatial processes differentially affect biogeochemical condition and pattern across a headwater stream network. We analyzed a high-resolution dataset consisting of 664 water samples collected every 100 m throughout 32 tributaries in an entire fifth-order stream network. These samples were analyzed for an exhaustive suite of chemical constituents. The fine grain and broad extent of this study design allowed us to quantify spatial patterns over a range of scales by using empirical semivariograms that explicitly incorporated network topology. Here, we show that spatial structure, as determined by the characteristic shape of the semivariograms, differed both among chemical constituents and by spatial relationship (flow-connected, flow-unconnected, or Euclidean). Spatial structure was apparent at either a single scale or at multiple nested scales, suggesting separate processes operating simultaneously within the stream network and surrounding terrestrial landscape. Expected patterns of spatial dependence for flow-connected relationships (e.g., increasing homogeneity with downstream distance) occurred for some chemical constituents (e.g., dissolved organic carbon, sulfate, and aluminum) but not for others (e.g., nitrate, sodium). By comparing semivariograms for the different chemical constituents and spatial relationships, we were able to separate effects on streamwater chemistry of (i) fine-scale versus broad-scale processes and (ii) in-stream processes versus landscape controls. These findings provide insight on the hierarchical scaling of local, longitudinal, and landscape processes that drive biogeochemical patterns in stream networks.

Network analysis reveals multiscale controls on streamwater chemistry

PubMed Central

McGuire, Kevin J.; Torgersen, Christian E.; Likens, Gene E.; Buso, Donald C.; Lowe, Winsor H.; Bailey, Scott W.

2014-01-01

By coupling synoptic data from a basin-wide assessment of streamwater chemistry with network-based geostatistical analysis, we show that spatial processes differentially affect biogeochemical condition and pattern across a headwater stream network. We analyzed a high-resolution dataset consisting of 664 water samples collected every 100 m throughout 32 tributaries in an entire fifth-order stream network. These samples were analyzed for an exhaustive suite of chemical constituents. The fine grain and broad extent of this study design allowed us to quantify spatial patterns over a range of scales by using empirical semivariograms that explicitly incorporated network topology. Here, we show that spatial structure, as determined by the characteristic shape of the semivariograms, differed both among chemical constituents and by spatial relationship (flow-connected, flow-unconnected, or Euclidean). Spatial structure was apparent at either a single scale or at multiple nested scales, suggesting separate processes operating simultaneously within the stream network and surrounding terrestrial landscape. Expected patterns of spatial dependence for flow-connected relationships (e.g., increasing homogeneity with downstream distance) occurred for some chemical constituents (e.g., dissolved organic carbon, sulfate, and aluminum) but not for others (e.g., nitrate, sodium). By comparing semivariograms for the different chemical constituents and spatial relationships, we were able to separate effects on streamwater chemistry of (i) fine-scale versus broad-scale processes and (ii) in-stream processes versus landscape controls. These findings provide insight on the hierarchical scaling of local, longitudinal, and landscape processes that drive biogeochemical patterns in stream networks. PMID:24753575

Network analysis reveals multiscale controls on streamwater chemistry.

PubMed

McGuire, Kevin J; Torgersen, Christian E; Likens, Gene E; Buso, Donald C; Lowe, Winsor H; Bailey, Scott W

2014-05-13

By coupling synoptic data from a basin-wide assessment of streamwater chemistry with network-based geostatistical analysis, we show that spatial processes differentially affect biogeochemical condition and pattern across a headwater stream network. We analyzed a high-resolution dataset consisting of 664 water samples collected every 100 m throughout 32 tributaries in an entire fifth-order stream network. These samples were analyzed for an exhaustive suite of chemical constituents. The fine grain and broad extent of this study design allowed us to quantify spatial patterns over a range of scales by using empirical semivariograms that explicitly incorporated network topology. Here, we show that spatial structure, as determined by the characteristic shape of the semivariograms, differed both among chemical constituents and by spatial relationship (flow-connected, flow-unconnected, or Euclidean). Spatial structure was apparent at either a single scale or at multiple nested scales, suggesting separate processes operating simultaneously within the stream network and surrounding terrestrial landscape. Expected patterns of spatial dependence for flow-connected relationships (e.g., increasing homogeneity with downstream distance) occurred for some chemical constituents (e.g., dissolved organic carbon, sulfate, and aluminum) but not for others (e.g., nitrate, sodium). By comparing semivariograms for the different chemical constituents and spatial relationships, we were able to separate effects on streamwater chemistry of (i) fine-scale versus broad-scale processes and (ii) in-stream processes versus landscape controls. These findings provide insight on the hierarchical scaling of local, longitudinal, and landscape processes that drive biogeochemical patterns in stream networks.

Multiple hypotheses testing of fish incidence patterns in an urbanized ecosystem

USGS Publications Warehouse

Chizinski, C.J.; Higgins, C.L.; Shavlik, C.E.; Pope, K.L.

2006-01-01

Ecological and evolutionary theories have focused traditionally on natural processes with little attempt to incorporate anthropogenic influences despite the fact that humans are such an integral part of virtually all ecosystems. A series of alternate models that incorporated anthropogenic factors and traditional ecological mechanisms of invasion to account for fish incidence patterns in urban lakes was tested. The models were based on fish biology, human intervention, and habitat characteristics. However, the only models to account for empirical patterns were those that included fish invasiveness, which incorporated species-specific information about overall tolerance and fecundity. This suggests that species-specific characteristics are more important in general distributional patterns than human-mediated dispersal. Better information of illegal stocking activities is needed to improve human-mediated models, and more insight into basic life history of ubiquitous species is needed to truly understand underlying mechanisms of biotic homogenization. ?? Springer 2005.

Liquid crystalline pattern formation in drying droplets of biopolymers

NASA Astrophysics Data System (ADS)

Smalyukh, Ivan; Zribi, Olena; Butler, John; Lavrentovich, Oleg; Wong, Gerard

2006-03-01

When a droplet of DNA in water dries out, a ring-like deposit is observed along the perimeter, similar to the stains in spilled drops of coffee. However, the dried ring of DNA is a self-similar birefringent pattern composed of extended molecules. We examine dynamics of the pattern formation at the droplet's rim. This gives us an insight into the underlining physics. During the major part of drying process the contact line is pinned so that DNA molecules are brought to the perimeter and extended by the radial capillary flow. Lyotropic nematic phase is formed in which highly concentrated DNA aligns along the triple line to minimize elastic energy. When the contact angle becomes small, the contact line starts to retract and the radial dilative stress causes buckling distortions at the rim which then propagate deep into the elastic liquid- crystalline medium and give rise to the pattern.

Insight on invasions and resilience derived from spatiotemporal discontinuities of biomass at local and regional scales

USGS Publications Warehouse

Angeler, David G.; Allen, Criag R.; Johnson, Richard K.

2012-01-01

Understanding the social and ecological consequences of species invasions is complicated by nonlinearities in processes, and differences in process and structure as scale is changed. Here we use discontinuity analyses to investigate nonlinear patterns in the distribution of biomass of an invasive nuisance species that could indicate scale-specific organization. We analyze biomass patterns in the flagellate Gonyostomum semen (Raphidophyta) in 75 boreal lakes during an 11-year period (1997-2007). With simulations using a unimodal null model and cluster analysis, we identified regional groupings of lakes based on their biomass patterns. We evaluated the variability of membership of individual lakes in regional biomass groups. Temporal trends in local and regional discontinuity patterns were analyzed using regressions and correlations with environmental variables that characterize nutrient conditions, acidity status, temperature variability, and water clarity. Regionally, there was a significant increase in the number of biomass groups over time, indicative of an increased number of scales at which algal biomass organizes across lakes. This increased complexity correlated with the invasion history of G. semen and broad-scale environmental change (recovery from acidification). Locally, no consistent patterns of lake membership to regional biomass groups were observed, and correlations with environmental variables were lake specific. The increased complexity of regional biomass patterns suggests that processes that act within or between scales reinforce the presence of G. semen and its potential to develop high-biomass blooms in boreal lakes. Emergent regional patterns combined with locally stochastic dynamics suggest a bleak future for managing G. semen, and more generally why invasive species can be ecologically successful.

Hierarchical analysis of spatial pattern and processes of Douglas-fir forests. Ph.D. Thesis, 10 Sep. 1991 Abstract Only

NASA Technical Reports Server (NTRS)

Bradshaw, G. A.

1995-01-01

There has been an increased interest in the quantification of pattern in ecological systems over the past years. This interest is motivated by the desire to construct valid models which extend across many scales. Spatial methods must quantify pattern, discriminate types of pattern, and relate hierarchical phenomena across scales. Wavelet analysis is introduced as a method to identify spatial structure in ecological transect data. The main advantage of the wavelet transform over other methods is its ability to preserve and display hierarchical information while allowing for pattern decomposition. Two applications of wavelet analysis are illustrated, as a means to: (1) quantify known spatial patterns in Douglas-fir forests at several scales, and (2) construct spatially-explicit hypotheses regarding pattern generating mechanisms. Application of the wavelet variance, derived from the wavelet transform, is developed for forest ecosystem analysis to obtain additional insight into spatially-explicit data. Specifically, the resolution capabilities of the wavelet variance are compared to the semi-variogram and Fourier power spectra for the description of spatial data using a set of one-dimensional stationary and non-stationary processes. The wavelet cross-covariance function is derived from the wavelet transform and introduced as a alternative method for the analysis of multivariate spatial data of understory vegetation and canopy in Douglas-fir forests of the western Cascades of Oregon.

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

PubMed

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

2007-01-01

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

Imbalanced target prediction with pattern discovery on clinical data repositories.

PubMed

Chan, Tak-Ming; Li, Yuxi; Chiau, Choo-Chiap; Zhu, Jane; Jiang, Jie; Huo, Yong

2017-04-20

Clinical data repositories (CDR) have great potential to improve outcome prediction and risk modeling. However, most clinical studies require careful study design, dedicated data collection efforts, and sophisticated modeling techniques before a hypothesis can be tested. We aim to bridge this gap, so that clinical domain users can perform first-hand prediction on existing repository data without complicated handling, and obtain insightful patterns of imbalanced targets for a formal study before it is conducted. We specifically target for interpretability for domain users where the model can be conveniently explained and applied in clinical practice. We propose an interpretable pattern model which is noise (missing) tolerant for practice data. To address the challenge of imbalanced targets of interest in clinical research, e.g., deaths less than a few percent, the geometric mean of sensitivity and specificity (G-mean) optimization criterion is employed, with which a simple but effective heuristic algorithm is developed. We compared pattern discovery to clinically interpretable methods on two retrospective clinical datasets. They contain 14.9% deaths in 1 year in the thoracic dataset and 9.1% deaths in the cardiac dataset, respectively. In spite of the imbalance challenge shown on other methods, pattern discovery consistently shows competitive cross-validated prediction performance. Compared to logistic regression, Naïve Bayes, and decision tree, pattern discovery achieves statistically significant (p-values < 0.01, Wilcoxon signed rank test) favorable averaged testing G-means and F1-scores (harmonic mean of precision and sensitivity). Without requiring sophisticated technical processing of data and tweaking, the prediction performance of pattern discovery is consistently comparable to the best achievable performance. Pattern discovery has demonstrated to be robust and valuable for target prediction on existing clinical data repositories with imbalance and noise. The prediction results and interpretable patterns can provide insights in an agile and inexpensive way for the potential formal studies.

Genomes in Turmoil: Frugality Drives Microbial Community Structure in Extremely Acidic Environments

NASA Astrophysics Data System (ADS)

Holmes, D. S.

2016-12-01

Extremely acidic environments (To gain insight into these issues, we have conducted deep bioinformatic analyses, including metabolic reconstruction of key assimilatory pathways, phylogenomics and network scrutiny of >160 genomes of acidophiles, including representatives from Archaea, Bacteria and Eukarya and at least ten metagenomes of acidic environments [Cardenas JP, et al. pp 179-197 in Acidophiles, eds R. Quatrini and D. B. Johnson, Caister Academic Press, UK (2016)]. Results yielded valuable insights into cellular processes, including carbon and nitrogen management and energy production, linking biogeochemical processes to organismal physiology. They also provided insight into the evolutionary forces that shape the genomic structure of members of acidophile communities. Niche partitioning can explain diversity patterns in rapidly changing acidic environments such as bioleaching heaps. However, in spatially and temporally homogeneous acidic environments genome flux appears to provide deeper insight into the composition and evolution of acidic consortia. Acidophiles have undergone genome streamlining by gene loss promoting mutual coexistence of species that exploit complementarity use of scarce resources consistent with the Black Queen hypothesis [Morris JJ et al. mBio 3: e00036-12 (2012)]. Acidophiles also have a large pool of accessory genes (the microbial super-genome) that can be accessed by horizontal gene transfer. This further promotes dependency relationships as drivers of community structure and the evolution of keystone species. Acknowledgements: Fondecyt 1130683; Basal CCTE PFB16

Seasonal and multi-year surface displacements measured by DInSAR in a High Arctic permafrost environment

NASA Astrophysics Data System (ADS)

Rudy, Ashley C. A.; Lamoureux, Scott F.; Treitz, Paul; Short, Naomi; Brisco, Brian

2018-02-01

Arctic landscapes undergo seasonal and long-term changes as the active layer thaws and freezes, which can result in localized or irregular subsidence leading to the formation of thermokarst terrain. Differential Interferometric Synthetic Aperture Radar (DInSAR) is a technique capable of measuring ground surface displacements resulting from thawing permafrost at centimetre precision and is quickly gaining acceptance as a means of measuring ground displacement in permafrost regions. Using RADARSAT-2 stacked DInSAR data from 2013 and 2015 we determined the magnitude and patterns of land surface change in a continuous permafrost environment. At our study site situated in the Canadian High Arctic, DInSAR seasonal ground displacement patterns were consistent with field observations of permafrost degradation. As expected, many DInSAR values are close to the detection threshold (i.e., 1 cm) and therefore do not indicate significant change; however, DInSAR seasonal ground displacement patterns aligned well with climatological and soil conditions and offer geomorphological insight into subsurface processes in permafrost environments. While our dataset is limited to two years of data representing a three-year time period, the displacements derived from DInSAR provide insight into permafrost change in a High Arctic environment and demonstrate that DInSAR is an applicable tool for understanding environmental change in remote permafrost regions.

Numerical investigation of coupled density-driven flow and hydrogeochemical processes below playas

NASA Astrophysics Data System (ADS)

Hamann, Enrico; Post, Vincent; Kohfahl, Claus; Prommer, Henning; Simmons, Craig T.

2015-11-01

Numerical modeling approaches with varying complexity were explored to investigate coupled groundwater flow and geochemical processes in saline basins. Long-term model simulations of a playa system gain insights into the complex feedback mechanisms between density-driven flow and the spatiotemporal patterns of precipitating evaporites and evolving brines. Using a reactive multicomponent transport model approach, the simulations reproduced, for the first time in a numerical study, the evaporite precipitation sequences frequently observed in saline basins ("bull's eyes"). Playa-specific flow, evapoconcentration, and chemical divides were found to be the primary controls for the location of evaporites formed, and the resulting brine chemistry. Comparative simulations with the computationally far less demanding surrogate single-species transport models showed that these were still able to replicate the major flow patterns obtained by the more complex reactive transport simulations. However, the simulated degree of salinization was clearly lower than in reactive multicomponent transport simulations. For example, in the late stages of the simulations, when the brine becomes halite-saturated, the nonreactive simulation overestimated the solute mass by almost 20%. The simulations highlight the importance of the consideration of reactive transport processes for understanding and quantifying geochemical patterns, concentrations of individual dissolved solutes, and evaporite evolution.

Ectopic Fgf signaling induces the intercalary response in developing chicken limb buds.

PubMed

Makanae, Aki; Satoh, Akira

2018-01-01

Intercalary pattern formation is an important regulatory step in amphibian limb regeneration. Amphibian limb regeneration is composed of multiple steps, including wounding, blastema formation, and intercalary pattern formation. Attempts have been made to transfer insights from regeneration-competent animals to regeneration-incompetent animalsat each step in the regeneration process. In the present study, we focused on the intercalary mechanism in chick limb buds. In amphibian limb regeneration, a proximodistal axis is organized as soon as a regenerating blastema is induced. Intermediate structures are subsequently induced (intercalated) between the established proximal and distal identities. Intercalary tissues are derived from proximal tissues. Fgf signaling mediates the intercalary response in amphibian limb regeneration. We attempted to transfer insights into intercalary regeneration from amphibian models to the chick limb bud. The zeugopodial part was dissected out, and the distal and proximal parts were conjunct at st. 24. Delivering ectopic Fgf2 + Fgf8 between the distal and proximal parts resulted in induction of zeugopodial elements. Examination of HoxA11 expression, apoptosis, and cell proliferation provides insights to compare with those in the intercalary mechanism of amphibian limb regeneration. Furthermore, the cellular contribution was investigated in both the chicken intercalary response and that of axolotl limb regeneration. We developed new insights into cellular contribution in amphibian intercalary regeneration, and found consistency between axolotl and chicken intercalary responses. Our findings demonstrate that the same principal of limb regeneration functions between regeneration-competent and -incompetent animals. In this context, we propose the feasibility of the induction of the regeneration response in amniotes.

Bioelectrical Signals and Ion Channels in the Modeling of Multicellular Patterns and Cancer Biophysics.

PubMed

Cervera, Javier; Alcaraz, Antonio; Mafe, Salvador

2016-02-04

Bioelectrical signals and ion channels are central to spatial patterns in cell ensembles, a problem of fundamental interest in positional information and cancer processes. We propose a model for electrically connected cells based on simple biological concepts: i) the membrane potential of a single cell characterizes its electrical state; ii) the long-range electrical coupling of the multicellular ensemble is realized by a network of gap junction channels between neighboring cells; and iii) the spatial distribution of an external biochemical agent can modify the conductances of the ion channels in a cell membrane and the multicellular electrical state. We focus on electrical effects in small multicellular ensembles, ignoring slow diffusional processes. The spatio-temporal patterns obtained for the local map of cell electric potentials illustrate the normalization of regions with abnormal cell electrical states. The effects of intercellular coupling and blocking of specific channels on the electrical patterns are described. These patterns can regulate the electrically-induced redistribution of charged nanoparticles over small regions of a model tissue. The inclusion of bioelectrical signals provides new insights for the modeling of cancer biophysics because collective multicellular states show electrical coupling mechanisms that are not readily deduced from biochemical descriptions at the individual cell level.

Bioelectrical Signals and Ion Channels in the Modeling of Multicellular Patterns and Cancer Biophysics

PubMed Central

Cervera, Javier; Alcaraz, Antonio; Mafe, Salvador

2016-01-01

Bioelectrical signals and ion channels are central to spatial patterns in cell ensembles, a problem of fundamental interest in positional information and cancer processes. We propose a model for electrically connected cells based on simple biological concepts: i) the membrane potential of a single cell characterizes its electrical state; ii) the long-range electrical coupling of the multicellular ensemble is realized by a network of gap junction channels between neighboring cells; and iii) the spatial distribution of an external biochemical agent can modify the conductances of the ion channels in a cell membrane and the multicellular electrical state. We focus on electrical effects in small multicellular ensembles, ignoring slow diffusional processes. The spatio-temporal patterns obtained for the local map of cell electric potentials illustrate the normalization of regions with abnormal cell electrical states. The effects of intercellular coupling and blocking of specific channels on the electrical patterns are described. These patterns can regulate the electrically-induced redistribution of charged nanoparticles over small regions of a model tissue. The inclusion of bioelectrical signals provides new insights for the modeling of cancer biophysics because collective multicellular states show electrical coupling mechanisms that are not readily deduced from biochemical descriptions at the individual cell level. PMID:26841954

Bioelectrical Signals and Ion Channels in the Modeling of Multicellular Patterns and Cancer Biophysics

NASA Astrophysics Data System (ADS)

Cervera, Javier; Alcaraz, Antonio; Mafe, Salvador

2016-02-01

Bioelectrical signals and ion channels are central to spatial patterns in cell ensembles, a problem of fundamental interest in positional information and cancer processes. We propose a model for electrically connected cells based on simple biological concepts: i) the membrane potential of a single cell characterizes its electrical state; ii) the long-range electrical coupling of the multicellular ensemble is realized by a network of gap junction channels between neighboring cells; and iii) the spatial distribution of an external biochemical agent can modify the conductances of the ion channels in a cell membrane and the multicellular electrical state. We focus on electrical effects in small multicellular ensembles, ignoring slow diffusional processes. The spatio-temporal patterns obtained for the local map of cell electric potentials illustrate the normalization of regions with abnormal cell electrical states. The effects of intercellular coupling and blocking of specific channels on the electrical patterns are described. These patterns can regulate the electrically-induced redistribution of charged nanoparticles over small regions of a model tissue. The inclusion of bioelectrical signals provides new insights for the modeling of cancer biophysics because collective multicellular states show electrical coupling mechanisms that are not readily deduced from biochemical descriptions at the individual cell level.

Field observation of diurnal dissolved oxygen fluctuations in shallow groundwater.

PubMed

Schilling, Keith E; Jacobson, Peter

2015-01-01

Dissolved oxygen (DO) concentrations influence many biogeochemical processes in groundwater systems but studies of temporal variability in DO are lacking. In this study, we used an optical DO probe to measure rapid changes in concentration due to plant-groundwater interaction at an alluvial aquifer field site in Iowa. Diurnal DO concentrations were observed during mid- to late-summer when soil conditions were dry, fluctuating approximately 0.2 to 0.3 mg/L on a daily basis. DO fluctuations in groundwater were out-of-phase with diurnal water table fluctuations, increasing during the day and decreasing at night. DO consumption at night is likely due to increased soil autotrophic and heterotrophic respiration linked with patterns of carbon supply derived from daytime photosynthetic activity, and consistent with available literature on diurnal soil respiration patterns. Although more work is needed to quantify specific processes, our results indicate the potential usefulness of the new optical DO technology to reveal insights regarding many ecohydrological processes. © 2014, National Ground Water Association.

RNA search engines empower the bacterial intranet.

PubMed

Dendooven, Tom; Luisi, Ben F

2017-08-15

RNA acts not only as an information bearer in the biogenesis of proteins from genes, but also as a regulator that participates in the control of gene expression. In bacteria, small RNA molecules (sRNAs) play controlling roles in numerous processes and help to orchestrate complex regulatory networks. Such processes include cell growth and development, response to stress and metabolic change, transcription termination, cell-to-cell communication, and the launching of programmes for host invasion. All these processes require recognition of target messenger RNAs by the sRNAs. This review summarizes recent results that have provided insights into how bacterial sRNAs are recruited into effector ribonucleoprotein complexes that can seek out and act upon target transcripts. The results hint at how sRNAs and their protein partners act as pattern-matching search engines that efficaciously regulate gene expression, by performing with specificity and speed while avoiding off-target effects. The requirements for efficient searches of RNA patterns appear to be common to all domains of life. © 2017 The Author(s).

Similar bowtie structures and distinct largest strong components are identified in the transcriptional regulatory networks of Arabidopsis thaliana during photomorphogenesis and heat shock.

PubMed

Luo, Shitao; Zhang, Fengming; Ruan, Yingfei; Li, Jie; Zhang, Zheng; Sun, Yan; Deng, Shixiong; Peng, Rui

2018-06-01

Photomorphogenesis and heat shock are critical biological processes of plants. A recent research constructed the transcriptional regulatory networks (TRNs) of Arabidopsis thaliana during these processes using DNase-seq. In this study, by strong decomposition, we revealed that each of these TRNs can be represented as a similar bowtie structure with only one non-trivial and distinct strong component. We further identified distinct patterns of variation of a few light-related genes in these bowtie structures during photomorphogenesis. These results suggest that bowtie structure may be a common property of TRNs of plants, and distinct variation patterns of genes in bowtie structures of TRNs during biological processes may reflect distinct functions. Overall, our study provides an insight into the molecular mechanisms underlying photomorphogenesis and heat shock, and emphasizes the necessity to investigate the strong connectivity structures while studying TRNs. Copyright © 2018 Elsevier B.V. All rights reserved.

RNA search engines empower the bacterial intranet

PubMed Central

Dendooven, Tom

2017-01-01

RNA acts not only as an information bearer in the biogenesis of proteins from genes, but also as a regulator that participates in the control of gene expression. In bacteria, small RNA molecules (sRNAs) play controlling roles in numerous processes and help to orchestrate complex regulatory networks. Such processes include cell growth and development, response to stress and metabolic change, transcription termination, cell-to-cell communication, and the launching of programmes for host invasion. All these processes require recognition of target messenger RNAs by the sRNAs. This review summarizes recent results that have provided insights into how bacterial sRNAs are recruited into effector ribonucleoprotein complexes that can seek out and act upon target transcripts. The results hint at how sRNAs and their protein partners act as pattern-matching search engines that efficaciously regulate gene expression, by performing with specificity and speed while avoiding off-target effects. The requirements for efficient searches of RNA patterns appear to be common to all domains of life. PMID:28710287

High aspect ratio 10-nm-scale nanoaperture arrays with template-guided metal dewetting

PubMed Central

Wang, Ying Min; Lu, Liangxing; Srinivasan, Bharathi Madurai; Asbahi, Mohamed; Zhang, Yong Wei; Yang, Joel K. W.

2015-01-01

We introduce an approach to fabricate ordered arrays of 10-nm-scale silica-filled apertures in a metal film without etching or liftoff. Using low temperature (<400°C) thermal dewetting of metal films guided by nano-patterned templates, apertures with aspect ratios up to 5:1 are demonstrated. Apertures form spontaneously during the thermal process without need for further processing. Although the phenomenon of dewetting has been well studied, this is the first demonstration of its use in the fabrication of nanoapertures in a spatially controllable manner. In particular, the achievement of 10-nm length-scale patterning at high aspect ratio with thermal dewetting is unprecedented. By varying the nanotemplate design, we show its strong influence over the positions and sizes of the nanoapertures. In addition, we construct a three-dimensional phase field model of metal dewetting on nano-patterned substrates. The simulation data obtained closely corroborates our experimental results and reveals new insights to template dewetting at the nanoscale. Taken together, this fabrication method and simulation model form a complete toolbox for 10-nm-scale patterning using template-guided dewetting that could be extended to a wide range of material systems and geometries. PMID:25858792

High aspect ratio 10-nm-scale nanoaperture arrays with template-guided metal dewetting.

PubMed

Wang, Ying Min; Lu, Liangxing; Srinivasan, Bharathi Madurai; Asbahi, Mohamed; Zhang, Yong Wei; Yang, Joel K W

2015-04-10

We introduce an approach to fabricate ordered arrays of 10-nm-scale silica-filled apertures in a metal film without etching or liftoff. Using low temperature (<400°C) thermal dewetting of metal films guided by nano-patterned templates, apertures with aspect ratios up to 5:1 are demonstrated. Apertures form spontaneously during the thermal process without need for further processing. Although the phenomenon of dewetting has been well studied, this is the first demonstration of its use in the fabrication of nanoapertures in a spatially controllable manner. In particular, the achievement of 10-nm length-scale patterning at high aspect ratio with thermal dewetting is unprecedented. By varying the nanotemplate design, we show its strong influence over the positions and sizes of the nanoapertures. In addition, we construct a three-dimensional phase field model of metal dewetting on nano-patterned substrates. The simulation data obtained closely corroborates our experimental results and reveals new insights to template dewetting at the nanoscale. Taken together, this fabrication method and simulation model form a complete toolbox for 10-nm-scale patterning using template-guided dewetting that could be extended to a wide range of material systems and geometries.

Reaction-diffusion controlled growth of complex structures

NASA Astrophysics Data System (ADS)

Noorduin, Willem; Mahadevan, L.; Aizenberg, Joanna

2013-03-01

Understanding how the emergence of complex forms and shapes in biominerals came about is both of fundamental and practical interest. Although biomineralization processes and organization strategies to give higher order architectures have been studied extensively, synthetic approaches to mimic these self-assembled structures are highly complex and have been difficult to emulate, let alone replicate. The emergence of solution patterns has been found in reaction-diffusion systems such as Turing patterns and the BZ reaction. Intrigued by this spontaneous formation of complexity we explored if similar processes can lead to patterns in the solid state. We here identify a reaction-diffusion system in which the shape of the solidified products is a direct readout of the environmental conditions. Based on insights in the underlying mechanism, we developed a toolbox of engineering strategies to deterministically sculpt patterns and shapes, and combine different morphologies to create a landscape of hierarchical multi scale-complex tectonic architectures with unprecedented levels of complexity. These findings may hold profound implications for understanding, mimicking and ultimately expanding upon nature's morphogenesis strategies, allowing the synthesis of advanced highly complex microscale materials and devices. WLN acknowledges the Netherlands Organization for Scientific Research for financial support

Post-patterning of an electronic homojunction in atomically thin monoclinic MoTe2

NASA Astrophysics Data System (ADS)

Kim, Sera; Kim, Jung Ho; Kim, Dohyun; Hwang, Geunwoo; Baik, Jaeyoon; Yang, Heejun; Cho, Suyeon

2017-06-01

Monoclinic group 6 transition metal dichalcogenides (TMDs) have been extensively studied for their intriguing 2D physics (e.g. spin Hall insulator) as well as for ohmic homojunction contacts in 2D device applications. A critical prerequisite for those applications is thickness control of the monoclinic 2D materials, which allows subtle engineering of the topological states or electronic bandgaps. Local thickness control enables the realization of clean homojunctions between different electronic states, and novel device operation in a single material. However, conventional fabrication processes, including chemical methods, typically produce non-homogeneous and relatively thick monoclinic TMDs, due to their distorted octahedral structures. Here, we report on a post-patterning technique using laser-irradiation to fabricate homojunctions between two different thickness areas in monoclinic MoTe2. A thickness-dependent electronic change from a metallic to semiconducting state, resulting in an electronic homojunction, was realized by the optical patterning of pristine MoTe2 flakes, and a pre-patterned device channel of monoclinic MoTe2 with a thickness-resolution of 5 nm. Our work provides insight on an optical post-process method for controlling thickness, as a promising approach for fabricating impurity-free 2D TMDs homojunction devices.

Polymer Film Dewetting by Water/Surfactant/Good-Solvent Mixtures: A Mechanistic Insight and Its Implications for the Conservation of Cultural Heritage.

PubMed

Baglioni, Michele; Montis, Costanza; Chelazzi, David; Giorgi, Rodorico; Berti, Debora; Baglioni, Piero

2018-06-18

Aqueous nanostructured fluids (NSFs) have been proposed to remove polymer coatings from the surface of works of art; this process usually involves film dewetting. The NSF cleaning mechanism was studied using several techniques that were employed to obtain mechanistic insight on the interaction of a methacrylic/acrylic copolymer (Paraloid B72) film laid on glass surfaces and several NSFs, based on two solvents and two surfactants. The experimental results provide a detailed picture of the dewetting process. The gyration radius and the reduction of the T g of Paraloid B72 fully swollen in the two solvents is larger for propylene carbonate than for methyl ethyl ketone, suggesting higher mobility of polymer chains for the former, while a nonionic alcohol ethoxylate surfactant was more effective than sodium dodecylsulfate in favoring the dewetting process. FTIR 2D imaging showed that the dewetting patterns observed on model samples are also present on polymer-coated mortar tiles when exposed to NSFs. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Geomorphology and the Restoration Ecology of Salmon

NASA Astrophysics Data System (ADS)

Montgomery, D. R.

2005-05-01

Natural and anthropogenic influences on watershed processes affect the distribution and abundance of salmon across a wide range of spatial and temporal scales, from differences in species use and density between individual pools and riffles to regional patterns of threatened, endangered, and extinct runs. The specific impacts of human activities (e.g., mining, logging, and urbanization) vary among regions and watersheds, as well as between different channel reaches in the same watershed. Understanding of both disturbance history and key biophysical processes are important for diagnosing the nature and causes of differences between historical and contemporary fluvial and watershed conditions based on evaluation of both historical and spatial contexts. In order to be most effective, the contribution of geomorphologic insight to salmon recovery efforts requires both assessment protocols commensurate with providing adequate knowledge of historical and spatial context, and experienced practitioners well versed in adapting general theory to local settings. The historical record of salmon management in Europe, New England and the Pacific Northwest indicates that there is substantial need to incorporate geomorphic insights on the effects of changes in watershed processes on salmon habitat and salmon abundance into salmon recovery efforts.

Evolution of aging: individual life history trade-offs and population heterogeneity account for mortality patterns across species.

PubMed

Le Cunff, Y; Baudisch, A; Pakdaman, K

2014-08-01

A broad range of mortality patterns has been documented across species, some even including decreasing mortality over age. Whether there exist a common denominator to explain both similarities and differences in these mortality patterns remains an open question. The disposable soma theory, an evolutionary theory of aging, proposes that universal intracellular trade-offs between maintenance/lifespan and reproduction would drive aging across species. The disposable soma theory has provided numerous insights concerning aging processes in single individuals. Yet, which specific population mortality patterns it can lead to is still largely unexplored. In this article, we propose a model exploring the mortality patterns which emerge from an evolutionary process including only the disposable soma theory core principles. We adapt a well-known model of genomic evolution to show that mortality curves producing a kink or mid-life plateaus derive from a common minimal evolutionary framework. These mortality shapes qualitatively correspond to those of Drosophila melanogaster, Caenorhabditis elegans, medflies, yeasts and humans. Species evolved in silico especially differ in their population diversity of maintenance strategies, which itself emerges as an adaptation to the environment over generations. Based on this integrative framework, we also derive predictions and interpretations concerning the effects of diet changes and heat-shock treatments on mortality patterns. © 2014 The Authors. Journal of Evolutionary Biology © 2014 European Society For Evolutionary Biology.

The role of pattern recognition in creative problem solving: a case study in search of new mathematics for biology.

PubMed

Hong, Felix T

2013-09-01

Rosen classified sciences into two categories: formalizable and unformalizable. Whereas formalizable sciences expressed in terms of mathematical theories were highly valued by Rutherford, Hutchins pointed out that unformalizable parts of soft sciences are of genuine interest and importance. Attempts to build mathematical theories for biology in the past century was met with modest and sporadic successes, and only in simple systems. In this article, a qualitative model of humans' high creativity is presented as a starting point to consider whether the gap between soft and hard sciences is bridgeable. Simonton's chance-configuration theory, which mimics the process of evolution, was modified and improved. By treating problem solving as a process of pattern recognition, the known dichotomy of visual thinking vs. verbal thinking can be recast in terms of analog pattern recognition (non-algorithmic process) and digital pattern recognition (algorithmic process), respectively. Additional concepts commonly encountered in computer science, operations research and artificial intelligence were also invoked: heuristic searching, parallel and sequential processing. The refurbished chance-configuration model is now capable of explaining several long-standing puzzles in human cognition: a) why novel discoveries often came without prior warning, b) why some creators had no ideas about the source of inspiration even after the fact, c) why some creators were consistently luckier than others, and, last but not least, d) why it was so difficult to explain what intuition, inspiration, insight, hunch, serendipity, etc. are all about. The predictive power of the present model was tested by means of resolving Zeno's paradox of Achilles and the Tortoise after one deliberately invoked visual thinking. Additional evidence of its predictive power must await future large-scale field studies. The analysis was further generalized to constructions of scientific theories in general. This approach is in line with Campbell's evolutionary epistemology. Instead of treating science as immutable Natural Laws, which already existed and which were just waiting to be discovered, scientific theories are regarded as humans' mental constructs, which must be invented to reconcile with observed natural phenomena. In this way, the pursuit of science is shifted from diligent and systematic (or random) searching for existing Natural Laws to firing up humans' imagination to comprehend Nature's behavioral pattern. The insights gained in understanding human creativity indicated that new mathematics that is capable of handling effectively parallel processing and human subjectivity is sorely needed. The past classification of formalizability vs. non-formalizability was made in reference to contemporary mathematics. Rosen's conclusion did not preclude future inventions of new biology-friendly mathematics. Copyright © 2013 Elsevier Ltd. All rights reserved.

Sponge budding is a spatiotemporal morphological patterning process: Insights from synchrotron radiation-based x-ray microtomography into the asexual reproduction of Tethya wilhelma.

PubMed

Hammel, Jörg U; Herzen, Julia; Beckmann, Felix; Nickel, Michael

2009-09-08

Primary agametic-asexual reproduction mechanisms such as budding and fission are present in all non-bilaterian and many bilaterian animal taxa and are likely to be metazoan ground pattern characters. Cnidarians display highly organized and regulated budding processes. In contrast, budding in poriferans was thought to be less specific and related to the general ability of this group to reorganize their tissues. Here we test the hypothesis of morphological pattern formation during sponge budding. We investigated the budding process in Tethya wilhelma (Demospongiae) by applying 3D morphometrics to high resolution synchrotron radiation-based x-ray microtomography (SR-muCT) image data. We followed the morphogenesis of characteristic body structures and identified distinct morphological states which indeed reveal characteristic spatiotemporal morphological patterns in sponge bud development. We discovered the distribution of skeletal elements, canal system and sponge tissue to be based on a sequential series of distinct morphological states. Based on morphometric data we defined four typical bud stages. Once they have reached the final stage buds are released as fully functional juvenile sponges which are morphologically and functionally equivalent to adult specimens. Our results demonstrate that budding in demosponges is considerably more highly organized and regulated than previously assumed. Morphological pattern formation in asexual reproduction with underlying genetic regulation seems to have evolved early in metazoans and was likely part of the developmental program of the last common ancestor of all Metazoa (LCAM).

Sponge budding is a spatiotemporal morphological patterning process: Insights from synchrotron radiation-based x-ray microtomography into the asexual reproduction of Tethya wilhelma

PubMed Central

Hammel, Jörg U; Herzen, Julia; Beckmann, Felix; Nickel, Michael

2009-01-01

Background Primary agametic-asexual reproduction mechanisms such as budding and fission are present in all non-bilaterian and many bilaterian animal taxa and are likely to be metazoan ground pattern characters. Cnidarians display highly organized and regulated budding processes. In contrast, budding in poriferans was thought to be less specific and related to the general ability of this group to reorganize their tissues. Here we test the hypothesis of morphological pattern formation during sponge budding. Results We investigated the budding process in Tethya wilhelma (Demospongiae) by applying 3D morphometrics to high resolution synchrotron radiation-based x-ray microtomography (SR-μCT) image data. We followed the morphogenesis of characteristic body structures and identified distinct morphological states which indeed reveal characteristic spatiotemporal morphological patterns in sponge bud development. We discovered the distribution of skeletal elements, canal system and sponge tissue to be based on a sequential series of distinct morphological states. Based on morphometric data we defined four typical bud stages. Once they have reached the final stage buds are released as fully functional juvenile sponges which are morphologically and functionally equivalent to adult specimens. Conclusion Our results demonstrate that budding in demosponges is considerably more highly organized and regulated than previously assumed. Morphological pattern formation in asexual reproduction with underlying genetic regulation seems to have evolved early in metazoans and was likely part of the developmental program of the last common ancestor of all Metazoa (LCAM). PMID:19737392

Delivering the lateral inhibition punchline: it's all about the timing.

PubMed

Axelrod, Jeffrey D

2010-10-26

Experimental and theoretical biologists have long been fascinated with the emergence of self-organizing patterns in developing organisms, and much attention has focused on Notch-mediated lateral inhibition. Within sheets of cells that may adopt either of two possible cell fates, lateral inhibition establishes patterns through the activity of a negative intercellular feedback loop involving the receptor, Notch, and its ligands Delta or Serrate. Despite a long history of intensive study in Drosophila, where the mechanism was first described, as well as in other organisms, new work continues to yield important insights. Mathematical modeling, combined with biological analyses, has now shed light on two features of the process: how antagonistic and activating ligand-receptor interactions work together to accelerate inhibition and ensure fidelity, and how filopodial dynamics contribute to the observed pattern refinement and spacing.

Benthic exchange and biogeochemical cycling in permeable sediments.

PubMed

Huettel, Markus; Berg, Peter; Kostka, Joel E

2014-01-01

The sandy sediments that blanket the inner shelf are situated in a zone where nutrient input from land and strong mixing produce maximum primary production and tight coupling between water column and sedimentary processes. The high permeability of the shelf sands renders them susceptible to pressure gradients generated by hydrodynamic and biological forces that modulate spatial and temporal patterns of water circulation through these sediments. The resulting dynamic three-dimensional patterns of particle and solute distribution generate a broad spectrum of biogeochemical reaction zones that facilitate effective decomposition of the pelagic and benthic primary production products. The intricate coupling between the water column and sediment makes it challenging to quantify the production and decomposition processes and the resultant fluxes in permeable shelf sands. Recent technical developments have led to insights into the high biogeochemical and biological activity of these permeable sediments and their role in the global cycles of matter.

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

PubMed

Grahn, Jessica A

2012-10-01

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

A flexible influence of affective feelings on creative and analytic performance.

PubMed

Huntsinger, Jeffrey R; Ray, Cara

2016-09-01

Considerable research shows that positive affect improves performance on creative tasks and negative affect improves performance on analytic tasks. The present research entertained the idea that affective feelings have flexible, rather than fixed, effects on cognitive performance. Consistent with the idea that positive and negative affect signal the value of accessible processing inclinations, the influence of affective feelings on performance on analytic or creative tasks was found to be flexibly responsive to the relative accessibility of different styles of processing (i.e., heuristic vs. systematic, global vs. local). When a global processing orientation was accessible happy participants generated more creative uses for a brick (Experiment 1), successfully solved more remote associates and insight problems (Experiment 2) and displayed broader categorization (Experiment 3) than those in sad moods. When a local processing orientation was accessible this pattern reversed. When a heuristic processing style was accessible happy participants were more likely to commit the conjunction fallacy (Experiment 3) and showed less pronounced anchoring effects (Experiment 4) than sad participants. When a systematic processing style was accessible this pattern reversed. Implications of these results for relevant affect-cognition models are discussed. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

Defense Against Pathogens: Structural Insights into the Mechanism of Chitin Induced Activation of Innate Immunity.

PubMed

Squeglia, Flavia; Berisio, Rita; Shibuya, Naoto; Kaku, Hanae

2017-11-24

Pattern recognition receptors on the plant cell surface mediate the recognition of microbe-associated molecular patterns, in a process which activates downstream immune signaling. These receptors are plasma membrane-localized kinases which need to be autophosphorylated to activate downstream responses. Perception of attacks from fungi occurs through recognition of chitin, a polymer of an N-acetylglucosamine which is a characteristic component of the cell walls of fungi. This process is regulated in Arabidopsis by chitin elicitor receptor kinase CERK1. A more complex process characterizes rice, in which regulation of chitin perception is operated by a complex composed of OsCERK1, a homolog of CERK1, and the chitin elicitor binding protein OsCEBiP. Recent literature has provided a mechanistic description of the complex regulation of activation of innate immunity in rice and an advance in the structural description of molecular players involved in this process. This review describes the current status of the understanding of molecular events involved in innate immunity activation in rice. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

The Role of Visual and Semantic Properties in the Emergence of Category-Specific Patterns of Neural Response in the Human Brain.

PubMed

Coggan, David D; Baker, Daniel H; Andrews, Timothy J

2016-01-01

Brain-imaging studies have found distinct spatial and temporal patterns of response to different object categories across the brain. However, the extent to which these categorical patterns of response reflect higher-level semantic or lower-level visual properties of the stimulus remains unclear. To address this question, we measured patterns of EEG response to intact and scrambled images in the human brain. Our rationale for using scrambled images is that they have many of the visual properties found in intact images, but do not convey any semantic information. Images from different object categories (bottle, face, house) were briefly presented (400 ms) in an event-related design. A multivariate pattern analysis revealed categorical patterns of response to intact images emerged ∼80-100 ms after stimulus onset and were still evident when the stimulus was no longer present (∼800 ms). Next, we measured the patterns of response to scrambled images. Categorical patterns of response to scrambled images also emerged ∼80-100 ms after stimulus onset. However, in contrast to the intact images, distinct patterns of response to scrambled images were mostly evident while the stimulus was present (∼400 ms). Moreover, scrambled images were able to account only for all the variance in the intact images at early stages of processing. This direct manipulation of visual and semantic content provides new insights into the temporal dynamics of object perception and the extent to which different stages of processing are dependent on lower-level or higher-level properties of the image.

Interannual to multidecadal climate forcings on groundwater resources of the U.S. West Coast

USGS Publications Warehouse

Velasco, Elzie M.; Gurdak, Jason J.; Dickinson, Jesse; Ferré, T.P.A.; Corona, Claudia

2017-01-01

Study regionThe U.S. West Coast, including the Pacific Northwest and California Coastal Basins aquifer systems.Study focusGroundwater response to interannual to multidecadal climate variability has important implications for security within the water–energy–food nexus. Here we use Singular Spectrum Analysis to quantify the teleconnections between AMO, PDO, ENSO, and PNA and precipitation and groundwater level fluctuations. The computer program DAMP was used to provide insight on the influence of soil texture, depth to water, and mean and period of a surface infiltration flux on the damping of climate signals in the vadose zone.New hydrological insights for the regionWe find that PDO, ENSO, and PNA have significant influence on precipitation and groundwater fluctuations across a north-south gradient of the West Coast, but the lower frequency climate modes (PDO) have a greater influence on hydrologic patterns than higher frequency climate modes (ENSO and PNA). Low frequency signals tend to be preserved better in groundwater fluctuations than high frequency signals, which is a function of the degree of damping of surface variable fluxes related to soil texture, depth to water, mean and period of the infiltration flux. The teleconnection patterns that exist in surface hydrologic processes are not necessarily the same as those preserved in subsurface processes, which are affected by damping of some climate variability signals within infiltrating water.

What do we know about Indonesian tropical lakes? Insights from high frequency measurement

NASA Astrophysics Data System (ADS)

Budi Santoso, Arianto; Triwisesa, Endra; Fakhrudin, Muh.; Harsono, Eko; Agita Rustini, Hadiid

2018-02-01

When measuring ecological variables in lakes, sampling frequency is critical in capturing an environmental pattern. Discrete sampling of traditional monitoring programs is likely to result in vital knowledge gaps in understanding any processes particularly those with fine temporal scale characteristics. The development of high frequency measurements offer a sophisticated range of information in recording any events in lakes at a finer time scale. We present physical indices of a tropical deep Lake Maninjau arrayed from OnLine Monitoring System (OLM). It is revealed that Lake Maninjau mostly has a diurnal thermal stratification pattern. The calculated lake stability (Schmidt stability), however, follows a seasonal pattern; low in December-January and around August, and high in May and September. Using a 3D numerical model simulation (ELCOM), we infer how wind and solar radiation intensity control lake’s temperature profiles. In this review, we highlight the needs of high frequency measurement establishment in Indonesian tropical lakes to better understand the unique processes and to support the authorities’ decision making in maximizing the provision of ecosystem services supplied by lakes and reservoirs.

Characteristics of vegetation phenology over the Alaskan landscape using AVHRR time-series data

USGS Publications Warehouse

Markon, Carl J.; Fleming, Michael D.; Binnian, Emily F.

1995-01-01

Advanced Very High Resolution Radiometer (AVHRR) satellite data were acquired and composited into twice-a-month periods from 1 May 1991 to 15 October 1991 in order to map vegetation characteristics of the Alaskan landscape. Unique spatial and temporal qualities of the AVHRR data provide information that leads to a better understanding of regional biophysical characteristics of vegetation communities and patterns. These data provided synoptic views of the landscape and depicted phenological diversity, temporal vegetation phenology (green-up, peak of green, and senescence), photosynthetic activity, and regional landscape patterns. Products generated from the data included a phenological class map, phenological composite maps (onset, peak, and duration), and photosynthetic activity maps (mean and maximum greenness). The time-series data provide opportunities to study phenological processes at small landscape scales over time periods of weeks, months, and years. Regional patterns identified on some of the maps are unique to specific areas; others correspond to biophysical or ecoregional boundaries. The data provide new insights to landscape processes, ecology, and landscape physiognomy that allow scientists to look at landscapes in ways that were previously difficult to achieve.

A discrete cell model with adaptive signalling for aggregation of Dictyostelium discoideum.

PubMed Central

Dallon, J C; Othmer, H G

1997-01-01

Dictyostelium discoideum (Dd) is a widely studied model system from which fundamental insights into cell movement, chemotaxis, aggregation and pattern formation can be gained. In this system aggregation results from the chemotactic response by dispersed amoebae to a travelling wave of the chemoattractant cAMP. We have developed a model in which the cells are treated as discrete points in a continuum field of the chemoattractant, and transduction of the extracellular cAMP signal into the intracellular signal is based on the G protein model developed by Tang & Othmer. The model reproduces a number of experimental observations and gives further insight into the aggregation process. We investigate different rules for cell movement the factors that influence stream formation the effect on aggregation of noise in the choice of the direction of movement and when spiral waves of chemoattractant and cell density are likely to occur. Our results give new insight into the origin of spiral waves and suggest that streaming is due to a finite amplitude instability. PMID:9134569

Nearly a decade-long repeatable seasonal diversity patterns of bacterioplankton communities in the eutrophic Lake Donghu (Wuhan, China)

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

Yan, Qingyun; Stegen, James C.; Yu, Yuhe

Uncovering which environmental factors have the greatest influence on community diversity patterns and how ecological processes govern community turnover are key questions related to understanding community assembly mechanisms. Although we have good understanding of plant and animal community assembly, the mechanisms regulating diversity patterns of aquatic bacterial communities in lake ecosystems remains poorly understood. Here we present nearly a decade-long time-series study of bacterioplankton communities from the eutrophic Lake Donghu (Wuhan, China) using 16S rRNA gene amplicon sequencing. We found strong repeatable seasonal patterns for the overall community, common (detected in more than 50% samples) and dominant bacterial taxa (relativemore » abundance > 1%). Moreover, community composition tracked the seasonal temperature gradient, indicating that temperature is an important environmental factor controlling observed diversity patterns. Total phosphorus also contributed significantly to the seasonal shifts in bacterioplankton composition. However, any spatial pattern across the main lake areas was overwhelmed by temporal variability in this eutrophic lake system. Phylogenetic analysis further indicated that 75%-82% of community turnover was governed by homogeneous selection, suggesting that the bacterioplankton communities are mainly controlled by niche-based processes. However, dominant niches available within seasons might be occupied by similar combinations of bacterial taxa with modest dispersal rates throughout this lake system. This study gives us important insights into community assembly and seasonal turnover of lake bacterioplankton, it may be also useful to predict temporal patterns of other planktonic communities.« less

Recent Insights into the Regulation of the Growth Plate

PubMed Central

Lui, Julian C.; Nilsson, Ola; Baron, Jeffrey

2014-01-01

For most bones, elongation is driven primarily by chondrogenesis at the growth plates. This process results from chondrocyte proliferation, hypertrophy, and extracellular matrix secretion and is carefully orchestrated by complex networks of local paracrine factors and modulated by endocrine factors. We review here recent advances in the understanding of growth plate physiology. These advances include new approaches to study expression patterns of large numbers of genes in the growth plate, using microdissection followed by microarray. This approach has been combined with genome-wide association studies to provide insights into the regulation of the human growth plate. We also review recent studies elucidating the roles of bone morphogenetic proteins, fibroblast growth factors, C-type natriuretic peptide, and suppressor of cytokine signaling in the local regulation of growth plate chondrogenesis and longitudinal bone growth. PMID:24740736

Plant hormone signaling during development: insights from computational models.

PubMed

Oliva, Marina; Farcot, Etienne; Vernoux, Teva

2013-02-01

Recent years have seen an impressive increase in our knowledge of the topology of plant hormone signaling networks. The complexity of these topologies has motivated the development of models for several hormones to aid understanding of how signaling networks process hormonal inputs. Such work has generated essential insights into the mechanisms of hormone perception and of regulation of cellular responses such as transcription in response to hormones. In addition, modeling approaches have contributed significantly to exploring how spatio-temporal regulation of hormone signaling contributes to plant growth and patterning. New tools have also been developed to obtain quantitative information on hormone distribution during development and to test model predictions, opening the way for quantitative understanding of the developmental roles of hormones. Copyright © 2012 Elsevier Ltd. All rights reserved.

Developmental distribution of the plasma membrane-enriched proteome in the maize primary root growth zone.

PubMed

Zhang, Zhe; Voothuluru, Priyamvada; Yamaguchi, Mineo; Sharp, Robert E; Peck, Scott C

2013-01-01

Within the growth zone of the maize primary root, there are well-defined patterns of spatial and temporal organization of cell division and elongation. However, the processes underlying this organization remain poorly understood. To gain additional insights into the differences amongst the defined regions, we performed a proteomic analysis focusing on fractions enriched for plasma membrane (PM) proteins. The PM is the interface between the plant cell and the apoplast and/or extracellular space. As such, it is a key structure involved in the exchange of nutrients and other molecules as well as in the integration of signals that regulate growth and development. Despite the important functions of PM-localized proteins in mediating these processes, a full understanding of dynamic changes in PM proteomes is often impeded by low relative concentrations relative to total proteins. Using a relatively simple strategy of treating microsomal fractions with Brij-58 detergent to enrich for PM proteins, we compared the developmental distribution of proteins within the root growth zone which revealed a number of previously known as well as novel proteins with interesting patterns of abundance. For instance, the quantitative proteomic analysis detected a gradient of PM aquaporin proteins similar to that previously reported using immunoblot analyses, confirming the veracity of this strategy. Cellulose synthases increased in abundance with increasing distance from the root apex, consistent with expected locations of cell wall deposition. The similar distribution pattern for Brittle-stalk-2-like protein implicates that this protein may also have cell wall related functions. These results show that the simplified PM enrichment method previously demonstrated in Arabidopsis can be successfully applied to completely unrelated plant tissues and provide insights into differences in the PM proteome throughout growth and development zones of the maize primary root.

High-resolution gene expression data from blastoderm embryos of the scuttle fly Megaselia abdita

PubMed Central

Wotton, Karl R; Jiménez-Guri, Eva; Crombach, Anton; Cicin-Sain, Damjan; Jaeger, Johannes

2015-01-01

Gap genes are involved in segment determination during early development in dipteran insects (flies, midges, and mosquitoes). We carried out a systematic quantitative comparative analysis of the gap gene network across different dipteran species. Our work provides mechanistic insights into the evolution of this pattern-forming network. As a central component of our project, we created a high-resolution quantitative spatio-temporal data set of gap and maternal co-ordinate gene expression in the blastoderm embryo of the non-drosophilid scuttle fly, Megaselia abdita. Our data include expression patterns in both wild-type and RNAi-treated embryos. The data—covering 10 genes, 10 time points, and over 1,000 individual embryos—consist of original embryo images, quantified expression profiles, extracted positions of expression boundaries, and integrated expression patterns, plus metadata and intermediate processing steps. These data provide a valuable resource for researchers interested in the comparative study of gene regulatory networks and pattern formation, an essential step towards a more quantitative and mechanistic understanding of developmental evolution. PMID:25977812

Lineage diversification and morphological evolution in a large-scale continental radiation: The neotropical ovenbirds and woodcreepers (Aves: Furnariidae)

USGS Publications Warehouse

Derryberry, Elizabeth P.; Claramunt, Santiago; Derryberry, Graham; Chesser, R. Terry; Cracraft, Joel; Aleixo, Alexandre; Pérez-Emán, Jorge; Remsen, J.V.; Brumfield, Robb T.

2011-01-01

Patterns of diversification in species-rich clades provide insight into the processes that generate biological diversity. We tested different models of lineage and phenotypic diversification in an exceptional continental radiation, the ovenbird family Furnariidae, using the most complete species-level phylogenetic hypothesis produced to date for a major avian clade (97% of 293 species). We found that the Furnariidae exhibit nearly constant rates of lineage accumulation but show evidence of constrained morphological evolution. This pattern of sustained high rates of speciation despite limitations on phenotypic evolution contrasts with the results of most previous studies of evolutionary radiations, which have found a pattern of decelerating diversity-dependent lineage accumulation coupled with decelerating or constrained phenotypic evolution. Our results suggest that lineage accumulation in tropical continental radiations may not be as limited by ecological opportunities as in temperate or island radiations. More studies examining patterns of both lineage and phenotypic diversification are needed to understand the often complex tempo and mode of evolutionary radiations on continents.

Cholinergic modulation of cognition: Insights from human pharmacological functional neuroimaging

PubMed Central

Bentley, Paul; Driver, Jon; Dolan, Raymond J.

2011-01-01

Evidence from lesion and cortical-slice studies implicate the neocortical cholinergic system in the modulation of sensory, attentional and memory processing. In this review we consider findings from sixty-three healthy human cholinergic functional neuroimaging studies that probe interactions of cholinergic drugs with brain activation profiles, and relate these to contemporary neurobiological models. Consistent patterns that emerge are: (1) the direction of cholinergic modulation of sensory cortex activations depends upon top-down influences; (2) cholinergic hyperstimulation reduces top-down selective modulation of sensory cortices; (3) cholinergic hyperstimulation interacts with task-specific frontoparietal activations according to one of several patterns, including: suppression of parietal-mediated reorienting; decreasing ‘effort’-associated activations in prefrontal regions; and deactivation of a ‘resting-state network’ in medial cortex, with reciprocal recruitment of dorsolateral frontoparietal regions during performance-challenging conditions; (4) encoding-related activations in both neocortical and hippocampal regions are disrupted by cholinergic blockade, or enhanced with cholinergic stimulation, while the opposite profile is observed during retrieval; (5) many examples exist of an ‘inverted-U shaped’ pattern of cholinergic influences by which the direction of functional neural activation (and performance) depends upon both task (e.g. relative difficulty) and subject (e.g. age) factors. Overall, human cholinergic functional neuroimaging studies both corroborate and extend physiological accounts of cholinergic function arising from other experimental contexts, while providing mechanistic insights into cholinergic-acting drugs and their potential clinical applications. PMID:21708219

Plasma metabolomics profiling of maintenance hemodialysis based on capillary electrophoresis - time of flight mass spectrometry.

PubMed

Liu, Shuxin; Wang, Lichao; Hu, Chunxiu; Huang, Xin; Liu, Hong; Xuan, Qiuhui; Lin, Xiaohui; Peng, Xiaojun; Lu, Xin; Chang, Ming; Xu, Guowang

2017-08-15

Uremia has been a rapidly increasing health problem in China. Hemodialysis (HD) is the main renal replacement therapy for uremia. The results of large-scale clinical trials have shown that the HD pattern is crucial for long-term prognosis of maintenance hemodialysis (MHD) in uremic patients. Plasma metabolism is very important for revealing the biological insights linked to the therapeutic effects of the HD pattern on uremia. Alteration of plasma metabolites in uremic patients in response to HD therapy has been reported. However, HD-pattern-dependent changes in plasma metabolites remain poorly understood. To this end, a capillary electrophoresis-time of flight mass spectrometry (CE-TOF/MS)-based metabolomics method was performed to systemically study the differences between HD and high flux hemodialysis (HFD) on plasma metabolite changes in patients. Three hundred and one plasma samples from three independent human cohorts (i.e., healthy controls, patients with pre-HD/post-HD, and patients with pre-HFD/post-HFD) were used in this study. Metabolites significantly changed (p < 0.05) after a single HD or HFD process. However, 11 uremic retention solutes could be more efficiently removed by HFD. Our findings indicate that a CE-TOF/MS-based metabolomics approach is promising for providing novel insights into understanding the effects of different dialysis methods on metabolite alterations of uremia.

Organisms on the move: ecology and evolution of dispersal.

PubMed

Gibbs, Melanie; Saastamoinen, Marjo; Coulon, Aurélie; Stevens, Virginie M

2010-04-23

The symposium and workshop 'Organisms on the move: ecology and evolution of dispersal', held in Ghent (Belgium), 14-18 September 2009, brought together a wide range of researchers using empirical and modelling approaches to examine the dispersal process. This meeting provided an opportunity to assess how much cross-fertilization there has been between empiricists and theoreticians, to present novel insights on dispersal patterns in plants, animals and micro-organisms and to measure the progress made in examining the causes and consequences of dispersal.

Using Bio-Optics to Reveal Phytoplankton Physiology from a Wirewalker Autonomous Platform

NASA Technical Reports Server (NTRS)

Omand, M. M.; Cetinic, I.; Lucas, A. J.

2017-01-01

Rapid, wave-powered profiling of bio-optical properties from an autonomous Wirewalker platform provides useful insights into phytoplankton physiology, including the patterns of diel growth, phytoplankton mortality, nonphotochemical quenching of chlorophyll a fluorescence, and natural (sun-induced) fluorescence of mixed communities. Methods are proposed to quantify each of these processes. Such autonomous measurements of phytoplankton physiological rates and responses open up new possibilities for studying phytoplankton in situ, over longer periods, and under a broader range of environmental conditions.

Gaining Insights on Nasopharyngeal Carcinoma Treatment Outcome Using Clinical Data Mining Techniques.

PubMed

Ghaibeh, A Ammar; Kasem, Asem; Ng, Xun Jin; Nair, Hema Latha Krishna; Hirose, Jun; Thiruchelvam, Vinesh

2018-01-01

The analysis of Electronic Health Records (EHRs) is attracting a lot of research attention in the medical informatics domain. Hospitals and medical institutes started to use data mining techniques to gain new insights from the massive amounts of data that can be made available through EHRs. Researchers in the medical field have often used descriptive statistics and classical statistical methods to prove assumed medical hypotheses. However, discovering new insights from large amounts of data solely based on experts' observations is difficult. Using data mining techniques and visualizations, practitioners can find hidden knowledge, identify interesting patterns, or formulate new hypotheses to be further investigated. This paper describes a work in progress on using data mining methods to analyze clinical data of Nasopharyngeal Carcinoma (NPC) cancer patients. NPC is the fifth most common cancer among Malaysians, and the data analyzed in this study was collected from three states in Malaysia (Kuala Lumpur, Sabah and Sarawak), and is considered to be the largest up-to-date dataset of its kind. This research is addressing the issue of cancer recurrence after the completion of radiotherapy and chemotherapy treatment. We describe the procedure, problems, and insights gained during the process.

Optical Pattern Formation in Cold Atoms: Explaining the Red-Blue Asymmetry

NASA Astrophysics Data System (ADS)

Schmittberger, Bonnie; Gauthier, Daniel

2013-05-01

The study of pattern formation in atomic systems has provided new insight into fundamental many-body physics and low-light-level nonlinear optics. Pattern formation in cold atoms in particular is of great interest in condensed matter physics and quantum information science because atoms undergo self-organization at ultralow input powers. We recently reported the first observation of pattern formation in cold atoms but found that our results were not accurately described by any existing theoretical model of pattern formation. Previous models describing pattern formation in cold atoms predict that pattern formation should occur using both red and blue-detuned pump beams, favoring a lower threshold for blue detunings. This disagrees with our recent work, in which we only observed pattern formation with red-detuned pump beams. Previous models also assume a two-level atom, which cannot account for the cooling processes that arise when beams counterpropagate through a cold atomic vapor. We describe a new model for pattern formation that accounts for Sisyphus cooling in multi-level atoms, which gives rise to a new nonlinearity via spatial organization of the atoms. This spatial organization causes a sharp red-blue detuning asymmetry, which agrees well with our experimental observations. We gratefully acknowledge the financial support of the NSF through Grant #PHY-1206040.

Direct patterning of silver particles on porous silicon by inkjet printing of a silver salt via in-situ reduction

PubMed Central

2012-01-01

We have developed a method for obtaining a direct pattern of silver nanoparticles (NPs) on porous silicon (p-Si) by means of inkjet printing (IjP) of a silver salt. Silver NPs were obtained by p-Si mediated in-situ reduction of Ag+ cations using solutions based on AgNO3 which were directly printed on p-Si according to specific geometries and process parameters. The main difference with respect to existing literature is that normally, inkjet printing is applied to silver (metal) NP suspensions, while in our experiment the NPs are formed after jetting the solution on the reactive substrate. We performed both optical and scanning electron microscopes on the NPs traces, correlating the morphology features with the IjP parameters, giving an insight on the synthesis kinetics. The patterned NPs show good performances as SERS substrates. PMID:22953722

Speech perception and production in bilinguals and monolinguals: Convergent and divergent patterns in adulthood and development

NASA Astrophysics Data System (ADS)

Sundara, Megha; Polka, Linda

2004-05-01

Most investigations of the role of language experience have looked at monolingual subjects. Data are presented from a series of experiments with consonant contrasts to highlight how bilingual adults exposed to Canadian-English and Canadian-French from birth accommodate two sets of input regularities in their perception and production behavior. Results from these investigations indicate that there are similarities as well as differences between adult simultaneous bilinguals and their monolingual peers. Recent findings from our lab exploring phonetic discrimination and word segmentation in monolingual and bilingual infants and children, which provide insights into the developmental roots of these adult patterns, are also presented. The findings from this work illustrate that during the developmental process bilingual infants and children differ from their monolingual peers in rate as well as pattern of development for some perceptual tasks but not others.

High-resolution Temporal Representations of Alcohol and Tobacco Behaviors from Social Media Data.

PubMed

Huang, Tom; Elghafari, Anas; Relia, Kunal; Chunara, Rumi

2017-11-01

Understanding tobacco- and alcohol-related behavioral patterns is critical for uncovering risk factors and potentially designing targeted social computing intervention systems. Given that we make choices multiple times per day, hourly and daily patterns are critical for better understanding behaviors. Here, we combine natural language processing, machine learning and time series analyses to assess Twitter activity specifically related to alcohol and tobacco consumption and their sub-daily, daily and weekly cycles. Twitter self-reports of alcohol and tobacco use are compared to other data streams available at similar temporal resolution. We assess if discussion of drinking by inferred underage versus legal age people or discussion of use of different types of tobacco products can be differentiated using these temporal patterns. We find that time and frequency domain representations of behaviors on social media can provide meaningful and unique insights, and we discuss the types of behaviors for which the approach may be most useful.

Mathematical study on robust tissue pattern formation in growing epididymal tubule.

PubMed

Hirashima, Tsuyoshi

2016-10-21

Tissue pattern formation during development is a reproducible morphogenetic process organized by a series of kinetic cellular activities, leading to the building of functional and stable organs. Recent studies focusing on mechanical aspects have revealed physical mechanisms on how the cellular activities contribute to the formation of reproducible tissue patterns; however, the understanding for what factors achieve the reproducibility of such patterning and how it occurs is far from complete. Here, I focus on a tube pattern formation during murine epididymal development, and show that two factors influencing physical design for the patterning, the proliferative zone within the tubule and the viscosity of tissues surrounding to the tubule, control the reproducibility of epididymal tubule pattern, using a mathematical model based on experimental data. Extensive numerical simulation of the simple mathematical model revealed that a spatially localized proliferative zone within the tubule, observed in experiments, results in more reproducible tubule pattern. Moreover, I found that the viscosity of tissues surrounding to the tubule imposes a trade-off regarding pattern reproducibility and spatial accuracy relating to the region where the tubule pattern is formed. This indicates an existence of optimality in material properties of tissues for the robust patterning of epididymal tubule. The results obtained by numerical analysis based on experimental observations provide a general insight on how physical design realizes robust tissue pattern formation. Copyright © 2016 Elsevier Ltd. All rights reserved.

INSIGHT responsive parenting intervention is associated with healthier patterns of dietary exposures in infants.

PubMed

Hohman, Emily E; Paul, Ian M; Birch, Leann L; Savage, Jennifer S

2017-01-01

To determine whether a responsive parenting (RP) intervention affects infant dietary patterns. Primiparous mother-newborn dyads (n = 291) were randomized to the Intervention Nurses Start Infants Growing on Healthy Trajectories (INSIGHT) RP intervention or control. Curricula were delivered at nurse home visits at ages 3, 16, 28, and 40 weeks. RP group feeding guidance advised responsive feeding, delayed introduction of solids, repeated exposure to novel foods, and age-appropriate portion sizes. Latent class analysis identified patterns of dietary exposure at 9 months. Class membership at 9 months was used to predict BMI percentile at 2 years. Five dietary patterns were identified: "Breastfed, Fruits and Vegetables," "Breastfed, Low Variety," "Formula, Fruits and Vegetables," "Formula, Low Variety," and "Formula, High Energy Density." Over 60% of infants had patterns low in fruits and vegetables or high in energy-dense foods. RP group infants were less likely than control to be in the "Formula, Low Variety" class (OR = 0.40, 95% CI 0.23-0.71) or "Formula, High Energy Density" class (OR = 0.28, 95% CI 0.12-0.61) relative to the "Formula, Fruits and Vegetables" class. Dietary pattern at 9 months was significantly associated with BMI percentile at 2 years. While a majority of infants consumed diets low in fruits and vegetables, the INSIGHT RP intervention was associated with healthier dietary patterns. © 2016 The Obesity Society.

Time-resolved double-slit interference pattern measurement with entangled photons

PubMed Central

Kolenderski, Piotr; Scarcella, Carmelo; Johnsen, Kelsey D.; Hamel, Deny R.; Holloway, Catherine; Shalm, Lynden K.; Tisa, Simone; Tosi, Alberto; Resch, Kevin J.; Jennewein, Thomas

2014-01-01

The double-slit experiment strikingly demonstrates the wave-particle duality of quantum objects. In this famous experiment, particles pass one-by-one through a pair of slits and are detected on a distant screen. A distinct wave-like pattern emerges after many discrete particle impacts as if each particle is passing through both slits and interfering with itself. Here we present a temporally- and spatially-resolved measurement of the double-slit interference pattern using single photons. We send single photons through a birefringent double-slit apparatus and use a linear array of single-photon detectors to observe the developing interference pattern. The analysis of the buildup allows us to compare quantum mechanics and the corpuscular model, which aims to explain the mystery of single-particle interference. Finally, we send one photon from an entangled pair through our double-slit setup and show the dependence of the resulting interference pattern on the twin photon's measured state. Our results provide new insight into the dynamics of the buildup process in the double-slit experiment, and can be used as a valuable resource in quantum information applications. PMID:24770360

Using Citizen Science Observations to Model Species Distributions Over Space, Through Time, and Across Scales

NASA Astrophysics Data System (ADS)

Kelling, S.

2017-12-01

The goal of Biodiversity research is to identify, explain, and predict why a species' distribution and abundance vary through time, space, and with features of the environment. Measuring these patterns and predicting their responses to change are not exercises in curiosity. Today, they are essential tasks for understanding the profound effects that humans have on earth's natural systems, and for developing science-based environmental policies. To gain insight about species' distribution patterns requires studying natural systems at appropriate scales, yet studies of ecological processes continue to be compromised by inadequate attention to scale issues. How spatial and temporal patterns in nature change with scale often reflects fundamental laws of physics, chemistry, or biology, and we can identify such basic, governing laws only by comparing patterns over a wide range of scales. This presentation will provide several examples that integrate bird observations made by volunteers, with NASA Earth Imagery using Big Data analysis techniques to analyze the temporal patterns of bird occurrence across scales—from hemisphere-wide views of bird distributions to the impact of powerful city lights on bird migration.

Patterns of genetic variability and habitat occupancy in Crepis triasii (Asteraceae) at different spatial scales: insights on evolutionary processes leading to diversification in continental islands.

PubMed

Mayol, Maria; Palau, Carles; Rosselló, Josep A; González-Martínez, Santiago C; Molins, Arántzazu; Riba, Miquel

2012-02-01

Archipelagos are unique systems for studying evolutionary processes promoting diversification and speciation. The islands of the Mediterranean basin are major areas of plant richness, including a high proportion of narrow endemics. Many endemic plants are currently found in rocky habitats, showing varying patterns of habitat occupancy at different spatial scales throughout their range. The aim of the present study was to understand the impact of varying patterns of population distribution on genetic diversity and structure to shed light on demographic and evolutionary processes leading to population diversification in Crepis triasii, an endemic plant from the eastern Balearic Islands. Using allozyme and chloroplast markers, we related patterns of genetic structure and diversity to those of habitat occupancy at a regional (between islands and among populations within islands) and landscape (population size and connectivity) scale. Genetic diversity was highly structured both at the regional and at the landscape level, and was positively correlated with population connectivity in the landscape. Populations located in small isolated mountains and coastal areas, with restricted patterns of regional occupancy, were genetically less diverse and much more differentiated. In addition, more isolated populations had stronger fine-scale genetic structure than well-connected ones. Changes in habitat availability and quality arising from marine transgressions during the Quaternary, as well as progressive fragmentation associated with the aridification of the climate since the last glaciation, are the most plausible factors leading to the observed patterns of genetic diversity and structure. Our results emphasize the importance of gene flow in preventing genetic erosion and maintaining the evolutionary potential of populations. They also agree with recent studies highlighting the importance of restricted gene flow and genetic drift as drivers of plant evolution in Mediterranean continental islands.

Object processing in the infant: lessons from neuroscience.

PubMed

Wilcox, Teresa; Biondi, Marisa

2015-07-01

Object identification is a fundamental cognitive capacity that forms the basis for complex thought and behavior. The adult cortex is organized into functionally distinct visual object-processing pathways that mediate this ability. Insights into the origin of these pathways have begun to emerge through the use of neuroimaging techniques with infant populations. The outcome of this work supports the view that, from the early days of life, object-processing pathways are organized in a way that resembles that of the adult. At the same time, theoretically important changes in patterns of cortical activation are observed during the first year. These findings lead to a new understanding of the cognitive and neural architecture in infants that supports their emerging object-processing capacities. Copyright © 2015 Elsevier Ltd. All rights reserved.

Mechanisms and neural basis of object and pattern recognition: a study with chess experts.

PubMed

Bilalić, Merim; Langner, Robert; Erb, Michael; Grodd, Wolfgang

2010-11-01

Comparing experts with novices offers unique insights into the functioning of cognition, based on the maximization of individual differences. Here we used this expertise approach to disentangle the mechanisms and neural basis behind two processes that contribute to everyday expertise: object and pattern recognition. We compared chess experts and novices performing chess-related and -unrelated (visual) search tasks. As expected, the superiority of experts was limited to the chess-specific task, as there were no differences in a control task that used the same chess stimuli but did not require chess-specific recognition. The analysis of eye movements showed that experts immediately and exclusively focused on the relevant aspects in the chess task, whereas novices also examined irrelevant aspects. With random chess positions, when pattern knowledge could not be used to guide perception, experts nevertheless maintained an advantage. Experts' superior domain-specific parafoveal vision, a consequence of their knowledge about individual domain-specific symbols, enabled improved object recognition. Functional magnetic resonance imaging corroborated this differentiation between object and pattern recognition and showed that chess-specific object recognition was accompanied by bilateral activation of the occipitotemporal junction, whereas chess-specific pattern recognition was related to bilateral activations in the middle part of the collateral sulci. Using the expertise approach together with carefully chosen controls and multiple dependent measures, we identified object and pattern recognition as two essential cognitive processes in expert visual cognition, which may also help to explain the mechanisms of everyday perception.

Taxonomic and Phylogenetic Determinants of Functional Composition of Bolivian Bat Assemblages

PubMed Central

Aguirre, Luis F.; Montaño-Centellas, Flavia A.; Gavilanez, M. Mercedes; Stevens, Richard D.

2016-01-01

Understanding diversity patterns and the potential mechanisms driving them is a fundamental goal in ecology. Examination of different dimensions of biodiversity can provide insights into the relative importance of different processes acting upon biotas to shape communities. Unfortunately, patterns of diversity are still poorly understood in hyper-diverse tropical countries. Here, we assess spatial variation of taxonomic, functional and phylogenetic diversity of bat assemblages in one of the least studied Neotropical countries, Bolivia, and determine whether changes in biodiversity are explained by the replacement of species or functional groups, or by differences in richness (i.e., gain or loss of species or functional groups). Further, we evaluate the contribution of phylogenetic and taxonomic changes in the resulting patterns of functional diversity of bats. Using well-sampled assemblages from published studies we examine noctilionoid bats at ten study sites across five ecoregions in Bolivia. Bat assemblages differed from each other in all dimensions of biodiversity considered; however, diversity patterns for each dimension were likely structured by different mechanisms. Within ecoregions, differences were largely explained by species richness, suggesting that the gain or loss of species or functional groups (as opposed to replacement) was driving dissimilarity patterns. Overall, our results suggest that whereas evolutionary processes (i.e., historical connection and dispersal routes across Bolivia) create a template of diversity patterns across the country, ecological mechanisms modify these templates, decoupling the observed patterns of functional, taxonomic and phylogenetic diversity in Bolivian bats. Our results suggests that elevation represents an important source of variability among diversity patterns for each dimension of diversity considered. Further, we found that neither phylogenetic nor taxonomic diversity can fully account for patterns of functional diversity, highlighting the need for examining different dimensions of biodiversity of bats in hyperdiverse ecosystems. PMID:27384441

Taxonomic and Phylogenetic Determinants of Functional Composition of Bolivian Bat Assemblages.

PubMed

Aguirre, Luis F; Montaño-Centellas, Flavia A; Gavilanez, M Mercedes; Stevens, Richard D

2016-01-01

Understanding diversity patterns and the potential mechanisms driving them is a fundamental goal in ecology. Examination of different dimensions of biodiversity can provide insights into the relative importance of different processes acting upon biotas to shape communities. Unfortunately, patterns of diversity are still poorly understood in hyper-diverse tropical countries. Here, we assess spatial variation of taxonomic, functional and phylogenetic diversity of bat assemblages in one of the least studied Neotropical countries, Bolivia, and determine whether changes in biodiversity are explained by the replacement of species or functional groups, or by differences in richness (i.e., gain or loss of species or functional groups). Further, we evaluate the contribution of phylogenetic and taxonomic changes in the resulting patterns of functional diversity of bats. Using well-sampled assemblages from published studies we examine noctilionoid bats at ten study sites across five ecoregions in Bolivia. Bat assemblages differed from each other in all dimensions of biodiversity considered; however, diversity patterns for each dimension were likely structured by different mechanisms. Within ecoregions, differences were largely explained by species richness, suggesting that the gain or loss of species or functional groups (as opposed to replacement) was driving dissimilarity patterns. Overall, our results suggest that whereas evolutionary processes (i.e., historical connection and dispersal routes across Bolivia) create a template of diversity patterns across the country, ecological mechanisms modify these templates, decoupling the observed patterns of functional, taxonomic and phylogenetic diversity in Bolivian bats. Our results suggests that elevation represents an important source of variability among diversity patterns for each dimension of diversity considered. Further, we found that neither phylogenetic nor taxonomic diversity can fully account for patterns of functional diversity, highlighting the need for examining different dimensions of biodiversity of bats in hyperdiverse ecosystems.

Biomarkers and taphonomic processes in fresh and fossil biosignatures from Hot Spring silica deposits in El Tatio Chile, as a Mars Analogue

NASA Astrophysics Data System (ADS)

Carrizo, D.; Sánchez-García, L.; Parro, V.; Cady, S. L.; Cabrol, N. A.

2017-09-01

Biomarkers characterization and taphonomic process of recent and fossil biosignatures in extreme environments with analogies to Mars is essential to understanding how life could develop and survive in this conditions. Siliceous sinter deposits on Mars where similar to those found in the hydrothermal hot springs and geysers from El Tatio, Chile. Organic preservation have been shown in this study. Many different labile functional groups (i.e., carboxylic acids, alcohols, aldehydes, etc.) were found in both "age" samples. A shift in congener pattern for the different lipids families were found and discuss. This results give insight in taphonomic processes actin in this extreme environment, which could be used as a baseline in Mars exploration.

Cognitive Architecture with Evolutionary Dynamics Solves Insight Problem.

PubMed

Fedor, Anna; Zachar, István; Szilágyi, András; Öllinger, Michael; de Vladar, Harold P; Szathmáry, Eörs

2017-01-01

In this paper, we show that a neurally implemented a cognitive architecture with evolutionary dynamics can solve the four-tree problem. Our model, called Darwinian Neurodynamics, assumes that the unconscious mechanism of problem solving during insight tasks is a Darwinian process. It is based on the evolution of patterns that represent candidate solutions to a problem, and are stored and reproduced by a population of attractor networks. In our first experiment, we used human data as a benchmark and showed that the model behaves comparably to humans: it shows an improvement in performance if it is pretrained and primed appropriately, just like human participants in Kershaw et al. (2013)'s experiment. In the second experiment, we further investigated the effects of pretraining and priming in a two-by-two design and found a beginner's luck type of effect: solution rate was highest in the condition that was primed, but not pretrained with patterns relevant for the task. In the third experiment, we showed that deficits in computational capacity and learning abilities decreased the performance of the model, as expected. We conclude that Darwinian Neurodynamics is a promising model of human problem solving that deserves further investigation.

Insights into cortical mechanisms of behavior from microstimulation experiments

PubMed Central

Histed, Mark H.; Ni, Amy M.; Maunsell, John H.R.

2012-01-01

Even the simplest behaviors depend on a large number of neurons that are distributed across many brain regions. Because electrical microstimulation can change the activity of localized subsets of neurons, it has provided valuable evidence that specific neurons contribute to particular behaviors. Here we review what has been learned about cortical function from behavioral studies using microstimulation in animals and humans. Experiments that examine how microstimulation affects the perception of stimuli have shown that the effects of microstimulation are usually highly specific and can be related to the stimuli preferred by neurons at the stimulated site. Experiments that ask subjects to detect cortical microstimulation in the absence of other stimuli have provided further insights. Although subjects typically can detect microstimulation of primary sensory or motor cortex, they are generally unable to detect stimulation of most of cortex without extensive practice. With practice, however, stimulation of any part of cortex can become detected. These training effects suggest that some patterns of cortical activity cannot be readily accessed to guide behavior, but that the adult brain retains enough plasticity to learn to process novel patterns of neuronal activity arising anywhere in cortex. PMID:22307059

Cognitive Architecture with Evolutionary Dynamics Solves Insight Problem

PubMed Central

Fedor, Anna; Zachar, István; Szilágyi, András; Öllinger, Michael; de Vladar, Harold P.; Szathmáry, Eörs

2017-01-01

In this paper, we show that a neurally implemented a cognitive architecture with evolutionary dynamics can solve the four-tree problem. Our model, called Darwinian Neurodynamics, assumes that the unconscious mechanism of problem solving during insight tasks is a Darwinian process. It is based on the evolution of patterns that represent candidate solutions to a problem, and are stored and reproduced by a population of attractor networks. In our first experiment, we used human data as a benchmark and showed that the model behaves comparably to humans: it shows an improvement in performance if it is pretrained and primed appropriately, just like human participants in Kershaw et al. (2013)'s experiment. In the second experiment, we further investigated the effects of pretraining and priming in a two-by-two design and found a beginner's luck type of effect: solution rate was highest in the condition that was primed, but not pretrained with patterns relevant for the task. In the third experiment, we showed that deficits in computational capacity and learning abilities decreased the performance of the model, as expected. We conclude that Darwinian Neurodynamics is a promising model of human problem solving that deserves further investigation. PMID:28405191

Trace-element patterns of fibrous and monocrystalline diamonds: Insights into mantle fluids

NASA Astrophysics Data System (ADS)

Rege, S.; Griffin, W. L.; Pearson, N. J.; Araujo, D.; Zedgenizov, D.; O'Reilly, S. Y.

2010-08-01

During their growth diamonds may trap micron-scale inclusions of the fluids from which they grew, and these "time capsules" provide insights into the metasomatic processes that have modified the subcontinental lithospheric mantle. LAM-ICPMS analysis of trace elements in > 500 fibrous and monocrystalline diamonds worldwide has been used to understand the nature of these fluids. Analyses of fibrous diamonds define two general types of pattern, a "fibrous-high" (FH) one with high contents of LREE, Ba and K, and a "fibrous-low" (FL) pattern characterized by depletion in LREE/MREE, Ba and K, negative anomalies in Sr and Y, and subchondritic Zr/Hf and Nb/Ta. Both types may be found in fibrous diamonds from single deposits, and in three Yakutian pipes some diamonds show abrupt transitions from inclusion-rich cores with FH patterns to clearer rims with FL patterns. Most monocrystalline diamonds show FL-type patterns, but some have patterns that resemble those of FH fibrous diamonds. Peridotitic and eclogitic monocrystalline diamonds may show either patterns with relatively flat REE, or patterns with more strongly depleted LREE. Kimberlites that contain peridotitic diamonds with "high" patterns also contain eclogitic diamonds with "high" patterns. Strong similarities in the patterns of these two groups of diamonds may suggest high fluid/rock ratios. Many diamonds of the "superdeep" paragenesis have trace-element patterns similar to those of other monocrystalline diamonds. This may be evidence that the trace-element compositions of deep-seated fluids are generally similar to those that form diamonds in the subcontinental lithospheric mantle. The element fractionations observed between the FH and FL patterns are consistent with the immiscible separation of a silicic fluid from a carbonatite-silicate fluid, leaving a residual carbonatitic fluid strongly enriched in LREE, Ba and alkalies. This model would suggest that most monocrystalline diamonds crystallized from the more silicic fraction. Comparison with studies of single fluid inclusions in fibrous diamonds suggests that the FH patterns reflect trapped inclusions of high-Mg and low-Mg carbonatitic high-density fluids. In terms of the rock-forming elements, the fluids that precipitated the rims of some fibrous diamonds (FL pattern) and most monocrystalline diamonds are broadly similar to some hydro-silicic high-density fluids found in fibrous diamonds. However, there are still significant differences between the trace-element patterns of most monocrystalline diamonds and known high-density fluids, and further research is required to understand the formation and growth of these diamonds.

Insight in paranoia: The role of experiential avoidance and internalized stigma.

PubMed

Valiente, Carmen; Provencio, Maria; Espinosa, Regina; Duque, Almudena; Everts, Franziska

2015-05-01

Evidence suggests that insight in psychosis has been related to treatment adherence, recovery and good prognosis, but also to depression, low self-esteem, and diminished quality of life. Thus, insight might not be advantageous under all circumstances. Internalized-stigma (i.e. self-acceptance of stigmatizing images of illness) and experiential avoidance (i.e. unwillingness to experience negative private events) have been proposed as moderating variables between insight, and psychological health variables and/or distress. We investigated the patterns of association of insight with satisfaction with life, self-esteem, depression, anxiety and psychotic psychopathology as moderated by self-stigmatizing beliefs and experiential avoidance, in a sample of 47 participants with persecutory beliefs and diagnosed with schizophrenia or other psychotic disorder. Moderation analyses confirm the importance of internalized-stigma and experiential avoidance. The presence of insight was associated with more depression when there were high levels of self-stigma. Whereas, the absence of insight was associated with a greater life satisfaction when there were high levels of experiential avoidance. To summarize, our results help understand the complex relationship between insight, psychological health variables and emotional distress, pointing to a differential pattern of moderation for negative and positive outcomes. We discuss the implications of these results for research and treatment of paranoia. Copyright © 2015 Elsevier B.V. All rights reserved.

Neural code alterations and abnormal time patterns in Parkinson’s disease

NASA Astrophysics Data System (ADS)

Andres, Daniela Sabrina; Cerquetti, Daniel; Merello, Marcelo

2015-04-01

Objective. The neural code used by the basal ganglia is a current question in neuroscience, relevant for the understanding of the pathophysiology of Parkinson’s disease. While a rate code is known to participate in the communication between the basal ganglia and the motor thalamus/cortex, different lines of evidence have also favored the presence of complex time patterns in the discharge of the basal ganglia. To gain insight into the way the basal ganglia code information, we studied the activity of the globus pallidus pars interna (GPi), an output node of the circuit. Approach. We implemented the 6-hydroxydopamine model of Parkinsonism in Sprague-Dawley rats, and recorded the spontaneous discharge of single GPi neurons, in head-restrained conditions at full alertness. Analyzing the temporal structure function, we looked for characteristic scales in the neuronal discharge of the GPi. Main results. At a low-scale, we observed the presence of dynamic processes, which allow the transmission of time patterns. Conversely, at a middle-scale, stochastic processes force the use of a rate code. Regarding the time patterns transmitted, we measured the word length and found that it is increased in Parkinson’s disease. Furthermore, it showed a positive correlation with the frequency of discharge, indicating that an exacerbation of this abnormal time pattern length can be expected, as the dopamine depletion progresses. Significance. We conclude that a rate code and a time pattern code can co-exist in the basal ganglia at different temporal scales. However, their normal balance is progressively altered and replaced by pathological time patterns in Parkinson’s disease.

Organization of nuclear architecture during adipocyte differentiation

PubMed Central

Charó, Nancy L.; Rodríguez Ceschan, María I.; Galigniana, Natalia M.; Toneatto, Judith; Piwien-Pilipuk, Graciela

2016-01-01

ABSTRACT Obesity is a serious health problem worldwide since it is a major risk factor for chronic diseases such as type II diabetes. Obesity is the result of hyperplasia (associated with increased adipogenesis) and hypertrophy (associated with decreased adipogenesis) of the adipose tissue. Therefore, understanding the molecular mechanisms underlying the process of adipocyte differentiation is relevant to delineate new therapeutic strategies for treatment of obesity. As in all differentiation processes, temporal patterns of transcription are exquisitely controlled, allowing the acquisition and maintenance of the adipocyte phenotype. The genome is spatially organized; therefore decoding local features of the chromatin language alone does not suffice to understand how cell type-specific gene expression patterns are generated. Elucidating how nuclear architecture is built during the process of adipogenesis is thus an indispensable step to gain insight in how gene expression is regulated to achieve the adipocyte phenotype. Here we will summarize the recent advances in our understanding of the organization of nuclear architecture as progenitor cells differentiate in adipocytes, and the questions that still remained to be answered. PMID:27416359

LateBiclustering: Efficient Heuristic Algorithm for Time-Lagged Bicluster Identification.

PubMed

Gonçalves, Joana P; Madeira, Sara C

2014-01-01

Identifying patterns in temporal data is key to uncover meaningful relationships in diverse domains, from stock trading to social interactions. Also of great interest are clinical and biological applications, namely monitoring patient response to treatment or characterizing activity at the molecular level. In biology, researchers seek to gain insight into gene functions and dynamics of biological processes, as well as potential perturbations of these leading to disease, through the study of patterns emerging from gene expression time series. Clustering can group genes exhibiting similar expression profiles, but focuses on global patterns denoting rather broad, unspecific responses. Biclustering reveals local patterns, which more naturally capture the intricate collaboration between biological players, particularly under a temporal setting. Despite the general biclustering formulation being NP-hard, considering specific properties of time series has led to efficient solutions for the discovery of temporally aligned patterns. Notably, the identification of biclusters with time-lagged patterns, suggestive of transcriptional cascades, remains a challenge due to the combinatorial explosion of delayed occurrences. Herein, we propose LateBiclustering, a sensible heuristic algorithm enabling a polynomial rather than exponential time solution for the problem. We show that it identifies meaningful time-lagged biclusters relevant to the response of Saccharomyces cerevisiae to heat stress.

Quantitative Aging Pattern in Mouse Urine Vapor as Measured by Gas-Liquid Chromatography

NASA Technical Reports Server (NTRS)

Robinson, Arthur B.; Dirren, Henri; Sheets, Alan; Miquel, Jaime; Lundgren, Paul R.

1975-01-01

We have discovered a quantitative aging pattern in mouse urine vapor. The diagnostic power of the pattern has been found to be high. We hope that this pattern will eventually allow quantitative estimates of physiological age and some insight into the biochemistry of aging.

Functional Characterization and Differential Coactivation Patterns of Two Cytoarchitectonic Visual Areas on the Human Posterior Fusiform Gyrus

PubMed Central

Caspers, Julian; Zilles, Karl; Amunts, Katrin; Laird, Angela R.; Fox, Peter T.; Eickhoff, Simon B.

2016-01-01

The ventral stream of the human extrastriate visual cortex shows a considerable functional heterogeneity from early visual processing (posterior) to higher, domain-specific processing (anterior). The fusiform gyrus hosts several of those “high-level” functional areas. We recently found a subdivision of the posterior fusiform gyrus on the microstructural level, that is, two distinct cytoarchitectonic areas, FG1 and FG2 (Caspers et al., Brain Structure & Function, 2013). To gain a first insight in the function of these two areas, here we studied their behavioral involvement and coactivation patterns by means of meta-analytic connectivity modeling based on the BrainMap database (www.brainmap.org), using probabilistic maps of these areas as seed regions. The coactivation patterns of the areas support the concept of a common involvement in a core network subserving different cognitive tasks, that is, object recognition, visual language perception, or visual attention. In addition, the analysis supports the previous cytoarchitectonic parcellation, indicating that FG1 appears as a transitional area between early and higher visual cortex and FG2 as a higher-order one. The latter area is furthermore lateralized, as it shows strong relations to the visual language processing system in the left hemisphere, while its right side is stronger associated with face selective regions. These findings indicate that functional lateralization of area FG2 relies on a different pattern of connectivity rather than side-specific cytoarchitectonic features. PMID:24038902

Free-standing carbon nanotube composite sensing skin for distributed strain sensing in structures

NASA Astrophysics Data System (ADS)

Burton, Andrew R.; Minegishi, Kaede; Kurata, Masahiro; Lynch, Jerome P.

2014-04-01

The technical challenges of managing the health of critical infrastructure systems necessitate greater structural sensing capabilities. Among these needs is the ability for quantitative, spatial damage detection on critical structural components. Advances in material science have now opened the door for novel and cost-effective spatial sensing solutions specially tailored for damage detection in structures. However, challenges remain before spatial damage detection can be realized. Some of the technical challenges include sensor installations and extensive signal processing requirements. This work addresses these challenges by developing a patterned carbon nanotube composite thin film sensor whose pattern has been optimized for measuring the spatial distribution of strain. The carbon nanotube-polymer nanocomposite sensing material is fabricated on a flexible polyimide substrate using a layer-by-layer deposition process. The thin film sensors are then patterned into sensing elements using optical lithography processes common to microelectromechanical systems (MEMS) technologies. The sensor array is designed as a series of sensing elements with varying width to provide insight on the limitations of such patterning and implications of pattern geometry on sensing signals. Once fabrication is complete, the substrate and attached sensor are epoxy bonded to a poly vinyl composite (PVC) bar that is then tested with a uniaxial, cyclic load pattern and mechanical response is characterized. The fabrication processes are then utilized on a larger-scale to develop and instrument a component-specific sensing skin in order to observe the strain distribution on the web of a steel beam. The instrumented beam is part of a larger steel beam-column connection with a concrete slab in composite action. The beam-column subassembly is laterally loaded and strain trends in the web are observed using the carbon nanotube composite sensing skin. The results are discussed in the context of understanding the properties of the thin film sensor and how it may be advanced toward structural sensing applications.

AFLP markers provide insights into the evolutionary relationships and diversification of New Caledonian Araucaria species (Araucariaceae).

PubMed

Gaudeul, Myriam; Rouhan, Germinal; Gardner, Martin F; Hollingsworth, Peter M

2012-01-01

Despite its small size, New Caledonia is characterized by a very diverse flora and striking environmental gradients, which make it an ideal setting to study species diversification. Thirteen of the 19 Araucaria species are endemic to the territory and form a monophyletic group, but patterns and processes that lead to such a high species richness are largely unexplored. We used 142 polymorphic AFLP markers and performed analyses based on Bayesian clustering algorithms, genetic distances, and cladistics on 71 samples representing all New Caledonian Araucaria species. We examined correlations between the inferred evolutionary relationships and shared morphological, ecological, or geographic parameters among species, to investigate evolutionary processes that may have driven speciation. We showed that genetic divergence among the present New Caledonian Araucaria species is low, suggesting recent diversification rather than pre-existence on Gondwana. We identified three genetic groups that included small-leaved, large-leaved, and coastal species, but detected no association with soil preference, ecological habitat, or rainfall. The observed patterns suggested that speciation events resulted from both differential adaptation and vicariance. Last, we hypothesize that speciation is ongoing and/or there are cryptic species in some genetically (sometimes also morphologically) divergent populations. Further data are required to provide better resolution and understanding of the diversification of New Caledonian Araucaria species. Nevertheless, our study allowed insights into their evolutionary relationships and provides a framework for future investigations on the evolution of this emblematic group of plants in one of the world's biodiversity hotspots.

Speech perception as an active cognitive process

PubMed Central

Heald, Shannon L. M.; Nusbaum, Howard C.

2014-01-01

One view of speech perception is that acoustic signals are transformed into representations for pattern matching to determine linguistic structure. This process can be taken as a statistical pattern-matching problem, assuming realtively stable linguistic categories are characterized by neural representations related to auditory properties of speech that can be compared to speech input. This kind of pattern matching can be termed a passive process which implies rigidity of processing with few demands on cognitive processing. An alternative view is that speech recognition, even in early stages, is an active process in which speech analysis is attentionally guided. Note that this does not mean consciously guided but that information-contingent changes in early auditory encoding can occur as a function of context and experience. Active processing assumes that attention, plasticity, and listening goals are important in considering how listeners cope with adverse circumstances that impair hearing by masking noise in the environment or hearing loss. Although theories of speech perception have begun to incorporate some active processing, they seldom treat early speech encoding as plastic and attentionally guided. Recent research has suggested that speech perception is the product of both feedforward and feedback interactions between a number of brain regions that include descending projections perhaps as far downstream as the cochlea. It is important to understand how the ambiguity of the speech signal and constraints of context dynamically determine cognitive resources recruited during perception including focused attention, learning, and working memory. Theories of speech perception need to go beyond the current corticocentric approach in order to account for the intrinsic dynamics of the auditory encoding of speech. In doing so, this may provide new insights into ways in which hearing disorders and loss may be treated either through augementation or therapy. PMID:24672438

New Experiments and a Model-Driven Approach for Interpreting Middle Stone Age Lithic Point Function Using the Edge Damage Distribution Method.

PubMed

Schoville, Benjamin J; Brown, Kyle S; Harris, Jacob A; Wilkins, Jayne

2016-01-01

The Middle Stone Age (MSA) is associated with early evidence for symbolic material culture and complex technological innovations. However, one of the most visible aspects of MSA technologies are unretouched triangular stone points that appear in the archaeological record as early as 500,000 years ago in Africa and persist throughout the MSA. How these tools were being used and discarded across a changing Pleistocene landscape can provide insight into how MSA populations prioritized technological and foraging decisions. Creating inferential links between experimental and archaeological tool use helps to establish prehistoric tool function, but is complicated by the overlaying of post-depositional damage onto behaviorally worn tools. Taphonomic damage patterning can provide insight into site formation history, but may preclude behavioral interpretations of tool function. Here, multiple experimental processes that form edge damage on unretouched lithic points from taphonomic and behavioral processes are presented. These provide experimental distributions of wear on tool edges from known processes that are then quantitatively compared to the archaeological patterning of stone point edge damage from three MSA lithic assemblages-Kathu Pan 1, Pinnacle Point Cave 13B, and Die Kelders Cave 1. By using a model-fitting approach, the results presented here provide evidence for variable MSA behavioral strategies of stone point utilization on the landscape consistent with armature tips at KP1, and cutting tools at PP13B and DK1, as well as damage contributions from post-depositional sources across assemblages. This study provides a method with which landscape-scale questions of early modern human tool-use and site-use can be addressed.

New Experiments and a Model-Driven Approach for Interpreting Middle Stone Age Lithic Point Function Using the Edge Damage Distribution Method

PubMed Central

Schoville, Benjamin J.; Brown, Kyle S.; Harris, Jacob A.; Wilkins, Jayne

2016-01-01

The Middle Stone Age (MSA) is associated with early evidence for symbolic material culture and complex technological innovations. However, one of the most visible aspects of MSA technologies are unretouched triangular stone points that appear in the archaeological record as early as 500,000 years ago in Africa and persist throughout the MSA. How these tools were being used and discarded across a changing Pleistocene landscape can provide insight into how MSA populations prioritized technological and foraging decisions. Creating inferential links between experimental and archaeological tool use helps to establish prehistoric tool function, but is complicated by the overlaying of post-depositional damage onto behaviorally worn tools. Taphonomic damage patterning can provide insight into site formation history, but may preclude behavioral interpretations of tool function. Here, multiple experimental processes that form edge damage on unretouched lithic points from taphonomic and behavioral processes are presented. These provide experimental distributions of wear on tool edges from known processes that are then quantitatively compared to the archaeological patterning of stone point edge damage from three MSA lithic assemblages—Kathu Pan 1, Pinnacle Point Cave 13B, and Die Kelders Cave 1. By using a model-fitting approach, the results presented here provide evidence for variable MSA behavioral strategies of stone point utilization on the landscape consistent with armature tips at KP1, and cutting tools at PP13B and DK1, as well as damage contributions from post-depositional sources across assemblages. This study provides a method with which landscape-scale questions of early modern human tool-use and site-use can be addressed. PMID:27736886

Congenital hypoplasia of the cerebellum: developmental causes and behavioral consequences

PubMed Central

Basson, M. Albert; Wingate, Richard J.

2013-01-01

Over the last 60 years, the spotlight of research has periodically returned to the cerebellum as new techniques and insights have emerged. Because of its simple homogeneous structure, limited diversity of cell types and characteristic behavioral pathologies, the cerebellum is a natural home for studies of cell specification, patterning, and neuronal migration. However, recent evidence has extended the traditional range of perceived cerebellar function to include modulation of cognitive processes and implicated cerebellar hypoplasia and Purkinje neuron hypo-cellularity with autistic spectrum disorder. In the light of this emerging frontier, we review the key stages and genetic mechanisms behind cerebellum development. In particular, we discuss the role of the midbrain hindbrain isthmic organizer in the development of the cerebellar vermis and the specification and differentiation of Purkinje cells and granule neurons. These developmental processes are then considered in relation to recent insights into selected human developmental cerebellar defects: Joubert syndrome, Dandy–Walker malformation, and pontocerebellar hypoplasia. Finally, we review current research that opens up the possibility of using the mouse as a genetic model to study the role of the cerebellum in cognitive function. PMID:24027500

Computational overlay metrology with adaptive data analytics

NASA Astrophysics Data System (ADS)

Schmitt-Weaver, Emil; Subramony, Venky; Ullah, Zakir; Matsunobu, Masazumi; Somasundaram, Ravin; Thomas, Joel; Zhang, Linmiao; Thul, Klaus; Bhattacharyya, Kaustuve; Goossens, Ronald; Lambregts, Cees; Tel, Wim; de Ruiter, Chris

2017-03-01

With photolithography as the fundamental patterning step in the modern nanofabrication process, every wafer within a semiconductor fab will pass through a lithographic apparatus multiple times. With more than 20,000 sensors producing more than 700GB of data per day across multiple subsystems, the combination of a light source and lithographic apparatus provide a massive amount of information for data analytics. This paper outlines how data analysis tools and techniques that extend insight into data that traditionally had been considered unmanageably large, known as adaptive analytics, can be used to show how data collected before the wafer is exposed can be used to detect small process dependent wafer-towafer changes in overlay.

Affinity communities in United Nations voting: Implications for democracy, cooperation, and conflict

NASA Astrophysics Data System (ADS)

Pauls, Scott D.; Cranmer, Skyler J.

2017-10-01

A network oriented examination of the co-voting network of the United Nations (UN) provides powerful insights into the international alignment of states, as well as normatively important processes such as democracy, defensive cooperation, and armed conflict. Here, we investigate the UN co-voting network using the tools of community detection and inductively identify "affinity communities" in which states articulate similar policy preferences through their voting patterns. Analysis of these communities reveals that there is more information contained in UN voting and co-voting patterns than has previously been thought. Affinity communities have complex relationships with some of the most normatively important international outcomes: they reflect transitions to democracy, have a feedback loop with the formation of defensive alliances, and actively help states avoid armed conflict.

Planar waveguide nanolaser configured by dye-doped hybrid nanofilm on substrate

NASA Astrophysics Data System (ADS)

Tikhonov, E. A.; Yashchuk, V. P.; Telbiz, G. M.

2018-04-01

Dye-doped hybrid silicate/titanium nanofilms on the glass substrate structures of asymmetrical waveguides were studied by way of laser systems. The threshold, spatial and spectral features of the laser oscillation of genuine and hollow waveguides were determined. The pattern of stimulated radiation included two concurrent processes: single-mode waveguide lasing and lateral small divergence emission. Comparison of the open angle of the lateral beams and grazing angles of the waveguide lasing mode provides an insight into the effect of leaky mode emission followed by Lummer-Gehrcke interference.

From Forest Landscape to Agricultural Landscape in the Developing Tropical Country of Malaysia: Pattern, Process, and Their Significance on Policy

NASA Astrophysics Data System (ADS)

Abdullah, Saiful Arif; Hezri, Adnan A.

2008-11-01

Agricultural expansion and deforestation are spatial processes of land transformation that impact on landscape pattern. In peninsular Malaysia, the conversion of forested areas into two major cash crops—rubber and oil palm plantations—has been identified as driving significant environmental change. To date, there has been insufficient literature studying the link between changes in landscape patterns and land-related development policies. Therefore, this paper examines: (i) the links between development policies and changes in land use/land cover and landscape pattern and (ii) the significance and implications of these links for future development policies. The objective is to generate insights on the changing process of land use/land cover and landscape pattern as a functional response to development policies and their consequences for environmental conditions. Over the last century, the development of cash crops has changed the country from one dominated by natural landscapes to one dominated by agricultural landscapes. But the last decade of the century saw urbanization beginning to impact significantly. This process aligned with the establishment of various development policies, from land development for agriculture between the mid 1950s and the 1970s to an emphasis on manufacturing from the 1980s onward. Based on a case study in Selangor, peninsular Malaysia, a model of landscape pattern change is presented. It contains three stages according to the relative importance of rubber (first stage: 1900-1950s), oil palm (second stage: 1960s-1970s), and urban (third stage: 1980s-1990s) development that influenced landscape fragmentation and heterogeneity. The environmental consequences of this change have been depicted through loss of biodiversity, geohazard incidences, and the spread of vector-borne diseases. The spatial ecological information can be useful to development policy formulation, allowing diagnosis of the country’s “health” and sustainability. The final section outlines the usefulness of landscape analysis in the policy-making process to prevent further fragmentation of the landscape and forest loss in Malaysia in the face of rapid economic development.

From forest landscape to agricultural landscape in the developing tropical country of Malaysia: pattern, process, and their significance on policy.

PubMed

Abdullah, Saiful Arif; Hezri, Adnan A

2008-11-01

Agricultural expansion and deforestation are spatial processes of land transformation that impact on landscape pattern. In peninsular Malaysia, the conversion of forested areas into two major cash crops--rubber and oil palm plantations--has been identified as driving significant environmental change. To date, there has been insufficient literature studying the link between changes in landscape patterns and land-related development policies. Therefore, this paper examines: (i) the links between development policies and changes in land use/land cover and landscape pattern and (ii) the significance and implications of these links for future development policies. The objective is to generate insights on the changing process of land use/land cover and landscape pattern as a functional response to development policies and their consequences for environmental conditions. Over the last century, the development of cash crops has changed the country from one dominated by natural landscapes to one dominated by agricultural landscapes. But the last decade of the century saw urbanization beginning to impact significantly. This process aligned with the establishment of various development policies, from land development for agriculture between the mid 1950s and the 1970s to an emphasis on manufacturing from the 1980s onward. Based on a case study in Selangor, peninsular Malaysia, a model of landscape pattern change is presented. It contains three stages according to the relative importance of rubber (first stage: 1900--1950s), oil palm (second stage: 1960s--1970s), and urban (third stage: 1980s--1990s) development that influenced landscape fragmentation and heterogeneity. The environmental consequences of this change have been depicted through loss of biodiversity, geohazard incidences, and the spread of vector-borne diseases. The spatial ecological information can be useful to development policy formulation, allowing diagnosis of the country's "health" and sustainability. The final section outlines the usefulness of landscape analysis in the policy-making process to prevent further fragmentation of the landscape and forest loss in Malaysia in the face of rapid economic development.

Entropy and gravity concepts as new methodological indexes to investigate technological convergence: patent network-based approach.

PubMed

Cho, Yongrae; Kim, Minsung

2014-01-01

The volatility and uncertainty in the process of technological developments are growing faster than ever due to rapid technological innovations. Such phenomena result in integration among disparate technology fields. At this point, it is a critical research issue to understand the different roles and the propensity of each element technology for technological convergence. In particular, the network-based approach provides a holistic view in terms of technological linkage structures. Furthermore, the development of new indicators based on network visualization can reveal the dynamic patterns among disparate technologies in the process of technological convergence and provide insights for future technological developments. This research attempts to analyze and discover the patterns of the international patent classification codes of the United States Patent and Trademark Office's patent data in printed electronics, which is a representative technology in the technological convergence process. To this end, we apply the physical idea as a new methodological approach to interpret technological convergence. More specifically, the concepts of entropy and gravity are applied to measure the activities among patent citations and the binding forces among heterogeneous technologies during technological convergence. By applying the entropy and gravity indexes, we could distinguish the characteristic role of each technology in printed electronics. At the technological convergence stage, each technology exhibits idiosyncratic dynamics which tend to decrease technological differences and heterogeneity. Furthermore, through nonlinear regression analysis, we have found the decreasing patterns of disparity over a given total period in the evolution of technological convergence. This research has discovered the specific role of each element technology field and has consequently identified the co-evolutionary patterns of technological convergence. These new findings on the evolutionary patterns of technological convergence provide some implications for engineering and technology foresight research, as well as for corporate strategy and technology policy.

Combining Population Structure with Historic Abitoic Processes to Better Understand Species and Community Range Shifts in Response to Climate Change

NASA Astrophysics Data System (ADS)

Graham, N. M.

2015-12-01

The evolution and speciation of plants is directly tied to the environment as the constrained stages of dispersal creates strong genetic differentiation among populations. This can result in differing genetic patterns between nuclear and chloroplast loci, where genes are inherited differently and dispersed via separate vectors. By developing distribution models based on genetic patterns found within a species, it is possible to begin understanding the influence of historic geomorphic and/or climatic processes on population evolution. If genetic patterns of the current range correlate with specific patterns of climate variability within the Pleistocene, it is possible that future shifts in species distribution in response to climate change can be more accurately modelled due to the historic signature that is found within inherited genes. Preliminary genetic analyses of Linanthus dichotomus, an annual herb distributed across California, suggests that the current taxonomic treatment does not accurately depict how this species is evolving. Genetic patterns of chloroplast genes suggest that populations are more correlated with biogeography than what the current nomenclature states. Additionally, chloroplast and nuclear genes show discrepancies in the dispersal across the landscape, suggesting pollinator driven gene flow overcoming seed dispersal boundaries. By comparing discrepancies between pollinator and seed induced gene flow we may be able to gain insight into historical pollinator communities within the Pleistocene. This information can then be applied to projected climate models to more accurately understand how species and/or communities will respond to a changing environment.

Transcriptomic variation of eyestalk reveals the genes and biological processes associated with molting in Portunus trituberculatus

PubMed Central

Zhang, Longtao; Liu, Ping; Li, Jian

2017-01-01

Background Molting is an essential biological process throughout the life history of crustaceans, which is regulated by many neuropeptide hormones expressed in the eyestalk. To better understand the molting mechanism in Portunus trituberculatus, we used digital gene expression (DGE) to analyze single eyestalk samples during the molting cycle by high-throughput sequencing. Results We obtained 14,387,942, 12,631,508 and 13,060,062 clean sequence reads from inter-molt (InM), pre-molt (PrM) and post-molt (PoM) cDNA libraries, respectively. A total of 1,394 molt-related differentially expressed genes (DEGs) were identified. GO and KEGG enrichment analysis identified some important processes and pathways with key roles in molting regulation, such as chitin metabolism, peptidase inhibitor activity, and the ribosome. We first observed a pattern associated with the neuromodulator-related pathways during the molting cycle, which were up-regulated in PrM and down-regulated in PoM. Four categories of important molting-related transcripts were clustered and most of them had similar expression patterns, which suggests that there is a connection between these genes throughout the molt cycle. Conclusion Our work is the first molt-related investigation of P. trituberculatus focusing on the eyestalk at the whole transcriptome level. Together, our results, including DEGs, identification of molting-related biological processes and pathways, and observed expression patterns of important genes, provide a novel insight into the function of the eyestalk in molting regulation. PMID:28394948

More than one way to see it: Individual heuristics in avian visual computation

PubMed Central

Ravignani, Andrea; Westphal-Fitch, Gesche; Aust, Ulrike; Schlumpp, Martin M.; Fitch, W. Tecumseh

2015-01-01

Comparative pattern learning experiments investigate how different species find regularities in sensory input, providing insights into cognitive processing in humans and other animals. Past research has focused either on one species’ ability to process pattern classes or different species’ performance in recognizing the same pattern, with little attention to individual and species-specific heuristics and decision strategies. We trained and tested two bird species, pigeons (Columba livia) and kea (Nestor notabilis, a parrot species), on visual patterns using touch-screen technology. Patterns were composed of several abstract elements and had varying degrees of structural complexity. We developed a model selection paradigm, based on regular expressions, that allowed us to reconstruct the specific decision strategies and cognitive heuristics adopted by a given individual in our task. Individual birds showed considerable differences in the number, type and heterogeneity of heuristic strategies adopted. Birds’ choices also exhibited consistent species-level differences. Kea adopted effective heuristic strategies, based on matching learned bigrams to stimulus edges. Individual pigeons, in contrast, adopted an idiosyncratic mix of strategies that included local transition probabilities and global string similarity. Although performance was above chance and quite high for kea, no individual of either species provided clear evidence of learning exactly the rule used to generate the training stimuli. Our results show that similar behavioral outcomes can be achieved using dramatically different strategies and highlight the dangers of combining multiple individuals in a group analysis. These findings, and our general approach, have implications for the design of future pattern learning experiments, and the interpretation of comparative cognition research more generally. PMID:26113444

Hydrogeological controls on spatial patterns of groundwater discharge in peatlands

NASA Astrophysics Data System (ADS)

Hare, Danielle K.; Boutt, David F.; Clement, William P.; Hatch, Christine E.; Davenport, Glorianna; Hackman, Alex

2017-11-01

Peatland environments provide important ecosystem services including water and carbon storage, nutrient processing and retention, and wildlife habitat. However, these systems and the services they provide have been degraded through historical anthropogenic agricultural conversion and dewatering practices. Effective wetland restoration requires incorporating site hydrology and understanding groundwater discharge spatial patterns. Groundwater discharge maintains wetland ecosystems by providing relatively stable hydrologic conditions, nutrient inputs, and thermal buffering important for ecological structure and function; however, a comprehensive site-specific evaluation is rarely feasible for such resource-constrained projects. An improved process-based understanding of groundwater discharge in peatlands may help guide ecological restoration design without the need for invasive methodologies and detailed site-specific investigation. Here we examine a kettle-hole peatland in southeast Massachusetts historically modified for commercial cranberry farming. During the time of our investigation, a large process-based ecological restoration project was in the assessment and design phases. To gain insight into the drivers of site hydrology, we evaluated the spatial patterning of groundwater discharge and the subsurface structure of the peatland complex using heat-tracing methods and ground-penetrating radar. Our results illustrate that two groundwater discharge processes contribute to the peatland hydrologic system: diffuse lower-flux marginal matrix seepage and discrete higher-flux preferential-flow-path seepage. Both types of groundwater discharge develop through interactions with subsurface peatland basin structure, often where the basin slope is at a high angle to the regional groundwater gradient. These field observations indicate strong correlation between subsurface structures and surficial groundwater discharge. Understanding these general patterns may allow resource managers to more efficiently predict and locate groundwater seepage, confirm these using remote sensing technologies, and incorporate this information into restoration design for these critical ecosystems.

Cultural evolution of military camouflage.

PubMed

Talas, Laszlo; Baddeley, Roland J; Cuthill, Innes C

2017-07-05

While one has evolved and the other been consciously created, animal and military camouflage are expected to show many similar design principles. Using a unique database of calibrated photographs of camouflage uniform patterns, processed using texture and colour analysis methods from computer vision, we show that the parallels with biology are deeper than design for effective concealment. Using two case studies we show that, like many animal colour patterns, military camouflage can serve multiple functions. Following the dissolution of the Warsaw Pact, countries that became more Western-facing in political terms converged on NATO patterns in camouflage texture and colour. Following the break-up of the former Yugoslavia, the resulting states diverged in design, becoming more similar to neighbouring countries than the ancestral design. None of these insights would have been obtained using extant military approaches to camouflage design, which focus solely on concealment. Moreover, our computational techniques for quantifying pattern offer new tools for comparative biologists studying animal coloration.This article is part of the themed issue 'Animal coloration: production, perception, function and application'. © 2017 The Author(s).

Lineage diversification and morphological evolution in a large-scale continental radiation: the neotropical ovenbirds and woodcreepers (aves: Furnariidae).

PubMed

Derryberry, Elizabeth P; Claramunt, Santiago; Derryberry, Graham; Chesser, R Terry; Cracraft, Joel; Aleixo, Alexandre; Pérez-Emán, Jorge; Remsen, J V; Brumfield, Robb T

2011-10-01

Patterns of diversification in species-rich clades provide insight into the processes that generate biological diversity. We tested different models of lineage and phenotypic diversification in an exceptional continental radiation, the ovenbird family Furnariidae, using the most complete species-level phylogenetic hypothesis produced to date for a major avian clade (97% of 293 species). We found that the Furnariidae exhibit nearly constant rates of lineage accumulation but show evidence of constrained morphological evolution. This pattern of sustained high rates of speciation despite limitations on phenotypic evolution contrasts with the results of most previous studies of evolutionary radiations, which have found a pattern of decelerating diversity-dependent lineage accumulation coupled with decelerating or constrained phenotypic evolution. Our results suggest that lineage accumulation in tropical continental radiations may not be as limited by ecological opportunities as in temperate or island radiations. More studies examining patterns of both lineage and phenotypic diversification are needed to understand the often complex tempo and mode of evolutionary radiations on continents. © 2011 The Author(s). Evolution© 2011 The Society for the Study of Evolution.

Neural signatures of attention: insights from decoding population activity patterns.

PubMed

Sapountzis, Panagiotis; Gregoriou, Georgia G

2018-01-01

Understanding brain function and the computations that individual neurons and neuronal ensembles carry out during cognitive functions is one of the biggest challenges in neuroscientific research. To this end, invasive electrophysiological studies have provided important insights by recording the activity of single neurons in behaving animals. To average out noise, responses are typically averaged across repetitions and across neurons that are usually recorded on different days. However, the brain makes decisions on short time scales based on limited exposure to sensory stimulation by interpreting responses of populations of neurons on a moment to moment basis. Recent studies have employed machine-learning algorithms in attention and other cognitive tasks to decode the information content of distributed activity patterns across neuronal ensembles on a single trial basis. Here, we review results from studies that have used pattern-classification decoding approaches to explore the population representation of cognitive functions. These studies have offered significant insights into population coding mechanisms. Moreover, we discuss how such advances can aid the development of cognitive brain-computer interfaces.

Stellar Abundance Observations and Heavy Element Formation

NASA Astrophysics Data System (ADS)

Cowan, J. J.

2005-05-01

Abundance observations indicate the presence of rapid-neutron capture (i.e., r-process) elements in old Galactic halo and globular cluster stars. These observations provide insight into the nature of the earliest generations of stars in the Galaxy -- the progenitors of the halo stars -- responsible for neutron-capture synthesis of the heavy elements. Abundance comparisons among the r-process-rich halo stars show that the heaviest neutron-capture elements (i.e., Ba and above) are consistent with a scaled solar system r-process abundance distribution, while the lighter neutron-capture elements do not conform to the solar pattern. These comparisons suggest the possibility of two r-process sites in stars. The large star-to-star scatter observed in the abundances of neutron-capture element/iron ratios at low metallicities -- which disappears with increasing metallicity or [Fe/H] -- suggests the formation of these heavy elements (presumably from certain types of supernovae) was rare in the early Galaxy. The stellar abundances also indicate a change from the r-process to the slow neutron capture (i.e., s-) process at higher metallicities in the Galaxy and provide insight into Galactic chemical evolution. Finally, the detection of thorium and uranium in halo and globular cluster stars offers an independent age-dating technique that can put lower limits on the age of the Galaxy, and hence the Universe. This work has been supported in part by NSF grant AST 03-07279 (J.J.C.) and by STScI grants GO-8111, GO-8342 and GO-9359.

Chronic alcoholism: insights from neurophysiology.

PubMed

Campanella, S; Petit, G; Maurage, P; Kornreich, C; Verbanck, P; Noël, X

2009-01-01

Increasing knowledge of the anatomical structures and cellular processes underlying psychiatric disorders may help bridge the gap between clinical signs and basic physiological processes. Accordingly, considerable insight has been gained in recent years into a common psychiatric condition, i.e., chronic alcoholism. We reviewed various physiological parameters that are altered in chronic alcoholic patients compared to healthy individuals--continuous electroencephalogram, oculomotor measures, cognitive event-related potentials and event-related oscillations--to identify links between these physiological parameters, altered cognitive processes and specific clinical symptoms. Alcoholic patients display: (1) high beta and theta power in the resting electroencephalogram, suggesting hyperarousal of their central nervous system; (2) abnormalities in smooth pursuit eye movements, in saccadic inhibition during antisaccade tasks, and in prepulse inhibition, suggesting disturbed attention modulation and abnormal patterns of prefrontal activation that may stem from the same prefrontal "inhibitory" cortical dysfunction; (3) decreased amplitude for cognitive event-related potentials situated along the continuum of information-processing, suggesting that alcoholism is associated with neurophysiological deficits at the level of the sensory cortex and not only disturbances involving associative cortices and limbic structures; and (4) decreased theta, gamma and delta oscillations, suggesting cognitive disinhibition at a functional level. The heterogeneity of alcoholic disorders in terms of symptomatology, course and outcome is the result of various pathophysiological processes that physiological parameters may help to define. These alterations may be related to precise cognitive processes that could be easily monitored neurophysiologically in order to create more homogeneous subgroups of alcoholic individuals.

The ghosts of mammals past: biological and geographical patterns of global mammalian extinction across the Holocene.

PubMed

Turvey, Samuel T; Fritz, Susanne A

2011-09-12

Although the recent historical period is usually treated as a temporal base-line for understanding patterns of mammal extinction, mammalian biodiversity loss has also taken place throughout the Late Quaternary. We explore the spatial, taxonomic and phylogenetic patterns of 241 mammal species extinctions known to have occurred during the Holocene up to the present day. To assess whether our understanding of mammalian threat processes has been affected by excluding these taxa, we incorporate extinct species data into analyses of the impact of body mass on extinction risk. We find that Holocene extinctions have been phylogenetically and spatially concentrated in specific taxa and geographical regions, which are often not congruent with those disproportionately at risk today. Large-bodied mammals have also been more extinction-prone in most geographical regions across the Holocene. Our data support the extinction filter hypothesis, whereby regional faunas from which susceptible species have already become extinct now appear less threatened; they may also suggest that different processes are responsible for driving past and present extinctions. We also find overall incompleteness and inter-regional biases in extinction data from the recent fossil record. Although direct use of fossil data in future projections of extinction risk is therefore not straightforward, insights into extinction processes from the Holocene record are still useful in understanding mammalian threat.

The ghosts of mammals past: biological and geographical patterns of global mammalian extinction across the Holocene

PubMed Central

Turvey, Samuel T.; Fritz, Susanne A.

2011-01-01

Although the recent historical period is usually treated as a temporal base-line for understanding patterns of mammal extinction, mammalian biodiversity loss has also taken place throughout the Late Quaternary. We explore the spatial, taxonomic and phylogenetic patterns of 241 mammal species extinctions known to have occurred during the Holocene up to the present day. To assess whether our understanding of mammalian threat processes has been affected by excluding these taxa, we incorporate extinct species data into analyses of the impact of body mass on extinction risk. We find that Holocene extinctions have been phylogenetically and spatially concentrated in specific taxa and geographical regions, which are often not congruent with those disproportionately at risk today. Large-bodied mammals have also been more extinction-prone in most geographical regions across the Holocene. Our data support the extinction filter hypothesis, whereby regional faunas from which susceptible species have already become extinct now appear less threatened; they may also suggest that different processes are responsible for driving past and present extinctions. We also find overall incompleteness and inter-regional biases in extinction data from the recent fossil record. Although direct use of fossil data in future projections of extinction risk is therefore not straightforward, insights into extinction processes from the Holocene record are still useful in understanding mammalian threat. PMID:21807737

Neural differences in the processing of true and false sentences: insights into the nature of 'truth' in language comprehension.

PubMed

Marques, J Frederico; Canessa, Nicola; Cappa, Stefano

2009-06-01

The inquiry on the nature of truth in language comprehension has a long history of opposite perspectives. These perspectives either consider that there are qualitative differences in the processing of true and false statements, or that these processes are fundamentally the same and only differ in quantitative terms. The present study evaluated the processing nature of true and false statements in terms of patterns of brain activity using event-related functional-Magnetic-Resonance-Imaging (fMRI). We show that when true and false concept-feature statements are controlled for relation strength/ambiguity, their processing is associated to qualitatively different processes. Verifying true statements activates the left inferior parietal cortex and the caudate nucleus, a neural correlate compatible with an extended search and matching process for particular stored information. In contrast, verifying false statements activates the fronto-polar cortex and is compatible with a reasoning process of finding and evaluating a contradiction between the sentence information and stored knowledge.

Structural Genomics: Correlation Blocks, Population Structure, and Genome Architecture

PubMed Central

Hu, Xin-Sheng; Yeh, Francis C.; Wang, Zhiquan

2011-01-01

An integration of the pattern of genome-wide inter-site associations with evolutionary forces is important for gaining insights into the genomic evolution in natural or artificial populations. Here, we assess the inter-site correlation blocks and their distributions along chromosomes. A correlation block is broadly termed as the DNA segment within which strong correlations exist between genetic diversities at any two sites. We bring together the population genetic structure and the genomic diversity structure that have been independently built on different scales and synthesize the existing theories and methods for characterizing genomic structure at the population level. We discuss how population structure could shape correlation blocks and their patterns within and between populations. Effects of evolutionary forces (selection, migration, genetic drift, and mutation) on the pattern of genome-wide correlation blocks are discussed. In eukaryote organisms, we briefly discuss the associations between the pattern of correlation blocks and genome assembly features in eukaryote organisms, including the impacts of multigene family, the perturbation of transposable elements, and the repetitive nongenic sequences and GC-rich isochores. Our reviews suggest that the observable pattern of correlation blocks can refine our understanding of the ecological and evolutionary processes underlying the genomic evolution at the population level. PMID:21886455

Discrimination of speech stimuli based on neuronal response phase patterns depends on acoustics but not comprehension.

PubMed

Howard, Mary F; Poeppel, David

2010-11-01

Speech stimuli give rise to neural activity in the listener that can be observed as waveforms using magnetoencephalography. Although waveforms vary greatly from trial to trial due to activity unrelated to the stimulus, it has been demonstrated that spoken sentences can be discriminated based on theta-band (3-7 Hz) phase patterns in single-trial response waveforms. Furthermore, manipulations of the speech signal envelope and fine structure that reduced intelligibility were found to produce correlated reductions in discrimination performance, suggesting a relationship between theta-band phase patterns and speech comprehension. This study investigates the nature of this relationship, hypothesizing that theta-band phase patterns primarily reflect cortical processing of low-frequency (<40 Hz) modulations present in the acoustic signal and required for intelligibility, rather than processing exclusively related to comprehension (e.g., lexical, syntactic, semantic). Using stimuli that are quite similar to normal spoken sentences in terms of low-frequency modulation characteristics but are unintelligible (i.e., their time-inverted counterparts), we find that discrimination performance based on theta-band phase patterns is equal for both types of stimuli. Consistent with earlier findings, we also observe that whereas theta-band phase patterns differ across stimuli, power patterns do not. We use a simulation model of the single-trial response to spoken sentence stimuli to demonstrate that phase-locked responses to low-frequency modulations of the acoustic signal can account not only for the phase but also for the power results. The simulation offers insight into the interpretation of the empirical results with respect to phase-resetting and power-enhancement models of the evoked response.

Word Naming in the L1 and L2: A Dynamic Perspective on Automatization and the Degree of Semantic Involvement in Naming.

PubMed

Plat, Rika; Lowie, Wander; de Bot, Kees

2017-01-01

Reaction time data have long been collected in order to gain insight into the underlying mechanisms involved in language processing. Means analyses often attempt to break down what factors relate to what portion of the total reaction time. From a dynamic systems theory perspective or an interaction dominant view of language processing, it is impossible to isolate discrete factors contributing to language processing, since these continually and interactively play a role. Non-linear analyses offer the tools to investigate the underlying process of language use in time, without having to isolate discrete factors. Patterns of variability in reaction time data may disclose the relative contribution of automatic (grapheme-to-phoneme conversion) processing and attention-demanding (semantic) processing. The presence of a fractal structure in the variability of a reaction time series indicates automaticity in the mental structures contributing to a task. A decorrelated pattern of variability will indicate a higher degree of attention-demanding processing. A focus on variability patterns allows us to examine the relative contribution of automatic and attention-demanding processing when a speaker is using the mother tongue (L1) or a second language (L2). A word naming task conducted in the L1 (Dutch) and L2 (English) shows L1 word processing to rely more on automatic spelling-to-sound conversion than L2 word processing. A word naming task with a semantic categorization subtask showed more reliance on attention-demanding semantic processing when using the L2. A comparison to L1 English data shows this was not only due to the amount of language use or language dominance, but also to the difference in orthographic depth between Dutch and English. An important implication of this finding is that when the same task is used to test and compare different languages, one cannot straightforwardly assume the same cognitive sub processes are involved to an equal degree using the same task in different languages.

Multiple filters affect tree species assembly in mid-latitude forest communities.

PubMed

Kubota, Y; Kusumoto, B; Shiono, T; Ulrich, W

2018-05-01

Species assembly patterns of local communities are shaped by the balance between multiple abiotic/biotic filters and dispersal that both select individuals from species pools at the regional scale. Knowledge regarding functional assembly can provide insight into the relative importance of the deterministic and stochastic processes that shape species assembly. We evaluated the hierarchical roles of the α niche and β niches by analyzing the influence of environmental filtering relative to functional traits on geographical patterns of tree species assembly in mid-latitude forests. Using forest plot datasets, we examined the α niche traits (leaf and wood traits) and β niche properties (cold/drought tolerance) of tree species, and tested non-randomness (clustering/over-dispersion) of trait assembly based on null models that assumed two types of species pools related to biogeographical regions. For most plots, species assembly patterns fell within the range of random expectation. However, particularly for cold/drought tolerance-related β niche properties, deviation from randomness was frequently found; non-random clustering was predominant in higher latitudes with harsh climates. Our findings demonstrate that both randomness and non-randomness in trait assembly emerged as a result of the α and β niches, although we suggest the potential role of dispersal processes and/or species equalization through trait similarities in generating the prevalence of randomness. Clustering of β niche traits along latitudinal climatic gradients provides clear evidence of species sorting by filtering particular traits. Our results reveal that multiple filters through functional niches and stochastic processes jointly shape geographical patterns of species assembly across mid-latitude forests.

Scale dependence in species turnover reflects variance in species occupancy.

PubMed

McGlinn, Daniel J; Hurlbert, Allen H

2012-02-01

Patterns of species turnover may reflect the processes driving community dynamics across scales. While the majority of studies on species turnover have examined pairwise comparison metrics (e.g., the average Jaccard dissimilarity), it has been proposed that the species-area relationship (SAR) also offers insight into patterns of species turnover because these two patterns may be analytically linked. However, these previous links only apply in a special case where turnover is scale invariant, and we demonstrate across three different plant communities that over 90% of the pairwise turnover values are larger than expected based on scale-invariant predictions from the SAR. Furthermore, the degree of scale dependence in turnover was negatively related to the degree of variance in the occupancy frequency distribution (OFD). These findings suggest that species turnover diverges from scale invariance, and as such pairwise turnover and the slope of the SAR are not redundant. Furthermore, models developed to explain the OFD should be linked with those developed to explain species turnover to achieve a more unified understanding of community structure.

High-resolution Temporal Representations of Alcohol and Tobacco Behaviors from Social Media Data

PubMed Central

Huang, Tom; Elghafari, Anas; Relia, Kunal; Chunara, Rumi

2017-01-01

Understanding tobacco- and alcohol-related behavioral patterns is critical for uncovering risk factors and potentially designing targeted social computing intervention systems. Given that we make choices multiple times per day, hourly and daily patterns are critical for better understanding behaviors. Here, we combine natural language processing, machine learning and time series analyses to assess Twitter activity specifically related to alcohol and tobacco consumption and their sub-daily, daily and weekly cycles. Twitter self-reports of alcohol and tobacco use are compared to other data streams available at similar temporal resolution. We assess if discussion of drinking by inferred underage versus legal age people or discussion of use of different types of tobacco products can be differentiated using these temporal patterns. We find that time and frequency domain representations of behaviors on social media can provide meaningful and unique insights, and we discuss the types of behaviors for which the approach may be most useful. PMID:29264592

The Role of Genetic Drift in Shaping Modern Human Cranial Evolution: A Test Using Microevolutionary Modeling

PubMed Central

Smith, Heather F.

2011-01-01

The means by which various microevolutionary processes have acted in the past to produce patterns of cranial variation that characterize modern humans is not thoroughly understood. Applying a microevolutionary framework, within- and among-population variance/covariance (V/CV) structure was compared for several functional and developmental modules of the skull across a worldwide sample of modern humans. V/CV patterns in the basicranium, temporal bone, and face are proportional within and among groups, which is consistent with a hypothesis of neutral evolution; however, mandibular morphology deviated from this pattern. Degree of intergroup similarity in facial, temporal bone, and mandibular morphology is significantly correlated with geographic distance; however, much of the variance remains unexplained. These findings provide insight into the evolutionary history of modern human cranial variation by identifying signatures of genetic drift, gene flow, and migration and set the stage for inferences regarding selective pressures that early humans encountered since their initial migrations around the world. PMID:21461369

Tree species exhibit complex patterns of distribution in bottomland hardwood forests

Treesearch

Luben D Dimov; Jim L Chambers; Brian R. Lockhart

2013-01-01

& Context Understanding tree interactions requires an insight into their spatial distribution. & Aims We looked for presence and extent of tree intraspecific spatial point pattern (random, aggregated, or overdispersed) and interspecific spatial point pattern (independent, aggregated, or segregated). & Methods We established twelve 0.64-ha plots in natural...

A dynamical system perspective to understanding badminton singles game play.

PubMed

Chow, Jia Yi; Seifert, Ludovic; Hérault, Romain; Chia, Shannon Jing Yi; Lee, Miriam Chang Yi

2014-02-01

By altering the task constraints of cooperative and competitive game contexts in badminton, insights can be obtained from a dynamical systems perspective to investigate the underlying processes that results in either a gradual shift or transition of playing patterns. Positional data of three pairs of skilled female badminton players (average age 20.5±1.38years) were captured and analyzed. Local correlation coefficient, which provides information on the relationship of players' displacement data, between each pair of players was computed for angle and distance from base position. Speed scalar product was in turn established from speed vectors of the players. The results revealed two patterns of playing behaviors (i.e., in-phase and anti-phase patterns) for movement displacement. Anti-phase relation was the dominant coupling pattern for speed scalar relationships among the pairs of players. Speed scalar product, as a collective variable, was different between cooperative and competitive plays with a greater variability in amplitude seen in competitive plays leading to a winning point. The findings from this study provide evidence for increasing stroke variability to perturb existing stable patterns of play and highlights the potential for speed scalar product to be a collective variable to distinguish different patterns of play (e.g., cooperative and competitive). Copyright © 2013 Elsevier B.V. All rights reserved.

Pathogenesis of vocal fold nodules: new insights from a modelling approach.

PubMed

Dejonckere, Philippe H; Kob, Malte

2009-01-01

To give new insights into the pathogenesis of vocal fold nodules: (a) why the female/male ratio is so extreme, (b) how an hourglass-shaped vibration pattern - eliciting a localized microtrauma - originates, and (c) what the roles of muscular tension imbalance and of behavioral aspects are. Simulations with a 3-dimensional computer model of the vibrating vocal folds. (1) A slightly incomplete dorsal vocal fold adduction is a first condition for inducing an hourglass vibration pattern. (2) A limited collision zone is only possible with a small degree of curving of the rest position of the vocal fold edges in their ventral portion. This is an anatomical characteristic of the adult female larynx. Muscular fatigue and resulting hypotonia seem to enhance this curving. (3) If both these conditions are fulfilled, a sufficient vibration amplitude is required to achieve a localized impact. (4) This third condition can be obtained by an increased subglottal pressure and/or by a decrease in active stress of the tension forces between the neighboring vocalis masses. These last aspects incorporate muscular tension imbalance (dyskinesia) and behavioral aspects in the modelling process. Decrease in active stress is a possible effect of fatigue, and increase in subglottal pressure a result of effort compensation. Copyright 2009 S. Karger AG, Basel.

Beyond modern landscape features: New insights in the archaeological area of Tiwanaku in Bolivia from satellite data

NASA Astrophysics Data System (ADS)

Lasaponara, Rosa; Masini, Nicola

2014-02-01

The aim of this paper is to investigate the cultural landscape of the archaeological area of Tiwanaku (Bolivia) using multiscale, multispectral and multitemporal satellite data. Geospatial analysis techniques were applied to the satellite data sets in order to enhance and map traces of past human activities and perform a spatial characterization of environmental and cultural patterns. In particular, in the Tiwanaku area, the approach based on local indicators of spatial autocorrelation (LISA) applied to ASTER data allowed us to identify traces of a possible ancient hydrographic network with a clear spatial relation with the well-known moat surrounding the core of the monumental area. The same approach applied to QuickBird data, allowed us to identify numerous traces of archaeological interest, in Mollo Kontu mound, less investigated than the monumental area. Some of these traces were in perfect accordance with the results of independent studies, other were completely unknown. As a whole, the detected features, composing a geometric pattern with roughly North-South orientation, closely match those of the other residential contexts at Tiwanaku. These new insights, captured from ASTER and QuickBird data processing, suggested new questions on the ancient landscape and provided important information for planning future field surveys and archaeogeophyical investigations.

Comparative Analysis of Proteomes and Functionomes Provides Insights into Origins of Cellular Diversification

PubMed Central

Caetano-Anollés, Gustavo

2013-01-01

Reconstructing the evolutionary history of modern species is a difficult problem complicated by the conceptual and technical limitations of phylogenetic tree building methods. Here, we propose a comparative proteomic and functionomic inferential framework for genome evolution that allows resolving the tripartite division of cells and sketching their history. Evolutionary inferences were derived from the spread of conserved molecular features, such as molecular structures and functions, in the proteomes and functionomes of contemporary organisms. Patterns of use and reuse of these traits yielded significant insights into the origins of cellular diversification. Results uncovered an unprecedented strong evolutionary association between Bacteria and Eukarya while revealing marked evolutionary reductive tendencies in the archaeal genomic repertoires. The effects of nonvertical evolutionary processes (e.g., HGT, convergent evolution) were found to be limited while reductive evolution and molecular innovation appeared to be prevalent during the evolution of cells. Our study revealed a strong vertical trace in the history of proteins and associated molecular functions, which was reliably recovered using the comparative genomics approach. The trace supported the existence of a stem line of descent and the very early appearance of Archaea as a diversified superkingdom, but failed to uncover a hidden canonical pattern in which Bacteria was the first superkingdom to deploy superkingdom-specific structures and functions. PMID:24492748

Fluctuating asymmetry and developmental instability in evolutionary biology: past, present and future.

PubMed

Dongen, S V

2006-11-01

The role of developmental instability (DI), as measured by fluctuating asymmetry (FA), in evolutionary biology has been the focus of a wealth of research for more than half a century. In spite of this long period and many published papers, our current state of knowledge reviewed here only allows us to conclude that patterns are heterogeneous and that very little is known about the underlying causes of this heterogeneity. In addition, the statistical properties of FA as a measure of DI are only poorly grasped because of a general lack of understanding of the underlying mechanisms that drive DI. If we want to avoid that this area of research becomes abandoned, more efforts should be made to understand the observed heterogeneity, and attempts should be made to develop a unifying statistical protocol. More specifically, and perhaps most importantly, it is argued here that more attention should be paid to the usefulness of FA as a measure of DI since many factors might blur this relationship. Furthermore, the genetic architecture, associations with fitness and the importance of compensatory growth should be investigated under a variety of stress situations. In addition, more focus should be directed to the underlying mechanisms of DI as well as how these processes map to the observable phenotype. These insights could yield more efficient statistical models and a unified approach to the analysis of patterns in FA and DI. The study of both DI and canalization is indispensable to obtain better insights in their possible common origin, especially because both have been suggested to play a role in both micro- and macro-evolutionary processes.

Song hybridization events during revolutionary song change provide insights into cultural transmission in humpback whales

PubMed Central

Garland, Ellen C.; Rendell, Luke; Lamoni, Luca; Poole, M. Michael; Noad, Michael J.

2017-01-01

Cultural processes occur in a wide variety of animal taxa, from insects to cetaceans. The songs of humpback whales are one of the most striking examples of the transmission of a cultural trait and social learning in any nonhuman animal. To understand how songs are learned, we investigate rare cases of song hybridization, where parts of an existing song are spliced with a new one, likely before an individual totally adopts the new song. Song unit sequences were extracted from over 9,300 phrases recorded during two song revolutions across the South Pacific Ocean, allowing fine-scale analysis of composition and sequencing. In hybrid songs the current and new songs were spliced together in two specific ways: (i) singers placed a single hybrid phrase, in which content from both songs were combined, between the two song types when transitioning from one to the other, and/or (ii) singers spliced complete themes from the revolutionary song into the current song. Sequence analysis indicated that both processes were governed by structural similarity rules. Hybrid phrases or theme substitutions occurred at points in the songs where both songs contained “similar sounds arranged in a similar pattern.” Songs appear to be learned as segments (themes/phrase types), akin to birdsong and human language acquisition, and these can be combined in predictable ways if the underlying structural pattern is similar. These snapshots of song change provide insights into the mechanisms underlying song learning in humpback whales, and comparative perspectives on the evolution of human language and culture. PMID:28739940

Song hybridization events during revolutionary song change provide insights into cultural transmission in humpback whales.

PubMed

Garland, Ellen C; Rendell, Luke; Lamoni, Luca; Poole, M Michael; Noad, Michael J

2017-07-24

Cultural processes occur in a wide variety of animal taxa, from insects to cetaceans. The songs of humpback whales are one of the most striking examples of the transmission of a cultural trait and social learning in any nonhuman animal. To understand how songs are learned, we investigate rare cases of song hybridization, where parts of an existing song are spliced with a new one, likely before an individual totally adopts the new song. Song unit sequences were extracted from over 9,300 phrases recorded during two song revolutions across the South Pacific Ocean, allowing fine-scale analysis of composition and sequencing. In hybrid songs the current and new songs were spliced together in two specific ways: ( i ) singers placed a single hybrid phrase, in which content from both songs were combined, between the two song types when transitioning from one to the other, and/or ( ii ) singers spliced complete themes from the revolutionary song into the current song. Sequence analysis indicated that both processes were governed by structural similarity rules. Hybrid phrases or theme substitutions occurred at points in the songs where both songs contained "similar sounds arranged in a similar pattern." Songs appear to be learned as segments (themes/phrase types), akin to birdsong and human language acquisition, and these can be combined in predictable ways if the underlying structural pattern is similar. These snapshots of song change provide insights into the mechanisms underlying song learning in humpback whales, and comparative perspectives on the evolution of human language and culture.

Expression of Geochemical Controls on Water Quality in Loch Vale, Rocky Mountain National Park

NASA Astrophysics Data System (ADS)

Podzorski, H.; Navarre-Sitchler, A.; Stets, E.; Clow, D. W.

2017-12-01

Relationships between concentrations of rock weathering products and discharge provide insight into the interactions between climate and solute dynamics. This concentration-discharge (C-Q) relationship is especially interesting in high alpine regions, due to their susceptibility to changes in the timing and magnitude of snowmelt. Previous studies looking at C-Q relationships have concluded that concentrations of conservative solutes remain relatively constant as discharge varies; however, these results may be due to relatively small sample sizes, especially at higher discharge values. Using water chemistry data collected regularly by the U.S. Geological Survey from Loch Vale, a high-elevation catchment in Rocky Mountain National Park, C-Q relationships were examined to determine possible geochemical controls on stream solute concentrations. A record of over 20 years of C-Q data resulted in a pattern that shows little variation in conservative solute concentrations during base flow and larger variations in concentrations around peak discharge. This observed pattern is consistent with accumulation of solutes in pore water during base flow, which are then flushed out and diluted by snowmelt. Further evidence of this flushing out mechanism is found in patterns of hysteresis that are present in annual C-Q relationships. Before peak discharge, concentrations of weathering products are higher than after peak discharge at similar values of discharge. Based on these observations, we hypothesize that the geochemical processes controlling stream chemistry vary by season. During the winter, solute concentrations are transport-limited due to slow subsurface flushing resulting in concentrations that are effectively constant and close to equilibrium. During the spring and summer, concentrations drop sharply after peak discharge due to a combination of dilution and reaction-limited processes under conditions with faster subsurface flow and continued snowmelt. This study provides insight into seasonal geochemical controls on conservative solute concentrations that can be overlooked with small, or seasonally biased, data sets.

Underwater microscopy for in situ studies of benthic ecosystems

NASA Astrophysics Data System (ADS)

Mullen, Andrew D.; Treibitz, Tali; Roberts, Paul L. D.; Kelly, Emily L. A.; Horwitz, Rael; Smith, Jennifer E.; Jaffe, Jules S.

2016-07-01

Microscopic-scale processes significantly influence benthic marine ecosystems such as coral reefs and kelp forests. Due to the ocean's complex and dynamic nature, it is most informative to study these processes in the natural environment yet it is inherently difficult. Here we present a system capable of non-invasively imaging seafloor environments and organisms in situ at nearly micrometre resolution. We overcome the challenges of underwater microscopy through the use of a long working distance microscopic objective, an electrically tunable lens and focused reflectance illumination. The diver-deployed instrument permits studies of both spatial and temporal processes such as the algal colonization and overgrowth of bleaching corals, as well as coral polyp behaviour and interspecific competition. By enabling in situ observations at previously unattainable scales, this instrument can provide important new insights into micro-scale processes in benthic ecosystems that shape observed patterns at much larger scales.

Confirming and denying in co-construction processes: a case study of an adult with cerebral palsy and two familiar partners.

PubMed

Hörmeyer, Ina; Renner, Gregor

2013-09-01

For individuals with complex communication needs, one of the most frequent communicative strategies is the co-construction of meaning with familiar partners. This preliminary single-case study gives insight into a special sequential pattern of co-construction processes - the search sequence - particularly in relation to the processes of confirming and denying meanings proposed by familiar interaction partners. Five different conversations between an adult with cerebral palsy and complex communication needs and two familiar co-participants were videotaped and analyzed using the methodology of conversation analysis (CA). The study revealed that confirmations and denials are not simply two alternative actions, but that several possibilities to realize confirmations and denials exist that differ in their frequency and that have different consequences for the sequential context. This study of confirmations and denials demonstrates that co-construction processes are more complex than have previously been documented.

Medication Overuse Headache: Pathophysiological Insights from Structural and Functional Brain MRI Research.

PubMed

Schwedt, Todd J; Chong, Catherine D

2017-07-01

Research imaging of brain structure and function has helped to elucidate the pathophysiology of medication overuse headache (MOH). This is a narrative review of imaging research studies that have investigated brain structural and functional alterations associated with MOH. Studies included in this review have investigated abnormal structure and function of pain processing regions in people with MOH, functional patterns that might predispose individuals to development of MOH, similarity of brain functional patterns in patients with MOH to those found in people with addiction, brain structure that could predict headache improvement following discontinuation of the overused medication, and changes in brain structure and function after discontinuation of medication overuse. MOH is associated with atypical structure and function of brain regions responsible for pain processing as well as brain regions that are commonly implicated in addiction. Several studies have shown "normalization" of structure and function in pain processing regions following discontinuation of the overused medication and resolution of MOH. However, some of the abnormalities in regions also implicated in addiction tend to persist following discontinuation of the overused medication, suggesting that they are a brain trait that predisposes certain individuals to medication overuse and MOH. © 2017 American Headache Society.

The effects of gender and self-insight on early semantic processing.

PubMed

Xu, Xu; Kang, Chunyan; Guo, Taomei

2014-01-01

This event-related potential (ERP) study explored individual differences associated with gender and level of self-insight in early semantic processing. Forty-eight Chinese native speakers completed a semantic judgment task with three different categories of words: abstract neutral words (e.g., logic, effect), concrete neutral words (e.g., teapot, table), and emotion words (e.g., despair, guilt). They then assessed their levels of self-insight. Results showed that women engaged in greater processing than did men. Gender differences also manifested in the relationship between level of self-insight and word processing. For women, level of self-insight was associated with level of semantic activation for emotion words and abstract neutral words, but not for concrete neutral words. For men, level of self-insight was related to processing speed, particularly in response to abstract and concrete neutral words. These findings provide electrophysiological evidence for the effects of gender and self-insight on semantic processing and highlight the need to take into consideration subject variables in related research.

Protein phosphorylation in plant immunity: insights into the regulation of pattern recognition receptor-mediated signaling

PubMed Central

Park, Chang-Jin; Caddell, Daniel F.; Ronald, Pamela C.

2012-01-01

Plants are continuously challenged by pathogens including viruses, bacteria, and fungi. The plant immune system recognizes invading pathogens and responds by activating an immune response. These responses occur rapidly and often involve post-translational modifications (PTMs) within the proteome. Protein phosphorylation is a common and intensively studied form of these PTMs and regulates many plant processes including plant growth, development, and immunity. Most well-characterized pattern recognition receptors (PRRs), including Xanthomonas resistance 21, flagellin sensitive 2, and elongation factor-Tu receptor, possess intrinsic protein kinase activity and regulate downstream signaling through phosphorylation events. Here, we focus on the phosphorylation events of plant PRRs that play important roles in the immune response. We also discuss the role of phosphorylation in regulating mitogen-associated protein kinase cascades and transcription factors in plant immune signaling. PMID:22876255

Three-Dimensional Analysis of Spiny Dendrites Using Straightening and Unrolling Transforms

PubMed Central

Morales, Juan; Benavides-Piccione, Ruth; Pastor, Luis; Yuste, Rafael; DeFelipe, Javier

2014-01-01

Current understanding of the synaptic organization of the brain depends to a large extent on knowledge about the synaptic inputs to the neurons. Indeed, the dendritic surfaces of pyramidal cells (the most common neuron in the cerebral cortex) are covered by thin protrusions named dendritic spines. These represent the targets of most excitatory synapses in the cerebral cortex and therefore, dendritic spines prove critical in learning, memory and cognition. This paper presents a new method that facilitates the analysis of the 3D structure of spine insertions in dendrites, providing insight on spine distribution patterns. This method is based both on the implementation of straightening and unrolling transformations to move the analysis process to a planar, unfolded arrangement, and on the design of DISPINE, an interactive environment that supports the visual analysis of 3D patterns. PMID:22644869

Turing mechanism underlying a branching model for lung morphogenesis.

PubMed

Xu, Hui; Sun, Mingzhu; Zhao, Xin

2017-01-01

The mammalian lung develops through branching morphogenesis. Two primary forms of branching, which occur in order, in the lung have been identified: tip bifurcation and side branching. However, the mechanisms of lung branching morphogenesis remain to be explored. In our previous study, a biological mechanism was presented for lung branching pattern formation through a branching model. Here, we provide a mathematical mechanism underlying the branching patterns. By decoupling the branching model, we demonstrated the existence of Turing instability. We performed Turing instability analysis to reveal the mathematical mechanism of the branching patterns. Our simulation results show that the Turing patterns underlying the branching patterns are spot patterns that exhibit high local morphogen concentration. The high local morphogen concentration induces the growth of branching. Furthermore, we found that the sparse spot patterns underlie the tip bifurcation patterns, while the dense spot patterns underlies the side branching patterns. The dispersion relation analysis shows that the Turing wavelength affects the branching structure. As the wavelength decreases, the spot patterns change from sparse to dense, the rate of tip bifurcation decreases and side branching eventually occurs instead. In the process of transformation, there may exists hybrid branching that mixes tip bifurcation and side branching. Since experimental studies have reported that branching mode switching from side branching to tip bifurcation in the lung is under genetic control, our simulation results suggest that genes control the switch of the branching mode by regulating the Turing wavelength. Our results provide a novel insight into and understanding of the formation of branching patterns in the lung and other biological systems.

Patterns of genetic variability and habitat occupancy in Crepis triasii (Asteraceae) at different spatial scales: insights on evolutionary processes leading to diversification in continental islands

PubMed Central

Mayol, Maria; Palau, Carles; Rosselló, Josep A.; González-Martínez, Santiago C.; Molins, Arántzazu; Riba, Miquel

2012-01-01

Background and Aims Archipelagos are unique systems for studying evolutionary processes promoting diversification and speciation. The islands of the Mediterranean basin are major areas of plant richness, including a high proportion of narrow endemics. Many endemic plants are currently found in rocky habitats, showing varying patterns of habitat occupancy at different spatial scales throughout their range. The aim of the present study was to understand the impact of varying patterns of population distribution on genetic diversity and structure to shed light on demographic and evolutionary processes leading to population diversification in Crepis triasii, an endemic plant from the eastern Balearic Islands. Methods Using allozyme and chloroplast markers, we related patterns of genetic structure and diversity to those of habitat occupancy at a regional (between islands and among populations within islands) and landscape (population size and connectivity) scale. Key Results Genetic diversity was highly structured both at the regional and at the landscape level, and was positively correlated with population connectivity in the landscape. Populations located in small isolated mountains and coastal areas, with restricted patterns of regional occupancy, were genetically less diverse and much more differentiated. In addition, more isolated populations had stronger fine-scale genetic structure than well-connected ones. Changes in habitat availability and quality arising from marine transgressions during the Quaternary, as well as progressive fragmentation associated with the aridification of the climate since the last glaciation, are the most plausible factors leading to the observed patterns of genetic diversity and structure. Conclusions Our results emphasize the importance of gene flow in preventing genetic erosion and maintaining the evolutionary potential of populations. They also agree with recent studies highlighting the importance of restricted gene flow and genetic drift as drivers of plant evolution in Mediterranean continental islands. PMID:22167790

Flower development: open questions and future directions.

PubMed

Wellmer, Frank; Bowman, John L; Davies, Brendan; Ferrándiz, Cristina; Fletcher, Jennifer C; Franks, Robert G; Graciet, Emmanuelle; Gregis, Veronica; Ito, Toshiro; Jack, Thomas P; Jiao, Yuling; Kater, Martin M; Ma, Hong; Meyerowitz, Elliot M; Prunet, Nathanaël; Riechmann, José Luis

2014-01-01

Almost three decades of genetic and molecular analyses have resulted in detailed insights into many of the processes that take place during flower development and in the identification of a large number of key regulatory genes that control these processes. Despite this impressive progress, many questions about how flower development is controlled in different angiosperm species remain unanswered. In this chapter, we discuss some of these open questions and the experimental strategies with which they could be addressed. Specifically, we focus on the areas of floral meristem development and patterning, floral organ specification and differentiation, as well as on the molecular mechanisms underlying the evolutionary changes that have led to the astounding variations in flower size and architecture among extant and extinct angiosperms.

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

PubMed

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

2001-01-01

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

Unraveling the insight paradox: One-year longitudinal study on the relationships between insight, self-stigma, and life satisfaction among people with schizophrenia spectrum disorders.

PubMed

Chio, Floria H N; Mak, Winnie W S; Chan, Randolph C H; Tong, Alan C Y

2018-01-30

The promotion of insight among people with schizophrenia spectrum disorders has posed a dilemma to service providers as higher insight has been linked to positive clinical outcomes but negative psychological outcomes. The negative meaning that people attached to the illness (self-stigma content) and the recurrence of such stigmatizing thoughts (self-stigma process) may explain why increased insight is associated with negative outcomes. The present study examined how the presence of high self-stigma content and self-stigma process may contribute to the negative association between insight and life satisfaction. A total of 181 people with schizophrenia spectrum disorders were assessed at baseline. 130 and 110 participants were retained and completed questionnaire at 6-month and 1-year follow-up, respectively. Results showed that baseline insight was associated with lower life satisfaction at 6-month when self-stigma process or self-stigma content was high. Furthermore, baseline insight was predictive of better life satisfaction at 1-year follow-up when self-stigma process was low. Findings suggested that the detrimental effects of insight can be a result from both the presence of cognitive content and habitual process of self-stigma. Future insight promotion interventions should also address self-stigma content and process among people with schizophrenia spectrum disorders so as to maximize the beneficial effects of insight. Copyright © 2018 Elsevier B.V. All rights reserved.

Pre-Service Elementary Teachers' Understanding of Pattern and Function

ERIC Educational Resources Information Center

Sharon, Valerie Vinyard

2010-01-01

Scope and method of study: The purpose of this study was to unpack the understandings pre-service elementary teachers have pertaining to the ideas of pattern and function. The intent was to bring insight into how mathematics teacher educators can use patterning activities to prepare pre-service elementary teachers to support the development of…

Regulation of Facial Morphogenesis by Endothelin Signaling: Insights from Mice and Fish

PubMed Central

Clouthier, David E.; Garcia, Elvin; Schilling, Thomas F.

2010-01-01

Craniofacial morphogenesis is accomplished through a complex set of developmental events, most of which are initiated in neural crest cells within the pharyngeal arches. Local patterning cues from the surrounding environment induce gene expression within neural crest cells, leading to formation of a diverse set of skeletal elements. Endothelin-1 (Edn1) is one of the primary signals that establish the identities of neural crest cells within the mandibular portion of the first pharyngeal arch. Signaling through its cognate receptor, the endothelin-A receptor, is critical for patterning the ventral/distal portion of the arch (lower jaw) and also participates with Hox genes in patterning more posterior arches. Edn1/Ednra signaling is highly conserved between mouse and zebrafish, and genetic analyses in these two species have provided complementary insights into the patterning cues responsible for establishing the craniofacial complex as well as the genetic basis of facial birth defect syndromes. PMID:20684004

Modeling and flow analysis of pure nylon polymer for injection molding process

NASA Astrophysics Data System (ADS)

Nuruzzaman, D. M.; Kusaseh, N.; Basri, S.; Oumer, A. N.; Hamedon, Z.

2016-02-01

In the production of complex plastic parts, injection molding is one of the most popular industrial processes. This paper addresses the modeling and analysis of the flow process of the nylon (polyamide) polymer for injection molding process. To determine the best molding conditions, a series of simulations are carried out using Autodesk Moldflow Insight software and the processing parameters are adjusted. This mold filling commercial software simulates the cavity filling pattern along with temperature and pressure distributions in the mold cavity. In the modeling, during the plastics flow inside the mold cavity, different flow parameters such as fill time, pressure, temperature, shear rate and warp at different locations in the cavity are analyzed. Overall, this Moldflow is able to perform a relatively sophisticated analysis of the flow process of pure nylon. Thus the prediction of the filling of a mold cavity is very important and it becomes useful before a nylon plastic part to be manufactured.

Glycoconjugate distribution in early human notochord and axial mesenchyme.

PubMed

Götz, W; Quondamatteo, F

2001-02-01

Glycosylation patterns of cells and tissues give insights into spatially and temporally regulated developmental processes and can be detected histochemically using plant lectins with specific affinities for sugar moieties. The early development of the vertebral column in man is a process which has never been investigated by lectin histochemistry. Therefore, we studied binding of several lectins (AIA, Con A, GSA II, LFA, LTA, PNA, RCA I, SBA, SNA, WGA) in formaldehyde-fixed sections of the axial mesenchyme of 5 human embryos in Carnegie stages 12-15. During these developmental stages, an unsegmented mesenchyme covers the notochord. Staining patterns did not show striking temporal variations except for SBA which stained the cranial axial mesenchyme only in the early stage 12 embryo and for PNA, of which the staining intensity in the mesenchyme decreased with age. The notochord appeared as a highly glycosylated tissue. Carbohydrates detected may correspond to adhesion molecules or to secreted substances like proteoglycans or proteins which could play an inductive role, for example, for the neural tube. The axial perinotochordal unsegmented mesenchyme showed strong PNA binding. Therefore, its function as a PNA-positive "barrier" tissue is discussed. The endoderm of the primitive gut showed a lectin-binding pattern that was similar to that of the notochord, which may correlate with interactions between these tissues during earlier developmental stages.

Unity and diversity of executive functions: Individual differences as a window on cognitive structure.

PubMed

Friedman, Naomi P; Miyake, Akira

2017-01-01

Executive functions (EFs) are high-level cognitive processes, often associated with the frontal lobes, that control lower level processes in the service of goal-directed behavior. They include abilities such as response inhibition, interference control, working memory updating, and set shifting. EFs show a general pattern of shared but distinct functions, a pattern described as "unity and diversity". We review studies of EF unity and diversity at the behavioral and genetic levels, focusing on studies of normal individual differences and what they reveal about the functional organization of these cognitive abilities. In particular, we review evidence that across multiple ages and populations, commonly studied EFs (a) are robustly correlated but separable when measured with latent variables; (b) are not the same as general intelligence or g; (c) are highly heritable at the latent level and seemingly also highly polygenic; and (d) activate both common and specific neural areas and can be linked to individual differences in neural activation, volume, and connectivity. We highlight how considering individual differences at the behavioral and neural levels can add considerable insight to the investigation of the functional organization of the brain, and conclude with some key points about individual differences to consider when interpreting neuropsychological patterns of dissociation. Copyright © 2016 Elsevier Ltd. All rights reserved.

Rett syndrome: basic features of visual processing-a pilot study of eye-tracking.

PubMed

Djukic, Aleksandra; Valicenti McDermott, Maria; Mavrommatis, Kathleen; Martins, Cristina L

2012-07-01

Consistently observed "strong eye gaze" has not been validated as a means of communication in girls with Rett syndrome, ubiquitously affected by apraxia, unable to reply either verbally or manually to questions during formal psychologic assessment. We examined nonverbal cognitive abilities and basic features of visual processing (visual discrimination attention/memory) by analyzing patterns of visual fixation in 44 girls with Rett syndrome, compared with typical control subjects. To determine features of visual fixation patterns, multiple pictures (with the location of the salient and presence/absence of novel stimuli as variables) were presented on the screen of a TS120 eye-tracker. Of the 44, 35 (80%) calibrated and exhibited meaningful patterns of visual fixation. They looked longer at salient stimuli (cartoon, 2.8 ± 2 seconds S.D., vs shape, 0.9 ± 1.2 seconds S.D.; P = 0.02), regardless of their position on the screen. They recognized novel stimuli, decreasing the fixation time on the central image when another image appeared on the periphery of the slide (2.7 ± 1 seconds S.D. vs 1.8 ± 1 seconds S.D., P = 0.002). Eye-tracking provides a feasible method for cognitive assessment and new insights into the "hidden" abilities of individuals with Rett syndrome. Copyright © 2012 Elsevier Inc. All rights reserved.

Dietary patterns, food groups and telomere length: a systematic review of current studies.

PubMed

Rafie, N; Golpour Hamedani, S; Barak, F; Safavi, S M; Miraghajani, M

2017-02-01

Telomere length (TL) is recognized as a biomarker of aging and shorter telomeres are linked with shorter lifespan. Inter-individual variability in telomere length is highly heritable. However, there has been a resurgence of interest in the controversial relationship between diet and TL. Evaluating the impact of diet at the food group and dietary pattern level will provide greater insight into the effect of diet on TL dynamics, which are of significant importance in health and longevity. This article reports the first systematic review of the relation between food groups, dietary patterns and TL in human populations based on PRISMA guidelines. PubMed, Science Direct, The Cochrane Library and Google Scholar databases were electronically searched for all relevant studies, up to November 2015. Among the 17 included studies, 3 and 10 of them were regarding the effect of dietary patterns and various food groups on TL, respectively. Also, in 4 studies, both dietary patterns and different food groups were assessed in relation to TL. Mediterranean dietary pattern was related to longer TL in 3 studies. Five studies indicated beneficial effect of fruits or vegetables on TL. In 7 studies, a reverse association between TL and intake of cereals, processed meat, and fats and oils was reported. Our systematic review supports the health benefits of adherence to Mediterranean diet on TL. Except for the fruits and vegetables, which showed positive association with TL, results were inconsistent for other dietary factors. Also, certain food categories including processed meat, cereals and sugar-sweetened beverages may be associated with shorter TLs. However, additional epidemiological evidence and clinical trials should be considered in future research in order to develop firm conclusions in this regard.

More than one way to see it: Individual heuristics in avian visual computation.

PubMed

Ravignani, Andrea; Westphal-Fitch, Gesche; Aust, Ulrike; Schlumpp, Martin M; Fitch, W Tecumseh

2015-10-01

Comparative pattern learning experiments investigate how different species find regularities in sensory input, providing insights into cognitive processing in humans and other animals. Past research has focused either on one species' ability to process pattern classes or different species' performance in recognizing the same pattern, with little attention to individual and species-specific heuristics and decision strategies. We trained and tested two bird species, pigeons (Columba livia) and kea (Nestor notabilis, a parrot species), on visual patterns using touch-screen technology. Patterns were composed of several abstract elements and had varying degrees of structural complexity. We developed a model selection paradigm, based on regular expressions, that allowed us to reconstruct the specific decision strategies and cognitive heuristics adopted by a given individual in our task. Individual birds showed considerable differences in the number, type and heterogeneity of heuristic strategies adopted. Birds' choices also exhibited consistent species-level differences. Kea adopted effective heuristic strategies, based on matching learned bigrams to stimulus edges. Individual pigeons, in contrast, adopted an idiosyncratic mix of strategies that included local transition probabilities and global string similarity. Although performance was above chance and quite high for kea, no individual of either species provided clear evidence of learning exactly the rule used to generate the training stimuli. Our results show that similar behavioral outcomes can be achieved using dramatically different strategies and highlight the dangers of combining multiple individuals in a group analysis. These findings, and our general approach, have implications for the design of future pattern learning experiments, and the interpretation of comparative cognition research more generally. Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.

Relationships of Leaf Net Photosynthesis, Stomatal Conductance, and Mesophyll Conductance to Primary Metabolism: A Multispecies Meta-Analysis Approach1

PubMed Central

Gago, Jorge; Daloso, Danilo de Menezes; Flexas, Jaume; Fernie, Alisdair Robert

2016-01-01

Plant metabolism drives plant development and plant-environment responses, and data readouts from this cellular level could provide insights in the underlying molecular processes. Existing studies have already related key in vivo leaf gas-exchange parameters with structural traits and nutrient components across multiple species. However, insights in the relationships of leaf gas-exchange with leaf primary metabolism are still limited. We investigated these relationships through a multispecies meta-analysis approach based on data sets from 17 published studies describing net photosynthesis (A) and stomatal (gs) and mesophyll (gm) conductances, alongside the 53 data profiles from primary metabolism of 14 species grown in different experiments. Modeling results highlighted the conserved patterns between the different species. Consideration of species-specific effects increased the explanatory power of the models for some metabolites, including Glc-6-P, Fru-6-P, malate, fumarate, Xyl, and ribose. Significant relationships of A with sugars and phosphorylated intermediates were observed. While gs was related to sugars, organic acids, myo-inositol, and shikimate, gm showed a more complex pattern in comparison to the two other traits. Some metabolites, such as malate and Man, appeared in the models for both conductances, suggesting a metabolic coregulation between gs and gm. The resulting statistical models provide the first hints for coregulation patterns involving primary metabolism plus leaf water and carbon balances that are conserved across plant species, as well as species-specific trends that can be used to determine new biotechnological targets for crop improvement. PMID:26977088

Toward Automating HIV Identification: Machine Learning for Rapid Identification of HIV-Related Social Media Data.

PubMed

Young, Sean D; Yu, Wenchao; Wang, Wei

2017-02-01

"Social big data" from technologies such as social media, wearable devices, and online searches continue to grow and can be used as tools for HIV research. Although researchers can uncover patterns and insights associated with HIV trends and transmission, the review process is time consuming and resource intensive. Machine learning methods derived from computer science might be used to assist HIV domain experts by learning how to rapidly and accurately identify patterns associated with HIV from a large set of social data. Using an existing social media data set that was associated with HIV and coded by an HIV domain expert, we tested whether 4 commonly used machine learning methods could learn the patterns associated with HIV risk behavior. We used the 10-fold cross-validation method to examine the speed and accuracy of these models in applying that knowledge to detect HIV content in social media data. Logistic regression and random forest resulted in the highest accuracy in detecting HIV-related social data (85.3%), whereas the Ridge Regression Classifier resulted in the lowest accuracy. Logistic regression yielded the fastest processing time (16.98 seconds). Machine learning can enable social big data to become a new and important tool in HIV research, helping to create a new field of "digital HIV epidemiology." If a domain expert can identify patterns in social data associated with HIV risk or HIV transmission, machine learning models could quickly and accurately learn those associations and identify potential HIV patterns in large social data sets.

Waiting in the wings: what can we learn about gene co-option from the diversification of butterfly wing patterns?

PubMed

Jiggins, Chris D; Wallbank, Richard W R; Hanly, Joseph J

2017-02-05

A major challenge is to understand how conserved gene regulatory networks control the wonderful diversity of form that we see among animals and plants. Butterfly wing patterns are an excellent example of this diversity. Butterfly wings form as imaginal discs in the caterpillar and are constructed by a gene regulatory network, much of which is conserved across the holometabolous insects. Recent work in Heliconius butterflies takes advantage of genomic approaches and offers insights into how the diversification of wing patterns is overlaid onto this conserved network. WntA is a patterning morphogen that alters spatial information in the wing. Optix is a transcription factor that acts later in development to paint specific wing regions red. Both of these loci fit the paradigm of conserved protein-coding loci with diverse regulatory elements and developmental roles that have taken on novel derived functions in patterning wings. These discoveries offer insights into the 'Nymphalid Ground Plan', which offers a unifying hypothesis for pattern formation across nymphalid butterflies. These loci also represent 'hotspots' for morphological change that have been targeted repeatedly during evolution. Both convergent and divergent evolution of a great diversity of patterns is controlled by complex alleles at just a few genes. We suggest that evolutionary change has become focused on one or a few genetic loci for two reasons. First, pre-existing complex cis-regulatory loci that already interact with potentially relevant transcription factors are more likely to acquire novel functions in wing patterning. Second, the shape of wing regulatory networks may constrain evolutionary change to one or a few loci. Overall, genomic approaches that have identified wing patterning loci in these butterflies offer broad insight into how gene regulatory networks evolve to produce diversity.This article is part of the themed issue 'Evo-devo in the genomics era, and the origins of morphological diversity'. © 2016 The Author(s).

Waiting in the wings: what can we learn about gene co-option from the diversification of butterfly wing patterns?

PubMed Central

Wallbank, Richard W. R.; Hanly, Joseph J.

2017-01-01

A major challenge is to understand how conserved gene regulatory networks control the wonderful diversity of form that we see among animals and plants. Butterfly wing patterns are an excellent example of this diversity. Butterfly wings form as imaginal discs in the caterpillar and are constructed by a gene regulatory network, much of which is conserved across the holometabolous insects. Recent work in Heliconius butterflies takes advantage of genomic approaches and offers insights into how the diversification of wing patterns is overlaid onto this conserved network. WntA is a patterning morphogen that alters spatial information in the wing. Optix is a transcription factor that acts later in development to paint specific wing regions red. Both of these loci fit the paradigm of conserved protein-coding loci with diverse regulatory elements and developmental roles that have taken on novel derived functions in patterning wings. These discoveries offer insights into the ‘Nymphalid Ground Plan’, which offers a unifying hypothesis for pattern formation across nymphalid butterflies. These loci also represent ‘hotspots’ for morphological change that have been targeted repeatedly during evolution. Both convergent and divergent evolution of a great diversity of patterns is controlled by complex alleles at just a few genes. We suggest that evolutionary change has become focused on one or a few genetic loci for two reasons. First, pre-existing complex cis-regulatory loci that already interact with potentially relevant transcription factors are more likely to acquire novel functions in wing patterning. Second, the shape of wing regulatory networks may constrain evolutionary change to one or a few loci. Overall, genomic approaches that have identified wing patterning loci in these butterflies offer broad insight into how gene regulatory networks evolve to produce diversity. This article is part of the themed issue ‘Evo-devo in the genomics era, and the origins of morphological diversity’. PMID:27994126

Hedgehog signal transduction: key players, oncogenic drivers, and cancer therapy

PubMed Central

Pak, Ekaterina; Segal, Rosalind A.

2016-01-01

Summary The Hedgehog (Hh) signaling pathway governs complex developmental processes, including proliferation and patterning within diverse tissues. These activities rely on a tightly-regulated transduction system that converts graded Hh input signals into specific levels of pathway activity. Uncontrolled activation of Hh signaling drives tumor initiation and maintenance. However, recent entry of pathway-specific inhibitors into the clinic reveals mixed patient responses and thus prompts further exploration of pathway activation and inhibition. In this review, we share emerging insights on regulated and oncogenic Hh signaling, supplemented with updates on the development and use of Hh pathway-targeted therapies. PMID:27554855

Propafenone effects on the stable structures of Aβ16-22 system

NASA Astrophysics Data System (ADS)

Tran, Linh; Ngo, Son Tung; Nguyen, Minh Tho

2018-03-01

An extensive replica exchange molecular dynamics (REMD) simulation was performed to investigate the progress patterns of the molecular interactions of propafenone and Aβ16-22 system. Distinct conformational equilibrium of Aβ16-22 system with and without propafenone was analyzed in detail. Propafenone can act to prevent the Alzheimer's disease (AD) by significantly inhibiting Aβ oligomerization. Our calculated results provide insights into the inhibition mechanism of propafenone on the oligomerization process to form Aβ16-22 peptide aggregation. These findings are valuable for the development of therapeutic drugs in the AD early stage.

Comparative primate genomics: emerging patterns of genome content and dynamics

PubMed Central

Rogers, Jeffrey; Gibbs, Richard A.

2014-01-01

Preface Advances in genome sequencing technologies have created new opportunities for comparative primate genomics. Genome assemblies have been published for several primates, with analyses of several others underway. Whole genome assemblies for the great apes provide remarkable new information about the evolutionary origins of the human genome and the processes involved. Genomic data for macaques and other nonhuman primates provide valuable insight into genetic similarities and differences among species used as models for disease-related research. This review summarizes current knowledge regarding primate genome content and dynamics and offers a series of goals for the near future. PMID:24709753

The economics of project analysis: Optimal investment criteria and methods of study

NASA Technical Reports Server (NTRS)

Scriven, M. C.

1979-01-01

Insight is provided toward the development of an optimal program for investment analysis of project proposals offering commercial potential and its components. This involves a critique of economic investment criteria viewed in relation to requirements of engineering economy analysis. An outline for a systems approach to project analysis is given Application of the Leontief input-output methodology to analysis of projects involving multiple processes and products is investigated. Effective application of elements of neoclassical economic theory to investment analysis of project components is demonstrated. Patterns of both static and dynamic activity levels are incorporated.

Comparative primate genomics: emerging patterns of genome content and dynamics.

PubMed

Rogers, Jeffrey; Gibbs, Richard A

2014-05-01

Advances in genome sequencing technologies have created new opportunities for comparative primate genomics. Genome assemblies have been published for various primate species, and analyses of several others are underway. Whole-genome assemblies for the great apes provide remarkable new information about the evolutionary origins of the human genome and the processes involved. Genomic data for macaques and other non-human primates offer valuable insights into genetic similarities and differences among species that are used as models for disease-related research. This Review summarizes current knowledge regarding primate genome content and dynamics, and proposes a series of goals for the near future.

Color synesthesia. Insight into perception, emotion, and consciousness

PubMed Central

Safran, Avinoam B.; Sanda, Nicolae

2015-01-01

Purpose of review Synesthesia is an extraordinary perceptual phenomenon, in which individuals experience unusual percepts elicited by the activation of an unrelated sensory modality or by a cognitive process. Emotional reactions are commonly associated. The condition prompted philosophical debates on the nature of perception and impacted the course of art history. It recently generated a considerable interest among neuroscientists, but its clinical significance apparently remains underevaluated. This review focuses on the recent studies regarding variants of color synesthesia, the commonest form of the condition. Recent findings Synesthesia is commonly classified as developmental and acquired. Developmental forms predispose to changes in primary sensory processing and cognitive functions, usually with better performances in certain aspects and worse in others, and to heightened creativity. Acquired forms of synesthesia commonly arise from drug ingestion or neurological disorders, including thalamic lesions and sensory deprivation (e.g., blindness). Cerebral exploration using structural and functional imaging has demonstrated distinct patterns in cortical activation and brain connectivity for controls and synesthetes. Artworks of affected painters are most illustrative of the nature of synesthetic experiences. Summary Results of the recent investigations on synesthesia offered a remarkable insight into the mechanisms of perception, emotion and consciousness, and deserve attention both from neuroscientists and from clinicians. PMID:25545055

Color synesthesia. Insight into perception, emotion, and consciousness.

PubMed

Safran, Avinoam B; Sanda, Nicolae

2015-02-01

Synesthesia is an extraordinary perceptual phenomenon, in which individuals experience unusual percepts elicited by the activation of an unrelated sensory modality or by a cognitive process. Emotional reactions are commonly associated. The condition prompted philosophical debates on the nature of perception and impacted the course of art history. It recently generated a considerable interest among neuroscientists, but its clinical significance apparently remains underevaluated. This review focuses on the recent studies regarding variants of color synesthesia, the commonest form of the condition. Synesthesia is commonly classified as developmental and acquired. Developmental forms predispose to changes in primary sensory processing and cognitive functions, usually with better performances in certain aspects and worse in others, and to heightened creativity. Acquired forms of synesthesia commonly arise from drug ingestion or neurological disorders, including thalamic lesions and sensory deprivation (e.g., blindness). Cerebral exploration using structural and functional imaging has demonstrated distinct patterns in cortical activation and brain connectivity for controls and synesthetes. Artworks of affected painters are most illustrative of the nature of synesthetic experiences. Results of the recent investigations on synesthesia offered a remarkable insight into the mechanisms of perception, emotion and consciousness, and deserve attention both from neuroscientists and from clinicians.

Sex Change in Clownfish: Molecular Insights from Transcriptome Analysis.

PubMed

Casas, Laura; Saborido-Rey, Fran; Ryu, Taewoo; Michell, Craig; Ravasi, Timothy; Irigoien, Xabier

2016-10-17

Sequential hermaphroditism is a unique reproductive strategy among teleosts that is displayed mainly in fish species living in the coral reef environment. The reproductive biology of hermaphrodites has long been intriguing; however, very little is known about the molecular pathways underlying their sex change. Here, we provide the first de novo transcriptome analyses of a hermaphrodite teleost´s undergoing sex change in its natural environment. Our study has examined relative gene expression across multiple groups-rather than just two contrasting conditions- and has allowed us to explore the differential expression patterns throughout the whole process. Our analysis has highlighted the rapid and complex genomic response of the brain associated with sex change, which is subsequently transmitted to the gonads, identifying a large number of candidate genes, some well-known and some novel, involved in the process. The present study provides strong evidence of the importance of the sex steroidogenic machinery during sex change in clownfish, with the aromatase gene playing a central role, both in the brain and the gonad. This work constitutes the first genome-wide study in a social sex-changing species and provides insights into the genetic mechanism governing social sex change and gonadal restructuring in protandrous hermaphrodites.

Interactive natural language acquisition in a multi-modal recurrent neural architecture

NASA Astrophysics Data System (ADS)

Heinrich, Stefan; Wermter, Stefan

2018-01-01

For the complex human brain that enables us to communicate in natural language, we gathered good understandings of principles underlying language acquisition and processing, knowledge about sociocultural conditions, and insights into activity patterns in the brain. However, we were not yet able to understand the behavioural and mechanistic characteristics for natural language and how mechanisms in the brain allow to acquire and process language. In bridging the insights from behavioural psychology and neuroscience, the goal of this paper is to contribute a computational understanding of appropriate characteristics that favour language acquisition. Accordingly, we provide concepts and refinements in cognitive modelling regarding principles and mechanisms in the brain and propose a neurocognitively plausible model for embodied language acquisition from real-world interaction of a humanoid robot with its environment. In particular, the architecture consists of a continuous time recurrent neural network, where parts have different leakage characteristics and thus operate on multiple timescales for every modality and the association of the higher level nodes of all modalities into cell assemblies. The model is capable of learning language production grounded in both, temporal dynamic somatosensation and vision, and features hierarchical concept abstraction, concept decomposition, multi-modal integration, and self-organisation of latent representations.

Experimental insights into the importance of aquatic bacterial community composition to the degradation of dissolved organic matter

PubMed Central

Logue, Jürg B; Stedmon, Colin A; Kellerman, Anne M; Nielsen, Nikoline J; Andersson, Anders F; Laudon, Hjalmar; Lindström, Eva S; Kritzberg, Emma S

2016-01-01

Bacteria play a central role in the cycling of carbon, yet our understanding of the relationship between the taxonomic composition and the degradation of dissolved organic matter (DOM) is still poor. In this experimental study, we were able to demonstrate a direct link between community composition and ecosystem functioning in that differently structured aquatic bacterial communities differed in their degradation of terrestrially derived DOM. Although the same amount of carbon was processed, both the temporal pattern of degradation and the compounds degraded differed among communities. We, moreover, uncovered that low-molecular-weight carbon was available to all communities for utilisation, whereas the ability to degrade carbon of greater molecular weight was a trait less widely distributed. Finally, whereas the degradation of either low- or high-molecular-weight carbon was not restricted to a single phylogenetic clade, our results illustrate that bacterial taxa of similar phylogenetic classification differed substantially in their association with the degradation of DOM compounds. Applying techniques that capture the diversity and complexity of both bacterial communities and DOM, our study provides new insight into how the structure of bacterial communities may affect processes of biogeochemical significance. PMID:26296065

Sex Change in Clownfish: Molecular Insights from Transcriptome Analysis

PubMed Central

Casas, Laura; Saborido-Rey, Fran; Ryu, Taewoo; Michell, Craig; Ravasi, Timothy; Irigoien, Xabier

2016-01-01

Sequential hermaphroditism is a unique reproductive strategy among teleosts that is displayed mainly in fish species living in the coral reef environment. The reproductive biology of hermaphrodites has long been intriguing; however, very little is known about the molecular pathways underlying their sex change. Here, we provide the first de novo transcriptome analyses of a hermaphrodite teleost´s undergoing sex change in its natural environment. Our study has examined relative gene expression across multiple groups—rather than just two contrasting conditions— and has allowed us to explore the differential expression patterns throughout the whole process. Our analysis has highlighted the rapid and complex genomic response of the brain associated with sex change, which is subsequently transmitted to the gonads, identifying a large number of candidate genes, some well-known and some novel, involved in the process. The present study provides strong evidence of the importance of the sex steroidogenic machinery during sex change in clownfish, with the aromatase gene playing a central role, both in the brain and the gonad. This work constitutes the first genome-wide study in a social sex-changing species and provides insights into the genetic mechanism governing social sex change and gonadal restructuring in protandrous hermaphrodites. PMID:27748421

Modeling Menstrual Cycle Length and Variability at the Approach of Menopause Using Hierarchical Change Point Models

PubMed Central

Huang, Xiaobi; Elliott, Michael R.; Harlow, Siobán D.

2013-01-01

SUMMARY As women approach menopause, the patterns of their menstrual cycle lengths change. To study these changes, we need to jointly model both the mean and variability of cycle length. Our proposed model incorporates separate mean and variance change points for each woman and a hierarchical model to link them together, along with regression components to include predictors of menopausal onset such as age at menarche and parity. Additional complexity arises from the fact that the calendar data have substantial missingness due to hormone use, surgery, and failure to report. We integrate multiple imputation and time-to event modeling in a Bayesian estimation framework to deal with different forms of the missingness. Posterior predictive model checks are applied to evaluate the model fit. Our method successfully models patterns of women’s menstrual cycle trajectories throughout their late reproductive life and identifies change points for mean and variability of segment length, providing insight into the menopausal process. More generally, our model points the way toward increasing use of joint mean-variance models to predict health outcomes and better understand disease processes. PMID:24729638

Bioplausible multiscale filtering in retino-cortical processing as a mechanism in perceptual grouping.

PubMed

Nematzadeh, Nasim; Powers, David M W; Lewis, Trent W

2017-12-01

Why does our visual system fail to reconstruct reality, when we look at certain patterns? Where do Geometrical illusions start to emerge in the visual pathway? How far should we take computational models of vision with the same visual ability to detect illusions as we do? This study addresses these questions, by focusing on a specific underlying neural mechanism involved in our visual experiences that affects our final perception. Among many types of visual illusion, 'Geometrical' and, in particular, 'Tilt Illusions' are rather important, being characterized by misperception of geometric patterns involving lines and tiles in combination with contrasting orientation, size or position. Over the last decade, many new neurophysiological experiments have led to new insights as to how, when and where retinal processing takes place, and the encoding nature of the retinal representation that is sent to the cortex for further processing. Based on these neurobiological discoveries, we provide computer simulation evidence from modelling retinal ganglion cells responses to some complex Tilt Illusions, suggesting that the emergence of tilt in these illusions is partially related to the interaction of multiscale visual processing performed in the retina. The output of our low-level filtering model is presented for several types of Tilt Illusion, predicting that the final tilt percept arises from multiple-scale processing of the Differences of Gaussians and the perceptual interaction of foreground and background elements. The model is a variation of classical receptive field implementation for simple cells in early stages of vision with the scales tuned to the object/texture sizes in the pattern. Our results suggest that this model has a high potential in revealing the underlying mechanism connecting low-level filtering approaches to mid- and high-level explanations such as 'Anchoring theory' and 'Perceptual grouping'.

Emergent Archetype Hydrological-Biogeochemical Response Patterns in Heterogeneous Catchments

NASA Astrophysics Data System (ADS)

Jawitz, J. W.; Gall, H. E.; Rao, P.

2013-12-01

What can spatiotemporally integrated patterns observed in stream hydrologic and biogeochemical signals generated in response to transient hydro-climatic and anthropogenic forcing tell us about the interactions between spatially heterogeneous soil-mediated hydrological and biogeochemical processes? We seek to understand how the spatial structure of solute sources coupled with hydrologic responses affect observed concentration-discharge (C-Q) patterns. These patterns are expressions of the spatiotemporal structure of solute loads exported from managed catchments, and their likely ecological consequences manifested in receiving water bodies (e.g., wetlands, rivers, lakes, and coastal waters). We investigated the following broad questions: (1) How does the correlation between flow-generating areas and biogeochemical source areas across a catchment evolve under stochastic hydro-climatic forcing? (2) What are the feasible hydrologic and biogeochemical responses that lead to the emergence of the observed archetype C-Q patterns? and; (3) What implications do these coupled dynamics have for catchment monitoring and implementation of management practices? We categorize the observed temporal signals into three archetypical C-Q patterns: dilution; accretion, and constant concentration. We introduce a parsimonious stochastic model of heterogeneous catchments, which act as hydrologic and biogeochemical filters, to examine the relationship between spatial heterogeneity and temporal history of solute export signals. The core concept of the modeling framework is considering the types and degree of spatial correlation between solute source zones and flow generating zones, and activation of different portions of the catchments during rainfall events. Our overarching hypothesis is that each of the archetype C-Q patterns can be generated by explicitly linking landscape-scale hydrologic responses and spatial distributions of solute source properties within a catchment. The model simulations reproduce the three major C-Q patterns observed in published data, offering valuable insight into coupled catchment processes. The findings have important implications for effective catchment management for water quality improvement, and stream monitoring strategies.

Fabrication of 3D surface structures using grayscale lithography

NASA Astrophysics Data System (ADS)

Stilson, Christopher; Pal, Rajan; Coutu, Ronald A.

2014-03-01

The ability to design and develop 3D microstructures is important for microelectromechanical systems (MEMS) fabrication. Previous techniques used to create 3D devices included tedious steps in direct writing and aligning patterns onto a substrate followed by multiple photolithography steps using expensive, customized equipment. Additionally, these techniques restricted batch processing and placed limits on achievable shapes. Gray-scale lithography enables the fabrication of a variety of shapes using a single photolithography step followed by reactive ion etching (RIE). Micromachining 3D silicon structures for MEMS can be accomplished using gray-scale lithography along with dry anisotropic etching. In this study, we investigated: using MATLAB for mask designs; feasibility of using 1 μm Heidelberg mask maker to direct write patterns onto photoresist; using RIE processing to etch patterns into a silicon substrate; and the ability to tailor etch selectivity for precise fabrication. To determine etch rates and to obtain desired etch selectivity, parameters such as gas mixture, gas flow, and electrode power were studied. This process successfully demonstrates the ability to use gray-scale lithography and RIE for use in the study of micro-contacts. These results were used to produce a known engineered non-planer surface for testing micro-contacts. Surface structures are between 5 μm and 20 μm wide with varying depths and slopes based on mask design and etch rate selectivity. The engineered surfaces will provide more insight into contact geometries and failure modes of fixed-fixed micro-contacts.

Estimation of Fractional Plant Lifeform Cover Using Landsat and Airborne LiDAR/hyperspectral Data

NASA Astrophysics Data System (ADS)

Parra, A. S.; Xu, Q.; Dilts, T.; Weisberg, P.; Greenberg, J. A.

2017-12-01

Land-cover change has generally been understood as the result of local, landscape or regional-scale processes with most studies focusing on case-study landscapes or smaller regions. However, as we observe similar types of land-cover change occurring across different biomes worldwide, it becomes clear that global-scale processes such as climate change and CO2 fertilization, in interaction with local influences, are underlying drivers in land-cover change patterns. Prior studies on global land-cover change may not have had a suitable spatial, temporal and thematic resolution for allowing the identification of such patterns. Furthermore, the lack of globally consistent spatial data products also constitutes a limiting factor in evaluating both proximate and ultimate causes of land-cover change. In this study, we derived a global model for broadleaf tree, needleleaf tree, shrub, herbaceous, and "other" fractional cover using Landsat imagery. Combined LiDAR/hyperspectral data sets were used for calibration and validation of the Landsat-derived products. Spatially explicit uncertainties were also created as part of the data products. Our results highlight the potential for large-scale studies that model local and global influences on land-cover transition types and rates at fine thematic, spatial, and temporal resolutions. These spatial data products are relevant for identifying patterns in land-cover change due to underlying global-scale processes and can provide valuable insights into climatic and land-use factors determining vegetation distributions.

The heuristic value of redundancy models of aging.

PubMed

Boonekamp, Jelle J; Briga, Michael; Verhulst, Simon

2015-11-01

Molecular studies of aging aim to unravel the cause(s) of aging bottom-up, but linking these mechanisms to organismal level processes remains a challenge. We propose that complementary top-down data-directed modelling of organismal level empirical findings may contribute to developing these links. To this end, we explore the heuristic value of redundancy models of aging to develop a deeper insight into the mechanisms causing variation in senescence and lifespan. We start by showing (i) how different redundancy model parameters affect projected aging and mortality, and (ii) how variation in redundancy model parameters relates to variation in parameters of the Gompertz equation. Lifestyle changes or medical interventions during life can modify mortality rate, and we investigate (iii) how interventions that change specific redundancy parameters within the model affect subsequent mortality and actuarial senescence. Lastly, as an example of data-directed modelling and the insights that can be gained from this, (iv) we fit a redundancy model to mortality patterns observed by Mair et al. (2003; Science 301: 1731-1733) in Drosophila that were subjected to dietary restriction and temperature manipulations. Mair et al. found that dietary restriction instantaneously reduced mortality rate without affecting aging, while temperature manipulations had more transient effects on mortality rate and did affect aging. We show that after adjusting model parameters the redundancy model describes both effects well, and a comparison of the parameter values yields a deeper insight in the mechanisms causing these contrasting effects. We see replacement of the redundancy model parameters by more detailed sub-models of these parameters as a next step in linking demographic patterns to underlying molecular mechanisms. Copyright © 2015 Elsevier Inc. All rights reserved.

Novel patterns of historical isolation, dispersal, and secondary contact across Baja California in the Rosy Boa (Lichanura trivirgata).

PubMed

Wood, Dustin A; Fisher, Robert N; Reeder, Tod W

2008-02-01

Mitochondrial DNA (mtDNA) sequence variation was examined in 131 individuals of the Rosy Boa (Lichanura trivirgata) from across the species range in southwestern North America. Bayesian inference and nested clade phylogeographic analyses (NCPA) were used to estimate relationships and infer evolutionary processes. These patterns were evaluated as they relate to previously hypothesized vicariant events and new insights are provided into the biogeographic and evolutionary processes important in Baja California and surrounding North American deserts. Three major lineages (Lineages A, B, and C) are revealed with very little overlap. Lineage A and B are predominately separated along the Colorado River and are found primarily within California and Arizona (respectively), while Lineage C consists of disjunct groups distributed along the Baja California peninsula as well as south-central Arizona, southward along the coastal regions of Sonora, Mexico. Estimated divergence time points (using a Bayesian relaxed molecular clock) and geographic congruence with postulated vicariant events suggest early extensions of the Gulf of California and subsequent development of the Colorado River during the Late Miocene-Pliocene led to the formation of these mtDNA lineages. Our results also suggest that vicariance hypotheses alone do not fully explain patterns of genetic variation. Therefore, we highlight the importance of dispersal to explain these patterns and current distribution of populations. We also compare the mtDNA lineages with those based on morphological variation and evaluate their implications for taxonomy.

Novel patterns of historical isolation, dispersal, and secondary contact across Baja California in the Rosy Boa (Lichanura trivirgata)

USGS Publications Warehouse

Wood, D.A.; Fisher, R.N.; Reeder, T.W.

2008-01-01

Mitochondrial DNA (mtDNA) sequence variation was examined in 131 individuals of the Rosy Boa (Lichanura trivirgata) from across the species range in southwestern North America. Bayesian inference and nested clade phylogeographic analyses (NCPA) were used to estimate relationships and infer evolutionary processes. These patterns were evaluated as they relate to previously hypothesized vicariant events and new insights are provided into the biogeographic and evolutionary processes important in Baja California and surrounding North American deserts. Three major lineages (Lineages A, B, and C) are revealed with very little overlap. Lineage A and B are predominately separated along the Colorado River and are found primarily within California and Arizona (respectively), while Lineage C consists of disjunct groups distributed along the Baja California peninsula as well as south-central Arizona, southward along the coastal regions of Sonora, Mexico. Estimated divergence time points (using a Bayesian relaxed molecular clock) and geographic congruence with postulated vicariant events suggest early extensions of the Gulf of California and subsequent development of the Colorado River during the Late Miocene-Pliocene led to the formation of these mtDNA lineages. Our results also suggest that vicariance hypotheses alone do not fully explain patterns of genetic variation. Therefore, we highlight the importance of dispersal to explain these patterns and current distribution of populations. We also compare the mtDNA lineages with those based on morphological variation and evaluate their implications for taxonomy. ?? 2007 Elsevier Inc. All rights reserved.

Interplay between membrane elasticity and active cytoskeleton forces regulates the aggregation dynamics of the immunological synapse

NASA Astrophysics Data System (ADS)

Dharan, Nadiv; Farago, Oded

Adhesion between a T cell and an antigen presenting cell is achieved by TCR-pMHC and LFA1-ICAM1 protein complexes. These segregate to form a special pattern, known as the immunological synapse (IS), consisting of a central quasi-circular domain of TCR-pMHC bonds surrounded by a peripheral domain of LFA1-ICAM1 complexes. Insights gained from imaging studies had led to the conclusion that the formation of the central adhesion domain in the IS is driven by active (ATP-driven) mechanisms. Recent studies, however, suggested that passive (thermodynamic) mechanisms may also play an important role in this process. Here, we present a simple physical model, taking into account the membrane-mediated thermodynamic attraction between the TCR-pMHC bonds and the effective forces that they experience due to ATP-driven actin retrograde flow and transport by dynein motor proteins. Monte Carlo simulations of the model exhibit a good spatio-temporal agreement with the experimentally observed pattern evolution of the TCR-pMHC microclusters. The agreement is lost when one of the aggregation mechanisms is "muted", which helps to identify the respective roles in the process. We conclude that actin retrograde flow drives the centripetal motion of TCR-pMHC bonds, while the membrane-mediated interactions facilitate microcluster formation and growth. In the absence of dynein motors, the system evolves into a ring-shaped pattern, which highlights the role of dynein motors in the formation of the final concentric pattern. The interplay between the passive and active mechanisms regulates the rate of the accumulation process, which in the absence of one them proceeds either too quickly or slowly.

Recolonization patterns of ants in a rehabilitated lignite mine in central Italy: Potential for the use of Mediterranean ants as indicators of restoration processes

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

Ottonetti, L.; Tucci, L.; Santini, G.

2006-03-15

Ant (Hymenoptera: Formicidae) assemblages were sampled with pitfall traps in three different habitats associated with a rehabilitated mine district and in undisturbed forests in Tuscany, Italy. The four habitats were (1) open fields (3-4 years old); (2) a middle-age mixed plantation (10 years); (3) an old-age mixed plantation (20 years); and (4) an oak woodland (40 years) not directly affected by mining activities. The aim of the study was to analyze ant recolonization patterns in order to provide insights on the use of Mediterranean ant fauna as indicators of restoration processes. Species richness and diversity were not significantly different amongmore » the four habitats. However, multivariate analyses showed that the assemblages in the different habitats were clearly differentiated, with similarity relationships reflecting a successional gradient among rehabilitated sites. The observed patterns of functional group changes along the gradient broadly accord with those of previous studies in other biogeographic regions. These were (1) a decrease of dominant Dolichoderinae and opportunists; (2) an increase in the proportion of cold-climate specialists; and (3) the appearance of the Cryptic species in the oldest plantations, with a maximum of abundance in the woodland. In conclusion, the results of our study supported the use of Mediterranean ants as a suitable tool for biomonitoring of restoration processes, and in particular, the functional group approach proved a valuable framework to better interpret local trends in terms of global ecological patterns. Further research is, however, needed in order to obtain a reliable classification of Mediterranean ant functional groups.« less

Femtosecond laser rapid fabrication of large-area rose-like micropatterns on freestanding flexible graphene films

PubMed Central

Shi, Xuesong; Li, Xin; Jiang, Lan; Qu, Liangti; Zhao, Yang; Ran, Peng; Wang, Qingsong; Cao, Qiang; Ma, Tianbao; Lu, Yongfeng

2015-01-01

We developed a simple, scalable and high-throughput method for fabrication of large-area three-dimensional rose-like microflowers with controlled size, shape and density on graphene films by femtosecond laser micromachining. The novel biomimetic microflower that composed of numerous turnup graphene nanoflakes can be fabricated by only a single femtosecond laser pulse, which is efficient enough for large-area patterning. The graphene films were composed of layer-by-layer graphene nanosheets separated by nanogaps (~10–50 nm), and graphene monolayers with an interlayer spacing of ~0.37 nm constituted each of the graphene nanosheets. This unique hierarchical layering structure of graphene films provides great possibilities for generation of tensile stress during femtosecond laser ablation to roll up the nanoflakes, which contributes to the formation of microflowers. By a simple scanning technique, patterned surfaces with controllable densities of flower patterns were obtained, which can exhibit adhesive superhydrophobicity. More importantly, this technique enables fabrication of the large-area patterned surfaces at centimeter scales in a simple and efficient way. This study not only presents new insights of ultrafast laser processing of novel graphene-based materials but also shows great promise of designing new materials combined with ultrafast laser surface patterning for future applications in functional coatings, sensors, actuators and microfluidics. PMID:26615800

Leisure Patterns among Four-Day Workers.

ERIC Educational Resources Information Center

Seltzer, Joseph; Wilson, James A.

1980-01-01

Insight into the patterns of leisure time usage may lead to a better understanding of the relationships between work and leisure and other aspects of an individual's life. A five-factor model was developed to explicate individual motivations for leisure pursuits. (JN)

Conserved and Divergent Molecular and Anatomic Features of Human and Mouse Nephron Patterning.

PubMed

Lindström, Nils O; Tran, Tracy; Guo, Jinjin; Rutledge, Elisabeth; Parvez, Riana K; Thornton, Matthew E; Grubbs, Brendan; McMahon, Jill A; McMahon, Andrew P

2018-03-01

The nephron is the functional unit of the kidney, but the mechanism of nephron formation during human development is unclear. We conducted a detailed analysis of nephron development in humans and mice by immunolabeling, and we compared human and mouse nephron patterning to describe conserved and divergent features. We created protein localization maps that highlight the emerging patterns along the proximal-distal axis of the developing nephron and benchmark expectations for localization of functionally important transcription factors, which revealed unanticipated cellular diversity. Moreover, we identified a novel nephron subdomain marked by Wnt4 expression that we fate-mapped to the proximal mature nephron. Significant conservation was observed between human and mouse patterning. We also determined the time at which markers for mature nephron cell types first emerge-critical data for the renal organoid field. These findings have conceptual implications for the evolutionary processes driving the diversity of mammalian organ systems. Furthermore, these findings provide practical insights beyond those gained with mouse and rat models that will guide in vitro efforts to harness the developmental programs necessary to build human kidney structures. Copyright © 2018 by the American Society of Nephrology.

Beyond Corroboration: Strengthening Model Validation by Looking for Unexpected Patterns

PubMed Central

Chérel, Guillaume; Cottineau, Clémentine; Reuillon, Romain

2015-01-01

Models of emergent phenomena are designed to provide an explanation to global-scale phenomena from local-scale processes. Model validation is commonly done by verifying that the model is able to reproduce the patterns to be explained. We argue that robust validation must not only be based on corroboration, but also on attempting to falsify the model, i.e. making sure that the model behaves soundly for any reasonable input and parameter values. We propose an open-ended evolutionary method based on Novelty Search to look for the diverse patterns a model can produce. The Pattern Space Exploration method was tested on a model of collective motion and compared to three common a priori sampling experiment designs. The method successfully discovered all known qualitatively different kinds of collective motion, and performed much better than the a priori sampling methods. The method was then applied to a case study of city system dynamics to explore the model’s predicted values of city hierarchisation and population growth. This case study showed that the method can provide insights on potential predictive scenarios as well as falsifiers of the model when the simulated dynamics are highly unrealistic. PMID:26368917

Use patterns of health information exchange through a multidimensional lens: conceptual framework and empirical validation.

PubMed

Politi, Liran; Codish, Shlomi; Sagy, Iftach; Fink, Lior

2014-12-01

Insights about patterns of system use are often gained through the analysis of system log files, which record the actual behavior of users. In a clinical context, however, few attempts have been made to typify system use through log file analysis. The present study offers a framework for identifying, describing, and discerning among patterns of use of a clinical information retrieval system. We use the session attributes of volume, diversity, granularity, duration, and content to define a multidimensional space in which each specific session can be positioned. We also describe an analytical method for identifying the common archetypes of system use in this multidimensional space. We demonstrate the value of the proposed framework with a log file of the use of a health information exchange (HIE) system by physicians in an emergency department (ED) of a large Israeli hospital. The analysis reveals five distinct patterns of system use, which have yet to be described in the relevant literature. The results of this study have the potential to inform the design of HIE systems for efficient and effective use, thus increasing their contribution to the clinical decision-making process. Copyright © 2014 Elsevier Inc. All rights reserved.

A gradient analysis on urban sprawl and urban landscape pattern between 1985 and 2000 in the Pearl River Delta, China

NASA Astrophysics Data System (ADS)

Dai, Erfu; Wu, Zhuo; Du, Xiaodian

2017-04-01

Urbanization is an irreversible trend worldwide, especially in rapidly developing China. Accelerated urbanization has resulted in rapid urban sprawl and urban landscape pattern changes. Quantifying the spatiotemporal dynamics of urban land use and landscape pattern not only can reveal the characteristics of social transfer and economic development, but also can provide insights into the driving mechanisms of land use changes. In this study, we integrated remote sensing (RS), geographic information system (GIS), landscape metrics, and gradient analysis to quantitatively compare the spatiotemporal dynamics of land use, urban sprawl, and landscape pattern for nine cities in the Pearl River Delta from 1985‒2000. For the whole study region, urbanization was obvious. The results show an increase in urban buildup land and shrinkage of cropland in the Pearl River Delta. However, the nine cities differed greatly in terms of the process and magnitude of urban sprawl for both the spatial and temporal dimensions. This was most evident for the cities of Guangzhou and Shenzhen. Gradient analysis on urban landscape changes could deepen understanding of the stages of urban development and provide a scientific foundation for future urban planning and land management strategies in China.

Logic programming to predict cell fate patterns and retrodict genotypes in organogenesis.

PubMed

Hall, Benjamin A; Jackson, Ethan; Hajnal, Alex; Fisher, Jasmin

2014-09-06

Caenorhabditis elegans vulval development is a paradigm system for understanding cell differentiation in the process of organogenesis. Through temporal and spatial controls, the fate pattern of six cells is determined by the competition of the LET-23 and the Notch signalling pathways. Modelling cell fate determination in vulval development using state-based models, coupled with formal analysis techniques, has been established as a powerful approach in predicting the outcome of combinations of mutations. However, computing the outcomes of complex and highly concurrent models can become prohibitive. Here, we show how logic programs derived from state machines describing the differentiation of C. elegans vulval precursor cells can increase the speed of prediction by four orders of magnitude relative to previous approaches. Moreover, this increase in speed allows us to infer, or 'retrodict', compatible genomes from cell fate patterns. We exploit this technique to predict highly variable cell fate patterns resulting from dig-1 reduced-function mutations and let-23 mosaics. In addition to the new insights offered, we propose our technique as a platform for aiding the design and analysis of experimental data. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

New insights into the phylogenetic relationships, character evolution, and phytogeographic patterns of Calceolaria (Calceolariaceae).

PubMed

Cosacov, Andrea; Sérsic, Alicia N; Sosa, Victoria; De-Nova, J Arturo; Nylinder, Stephan; Cocucci, Andrea A

2009-12-01

Biogeographical patterns and diversification processes in Andean and Patagonian flora are not yet well understood. Calceolaria is a highly diversified genus of these areas, representing one of the most specialized plant-pollinator systems because flowers produce nonvolatile oils, a very unusual floral reward. Phylogenetic analyses with molecular (ITS and matK) and morphological characters from 103 Calceolaria species were conducted to examine relationships, to understand biogeographic patterns, and to detect evolutionary patterns of floral and ecological characters. Total evidence analysis retrieved three major clades, which strongly correspond to the three previously recognized subgenera, although only subgenus Rosula was retrieved as a monophyletic group. A single historical event explains the expansion from the southern to central Andes, while different parallel evolutionary lines show a northward expansion from the central to northern Andes across the Huancabamba Deflection, an important geographical barrier in northern Peru. Polyploidy, acquisition of elaiophores, and a nototribic pollination mechanism are key aspects of the evolutionary history of Calceolaria. Pollination interactions were more frequently established with Centris than with Chalepogenus oil-collecting bee species. The repeated loss of the oil gland and shifts to pollen as the only reward suggest an evolutionary tendency from highly to moderately specialized pollination systems.

Engineering paradigms and anthropogenic global change

NASA Astrophysics Data System (ADS)

Bohle, Martin

2016-04-01

This essay discusses 'paradigms' as means to conceive anthropogenic global change. Humankind alters earth-systems because of the number of people, the patterns of consumption of resources, and the alterations of environments. This process of anthropogenic global change is a composite consisting of societal (in the 'noosphere') and natural (in the 'bio-geosphere') features. Engineering intercedes these features; e.g. observing stratospheric ozone depletion has led to understanding it as a collateral artefact of a particular set of engineering choices. Beyond any specific use-case, engineering works have a common function; e.g. civil-engineering intersects economic activity and geosphere. People conceive their actions in the noosphere including giving purpose to their engineering. The 'noosphere' is the ensemble of social, cultural or political concepts ('shared subjective mental insights') of people. Among people's concepts are the paradigms how to shape environments, production systems and consumption patterns given their societal preferences. In that context, engineering is a means to implement a given development path. Four paradigms currently are distinguishable how to make anthropogenic global change happening. Among the 'engineering paradigms' for anthropogenic global change, 'adaptation' is a paradigm for a business-as-usual scenario and steady development paths of societies. Applying this paradigm implies to forecast the change to come, to appropriately design engineering works, and to maintain as far as possible the current production and consumption patterns. An alternative would be to adjust incrementally development paths of societies, namely to 'dovetail' anthropogenic and natural fluxes of matter and energy. To apply that paradigm research has to identify 'natural boundaries', how to modify production and consumption patterns, and how to tackle process in the noosphere to render alterations of common development paths acceptable. A further alternative, the paradigm of 'ecomodernism' implies to accentuate some of the current development paths of societies with the goal to 'decouple' anthropogenic and natural fluxes of matter and energy. Applying the paradigm 'geoengineering', engineering works shall 'modulate' natural fluxes of matter to counter the effect of anthropogenic fluxes of matter instead to alter the development paths of societies. Thus, anthropogenic global change is a composite process in which engineering intercedes the 'noosphere' and in the 'bio-geosphere'. Paradigms 'how to engineering earth systems' reflect different concepts ('shared subjective insights') how to combine knowledge with use, function and purpose. Currently, four paradigms are distinguishable how to engineer anthropogenic global change. They convene recipes human activity and bio-geosphere should intersect.

Measuring spatial patterns in floodplains: A step towards understanding the complexity of floodplain ecosystems: Chapter 6

USGS Publications Warehouse

Scown, Murray W.; Thoms, Martin C.; DeJager, Nathan R.; Gilvear, David J.; Greenwood, Malcolm T.; Thoms, Martin C.; Wood, Paul J.

2016-01-01

Floodplains can be viewed as complex adaptive systems (Levin, 1998) because they are comprised of many different biophysical components, such as morphological features, soil groups and vegetation communities as well as being sites of key biogeochemical processing (Stanford et al., 2005). Interactions and feedbacks among the biophysical components often result in additional phenomena occuring over a range of scales, often in the absence of any controlling factors (sensu Hallet, 1990). This emergence of new biophysical features and rates of processing can lead to alternative stable states which feed back into floodplain adaptive cycles (cf. Hughes, 1997; Stanford et al., 2005). Interactions between different biophysical components, feedbacks, self emergence and scale are all key properties of complex adaptive systems (Levin, 1998; Phillips, 2003; Murray et al., 2014) and therefore will influence the manner in which we study and view spatial patterns. Measuring the spatial patterns of floodplain biophysical components is a prerequisite to examining and understanding these ecosystems as complex adaptive systems. Elucidating relationships between pattern and process, which are intrinsically linked within floodplains (Ward et al., 2002), is dependent upon an understanding of spatial pattern. This knowledge can help river scientists determine the major drivers, controllers and responses of floodplain structure and function, as well as the consequences of altering those drivers and controllers (Hughes and Cass, 1997; Whited et al., 2007). Interactions and feedbacks between physical, chemical and biological components of floodplain ecosystems create and maintain a structurally diverse and dynamic template (Stanford et al., 2005). This template influences subsequent interactions between components that consequently affect system trajectories within floodplains (sensu Bak et al., 1988). Constructing and evaluating models used to predict floodplain ecosystem responses to natural and anthropogenic disturbances therefore require quantification of spatial pattern (Asselman and Middelkoop, 1995; Walling and He, 1998). Quantifying these patterns also provides insights into the spatial and temporal domains of structuring processes as well as enabling the detection of self-emergent phenomena, environmental constraints or anthropogenic interference (Turner et al., 1990; Holling, 1992; De Jager and Rohweder, 2012). Thus, quantifying spatial pattern is an important building block on which to examine floodplains as complex adaptive systems (Levin, 1998). Approaches to measuring spatial pattern in floodplains must be cognisant of scale, self-emergent phenomena, spatial organisation, and location. Fundamental problems may arise when patterns observed at a site or transect scale are scaled-up to infer processes and patterns over entire floodplain surfaces (Wiens, 2002; Thorp et al., 2008). Likewise, patterns observed over the entire spatial extent of a landscape can mask important variation and detail at finer scales (Riitters et al., 2002). Indeed, different patterns often emerge at different scales (Turner et al., 1990) because of hierarchical structuring processes (O'Neill et al., 1991). Categorising data into discrete, homogeneous and predefined spatial units at a particular scale (e.g. polygons) creates issues and errors associated with scale and subjective classification (McGarigal et al., 2009; Cushman et al., 2010). These include, loss of information within classified ‘patches’, as well as the ability to detect the emergence of new features that do not fit the original classification scheme. Many of these issues arise because floodplains are highly heterogeneous and have complex spatial organizations (Carbonneau et al., 2012; Legleiter, 2013). As a result, the scale and location at which measurements are made can influence the observed spatial patterns; and patterns may not be scale independent or applicable in different geomorp

The association of lifetime insight and cognition in psychosis.

PubMed

Sánchez-Torres, Ana M; Zarzuela, Amalia; Peralta, Victor; Cuesta, Manuel J

2015-03-01

Poor insight has been related to poor course in psychosis. However, the role of cognition in insight remains unclear. The aim of this study was to examine the influence of cognition and lifetime psychopathological dimensions on insight in psychosis. We followed up 42 patients with psychotic disorders over 10years. Lifetime psychopathological dimensions and cognitive performance were assessed. Patients were divided into two groups by lifetime patterns of insight and compared with 42 healthy volunteers. Lower IQ and poorer social cognition were associated with higher risks of poorer lifetime insight of feeling ill and global insight respectively. Lifetime negative symptoms were associated with a higher risk of poorer lifetime insight into symptoms. Lifetime lack of insight is independent of cognitive impairment in specific domains, except for social cognition. Higher IQ may contribute to better lifetime awareness of illness, while better ability to manage emotions is involved in lifetime global insight. Copyright © 2014 Elsevier B.V. All rights reserved.

Regional Patterns and Spatial Clusters of Nonstationarities in Annual Peak Instantaneous Streamflow

NASA Astrophysics Data System (ADS)

White, K. D.; Baker, B.; Mueller, C.; Villarini, G.; Foley, P.; Friedman, D.

2017-12-01

Information about hydrologic changes resulting from changes in climate, land use, and land cover is a necessity planning and design or water resources infrastructure. The United States Army Corps of Engineers (USACE) evaluated and selected 12 methods to detect abrupt and slowly varying nonstationarities in records of maximum peak annual flows. They deployed a publicly available tool[1]in 2016 and a guidance document in 2017 to support identification of nonstationarities in a reproducible manner using a robust statistical framework. This statistical framework has now been applied to streamflow records across the continental United States to explore the presence of regional patterns and spatial clusters of nonstationarities in peak annual flow. Incorporating this geographic dimension into the detection of nonstationarities provides valuable insight for the process of attribution of these significant changes. This poster summarizes the methods used and provides the results of the regional analysis. [1] Available here - http://www.corpsclimate.us/ptcih.cfm

Impact of Plant Functional Types on Coherence Between Precipitation and Soil Moisture: A Wavelet Analysis

NASA Astrophysics Data System (ADS)

Liu, Qi; Hao, Yonghong; Stebler, Elaine; Tanaka, Nobuaki; Zou, Chris B.

2017-12-01

Mapping the spatiotemporal patterns of soil moisture within heterogeneous landscapes is important for resource management and for the understanding of hydrological processes. A critical challenge in this mapping is comparing remotely sensed or in situ observations from areas with different vegetation cover but subject to the same precipitation regime. We address this challenge by wavelet analysis of multiyear observations of soil moisture profiles from adjacent areas with contrasting plant functional types (grassland, woodland, and encroached) and precipitation. The analysis reveals the differing soil moisture patterns and dynamics between plant functional types. The coherence at high-frequency periodicities between precipitation and soil moisture generally decreases with depth but this is much more pronounced under woodland compared to grassland. Wavelet analysis provides new insights on soil moisture dynamics across plant functional types and is useful for assessing differences and similarities in landscapes with heterogeneous vegetation cover.

Static lung compliance and body pressures in Tupinambis merianae with and without post-hepatic septum.

PubMed

Klein, Wilfried; Abe, Augusto S; Perry, Steven F

2003-04-15

The surgical removal of the post-hepatic septum (PHS) in the tegu lizard, Tupinambis merianae, significantly reduces resting lung volume (V(Lr)) and maximal lung volume (V(Lm)) when compared with tegus with intact PHS. Standardised for body mass (M(B)), static lung compliance was significantly less in tegus without PHS. Pleural and abdominal pressures followed, like ventilation, a biphasic pattern. In general, pressures increased during expiration and decreased during inspiration. However, during expiration pressure changes showed a marked intra- and interindividual variation. The removal of the PHS resulted in a lower cranio-caudal intracoelomic pressure differential, but had no effect on the general pattern of pressure changes accompanying ventilation. These results show that a perforated PHS that lacks striated muscle has significant influence on static breathing mechanics in Tupinambis and by analogy provides valuable insight into similar processes that led to the evolution of the mammalian diaphragm.

Species richness and morphological diversity of passerine birds

PubMed Central

Ricklefs, Robert E.

2012-01-01

The relationship between species richness and the occupation of niche space can provide insight into the processes that shape patterns of biodiversity. For example, if species interactions constrained coexistence, one might expect tendencies toward even spacing within niche space and positive relationships between diversity and total niche volume. I use morphological diversity of passerine birds as a proxy for diet, foraging maneuvers, and foraging substrates and examine the morphological space occupied by regional and local passerine avifaunas. Although independently diversified regional faunas exhibit convergent morphology, species are clustered rather than evenly distributed, the volume of the morphological space is weakly related to number of species per taxonomic family, and morphological volume is unrelated to number of species within both regional avifaunas and local assemblages. These results seemingly contradict patterns expected when species interactions constrain regional or local diversity, and they suggest a larger role for diversification, extinction, and dispersal limitation in shaping species richness. PMID:22908271

Delay and probability discounting among payday and title loan recipients.

PubMed

Mahoney, Colin T; Lawyer, Steven R

2016-04-01

Payday and title loans are short-term loans associated with significant economic impact. Behavioral theories of impulsive choice may provide insight into behavioral processes that underlie the propensity to take out payday and title loans. Adults between the ages of 18 and 30 recruited from the community completed delay and probability discounting tasks for hypothetical money as well as measures of substance use. Patterns of discounting were characterized using a hyperbolic decay model and area under the curve. Participants who took out a payday and/or title loan in the past (n=41) exhibited more impulsive choice patterns on the delay discounting task than did those who did not (n=255). Substance use mediated this relationship between payday and title loan retention and delay discounting. These findings suggest potentially important relationships between payday/title loan borrowing, substance use, and delay discounting. Copyright © 2016 Elsevier B.V. All rights reserved.

Biological substrates of schizophrenia.

PubMed

Kovelman, J A; Scheibel, A B

1986-01-01

Schizophrenia is increasingly believed to represent a group of organic disorders which primarily, although not exclusively, affect the central nervous system. Our purpose is to review a representative sample of twentieth-century literature which speaks to the biological substrates of the syndrome. Subjects reviewed include genetic and environmental contributions to the onset of illness, early and recent findings of gross structural anomalies, and apparent histopathological alterations in cerebral cortex, cerebellar vermis, limbic system, and brain stem, as well as problems of cerebral asymmetry. Data from a diverse group of electrophysiological studies reveal several promising correlates of these areas of investigation. Despite the inconsistent nature of the findings to date, several themes have begun to emerge, including patterns of hypofrontal/hyperparietal regional cerebral flow and glucose utilization, left hemispheric dysfunction, and deficits of interhemispheric information processing. The interpretation and significance of these emerging patterns remains unclear and must await more profound insights into the nature of normal and abnormal cerebral function.

Phonological Concept Learning.

PubMed

Moreton, Elliott; Pater, Joe; Pertsova, Katya

2017-01-01

Linguistic and non-linguistic pattern learning have been studied separately, but we argue for a comparative approach. Analogous inductive problems arise in phonological and visual pattern learning. Evidence from three experiments shows that human learners can solve them in analogous ways, and that human performance in both cases can be captured by the same models. We test GMECCS (Gradual Maximum Entropy with a Conjunctive Constraint Schema), an implementation of the Configural Cue Model (Gluck & Bower, ) in a Maximum Entropy phonotactic-learning framework (Goldwater & Johnson, ; Hayes & Wilson, ) with a single free parameter, against the alternative hypothesis that learners seek featurally simple algebraic rules ("rule-seeking"). We study the full typology of patterns introduced by Shepard, Hovland, and Jenkins () ("SHJ"), instantiated as both phonotactic patterns and visual analogs, using unsupervised training. Unlike SHJ, Experiments 1 and 2 found that both phonotactic and visual patterns that depended on fewer features could be more difficult than those that depended on more features, as predicted by GMECCS but not by rule-seeking. GMECCS also correctly predicted performance differences between stimulus subclasses within each pattern. A third experiment tried supervised training (which can facilitate rule-seeking in visual learning) to elicit simple rule-seeking phonotactic learning, but cue-based behavior persisted. We conclude that similar cue-based cognitive processes are available for phonological and visual concept learning, and hence that studying either kind of learning can lead to significant insights about the other. Copyright © 2015 Cognitive Science Society, Inc.

The Functional Basis of Wing Patterning in Heliconius Butterflies: The Molecules Behind Mimicry

PubMed Central

Kronforst, Marcus R.; Papa, Riccardo

2015-01-01

Wing-pattern mimicry in butterflies has provided an important example of adaptation since Charles Darwin and Alfred Russell Wallace proposed evolution by natural selection >150 years ago. The neotropical butterfly genus Heliconius played a central role in the development of mimicry theory and has since been studied extensively in the context of ecology and population biology, behavior, and mimicry genetics. Heliconius species are notable for their diverse color patterns, and previous crossing experiments revealed that much of this variation is controlled by a small number of large-effect, Mendelian switch loci. Recent comparative analyses have shown that the same switch loci control wing-pattern diversity throughout the genus, and a number of these have now been positionally cloned. Using a combination of comparative genetic mapping, association tests, and gene expression analyses, variation in red wing patterning throughout Heliconius has been traced back to the action of the transcription factor optix. Similarly, the signaling ligand WntA has been shown to control variation in melanin patterning across Heliconius and other butterflies. Our understanding of the molecular basis of Heliconius mimicry is now providing important insights into a variety of additional evolutionary phenomena, including the origin of supergenes, the interplay between constraint and evolvability, the genetic basis of convergence, the potential for introgression to facilitate adaptation, the mechanisms of hybrid speciation in animals, and the process of ecological speciation. PMID:25953905

Mechanism of single-pulse ablative generation of laser-induced periodic surface structures

NASA Astrophysics Data System (ADS)

Shugaev, Maxim V.; Gnilitskyi, Iaroslav; Bulgakova, Nadezhda M.; Zhigilei, Leonid V.

2017-11-01

One of the remarkable capabilities of ultrashort polarized laser pulses is the generation of laser-induced periodic surface structures (LIPSS). The origin of this phenomenon is largely attributed to the interference of the incident laser wave and surface electromagnetic wave that creates a periodic absorption pattern. Although, commonly, LIPSS are produced by repetitive irradiation of the same area by multiple laser pulses in the regime of surface melting and resolidification, recent reports demonstrate the formation of LIPSS in the single-pulse irradiation regime at laser fluences well above the ablation threshold. In this paper, we report results of a large-scale molecular dynamics simulation aimed at providing insights into the mechanisms of single-pulse ablative LIPSS formation. The simulation performed for a Cr target reveals an interplay of material removal and redistribution in the course of spatially modulated ablation, leading to the transient formation of an elongated liquid wall extending up to ˜600 nm above the surface of the target at the locations of the minima of the laser energy deposition. The upper part of the liquid wall disintegrates into droplets while the base of the wall solidifies on the time scale of ˜2 ns, producing a ˜100 -nm-tall frozen surface feature extending above the level of the initial surface of the target. The properties of the surface region of the target are modified by the presence of high densities of dislocations and vacancies generated due to the rapid and highly nonequilibrium nature of the melting and resolidification processes. The insights into the LIPSS formation mechanisms may help in designing approaches for increasing the processing speed and improving the quality of the laser-patterned periodic surface structures.

Cognitive inflexibility in obsessive-compulsive disorder

PubMed Central

Gruner, Patricia; Pittenger, Christopher

2016-01-01

Obsessive-Compulsive Disorder (OCD) is characterized by maladaptive patterns of repetitive, inflexible cognition and behavior that suggest a lack of cognitive flexibility. Consistent with this clinical observation, many neurocognitive studies suggest behavioral and neurobiological abnormalities in cognitive flexibility in individuals with OCD. Meta-analytic reviews support a pattern of cognitive inflexibility, with effect sizes generally in the medium range. Heterogeneity in assessments and the way underlying constructs have been operationalized point to the need for better standardization across studies, as well as more refined overarching models of cognitive flexibility and executive function. Neuropsychological assessments of cognitive flexibility include measures of attentional set shifting, reversal and alternation, cued task switching paradigms, cognitive control measures such as the Trail-Making and Stroop tasks, and several measures of motor inhibition. Differences in the cognitive constructs and neural substrates associated with these measures suggest that performance within these different domains should be examined separately. Additional factors, such as the number of consistent trials prior to a shift and whether a shift is explicitly signaled or must be inferred from a change in reward contingencies, may influence performance, and thus mask or accentuate deficits. Several studies have described abnormalities in neural activation in the absence of differences in behavioral performance, suggesting that our behavioral probes may not be adequately sensitive, but also offering important insights into potential compensatory processes. The fact that deficits of moderate effect size are seen across a broad range of classic neuropsychological tests in OCD presents a conceptual challenge, as clinical symptomatology suggests greater specificity. Traditional cognitive probes may not be sufficient to delineate specific domains of deficit in this and other neuropsychiatric disorders; a new generation of behavioral tasks that test more specific underlying constructs, supplemented by neuroimaging to provide greater insight into the underlying processes, may be needed. PMID:27491478

A review of mixing and propulsion of chyme in the small intestine: fresh insights from new methods.

PubMed

Lentle, R G; de Loubens, C

2015-05-01

The small intestine is a convoluted flexible tube of inconstant form and capacity through which chyme is propelled and mixed by varying patterns of contraction. These inconstancies have prevented quantitative comparisons of the manner in which contractile activity engenders mixing of contained chyme. Recent quantitative work based on spatiotemporal mapping of intestinal contractions, macro- and micro-rheology, particle image velocimetry and real-time modelling has provided new insights into this process. Evidence indicates that the speeds and patterns of the various types of small intestinal contraction are insufficient to secure optimal mixing and enzymatic digestion over a minimal length of intestine. Hence particulate substrates and soluble nutrients become dispersed along the length of the lumen. Mixing within the lumen is not turbulent but results from localised folding and kneading of the contents by contractions but is augmented by the inconstant spatial disposition of the contractions and their component contractile processes. The latter include inconstancies in the sites of commencement and the directions of propagation of contraction in component groups of smooth muscle cells and in the coordination of the radial and circular components of smooth muscle contraction. Evidence suggests there is ongoing augmentation of mixing at the periphery of the lumen, during both the post-prandial and inter-meal periods, to promote flow around and between adjacent villi. This results largely from folding of the relatively inelastic mucosa during repeated radial and longitudinal muscular contraction, causing chyme to be displaced by periodic crowding and separation of the tips of the relatively rigid villi. Further, micro-rheological studies indicate that such peripheral mixing may extend to the apices of enterocytes owing to discontinuities in the mobile mucus layer that covers the ileal mucosa.

Predicting animal home-range structure and transitions using a multistate Ornstein-Uhlenbeck biased random walk

USGS Publications Warehouse

Breed, Greg A.; Golson, Emily A.; Tinker, M. Tim

2017-01-01

The home‐range concept is central in animal ecology and behavior, and numerous mechanistic models have been developed to understand home range formation and maintenance. These mechanistic models usually assume a single, contiguous home range. Here we describe and implement a simple home‐range model that can accommodate multiple home‐range centers, form complex shapes, allow discontinuities in use patterns, and infer how external and internal variables affect movement and use patterns. The model assumes individuals associate with two or more home‐range centers and move among them with some estimable probability. Movement in and around home‐range centers is governed by a two‐dimensional Ornstein‐Uhlenbeck process, while transitions between centers are modeled as a stochastic state‐switching process. We augmented this base model by introducing environmental and demographic covariates that modify transition probabilities between home‐range centers and can be estimated to provide insight into the movement process. We demonstrate the model using telemetry data from sea otters (Enhydra lutris) in California. The model was fit using a Bayesian Markov Chain Monte Carlo method, which estimated transition probabilities, as well as unique Ornstein‐Uhlenbeck diffusion and centralizing tendency parameters. Estimated parameters could then be used to simulate movement and space use that was virtually indistinguishable from real data. We used Deviance Information Criterion (DIC) scores to assess model fit and determined that both wind and reproductive status were predictive of transitions between home‐range centers. Females were less likely to move between home‐range centers on windy days, less likely to move between centers when tending pups, and much more likely to move between centers just after weaning a pup. These tendencies are predicted by theoretical movement rules but were not previously known and show that our model can extract meaningful behavioral insight from complex movement data.

Natural thermodynamics

NASA Astrophysics Data System (ADS)

Annila, Arto

2016-02-01

The principle of increasing entropy is derived from statistical physics of open systems assuming that quanta of actions, as undividable basic build blocks, embody everything. According to this tenet, all systems evolve from one state to another either by acquiring quanta from their surroundings or by discarding quanta to the surroundings in order to attain energetic balance in least time. These natural processes result in ubiquitous scale-free patterns: skewed distributions that accumulate in a sigmoid manner and hence span log-log scales mostly as straight lines. Moreover, the equation for least-time motions reveals that evolution is by nature a non-deterministic process. Although the obtained insight in thermodynamics from the notion of quanta in motion yields nothing new, it accentuates that contemporary comprehension is impaired when modeling evolution as a computable process by imposing conservation of energy and thereby ignoring that quantum of actions are the carriers of energy from the system to its surroundings.

Diet and Exercise in Parenthood: A Social Control Perspective

PubMed Central

Reczek, Corinne; Beth Thomeer, Mieke; Lodge, Amy C.; Umberson, Debra; Underhill, Megan

2014-01-01

Previous work on social control—the direct and indirect regulation of an individual’s health behaviors by others—suggests that parent–child relationships promote healthy diet and exercise. Yet parenthood is associated with less healthy diet and exercise patterns. The authors investigated this paradox by examining social control processes in 40 in-depth interviews with mothers and fathers. They found that parenthood involves social control processes that both promote and compromise healthy behavior, contributing to contradictory perceived effects of parenthood on health behavior. Moreover, the dynamics of social control appear to unfold in different ways for mothers and fathers and depend on the child’s gender and life stage, suggesting that gender and age dyads are central to understanding the seemingly contradictory consequences of parenthood at the population level. These articulations of gendered social control processes provide new insight into the consequences of the gendered organization of parenthood for diet and exercise. PMID:25328244

Large-Scale Fluorescence Calcium-Imaging Methods for Studies of Long-Term Memory in Behaving Mammals

PubMed Central

Jercog, Pablo; Rogerson, Thomas; Schnitzer, Mark J.

2016-01-01

During long-term memory formation, cellular and molecular processes reshape how individual neurons respond to specific patterns of synaptic input. It remains poorly understood how such changes impact information processing across networks of mammalian neurons. To observe how networks encode, store, and retrieve information, neuroscientists must track the dynamics of large ensembles of individual cells in behaving animals, over timescales commensurate with long-term memory. Fluorescence Ca2+-imaging techniques can monitor hundreds of neurons in behaving mice, opening exciting avenues for studies of learning and memory at the network level. Genetically encoded Ca2+ indicators allow neurons to be targeted by genetic type or connectivity. Chronic animal preparations permit repeated imaging of neural Ca2+ dynamics over multiple weeks. Together, these capabilities should enable unprecedented analyses of how ensemble neural codes evolve throughout memory processing and provide new insights into how memories are organized in the brain. PMID:27048190

Induced Seismicity

NASA Astrophysics Data System (ADS)

Keranen, Katie M.; Weingarten, Matthew

2018-05-01

The ability of fluid-generated subsurface stress changes to trigger earthquakes has long been recognized. However, the dramatic rise in the rate of human-induced earthquakes in the past decade has created abundant opportunities to study induced earthquakes and triggering processes. This review briefly summarizes early studies but focuses on results from induced earthquakes during the past 10 years related to fluid injection in petroleum fields. Study of these earthquakes has resulted in insights into physical processes and has identified knowledge gaps and future research directions. Induced earthquakes are challenging to identify using seismological methods, and faults and reefs strongly modulate spatial and temporal patterns of induced seismicity. However, the similarity of induced and natural seismicity provides an effective tool for studying earthquake processes. With continuing development of energy resources, increased interest in carbon sequestration, and construction of large dams, induced seismicity will continue to pose a hazard in coming years.

Hydrozoan insights in animal development and evolution.

PubMed

Leclère, Lucas; Copley, Richard R; Momose, Tsuyoshi; Houliston, Evelyn

2016-08-01

The fresh water polyp Hydra provides textbook experimental demonstration of positional information gradients and regeneration processes. Developmental biologists are thus familiar with Hydra, but may not appreciate that it is a relatively simple member of the Hydrozoa, a group of mostly marine cnidarians with complex and diverse life cycles, exhibiting extensive phenotypic plasticity and regenerative capabilities. Hydrozoan species offer extensive opportunities to address many developmental mechanisms relevant across the animal kingdom. Here we review recent work from non-Hydra hydrozoans - hydromedusae, hydroids and siphonophores - shedding light on mechanisms of oogenesis, embryonic patterning, allorecognition, stem cell regulation and regeneration. We also highlight potential research directions in which hydrozoan diversity can illuminate the evolution of developmental processes at micro- and macro-evolutionary time scales. Copyright © 2016 Elsevier Ltd. All rights reserved.

On the relation between dependency distance, crossing dependencies, and parsing. Comment on "Dependency distance: a new perspective on syntactic patterns in natural languages" by Haitao Liu et al.

NASA Astrophysics Data System (ADS)

Gómez-Rodríguez, Carlos

2017-07-01

Liu et al. [1] provide a comprehensive account of research on dependency distance in human languages. While the article is a very rich and useful report on this complex subject, here I will expand on a few specific issues where research in computational linguistics (specifically natural language processing) can inform DDM research, and vice versa. These aspects have not been explored much in [1] or elsewhere, probably due to the little overlap between both research communities, but they may provide interesting insights for improving our understanding of the evolution of human languages, the mechanisms by which the brain processes and understands language, and the construction of effective computer systems to achieve this goal.

The brain in time: insights from neuromagnetic recordings.

PubMed

Hari, Riitta; Parkkonen, Lauri; Nangini, Cathy

2010-03-01

The millisecond time resolution of magnetoencephalography (MEG) is instrumental for investigating the brain basis of sensory processing, motor planning, cognition, and social interaction. We review the basic principles, recent progress, and future potential of MEG in noninvasive tracking of human brain activity. Cortical activation sequences from tens to hundreds of milliseconds can be followed during, e.g., perception, motor action, imitation, and language processing by recording both spontaneous and evoked brain signals. Moreover, tagging of sensory input can be used to reveal neuronal mechanisms of binaural interaction and perception of ambiguous images. The results support the emerging ideas of multiple, hierarchically organized temporal scales in human brain function. Instrumentation and data analysis methods are rapidly progressing, enabling attempts to decode the four-dimensional spatiotemporal signal patterns to reveal correlates of behavior and mental contents.

Age-related epigenetic drift and phenotypic plasticity loss: implications in prevention of age-related human diseases

PubMed Central

Li, Yuanyuan; Tollefsbol, Trygve O

2016-01-01

Aging is considered as one of the most important developmental processes in organisms and is closely associated with global deteriorations of epigenetic markers such as aberrant methylomic patterns. This altered epigenomic state, referred to ‘epigenetic drift’, reflects deficient maintenance of epigenetic marks and contributes to impaired cellular and molecular functions in aged cells. Epigenetic drift-induced abnormal changes during aging are scantily repaired by epigenetic modulators. This inflexibility in the aged epigenome may lead to an age-related decline in phenotypic plasticity at the cellular and molecular levels due to epigenetic drift. This perspective aims to provide novel concepts for understanding epigenetic effects on the aging process and to provide insights into epigenetic prevention and therapeutic strategies for age-related human disease. PMID:27882781

Teacher change in beliefs and practices in science and literacy instruction with English language learners

NASA Astrophysics Data System (ADS)

Lee, Okhee

2004-01-01

This study examined patterns of change in beliefs and practices as elementary teachers learned to establish instructional congruence, a process of mediating academic disciplines with linguistic and cultural experiences of diverse student groups. The study focused on six bilingual Hispanic teachers working with fourth-grade, mostly Hispanic students. The results indicated that teacher learning and change occurred in different ways in the areas of science instruction, students' language and culture, English language and literacy instruction, and integration of these areas in establishing instructional congruence. The results also indicated that establishing instructional congruence was a gradual and demanding process requiring teacher reflection and insight, formal training, and extensive support and sharing. Implications for further research in promoting achievement for all students are discussed.

Insights into Learning Profiles and Learning Outcomes within Introductory Accounting

ERIC Educational Resources Information Center

Teixeira, Cláudia; Gomes, Delfina

2017-01-01

This paper reports an empirical study aiming to explore aspects of learning and studying introductory accounting in Portuguese higher education. It specifically provides insight into patterns of learning and learning outcomes. To do so, it draws on qualitative data collected from students' answers to a semi-structured interview about their…

The Manifest Association Structure of the Single-Factor Model: Insights from Partial Correlations

ERIC Educational Resources Information Center

Salgueiro, Maria de Fatima; Smith, Peter W. F.; McDonald, John W.

2008-01-01

The association structure between manifest variables arising from the single-factor model is investigated using partial correlations. The additional insights to the practitioner provided by partial correlations for detecting a single-factor model are discussed. The parameter space for the partial correlations is presented, as are the patterns of…

Alternative Work Patterns: Implications for Worklife Education and Training. Worker Education and Training Policies Project.

ERIC Educational Resources Information Center

Shore, Jane

This monograph explores the major categories of alternative work patterns, e.g., flexitime, permanent part-time employment, job sharing, the compressed work week, and reduced work time. Advantages and disadvantages of each type are discussed, and new insight is offered into an unexplored dimension of the major types of alternative work patterns:…

Genomic insights into the Ixodes scapularis tick vector of Lyme disease

PubMed Central

Gulia-Nuss, Monika; Nuss, Andrew B.; Meyer, Jason M.; Sonenshine, Daniel E.; Roe, R. Michael; Waterhouse, Robert M.; Sattelle, David B.; de la Fuente, José; Ribeiro, Jose M.; Megy, Karine; Thimmapuram, Jyothi; Miller, Jason R.; Walenz, Brian P.; Koren, Sergey; Hostetler, Jessica B.; Thiagarajan, Mathangi; Joardar, Vinita S.; Hannick, Linda I.; Bidwell, Shelby; Hammond, Martin P.; Young, Sarah; Zeng, Qiandong; Abrudan, Jenica L.; Almeida, Francisca C.; Ayllón, Nieves; Bhide, Ketaki; Bissinger, Brooke W.; Bonzon-Kulichenko, Elena; Buckingham, Steven D.; Caffrey, Daniel R.; Caimano, Melissa J.; Croset, Vincent; Driscoll, Timothy; Gilbert, Don; Gillespie, Joseph J.; Giraldo-Calderón, Gloria I.; Grabowski, Jeffrey M.; Jiang, David; Khalil, Sayed M. S.; Kim, Donghun; Kocan, Katherine M.; Koči, Juraj; Kuhn, Richard J.; Kurtti, Timothy J.; Lees, Kristin; Lang, Emma G.; Kennedy, Ryan C.; Kwon, Hyeogsun; Perera, Rushika; Qi, Yumin; Radolf, Justin D.; Sakamoto, Joyce M.; Sánchez-Gracia, Alejandro; Severo, Maiara S.; Silverman, Neal; Šimo, Ladislav; Tojo, Marta; Tornador, Cristian; Van Zee, Janice P.; Vázquez, Jesús; Vieira, Filipe G.; Villar, Margarita; Wespiser, Adam R.; Yang, Yunlong; Zhu, Jiwei; Arensburger, Peter; Pietrantonio, Patricia V.; Barker, Stephen C.; Shao, Renfu; Zdobnov, Evgeny M.; Hauser, Frank; Grimmelikhuijzen, Cornelis J. P.; Park, Yoonseong; Rozas, Julio; Benton, Richard; Pedra, Joao H. F.; Nelson, David R.; Unger, Maria F.; Tubio, Jose M. C.; Tu, Zhijian; Robertson, Hugh M.; Shumway, Martin; Sutton, Granger; Wortman, Jennifer R.; Lawson, Daniel; Wikel, Stephen K.; Nene, Vishvanath M.; Fraser, Claire M.; Collins, Frank H.; Birren, Bruce; Nelson, Karen E.; Caler, Elisabet; Hill, Catherine A.

2016-01-01

Ticks transmit more pathogens to humans and animals than any other arthropod. We describe the 2.1 Gbp nuclear genome of the tick, Ixodes scapularis (Say), which vectors pathogens that cause Lyme disease, human granulocytic anaplasmosis, babesiosis and other diseases. The large genome reflects accumulation of repetitive DNA, new lineages of retro-transposons, and gene architecture patterns resembling ancient metazoans rather than pancrustaceans. Annotation of scaffolds representing ∼57% of the genome, reveals 20,486 protein-coding genes and expansions of gene families associated with tick–host interactions. We report insights from genome analyses into parasitic processes unique to ticks, including host ‘questing', prolonged feeding, cuticle synthesis, blood meal concentration, novel methods of haemoglobin digestion, haem detoxification, vitellogenesis and prolonged off-host survival. We identify proteins associated with the agent of human granulocytic anaplasmosis, an emerging disease, and the encephalitis-causing Langat virus, and a population structure correlated to life-history traits and transmission of the Lyme disease agent. PMID:26856261

Gene expression analysis of aquatic angiosperms podostemaceae to gain insight into the evolution of their enigmatic morphology.

PubMed

Koi, Satoshi; Katayama, Natsu

2013-01-01

Podostemaceae is a family of aquatic angiosperms growing submerged on rocks in fast-flowing water and called moss-like or alga-like riverweeds. It evolved remarkable innovations to adapt to such an extreme environment, one of which is reduced shoots borne on roots adhering to rock surface. Recent observations revealed that the basal subfamily Tristichoideae, like most other angiosperms, has typical shoot apical meristems (SAMs). In species of the subfamily Podostemoideae, however, shoot apical meristems (SAMs) are not formed during development and new leaves arise from the meristematic basal region of preexisting leaves. The genetic basis of this shoot organogenesis process, e.g., the expression patterns of genes homologous to transcription factors regulating shoot development, is essential to better understand the evolution of Podostemaceae. A gene expression analysis found that the SAM-less Podostemoideae leaf has mixed identity of SAM and leaf, and provided insight into the evolution of the shoot in Podostemaceae.

Genomic insights into the Ixodes scapularis tick vector of Lyme disease.

PubMed

Gulia-Nuss, Monika; Nuss, Andrew B; Meyer, Jason M; Sonenshine, Daniel E; Roe, R Michael; Waterhouse, Robert M; Sattelle, David B; de la Fuente, José; Ribeiro, Jose M; Megy, Karine; Thimmapuram, Jyothi; Miller, Jason R; Walenz, Brian P; Koren, Sergey; Hostetler, Jessica B; Thiagarajan, Mathangi; Joardar, Vinita S; Hannick, Linda I; Bidwell, Shelby; Hammond, Martin P; Young, Sarah; Zeng, Qiandong; Abrudan, Jenica L; Almeida, Francisca C; Ayllón, Nieves; Bhide, Ketaki; Bissinger, Brooke W; Bonzon-Kulichenko, Elena; Buckingham, Steven D; Caffrey, Daniel R; Caimano, Melissa J; Croset, Vincent; Driscoll, Timothy; Gilbert, Don; Gillespie, Joseph J; Giraldo-Calderón, Gloria I; Grabowski, Jeffrey M; Jiang, David; Khalil, Sayed M S; Kim, Donghun; Kocan, Katherine M; Koči, Juraj; Kuhn, Richard J; Kurtti, Timothy J; Lees, Kristin; Lang, Emma G; Kennedy, Ryan C; Kwon, Hyeogsun; Perera, Rushika; Qi, Yumin; Radolf, Justin D; Sakamoto, Joyce M; Sánchez-Gracia, Alejandro; Severo, Maiara S; Silverman, Neal; Šimo, Ladislav; Tojo, Marta; Tornador, Cristian; Van Zee, Janice P; Vázquez, Jesús; Vieira, Filipe G; Villar, Margarita; Wespiser, Adam R; Yang, Yunlong; Zhu, Jiwei; Arensburger, Peter; Pietrantonio, Patricia V; Barker, Stephen C; Shao, Renfu; Zdobnov, Evgeny M; Hauser, Frank; Grimmelikhuijzen, Cornelis J P; Park, Yoonseong; Rozas, Julio; Benton, Richard; Pedra, Joao H F; Nelson, David R; Unger, Maria F; Tubio, Jose M C; Tu, Zhijian; Robertson, Hugh M; Shumway, Martin; Sutton, Granger; Wortman, Jennifer R; Lawson, Daniel; Wikel, Stephen K; Nene, Vishvanath M; Fraser, Claire M; Collins, Frank H; Birren, Bruce; Nelson, Karen E; Caler, Elisabet; Hill, Catherine A

2016-02-09

Ticks transmit more pathogens to humans and animals than any other arthropod. We describe the 2.1 Gbp nuclear genome of the tick, Ixodes scapularis (Say), which vectors pathogens that cause Lyme disease, human granulocytic anaplasmosis, babesiosis and other diseases. The large genome reflects accumulation of repetitive DNA, new lineages of retro-transposons, and gene architecture patterns resembling ancient metazoans rather than pancrustaceans. Annotation of scaffolds representing ∼57% of the genome, reveals 20,486 protein-coding genes and expansions of gene families associated with tick-host interactions. We report insights from genome analyses into parasitic processes unique to ticks, including host 'questing', prolonged feeding, cuticle synthesis, blood meal concentration, novel methods of haemoglobin digestion, haem detoxification, vitellogenesis and prolonged off-host survival. We identify proteins associated with the agent of human granulocytic anaplasmosis, an emerging disease, and the encephalitis-causing Langat virus, and a population structure correlated to life-history traits and transmission of the Lyme disease agent.

The Added Value of Log File Analyses of the Use of a Personal Health Record for Patients With Type 2 Diabetes Mellitus

PubMed Central

Kelders, Saskia M.; Braakman-Jansen, Louise M. A.; van Gemert-Pijnen, Julia E. W. C.

2014-01-01

The electronic personal health record (PHR) is a promising technology for improving the quality of chronic disease management. Until now, evaluations of such systems have provided only little insight into why a particular outcome occurred. The aim of this study is to gain insight into the navigation process (what functionalities are used, and in what sequence) of e-Vita, a PHR for patients with type 2 diabetes mellitus (T2DM), to increase the efficiency of the system and improve the long-term adherence. Log data of the first visits in the first 6 weeks after the release of a renewed version of e-Vita were analyzed to identify the usage patterns that emerge when users explore a new application. After receiving the invitation, 28% of all registered users visited e-Vita. In total, 70 unique usage patterns could be identified. When users visited the education service first, 93% of all users ended their session. Most users visited either 1 or 5 or more services during their first session, but the distribution of the routes was diffuse. In conclusion, log file analyses can provide valuable prompts for improving the system design of a PHR. In this way, the match between the system and its users and the long-term adherence has the potential to increase. PMID:24876574

Entropy and Gravity Concepts as New Methodological Indexes to Investigate Technological Convergence: Patent Network-Based Approach

PubMed Central

Cho, Yongrae; Kim, Minsung

2014-01-01

The volatility and uncertainty in the process of technological developments are growing faster than ever due to rapid technological innovations. Such phenomena result in integration among disparate technology fields. At this point, it is a critical research issue to understand the different roles and the propensity of each element technology for technological convergence. In particular, the network-based approach provides a holistic view in terms of technological linkage structures. Furthermore, the development of new indicators based on network visualization can reveal the dynamic patterns among disparate technologies in the process of technological convergence and provide insights for future technological developments. This research attempts to analyze and discover the patterns of the international patent classification codes of the United States Patent and Trademark Office's patent data in printed electronics, which is a representative technology in the technological convergence process. To this end, we apply the physical idea as a new methodological approach to interpret technological convergence. More specifically, the concepts of entropy and gravity are applied to measure the activities among patent citations and the binding forces among heterogeneous technologies during technological convergence. By applying the entropy and gravity indexes, we could distinguish the characteristic role of each technology in printed electronics. At the technological convergence stage, each technology exhibits idiosyncratic dynamics which tend to decrease technological differences and heterogeneity. Furthermore, through nonlinear regression analysis, we have found the decreasing patterns of disparity over a given total period in the evolution of technological convergence. This research has discovered the specific role of each element technology field and has consequently identified the co-evolutionary patterns of technological convergence. These new findings on the evolutionary patterns of technological convergence provide some implications for engineering and technology foresight research, as well as for corporate strategy and technology policy. PMID:24914959

Word Naming in the L1 and L2: A Dynamic Perspective on Automatization and the Degree of Semantic Involvement in Naming

PubMed Central

Plat, Rika; Lowie, Wander; de Bot, Kees

2018-01-01

Reaction time data have long been collected in order to gain insight into the underlying mechanisms involved in language processing. Means analyses often attempt to break down what factors relate to what portion of the total reaction time. From a dynamic systems theory perspective or an interaction dominant view of language processing, it is impossible to isolate discrete factors contributing to language processing, since these continually and interactively play a role. Non-linear analyses offer the tools to investigate the underlying process of language use in time, without having to isolate discrete factors. Patterns of variability in reaction time data may disclose the relative contribution of automatic (grapheme-to-phoneme conversion) processing and attention-demanding (semantic) processing. The presence of a fractal structure in the variability of a reaction time series indicates automaticity in the mental structures contributing to a task. A decorrelated pattern of variability will indicate a higher degree of attention-demanding processing. A focus on variability patterns allows us to examine the relative contribution of automatic and attention-demanding processing when a speaker is using the mother tongue (L1) or a second language (L2). A word naming task conducted in the L1 (Dutch) and L2 (English) shows L1 word processing to rely more on automatic spelling-to-sound conversion than L2 word processing. A word naming task with a semantic categorization subtask showed more reliance on attention-demanding semantic processing when using the L2. A comparison to L1 English data shows this was not only due to the amount of language use or language dominance, but also to the difference in orthographic depth between Dutch and English. An important implication of this finding is that when the same task is used to test and compare different languages, one cannot straightforwardly assume the same cognitive sub processes are involved to an equal degree using the same task in different languages. PMID:29403404

A cross correlation method for chemical profiles in minerals, with an application to zircons of the Kilgore Tuff (USA)

NASA Astrophysics Data System (ADS)

Probst, L. C.; Sheldrake, T. E.; Gander, M. J.; Wallace, G.; Simpson, G.; Caricchi, L.

2018-03-01

Magmatic crystals are characterised by chemical zonation patterns that reflect the thermal and chemical conditions within magma reservoirs in which they grew. Crystals that exhibit similar patterns of zonation are often interpreted to have experienced similar conditions of growth. These patterns of zonation may represent continuous processes such as cooling, or more instantaneous events such as magma injection, and provide an insight into the structure and evolution of a magmatic system, both temporally and spatially. We have developed an algorithm that is objectively able to quantify the similarity within and between suites of magmatic crystals from different samples. Significantly, the algorithm is able to identify correlation that occurs between the interiors of two crystals, but does not extend to the rim, which provides an opportunity to understand the long-term evolution of magmatic systems. We develop and explain the mathematical basis for our algorithm and introduce its application using cathodoluminescence images of zircons from the Kilgore Tuff (USA). The results allow us to correlate samples from two different outcrops that are found over 80 km apart.

Bi-PROF

PubMed Central

Gries, Jasmin; Schumacher, Dirk; Arand, Julia; Lutsik, Pavlo; Markelova, Maria Rivera; Fichtner, Iduna; Walter, Jörn; Sers, Christine; Tierling, Sascha

2013-01-01

The use of next generation sequencing has expanded our view on whole mammalian methylome patterns. In particular, it provides a genome-wide insight of local DNA methylation diversity at single nucleotide level and enables the examination of single chromosome sequence sections at a sufficient statistical power. We describe a bisulfite-based sequence profiling pipeline, Bi-PROF, which is based on the 454 GS-FLX Titanium technology that allows to obtain up to one million sequence stretches at single base pair resolution without laborious subcloning. To illustrate the performance of the experimental workflow connected to a bioinformatics program pipeline (BiQ Analyzer HT) we present a test analysis set of 68 different epigenetic marker regions (amplicons) in five individual patient-derived xenograft tissue samples of colorectal cancer and one healthy colon epithelium sample as a control. After the 454 GS-FLX Titanium run, sequence read processing and sample decoding, the obtained alignments are quality controlled and statistically evaluated. Comprehensive methylation pattern interpretation (profiling) assessed by analyzing 102-104 sequence reads per amplicon allows an unprecedented deep view on pattern formation and methylation marker heterogeneity in tissues concerned by complex diseases like cancer. PMID:23803588

Graph Theoretical Framework of Brain Networks in Multiple Sclerosis: A Review of Concepts.

PubMed

Fleischer, Vinzenz; Radetz, Angela; Ciolac, Dumitru; Muthuraman, Muthuraman; Gonzalez-Escamilla, Gabriel; Zipp, Frauke; Groppa, Sergiu

2017-11-01

Network science provides powerful access to essential organizational principles of the human brain. It has been applied in combination with graph theory to characterize brain connectivity patterns. In multiple sclerosis (MS), analysis of the brain networks derived from either structural or functional imaging provides new insights into pathological processes within the gray and white matter. Beyond focal lesions and diffuse tissue damage, network connectivity patterns could be important for closely tracking and predicting the disease course. In this review, we describe concepts of graph theory, highlight novel issues of tissue reorganization in acute and chronic neuroinflammation and address pitfalls with regard to network analysis in MS patients. We further provide an outline of functional and structural connectivity patterns observed in MS, spanning from disconnection and disruption on one hand to adaptation and compensation on the other. Moreover, we link network changes and their relation to clinical disability based on the current literature. Finally, we discuss the perspective of network science in MS for future research and postulate its role in the clinical framework. Copyright © 2017 IBRO. Published by Elsevier Ltd. All rights reserved.

Learning Midlevel Auditory Codes from Natural Sound Statistics.

PubMed

Młynarski, Wiktor; McDermott, Josh H

2018-03-01

Interaction with the world requires an organism to transform sensory signals into representations in which behaviorally meaningful properties of the environment are made explicit. These representations are derived through cascades of neuronal processing stages in which neurons at each stage recode the output of preceding stages. Explanations of sensory coding may thus involve understanding how low-level patterns are combined into more complex structures. To gain insight into such midlevel representations for sound, we designed a hierarchical generative model of natural sounds that learns combinations of spectrotemporal features from natural stimulus statistics. In the first layer, the model forms a sparse convolutional code of spectrograms using a dictionary of learned spectrotemporal kernels. To generalize from specific kernel activation patterns, the second layer encodes patterns of time-varying magnitude of multiple first-layer coefficients. When trained on corpora of speech and environmental sounds, some second-layer units learned to group similar spectrotemporal features. Others instantiate opponency between distinct sets of features. Such groupings might be instantiated by neurons in the auditory cortex, providing a hypothesis for midlevel neuronal computation.

Area-based tests for association between spatial patterns

NASA Astrophysics Data System (ADS)

Maruca, Susan L.; Jacquez, Geoffrey M.

Edge effects pervade natural systems, and the processes that determine spatial heterogeneity (e.g. physical, geochemical, biological, ecological factors) occur on diverse spatial scales. Hence, tests for association between spatial patterns should be unbiased by edge effects and be based on null spatial models that incorporate the spatial heterogeneity characteristic of real-world systems. This paper develops probabilistic pattern association tests that are appropriate when edge effects are present, polygon size is heterogeneous, and the number of polygons varies from one classification to another. The tests are based on the amount of overlap between polygons in each of two partitions. Unweighted and area-weighted versions of the statistics are developed and verified using scenarios representing both polygon overlap and avoidance at different spatial scales and for different distributions of polygon sizes. These statistics were applied to Soda Butte Creek, Wyoming, to determine whether stream microhabitats, such as riffles, pools and glides, can be identified remotely using high spatial resolution hyperspectral imagery. These new ``spatially explicit'' techniques provide information and insights that cannot be obtained from the spectral information alone.

Multiscale analysis of information dynamics for linear multivariate processes.

PubMed

Faes, Luca; Montalto, Alessandro; Stramaglia, Sebastiano; Nollo, Giandomenico; Marinazzo, Daniele

2016-08-01

In the study of complex physical and physiological systems represented by multivariate time series, an issue of great interest is the description of the system dynamics over a range of different temporal scales. While information-theoretic approaches to the multiscale analysis of complex dynamics are being increasingly used, the theoretical properties of the applied measures are poorly understood. This study introduces for the first time a framework for the analytical computation of information dynamics for linear multivariate stochastic processes explored at different time scales. After showing that the multiscale processing of a vector autoregressive (VAR) process introduces a moving average (MA) component, we describe how to represent the resulting VARMA process using statespace (SS) models and how to exploit the SS model parameters to compute analytical measures of information storage and information transfer for the original and rescaled processes. The framework is then used to quantify multiscale information dynamics for simulated unidirectionally and bidirectionally coupled VAR processes, showing that rescaling may lead to insightful patterns of information storage and transfer but also to potentially misleading behaviors.

Normalized burn ratios link fire severity with patterns of avian occurrence

USGS Publications Warehouse

Rose, Eli T.; Simons, Theodore R.; Klein, Rob; McKerrow, Alexa

2016-01-01

ContextRemotely sensed differenced normalized burn ratios (DNBR) provide an index of fire severity across the footprint of a fire. We asked whether this index was useful for explaining patterns of bird occurrence within fire adapted xeric pine-oak forests of the southern Appalachian Mountains.ObjectivesWe evaluated the use of DNBR indices for linking ecosystem process with patterns of bird occurrence. We compared field-based and remotely sensed fire severity indices and used each to develop occupancy models for six bird species to identify patterns of bird occurrence following fire.MethodsWe identified and sampled 228 points within fires that recently burned within Great Smoky Mountains National Park. We performed avian point counts and field-assessed fire severity at each bird census point. We also used Landsat™ imagery acquired before and after each fire to quantify fire severity using DNBR. We used non-parametric methods to quantify agreement between fire severity indices, and evaluated single season occupancy models incorporating fire severity summarized at different spatial scales.ResultsAgreement between field-derived and remotely sensed measures of fire severity was influenced by vegetation type. Although occurrence models using field-derived indices of fire severity outperformed those using DNBR, summarizing DNBR at multiple spatial scales provided additional insights into patterns of occurrence associated with different sized patches of high severity fire.ConclusionsDNBR is useful for linking the effects of fire severity to patterns of bird occurrence, and informing how high severity fire shapes patterns of bird species occurrence on the landscape.

Scaling Effects of Cr(VI) Reduction Kinetics. The Role of Geochemical Heterogeneity

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

Wang, Li; Li, Li

2015-10-22

The natural subsurface is highly heterogeneous with minerals distributed in different spatial patterns. Fundamental understanding of how mineral spatial distribution patterns regulate sorption process is important for predicting the transport and fate of chemicals. Existing studies about the sorption was carried out in well-mixed batch reactors or uniformly packed columns, with few data available on the effects of spatial heterogeneities. As a result, there is a lack of data and understanding on how spatial heterogeneities control sorption processes. In this project, we aim to understand and develop modeling capabilities to predict the sorption of Cr(VI), an omnipresent contaminant in naturalmore » systems due to its natural occurrence and industrial utilization. We systematically examine the role of spatial patterns of illite, a common clay, in determining the extent of transport limitation and scaling effects associated with Cr(VI) sorption capacity and kinetics using column experiments and reactive transport modeling. Our results showed that the sorbed mass and rates can differ by an order of magnitude due to of the illite spatial heterogeneities and transport limitation. With constraints from data, we also developed the capabilities of modeling Cr(VI) in heterogeneous media. The developed model is then utilized to understand the general principles that govern the relationship between sorption and connectivity, a key measure of the spatial pattern characteristics. This correlation can be used to estimate Cr(VI) sorption characteristics in heterogeneous porous media. Insights gained here bridge gaps between laboratory and field application in hydrogeology and geochemical field, and advance predictive understanding of reactive transport processes in the natural heterogeneous subsurface. We believe that these findings will be of interest to a large number of environmental geochemists and engineers, hydrogeologists, and those interested in contaminant fate and transport, water quality and water composition, and natural attenuation processes in natural systems.« less

Finite Element Analysis of the Implantation Process of Overlapping Stents

PubMed Central

Xu, Jiang; Yang, Jie; Sohrabi, Salman; Zhou, Yihua; Liu, Yaling

2017-01-01

Overlapping stents are widely used in vascular stent surgeries. However, the rate of stent fractures (SF) and in-stent restenosis (ISR) after using overlapping stents is higher than that of single stent implantations. Published studies investigating the nature of overlapping stents rely primarily on medical images, which can only reveal the effect of the surgery without providing insights into how stent overlap influences the implantation process. In this paper, a finite element analysis of the overlapping stent implantation process was performed to study the interaction between overlapping stents. Four different cases, based on three typical stent overlap modes and two classical balloons, were investigated. The results showed that overlapping contact patterns among struts were edge-to-edge, edge-to-surface, and noncontact. These were mainly induced by the nonuniform deformation of the stent in the radial direction and stent tubular structures. Meanwhile, the results also revealed that the contact pressure was concentrated in the edge of overlapping struts. During the stent overlap process, the contact pattern was primarily edge-to-edge contact at the beginning and edge-to-surface contact as the contact pressure increased. The interactions between overlapping stents suggest that the failure of overlapping stents frequently occurs along stent edges, which agrees with the previous experimental research regarding the safety of overlapping stents. This paper also provides a fundamental understanding of the mechanical properties of overlapping stents. PMID:28690712

The developing human connectome project: A minimal processing pipeline for neonatal cortical surface reconstruction.

PubMed

Makropoulos, Antonios; Robinson, Emma C; Schuh, Andreas; Wright, Robert; Fitzgibbon, Sean; Bozek, Jelena; Counsell, Serena J; Steinweg, Johannes; Vecchiato, Katy; Passerat-Palmbach, Jonathan; Lenz, Gregor; Mortari, Filippo; Tenev, Tencho; Duff, Eugene P; Bastiani, Matteo; Cordero-Grande, Lucilio; Hughes, Emer; Tusor, Nora; Tournier, Jacques-Donald; Hutter, Jana; Price, Anthony N; Teixeira, Rui Pedro A G; Murgasova, Maria; Victor, Suresh; Kelly, Christopher; Rutherford, Mary A; Smith, Stephen M; Edwards, A David; Hajnal, Joseph V; Jenkinson, Mark; Rueckert, Daniel

2018-06-01

The Developing Human Connectome Project (dHCP) seeks to create the first 4-dimensional connectome of early life. Understanding this connectome in detail may provide insights into normal as well as abnormal patterns of brain development. Following established best practices adopted by the WU-MINN Human Connectome Project (HCP), and pioneered by FreeSurfer, the project utilises cortical surface-based processing pipelines. In this paper, we propose a fully automated processing pipeline for the structural Magnetic Resonance Imaging (MRI) of the developing neonatal brain. This proposed pipeline consists of a refined framework for cortical and sub-cortical volume segmentation, cortical surface extraction, and cortical surface inflation, which has been specifically designed to address considerable differences between adult and neonatal brains, as imaged using MRI. Using the proposed pipeline our results demonstrate that images collected from 465 subjects ranging from 28 to 45 weeks post-menstrual age (PMA) can be processed fully automatically; generating cortical surface models that are topologically correct, and correspond well with manual evaluations of tissue boundaries in 85% of cases. Results improve on state-of-the-art neonatal tissue segmentation models and significant errors were found in only 2% of cases, where these corresponded to subjects with high motion. Downstream, these surfaces will enhance comparisons of functional and diffusion MRI datasets, supporting the modelling of emerging patterns of brain connectivity. Copyright © 2018 Elsevier Inc. All rights reserved.

Orthographic influences on division of labor in learning to read Chinese and English: Insights from computational modeling

PubMed Central

Yang, Jianfeng; Shu, Hua; McCandliss, Bruce D.; Zevin, Jason D.

2013-01-01

Learning to read any language requires learning to map among print, sound and meaning. Writing systems differ in a number of factors that influence both the ease and rate with which reading skill can be acquired, as well as the eventual division of labor between phonological and semantic processes. Further, developmental reading disability manifests differently across writing systems, and may be related to different deficits in constitutive processes. Here we simulate some aspects of reading acquisition in Chinese and English using the same model architecture for both writing systems. The contribution of semantic and phonological processing to literacy acquisition in the two languages is simulated, including specific effects of phonological and semantic deficits. Further, we demonstrate that similar patterns of performance are observed when the same model is trained on both Chinese and English as an "early bilingual." The results are consistent with the view that reading skill is acquired by the application of statistical learning rules to mappings among print, sound and meaning, and that differences in the typical and disordered acquisition of reading skill between writing systems are driven by differences in the statistical patterns of the writing systems themselves, rather than differences in cognitive architecture of the learner. PMID:24587693

What can be found in scalp EEG spectrum beyond common frequency bands. EEG-fMRI study

NASA Astrophysics Data System (ADS)

Marecek, R.; Lamos, M.; Mikl, M.; Barton, M.; Fajkus, J.; I, Rektor; Brazdil, M.

2016-08-01

Objective. The scalp EEG spectrum is a frequently used marker of neural activity. Commonly, the preprocessing of EEG utilizes constraints, e.g. dealing with a predefined subset of electrodes or a predefined frequency band of interest. Such treatment of the EEG spectrum neglects the fact that particular neural processes may be reflected in several frequency bands and/or several electrodes concurrently, and can overlook the complexity of the structure of the EEG spectrum. Approach. We showed that the EEG spectrum structure can be described by parallel factor analysis (PARAFAC), a method which blindly uncovers the spatial-temporal-spectral patterns of EEG. We used an algorithm based on variational Bayesian statistics to reveal nine patterns from the EEG of 38 healthy subjects, acquired during a semantic decision task. The patterns reflected neural activity synchronized across theta, alpha, beta and gamma bands and spread over many electrodes, as well as various EEG artifacts. Main results. Specifically, one of the patterns showed significant correlation with the stimuli timing. The correlation was higher when compared to commonly used models of neural activity (power fluctuations in distinct frequency band averaged across a subset of electrodes) and we found significantly correlated hemodynamic fluctuations in simultaneously acquired fMRI data in regions known to be involved in speech processing. Further, we show that the pattern also occurs in EEG data which were acquired outside the MR machine. Two other patterns reflected brain rhythms linked to the attentional and basal ganglia large scale networks. The other patterns were related to various EEG artifacts. Significance. These results show that PARAFAC blindly identifies neural activity in the EEG spectrum and that it naturally handles the correlations among frequency bands and electrodes. We conclude that PARAFAC seems to be a powerful tool for analysis of the EEG spectrum and might bring novel insight to the relationships between EEG activity and brain hemodynamics.

Off-road truck-related accidents in U.S. mines

PubMed Central

Dindarloo, Saeid R.; Pollard, Jonisha P.; Siami-Irdemoosa, Elnaz

2016-01-01

Introduction Off-road trucks are one of the major sources of equipment-related accidents in the U.S. mining industries. A systematic analysis of all off-road truck-related accidents, injuries, and illnesses, which are reported and published by the Mine Safety and Health Administration (MSHA), is expected to provide practical insights for identifying the accident patterns and trends in the available raw database. Therefore, appropriate safety management measures can be administered and implemented based on these accident patterns/trends. Methods A hybrid clustering-classification methodology using K-means clustering and gene expression programming (GEP) is proposed for the analysis of severe and non-severe off-road truck-related injuries at U.S. mines. Using the GEP sub-model, a small subset of the 36 recorded attributes was found to be correlated to the severity level. Results Given the set of specified attributes, the clustering sub-model was able to cluster the accident records into 5 distinct groups. For instance, the first cluster contained accidents related to minerals processing mills and coal preparation plants (91%). More than two-thirds of the victims in this cluster had less than 5 years of job experience. This cluster was associated with the highest percentage of severe injuries (22 severe accidents, 3.4%). Almost 50% of all accidents in this cluster occurred at stone operations. Similarly, the other four clusters were characterized to highlight important patterns that can be used to determine areas of focus for safety initiatives. Conclusions The identified clusters of accidents may play a vital role in the prevention of severe injuries in mining. Further research into the cluster attributes and identified patterns will be necessary to determine how these factors can be mitigated to reduce the risk of severe injuries. Practical application Analyzing injury data using data mining techniques provides some insight into attributes that are associated with high accuracies for predicting injury severity. PMID:27620937

Off-road truck-related accidents in U.S. mines.

PubMed

Dindarloo, Saeid R; Pollard, Jonisha P; Siami-Irdemoosa, Elnaz

2016-09-01

Off-road trucks are one of the major sources of equipment-related accidents in the U.S. mining industries. A systematic analysis of all off-road truck-related accidents, injuries, and illnesses, which are reported and published by the Mine Safety and Health Administration (MSHA), is expected to provide practical insights for identifying the accident patterns and trends in the available raw database. Therefore, appropriate safety management measures can be administered and implemented based on these accident patterns/trends. A hybrid clustering-classification methodology using K-means clustering and gene expression programming (GEP) is proposed for the analysis of severe and non-severe off-road truck-related injuries at U.S. mines. Using the GEP sub-model, a small subset of the 36 recorded attributes was found to be correlated to the severity level. Given the set of specified attributes, the clustering sub-model was able to cluster the accident records into 5 distinct groups. For instance, the first cluster contained accidents related to minerals processing mills and coal preparation plants (91%). More than two-thirds of the victims in this cluster had less than 5years of job experience. This cluster was associated with the highest percentage of severe injuries (22 severe accidents, 3.4%). Almost 50% of all accidents in this cluster occurred at stone operations. Similarly, the other four clusters were characterized to highlight important patterns that can be used to determine areas of focus for safety initiatives. The identified clusters of accidents may play a vital role in the prevention of severe injuries in mining. Further research into the cluster attributes and identified patterns will be necessary to determine how these factors can be mitigated to reduce the risk of severe injuries. Analyzing injury data using data mining techniques provides some insight into attributes that are associated with high accuracies for predicting injury severity. Copyright © 2016 Elsevier Ltd and National Safety Council. All rights reserved.

Macroscale patterns in body size of intertidal crustaceans provide insights on climate change effects.

PubMed

Jaramillo, Eduardo; Dugan, Jenifer E; Hubbard, David M; Contreras, Heraldo; Duarte, Cristian; Acuña, Emilio; Schoeman, David S

2017-01-01

Predicting responses of coastal ecosystems to altered sea surface temperatures (SST) associated with global climate change, requires knowledge of demographic responses of individual species. Body size is an excellent metric because it scales strongly with growth and fecundity for many ectotherms. These attributes can underpin demographic as well as community and ecosystem level processes, providing valuable insights for responses of vulnerable coastal ecosystems to changing climate. We investigated contemporary macroscale patterns in body size among widely distributed crustaceans that comprise the majority of intertidal abundance and biomass of sandy beach ecosystems of the eastern Pacific coasts of Chile and California, USA. We focused on ecologically important species representing different tidal zones, trophic guilds and developmental modes, including a high-shore macroalga-consuming talitrid amphipod (Orchestoidea tuberculata), two mid-shore scavenging cirolanid isopods (Excirolana braziliensis and E. hirsuticauda), and a low-shore suspension-feeding hippid crab (Emerita analoga) with an amphitropical distribution. Significant latitudinal patterns in body sizes were observed for all species in Chile (21° - 42°S), with similar but steeper patterns in Emerita analoga, in California (32°- 41°N). Sea surface temperature was a strong predictor of body size (-4% to -35% °C-1) in all species. Beach characteristics were subsidiary predictors of body size. Alterations in ocean temperatures of even a few degrees associated with global climate change are likely to affect body sizes of important intertidal ectotherms, with consequences for population demography, life history, community structure, trophic interactions, food-webs, and indirect effects such as ecosystem function. The consistency of results for body size and temperature across species with different life histories, feeding modes, ecological roles, and microhabitats inhabiting a single widespread coastal ecosystem, and for one species, across hemispheres in this space-for-time substitution, suggests predictions of ecosystem responses to thermal effects of climate change may potentially be generalised, with important implications for coastal conservation.

Macroscale patterns in body size of intertidal crustaceans provide insights on climate change effects

PubMed Central

Dugan, Jenifer E.; Hubbard, David M.; Contreras, Heraldo; Duarte, Cristian; Acuña, Emilio; Schoeman, David S.

2017-01-01

Predicting responses of coastal ecosystems to altered sea surface temperatures (SST) associated with global climate change, requires knowledge of demographic responses of individual species. Body size is an excellent metric because it scales strongly with growth and fecundity for many ectotherms. These attributes can underpin demographic as well as community and ecosystem level processes, providing valuable insights for responses of vulnerable coastal ecosystems to changing climate. We investigated contemporary macroscale patterns in body size among widely distributed crustaceans that comprise the majority of intertidal abundance and biomass of sandy beach ecosystems of the eastern Pacific coasts of Chile and California, USA. We focused on ecologically important species representing different tidal zones, trophic guilds and developmental modes, including a high-shore macroalga-consuming talitrid amphipod (Orchestoidea tuberculata), two mid-shore scavenging cirolanid isopods (Excirolana braziliensis and E. hirsuticauda), and a low-shore suspension-feeding hippid crab (Emerita analoga) with an amphitropical distribution. Significant latitudinal patterns in body sizes were observed for all species in Chile (21° - 42°S), with similar but steeper patterns in Emerita analoga, in California (32°- 41°N). Sea surface temperature was a strong predictor of body size (-4% to -35% °C-1) in all species. Beach characteristics were subsidiary predictors of body size. Alterations in ocean temperatures of even a few degrees associated with global climate change are likely to affect body sizes of important intertidal ectotherms, with consequences for population demography, life history, community structure, trophic interactions, food-webs, and indirect effects such as ecosystem function. The consistency of results for body size and temperature across species with different life histories, feeding modes, ecological roles, and microhabitats inhabiting a single widespread coastal ecosystem, and for one species, across hemispheres in this space-for-time substitution, suggests predictions of ecosystem responses to thermal effects of climate change may potentially be generalised, with important implications for coastal conservation. PMID:28481897

Comparison of glomerular activity patterns by fMRI and wide-field calcium imaging: implications for principles underlying odor mapping

PubMed Central

Sanganahalli, Basavaraju G.; Rebello, Michelle R.; Herman, Peter; Papademetris, Xenophon; Shepherd, Gordon M.; Verhagen, Justus V.; Hyder, Fahmeed

2015-01-01

Functional imaging signals arise from distinct metabolic and hemodynamic events at the neuropil, but how these processes are influenced by pre- and post-synaptic activities need to be understood for quantitative interpretation of stimulus-evoked mapping data. The olfactory bulb (OB) glomeruli, spherical neuropil regions with well-defined neuronal circuitry, can provide insights into this issue. Optical calcium-sensitive fluorescent dye imaging (OICa2+) reflects dynamics of pre-synaptic input to glomeruli, whereas high-resolution functional magnetic resonance imaging (fMRI) using deoxyhemoglobin contrast reveals neuropil function within the glomerular layer where both pre- and post-synaptic activities contribute. We imaged odor-specific activity patterns of the dorsal OB in the same anesthetized rats with fMRI and OICa2+ and then co-registered the respective maps to compare patterns in the same space. Maps by each modality were very reproducible as trial-to-trial patterns for a given odor, overlapping by ~80%. Maps evoked by ethyl butyrate and methyl valerate for a given modality overlapped by ~80%, suggesting activation of similar dorsal glomerular networks by these odors. Comparison of maps generated by both methods for a given odor showed ~70% overlap, indicating similar odor-specific maps by each method. These results suggest that odor-specific glomerular patterns by high-resolution fMRI primarily tracks pre-synaptic input to the OB. Thus combining OICa2+ and fMRI lays the framework for studies of OB processing over a range of spatiotemporal scales, where OICa2+ can feature the fast dynamics of dorsal glomerular clusters and fMRI can map the entire glomerular sheet in the OB. PMID:26631819

High-frequency DOC and nitrate measurements provide new insights into their export and their relationships to rainfall-runoff processes

NASA Astrophysics Data System (ADS)

Schwab, Michael; Klaus, Julian; Pfister, Laurent; Weiler, Markus

2015-04-01

Over the past decades, stream sampling protocols for environmental tracers were often limited by logistical and technological constraints. Long-term sampling programs would typically rely on weekly sampling campaigns, while high-frequency sampling would remain restricted to a few days or hours at best. We stipulate that the currently predominant sampling protocols are too coarse to capture and understand the full amplitude of rainfall-runoff processes and its relation to water quality fluctuations. Weekly sampling protocols are not suited to get insights into the hydrological system during high flow conditions. Likewise, high frequency measurements of a few isolated events do not allow grasping inter-event variability in contributions and processes. Our working hypothesis is based on the potential of a new generation of field-deployable instruments for measuring environmental tracers at high temporal frequencies over an extended period. With this new generation of instruments we expect to gain new insights into rainfall-runoff dynamics, both at intra- and inter-event scales. Here, we present the results of one year of DOC and nitrate measurements with the field deployable UV-Vis spectrometer spectro::lyser (scan Messtechnik GmbH). The instrument measures the absorption spectrum from 220 to 720 nm in situ and at high frequencies and derives DOC and nitrate concentrations. The measurements were carried out at 15 minutes intervals in the Weierbach catchment (0.47 km2) in Luxemburg. This fully forested catchment is characterized by cambisol soils and fractured schist as underlying bedrock. The time series of DOC and nitrate give insights into the high frequency dynamics of stream water. Peaks in DOC concentrations are closely linked to discharge peaks that occur during or right after a rainfall event. Those first discharge peaks can be linked to fast near surface runoff processes and are responsible for a remarkable amount of DOC export. A special characterisation of the Weierbach catchment are the delayed second peaks a few days after the rainfall event. Nitrate concentrations are following this second peak. We assume that this delayed response is going back to subsurface or upper groundwater flows, with nitrate enriched water. On an inter-event scale during low flow / base flow conditions, we observe interesting diurnal patterns of both DOC and nitrate concentrations. Overall, the long-term high-frequency measurements of DOC and nitrate provide us the opportunity to separate different rainfall-runoff processes and link the amount of DOC and nitrate export to them to quantify the overall relevance of the different processes.

Patterns of Circulating Inflammatory Biomarkers in Older Persons with Varying Levels of Physical Performance: A Partial Least Squares-Discriminant Analysis Approach

PubMed Central

Marzetti, Emanuele; Landi, Francesco; Marini, Federico; Cesari, Matteo; Buford, Thomas W.; Manini, Todd M.; Onder, Graziano; Pahor, Marco; Bernabei, Roberto; Leeuwenburgh, Christiaan; Calvani, Riccardo

2014-01-01

Background: Chronic, low-grade inflammation and declining physical function are hallmarks of the aging process. However, previous attempts to correlate individual inflammatory biomarkers with physical performance in older people have produced mixed results. Given the complexity of the inflammatory response, the simultaneous analysis of an array of inflammatory mediators may provide more insights into the relationship between inflammation and age-related physical function decline. This study was designed to explore the association between a panel of inflammatory markers and physical performance in older adults through a multivariate statistical approach. Methods: Community-dwelling older persons were categorized into “normal walkers” (NWs; n = 27) or “slow walkers” (SWs; n = 11) groups using 0.8 m s−1 as the 4-m gait speed cutoff. A panel of 14 circulating inflammatory biomarkers was assayed by multiplex analysis. Partial least squares-discriminant analysis (PLS-DA) was used to identify patterns of inflammatory mediators associated with gait speed categories. Results: The optimal complexity of the PLS-DA model was found to be five latent variables. The proportion of correct classification was 88.9% for NW subjects (74.1% in cross-validation) and 90.9% for SW individuals (81.8% in cross-validation). Discriminant biomarkers in the model were interleukin 8, myeloperoxidase, and tumor necrosis factor alpha (all higher in the SW group), and P-selectin, interferon gamma, and granulocyte–macrophage colony-stimulating factor (all higher in the NW group). Conclusion: Distinct profiles of circulating inflammatory biomarkers characterize older subjects with different levels of physical performance. The dissection of these patterns may provide novel insights into the role played by inflammation in the disabling cascade and possible new targets for interventions. PMID:25593902

Capable Copper Electrodeposition Process for Integrated Circuit - substrate Packaging Manufacturing

NASA Astrophysics Data System (ADS)

Ghanbari, Nasrin

This work demonstrates a capable reverse pulse deposition methodology to influence gap fill behavior inside microvia along with a uniform deposit in the fine line patterned regions for substrate packaging applications. Interconnect circuitry in IC substrate packages comprises of stacked microvia that varies in depth from 20microm to 100microm with an aspect ratio of 0.5 to 1.5 and fine line patterns defined by photolithography. Photolithography defined pattern regions incorporate a wide variety of feature sizes including large circular pad structures with diameter of 20microm - 200microm, fine traces with varying widths of 3microm - 30microm and additional planar regions to define a IC substrate package. Electrodeposition of copper is performed to establish the desired circuit. Electrodeposition of copper in IC substrate applications holds certain unique challenges in that they require a low cost manufacturing process that enables a void-free gap fill inside the microvia along with uniform deposition of copper on exposed patterned regions. Deposition time scales to establish the desired metal thickness for such packages could range from several minutes to few hours. This work showcases a reverse pulse electrodeposition methodology that achieves void-free gap fill inside the microvia and uniform plating in FLS (Fine Lines and Spaces) regions with significantly higher deposition rates than traditional approaches. In order to achieve this capability, systematic experimental and simulation studies were performed. A strong correlation of independent parameters that govern the electrodeposition process such as bath temperature, reverse pulse plating parameters and the ratio of electrolyte concentrations is shown to the deposition kinetics and deposition uniformity in fine patterned regions and gap fill rate inside the microvia. Additionally, insight into the physics of via fill process is presented with secondary and tertiary current simulation efforts. Such efforts lead to show "smart" control of deposition rate at the top and bottom of via to avoid void formation. Finally, a parametric effect on grain size and the ensuing copper metallurgical characteristics of bulk copper is also shown to enable high reliability substrate packages for the IC packaging industry.

Drosophila Polypyrimidine Tract-Binding Protein (DmPTB) Regulates Dorso-Ventral Patterning Genes in Embryos

PubMed Central

Huntley, Jim; Wesley, Cedric S.; Singh, Ravinder

2014-01-01

The Drosophila polypyrimidine tract-binding protein (dmPTB or hephaestus) plays an important role during embryogenesis. A loss of function mutation, heph03429, results in varied defects in embryonic developmental processes, leading to embryonic lethality. However, the suite of molecular functions that are disrupted in the mutant remains unknown. We have used an unbiased high throughput sequencing approach to identify transcripts that are misregulated in this mutant. Misregulated transcripts show evidence of significantly altered patterns of splicing (exon skipping, 5′ and 3′ splice site switching), alternative 5′ ends, and mRNA level changes (up and down regulation). These findings are independently supported by reverse-transcription-polymerase chain reaction (RT-PCR) analysis and in situ hybridization. We show that a group of genes, such as Zerknüllt, z600 and screw are among the most upregulated in the mutant and have been functionally linked to dorso-ventral patterning and/or dorsal closure processes. Thus, loss of dmPTB function results in specific misregulated transcripts, including those that provide the missing link between the loss of dmPTB function and observed developmental defects in embryogenesis. This study provides the first comprehensive repertoire of genes affected in vivo in the heph mutant in Drosophila and offers insight into the role of dmPTB during embryonic development. PMID:25014769

Biological robustness.

PubMed

Kitano, Hiroaki

2004-11-01

Robustness is a ubiquitously observed property of biological systems. It is considered to be a fundamental feature of complex evolvable systems. It is attained by several underlying principles that are universal to both biological organisms and sophisticated engineering systems. Robustness facilitates evolvability and robust traits are often selected by evolution. Such a mutually beneficial process is made possible by specific architectural features observed in robust systems. But there are trade-offs between robustness, fragility, performance and resource demands, which explain system behaviour, including the patterns of failure. Insights into inherent properties of robust systems will provide us with a better understanding of complex diseases and a guiding principle for therapy design.

Modeling plant growth and development.

PubMed

Prusinkiewicz, Przemyslaw

2004-02-01

Computational plant models or 'virtual plants' are increasingly seen as a useful tool for comprehending complex relationships between gene function, plant physiology, plant development, and the resulting plant form. The theory of L-systems, which was introduced by Lindemayer in 1968, has led to a well-established methodology for simulating the branching architecture of plants. Many current architectural models provide insights into the mechanisms of plant development by incorporating physiological processes, such as the transport and allocation of carbon. Other models aim at elucidating the geometry of plant organs, including flower petals and apical meristems, and are beginning to address the relationship between patterns of gene expression and the resulting plant form.

Ultracold Heteronuclear Three-Body Systems: How Diabaticity Limits the Universality of Recombination into Shallow Dimers

NASA Astrophysics Data System (ADS)

Giannakeas, P.; Greene, Chris H.

2018-01-01

The mass-imbalanced three-body recombination process that forms a shallow dimer is shown to possess a rich Efimov-Stückelberg landscape, with corresponding spectra that differ fundamentally from the homonuclear case. A semianalytical treatment of the three-body recombination predicts unusual spectra with intertwined resonance peaks and minima and yields in-depth insight into the behavior of the corresponding Efimov spectra. In particular, the patterns of the Efimov-Stückelberg landscape are shown to depend inherently on the degree of diabaticity of the three-body collisions, which strongly affects the universality of the heteronuclear Efimov states.

Final Technical Report for DE-SC0008149

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

Buchanan, Kristen

The major goal of this project is to study spin waves in magnetic thin films, especially how spin waves respond to external stimuli. This is expected to lead to new insight into dynamic processes and new ideas for methods to control spin waves. Experimental studies are being done primarily using time- and spatially-resolved Brillouin light scattering (BLS) measurements on extended and patterned magnetic thin films. BLS is a versatile tool that provides a non-invasive probe of spin dynamics with frequencies of ~1 GHz to well over 100 GHz, diffraction-limited spatial resolution, 250-ps temporal resolution, and it is sensitive enough tomore » detect thermal magnons.« less

DeDaL: Cytoscape 3 app for producing and morphing data-driven and structure-driven network layouts.

PubMed

Czerwinska, Urszula; Calzone, Laurence; Barillot, Emmanuel; Zinovyev, Andrei

2015-08-14

Visualization and analysis of molecular profiling data together with biological networks are able to provide new mechanistic insights into biological functions. Currently, it is possible to visualize high-throughput data on top of pre-defined network layouts, but they are not always adapted to a given data analysis task. A network layout based simultaneously on the network structure and the associated multidimensional data might be advantageous for data visualization and analysis in some cases. We developed a Cytoscape app, which allows constructing biological network layouts based on the data from molecular profiles imported as values of node attributes. DeDaL is a Cytoscape 3 app, which uses linear and non-linear algorithms of dimension reduction to produce data-driven network layouts based on multidimensional data (typically gene expression). DeDaL implements several data pre-processing and layout post-processing steps such as continuous morphing between two arbitrary network layouts and aligning one network layout with respect to another one by rotating and mirroring. The combination of all these functionalities facilitates the creation of insightful network layouts representing both structural network features and correlation patterns in multivariate data. We demonstrate the added value of applying DeDaL in several practical applications, including an example of a large protein-protein interaction network. DeDaL is a convenient tool for applying data dimensionality reduction methods and for designing insightful data displays based on data-driven layouts of biological networks, built within Cytoscape environment. DeDaL is freely available for downloading at http://bioinfo-out.curie.fr/projects/dedal/.

The Growth of Developmental Thought: Implications for a New Evolutionary Psychology

PubMed Central

Lickliter, Robert

2009-01-01

Evolution has come to be increasingly discussed in terms of changes in developmental processes rather than simply in terms of changes in gene frequencies. This shift is based in large part on the recognition that since all phenotypic traits arise during ontogeny as products of individual development, a primary basis for evolutionary change must be variations in the patterns and processes of development. Further, the products of development are epigenetic, not just genetic, and this is the case even when considering the evolutionary process. These insights have led investigators to reconsider the established notion of genes as the primary cause of development, opening the door to research programs focused on identifying how genetic and non-genetic factors coact to guide and constrain the process of development and its outcomes. I explore this growth of developmental thought and its implications for the achievement of a unified theory of heredity, development, and evolution and consider its implications for the realization of a new, developmentally-based evolutionary psychology. PMID:19956346

How product trial changes quality perception of four new processed beef products.

PubMed

Saeed, Faiza; Grunert, Klaus G; Therkildsen, Margrethe

2013-01-01

The purpose of this paper is the quantitative analysis of the change in quality perception of four new processed beef products from pre to post trial phases. Based on the Total Food Quality Model, differences in pre and post-trial phases were measured using repeated measures technique for cue evaluation, quality evaluation and purchase motive fulfillment. For two of the tested products, trial resulted in a decline of the evaluation of cues, quality and purchase motive fulfillment compared to pre-trial expectations. For these products, positive expectations were created by giving information about ingredients and ways of processing, which were not confirmed during trial. For the other two products, evaluations on key sensory dimensions based on trial exceeded expectations, whereas the other evaluations remained unchanged. Several demographic factors influenced the pattern of results, notably age and gender, which may be due to underlying differences in previous experience. The study gives useful insights for testing of new processed meat products before market introduction. Copyright © 2012 Elsevier Ltd. All rights reserved.

Computer simulation studies on passive recruitment dynamics of lipids induced by the adsorption of charged nanoparticles.

PubMed

Li, Yang

2014-07-07

The recruitment dynamics of lipids in the biomembrane is believed to play an important role in a variety of cellular processes. In this work, we investigate the nanoparticle-induced recruitment dynamics of lipids in the heterogeneous phospholipid bilayers of distearoyl-phosphatidylcholine (DSPC) and dioleoyl-phosphatidylglycerol (DOPG) via coarse-grained molecular dynamics simulations. Three dynamic modes of individual charged DOPG lipid molecules have been taken into account in the recruitment process: lateral diffusion, protrusions, and flip-flops. Based on analysis of the mobility pattern of lipids, structural variations in the membrane as well as activation energy of the structure of lipid eyelids characterized by the potential of mean force, we have concluded that the electrostatic attraction of nanoparticles plays a crucial role in the recruitment process of lipids in phospholipid bilayers. These studies are consistent with experimental observations and to some extent give insight into the origin of some cellular processes such as signaling, formation of lipid rafts, and endocytosis.

Print-specific N170 involves multiple subcomponents for Japanese Hiragana.

PubMed

Uno, Tomoki; Okumura, Yasuko; Kasai, Tetsuko

2017-05-22

Print-specific N170 in event-related potentials is generally considered to reflect relatively automatic processing for letter strings, which is crucial for fluent reading. However, our previous studies demonstrated that print-specific N170 for transparent Japanese Hiragana script consists of at least two subcomponents under rapid stimulus presentation: an attention-related left-lateralized N170 and a bilateral N170 associated with more automatic orthographic processes (Okumura, Kasai & Murohashi, 2014, 2015). The present study aimed to confirm the latter component by controlling presentation frequency of letters and nonlinguistic visual controls (i.e., symbols), but found a quite different pattern of results; an enhanced occipito-temporal positivity for words (80-120ms poststimulus) followed by the typical left-lateralized N170 and an enhanced parietal negativity for nonwords (150-200ms). These results should provide further insights into the interaction processes between attention and early stages of print processing. Copyright © 2017 Elsevier B.V. All rights reserved.

The Development of Theory on Gendered Patterns of Achievement in the Anglophone Caribbean: Insights, Contradictions, and Silences

ERIC Educational Resources Information Center

De Lisle, Jerome

2018-01-01

Gendered patterns of achievement emerged as a critical policy concern for the small island developing states of the Anglophone Caribbean as early as 1986. Although these patterns are mostly variegated, some males do appear to be disadvantaged on key schooling outcomes as evident in the literacy attainment gap for Trinidad and Tobago in PISA 2009…

Using Facebook Page Insights Data to Determine Posting Best Practices in an Academic Health Sciences Library

ERIC Educational Resources Information Center

Houk, Kathryn M.; Thornhill, Kate

2013-01-01

Tufts University Hirsh Health Sciences Library created a Facebook page and a corresponding managing committee in March 2010. Facebook Page Insights data collected from the library's Facebook page were statistically analyzed to investigate patterns of user engagement. The committee hoped to improve posting practices and increase user engagement…

Psychocentricity and participant profiles: implications for lexical processing among multilinguals

PubMed Central

Libben, Gary; Curtiss, Kaitlin; Weber, Silke

2014-01-01

Lexical processing among bilinguals is often affected by complex patterns of individual experience. In this paper we discuss the psychocentric perspective on language representation and processing, which highlights the centrality of individual experience in psycholinguistic experimentation. We discuss applications to the investigation of lexical processing among multilinguals and explore the advantages of using high-density experiments with multilinguals. High density experiments are designed to co-index measures of lexical perception and production, as well as participant profiles. We discuss the challenges associated with the characterization of participant profiles and present a new data visualization technique, that we term Facial Profiles. This technique is based on Chernoff faces developed over 40 years ago. The Facial Profile technique seeks to overcome some of the challenges associated with the use of Chernoff faces, while maintaining the core insight that recoding multivariate data as facial features can engage the human face recognition system and thus enhance our ability to detect and interpret patterns within multivariate datasets. We demonstrate that Facial Profiles can code participant characteristics in lexical processing studies by recoding variables such as reading ability, speaking ability, and listening ability into iconically-related relative sizes of eye, mouth, and ear, respectively. The balance of ability in bilinguals can be captured by creating composite facial profiles or Janus Facial Profiles. We demonstrate the use of Facial Profiles and Janus Facial Profiles in the characterization of participant effects in the study of lexical perception and production. PMID:25071614

Hill slope and erosional controls on soil organic geochemistry in intensely managed landscapes

NASA Astrophysics Data System (ADS)

Filley, T. R.; Hou, T.; Hughes, M.; Tong, Y.; Papanicolaou, T.; Wacha, K.; Abban, B. K.; Boys, J.; Wilson, C. G.

2015-12-01

Like many regions of North America, the last 100 years of agriculture in the glaciated upper Midwest has lead to a major redistribution of soil carbon and nitrogen on the landscape. Through the natural coevolution of geomorphic, pedogenic, and ecological processes in the critical zone or by punctual changes in these processes as a result of intensive management, landscapes established characteristic hierarchies of physicochemical controls on organic matter stability. In the Intensively-Managed Landscapes - Critical Zone Observatory (IML-CZO) in Iowa and Illinois these processes are being studied with a combination of surface soil geochemical surveys and simulated rainfall/erosion experiments to document how the organic geochemistry of hill slopes, under land management ranging from row crop to restored prairie, are currently evolving, and how they evolved during early management and pre settlement. Using a combination of soil analyses including elemental, stable isotope, textural, and soil biopolymers (lignin and cutin/suberin fatty acids (SFA)) we investigated the spatial patterns of static surface soil properties and time course rainfall-erosional experiments along the same slopes to gain insight into soil carbon and biopolymer enrichment patterns in east-central Iowa within the Clear Creek Watershed. Both lignin and substituted fatty acid concentration and their molecular ratios highlighted differences in C3/C4 (soy/corn) management activities in surface soils while over 40 years of prairie restoration dramatically altered surface soil profiles. For example, a general pattern in static baseline samples was an enrichment of 15N in soils down slope and an opposite pattern of accumulation/loss of lignin and SFA in topographic highs and lows. Transport of soil particles, associated biopolymers, and elemental and isotope signatures, exhibited distinct patterns based upon both position of the hill slope and directionality of flow with respect to rill/gully direction created by tillage activity. This indicates that particle/chemistry transport and enrichment of organic chemical signatures down slope and into associated flood plains and streams in modern intensively managed systems should be distinct from pre-settlement patterns and help interpret pre- and post settlement alluvium sediment.

About the unidirectionality of interference: insight from the musical Stroop effect.

PubMed

Grégoire, Laurent; Perruchet, Pierre; Poulin-Charronnat, Bénédicte

2014-01-01

The asymmetry of interference in a Stroop task usually refers to the well-documented result that incongruent colour words slow colour naming (Stroop effect) but incongruent colours do not slow colour word reading (no reverse Stroop effect). A few other studies have suggested that, more generally, a reverse Stroop effect can be occasionally observed but at the expense of the Stroop effect itself, as if interference was inherently unidirectional, from the stronger to the weaker of the two competing processes. We describe here a situation conducive to a pervasive mutual interference effect. Musicians were exposed to congruent and incongruent note name/note position patterns, and they were asked either to read the word while ignoring the location of the note within the staff, or to name the note while ignoring the note name written inside the note picture. Most of the participants exhibited interference in the two tasks. Overall, this result pattern runs against the still prevalent model of the Stroop phenomenon [Cohen, J. D., Dunbar, K., & McClelland, J. L. (1990). On the control of automatic processes: A parallel distributed processing account of the Stroop effect. Psychological Review, 97(3), 332-361]. However, further analyses lend support to one of the key tenets of the model, namely that the pattern of interference depends on the relative strength of the two competing pathways. The reasons for the impressive differences between the results collected in the present study and in the standard colour-word (or picture-word) paradigms are also examined. We suggest that these differences reveal the importance of stimulus-response contingency in the formation of automatisms.

Genetic diversity, structure, and patterns of differentiation in the genus vitis

USDA-ARS?s Scientific Manuscript database

Vitis (Vitaceae) is a taxonomically complicated genus with ca. 60 taxa divided into two subgenera, Vitis and Muscadinia. We used population genetic approaches to gain insights into the genetic diversity, patterns of evolutionary differentiation and to decipher the taxonomic status of some of the con...

Feasibility of Explicit Instruction in Adult Basic Education: Instructor-Learner Interaction Patterns

ERIC Educational Resources Information Center

Mellard, Daryl; Scanlon, David

2006-01-01

A strategic instruction model introduced into adult basic education classrooms yields insight into the feasibility of using direct and explicit instruction with adults with learning disabilities or other cognitive barriers to learning. Ecobehavioral assessment was used to describe and compare instructor-learner interaction patterns during learning…

Supporting cognition in systems biology analysis: findings on users' processes and design implications.

PubMed

Mirel, Barbara

2009-02-13

Current usability studies of bioinformatics tools suggest that tools for exploratory analysis support some tasks related to finding relationships of interest but not the deep causal insights necessary for formulating plausible and credible hypotheses. To better understand design requirements for gaining these causal insights in systems biology analyses a longitudinal field study of 15 biomedical researchers was conducted. Researchers interacted with the same protein-protein interaction tools to discover possible disease mechanisms for further experimentation. Findings reveal patterns in scientists' exploratory and explanatory analysis and reveal that tools positively supported a number of well-structured query and analysis tasks. But for several of scientists' more complex, higher order ways of knowing and reasoning the tools did not offer adequate support. Results show that for a better fit with scientists' cognition for exploratory analysis systems biology tools need to better match scientists' processes for validating, for making a transition from classification to model-based reasoning, and for engaging in causal mental modelling. As the next great frontier in bioinformatics usability, tool designs for exploratory systems biology analysis need to move beyond the successes already achieved in supporting formulaic query and analysis tasks and now reduce current mismatches with several of scientists' higher order analytical practices. The implications of results for tool designs are discussed.

Insight into the precuneus: a novel seizure semiology in a child with epilepsy arising from the right posterior precuneus.

PubMed

Mailo, Janette; Tang-Wai, Richard

2015-09-01

To date, there is limited understanding of the role of the precuneus. fMRI studies have suggested its involvement in a wide spectrum of highly integrated tasks, including spatially-guided behaviour, visuo-spatial imagery, and consciousness. We present a patient with intractable parietal lobe epilepsy arising from a lesion localized to the right precuneus. Two seizure types with distinct semiologies were captured on video-EEG monitoring. The first type consisted of an urge described as a "feeling of wanting to move". On video analysis, the patient is seen to turn his head and body to his left. He remains conscious, he is able to answer questions and when asked, he can look to his right. This seizure was associated with an ictal pattern localized to the right parieto-occipital region. The second seizure type consisted of reading-induced visual distortion with macropsia and micropsia. Interictally, intermittent rhythmic slowing and spikes were seen and localized to the parietal midline and the right parieto-occipital regions. Our patient's seizures are positive phenomena of the right precuneus and its related processing network. They represent unique seizure semiologies that offer further insight into the role of the precuneus in spatial awareness, visuo-spatial processing and consciousness.

High-resolution liquid patterns via three-dimensional droplet shape control.

PubMed

Raj, Rishi; Adera, Solomon; Enright, Ryan; Wang, Evelyn N

2014-09-25

Understanding liquid dynamics on surfaces can provide insight into nature's design and enable fine manipulation capability in biological, manufacturing, microfluidic and thermal management applications. Of particular interest is the ability to control the shape of the droplet contact area on the surface, which is typically circular on a smooth homogeneous surface. Here, we show the ability to tailor various droplet contact area shapes ranging from squares, rectangles, hexagons, octagons, to dodecagons via the design of the structure or chemical heterogeneity on the surface. We simultaneously obtain the necessary physical insights to develop a universal model for the three-dimensional droplet shape by characterizing the droplet side and top profiles. Furthermore, arrays of droplets with controlled shapes and high spatial resolution can be achieved using this approach. This liquid-based patterning strategy promises low-cost fabrication of integrated circuits, conductive patterns and bio-microarrays for high-density information storage and miniaturized biochips and biosensors, among others.

Citizen science: A new perspective to advance spatial pattern evaluation in hydrology.

PubMed

Koch, Julian; Stisen, Simon

2017-01-01

Citizen science opens new pathways that can complement traditional scientific practice. Intuition and reasoning often make humans more effective than computer algorithms in various realms of problem solving. In particular, a simple visual comparison of spatial patterns is a task where humans are often considered to be more reliable than computer algorithms. However, in practice, science still largely depends on computer based solutions, which inevitably gives benefits such as speed and the possibility to automatize processes. However, the human vision can be harnessed to evaluate the reliability of algorithms which are tailored to quantify similarity in spatial patterns. We established a citizen science project to employ the human perception to rate similarity and dissimilarity between simulated spatial patterns of several scenarios of a hydrological catchment model. In total, the turnout counts more than 2500 volunteers that provided over 43000 classifications of 1095 individual subjects. We investigate the capability of a set of advanced statistical performance metrics to mimic the human perception to distinguish between similarity and dissimilarity. Results suggest that more complex metrics are not necessarily better at emulating the human perception, but clearly provide auxiliary information that is valuable for model diagnostics. The metrics clearly differ in their ability to unambiguously distinguish between similar and dissimilar patterns which is regarded a key feature of a reliable metric. The obtained dataset can provide an insightful benchmark to the community to test novel spatial metrics.

Effects of intrinsic stochasticity on delayed reaction-diffusion patterning systems.

PubMed

Woolley, Thomas E; Baker, Ruth E; Gaffney, Eamonn A; Maini, Philip K; Seirin-Lee, Sungrim

2012-05-01

Cellular gene expression is a complex process involving many steps, including the transcription of DNA and translation of mRNA; hence the synthesis of proteins requires a considerable amount of time, from ten minutes to several hours. Since diffusion-driven instability has been observed to be sensitive to perturbations in kinetic delays, the application of Turing patterning mechanisms to the problem of producing spatially heterogeneous differential gene expression has been questioned. In deterministic systems a small delay in the reactions can cause a large increase in the time it takes a system to pattern. Recently, it has been observed that in undelayed systems intrinsic stochasticity can cause pattern initiation to occur earlier than in the analogous deterministic simulations. Here we are interested in adding both stochasticity and delays to Turing systems in order to assess whether stochasticity can reduce the patterning time scale in delayed Turing systems. As analytical insights to this problem are difficult to attain and often limited in their use, we focus on stochastically simulating delayed systems. We consider four different Turing systems and two different forms of delay. Our results are mixed and lead to the conclusion that, although the sensitivity to delays in the Turing mechanism is not completely removed by the addition of intrinsic noise, the effects of the delays are clearly ameliorated in certain specific cases.

On the distribution of interspecies correlation for Markov models of character evolution on Yule trees.

PubMed

Mulder, Willem H; Crawford, Forrest W

2015-01-07

Efforts to reconstruct phylogenetic trees and understand evolutionary processes depend fundamentally on stochastic models of speciation and mutation. The simplest continuous-time model for speciation in phylogenetic trees is the Yule process, in which new species are "born" from existing lineages at a constant rate. Recent work has illuminated some of the structural properties of Yule trees, but it remains mostly unknown how these properties affect sequence and trait patterns observed at the tips of the phylogenetic tree. Understanding the interplay between speciation and mutation under simple models of evolution is essential for deriving valid phylogenetic inference methods and gives insight into the optimal design of phylogenetic studies. In this work, we derive the probability distribution of interspecies covariance under Brownian motion and Ornstein-Uhlenbeck models of phenotypic change on a Yule tree. We compute the probability distribution of the number of mutations shared between two randomly chosen taxa in a Yule tree under discrete Markov mutation models. Our results suggest summary measures of phylogenetic information content, illuminate the correlation between site patterns in sequences or traits of related organisms, and provide heuristics for experimental design and reconstruction of phylogenetic trees. Copyright © 2014 Elsevier Ltd. All rights reserved.

Modelling the Wind-Borne Spread of Highly Pathogenic Avian Influenza Virus between Farms

PubMed Central

Ssematimba, Amos; Hagenaars, Thomas J.; de Jong, Mart C. M.

2012-01-01

A quantitative understanding of the spread of contaminated farm dust between locations is a prerequisite for obtaining much-needed insight into one of the possible mechanisms of disease spread between farms. Here, we develop a model to calculate the quantity of contaminated farm-dust particles deposited at various locations downwind of a source farm and apply the model to assess the possible contribution of the wind-borne route to the transmission of Highly Pathogenic Avian Influenza virus (HPAI) during the 2003 epidemic in the Netherlands. The model is obtained from a Gaussian Plume Model by incorporating the dust deposition process, pathogen decay, and a model for the infection process on exposed farms. Using poultry- and avian influenza-specific parameter values we calculate the distance-dependent probability of between-farm transmission by this route. A comparison between the transmission risk pattern predicted by the model and the pattern observed during the 2003 epidemic reveals that the wind-borne route alone is insufficient to explain the observations although it could contribute substantially to the spread over short distance ranges, for example, explaining 24% of the transmission over distances up to 25 km. PMID:22348042

Modelling the wind-borne spread of highly pathogenic avian influenza virus between farms.

PubMed

Ssematimba, Amos; Hagenaars, Thomas J; de Jong, Mart C M

2012-01-01

A quantitative understanding of the spread of contaminated farm dust between locations is a prerequisite for obtaining much-needed insight into one of the possible mechanisms of disease spread between farms. Here, we develop a model to calculate the quantity of contaminated farm-dust particles deposited at various locations downwind of a source farm and apply the model to assess the possible contribution of the wind-borne route to the transmission of Highly Pathogenic Avian Influenza virus (HPAI) during the 2003 epidemic in the Netherlands. The model is obtained from a Gaussian Plume Model by incorporating the dust deposition process, pathogen decay, and a model for the infection process on exposed farms. Using poultry- and avian influenza-specific parameter values we calculate the distance-dependent probability of between-farm transmission by this route. A comparison between the transmission risk pattern predicted by the model and the pattern observed during the 2003 epidemic reveals that the wind-borne route alone is insufficient to explain the observations although it could contribute substantially to the spread over short distance ranges, for example, explaining 24% of the transmission over distances up to 25 km.

Do arms races punctuate evolutionary stasis? Unified insights from phylogeny, phylogeography and microevolutionary processes.

PubMed

Toju, Hirokazu; Sota, Teiji

2009-09-01

One of the major controversies in evolutionary biology concerns the processes underlying macroevolutionary patterns in which prolonged stasis is disrupted by rapid, short-term evolution that leads species to new adaptive zones. Recent advances in the understanding of contemporary evolution have suggested that such rapid evolution can occur in the wild as a result of environmental changes. Here, we examined a novel hypothesis that evolutionary stasis is punctuated by co-evolutionary arms races, which continuously alter adaptive peaks and landscapes. Based on the phylogeny of long-mouthed weevils in the genus Curculio, likelihood ratio tests showed that the macroevolutionary pattern of the weevils coincides with the punctuational evolution model. A coalescent analysis of a species, Curculio camelliae, the mouthpart of which has diverged considerably among populations because of an arms race with its host plant, further suggested that major evolutionary shifts had occurred within 7000 generations. Through a microevolutionary analysis of the species, we also found that natural selection acting through co-evolutionary interactions is potentially strong enough to drive rapid evolutionary shifts between adaptive zones. Overall, we posit that co-evolution is an important factor driving the history of organismal evolution.

Rejuvenation of Gene Expression Pattern of Aged Human Skin by Broadband Light Treatment: A Pilot Study

PubMed Central

Chang, Anne Lynn S; Bitter, Patrick H; Qu, Kun; Lin, Meihong; Rapicavoli, Nicole A; Chang, Howard Y

2013-01-01

Studies in model organisms suggest that aged cells can be functionally rejuvenated, but whether this concept applies to human skin is unclear. Here we apply 3′-end sequencing for expression quantification (“3-seq”) to discover the gene expression program associated with human photoaging and intrinsic skin aging (collectively termed “skin aging”), and the impact of broadband light (BBL) treatment. We find that skin aging was associated with a significantly altered expression level of 2,265 coding and noncoding RNAs, of which 1,293 became “rejuvenated” after BBL treatment; i.e., they became more similar to their expression level in youthful skin. Rejuvenated genes (RGs) included several known key regulators of organismal longevity and their proximal long noncoding RNAs. Skin aging is not associated with systematic changes in 3′-end mRNA processing. Hence, BBL treatment can restore gene expression pattern of photoaged and intrinsically aged human skin to resemble young skin. In addition, our data reveal, to our knowledge, a previously unreported set of targets that may lead to new insights into the human skin aging process. PMID:22931923

Competitive and demographic leverage points of community shifts under climate warming

PubMed Central

Sorte, Cascade J. B.; White, J. Wilson

2013-01-01

Accelerating rates of climate change and a paucity of whole-community studies of climate impacts limit our ability to forecast shifts in ecosystem structure and dynamics, particularly because climate change can lead to idiosyncratic responses via both demographic effects and altered species interactions. We used a multispecies model to predict which processes and species' responses are likely to drive shifts in the composition of a space-limited benthic marine community. Our model was parametrized from experimental manipulations of the community. Model simulations indicated shifts in species dominance patterns as temperatures increase, with projected shifts in composition primarily owing to the temperature dependence of growth, mortality and competition for three critical species. By contrast, warming impacts on two other species (rendering them weaker competitors for space) and recruitment rates of all species were of lesser importance in determining projected community changes. Our analysis reveals the importance of temperature-dependent competitive interactions for predicting effects of changing climate on such communities. Furthermore, by identifying processes and species that could disproportionately leverage shifts in community composition, our results contribute to a mechanistic understanding of climate change impacts, thereby allowing more insightful predictions of future biodiversity patterns. PMID:23658199

Management of change through force field analysis.

PubMed

Baulcomb, Jean Sandra

2003-07-01

Today's NHS is rapidly changing, placing more emphasis on the managerial responsibilities of ward managers. Managing change is seen as being skilled at creating, acquiring and transferring knowledge to reflect new knowledge and insights. Defining core concepts is often difficult and requires the drawing on models/theories of change for guidance. Guidance from Lewin's (1951) force field analysis demonstrates the complexities of the change process and how driving and resisting forces were incorporated within the planning and implementation phases. Findings outline the benefits of a small scale change for staff, patients and the organization when successfully used to introduce a change of shift pattern within a progressively busy haematology day unit, in order to meet service demands without additional funding. Conclusions have been drawn in relation to the process and recommendations for practice made to further enhance care delivery within the unit.

Transition in the decay rates of stationary distributions of Lévy motion in an energy landscape.

PubMed

Kaleta, Kamil; Lőrinczi, József

2016-02-01

The time evolution of random variables with Lévy statistics has the ability to develop jumps, displaying very different behaviors from continuously fluctuating cases. Such patterns appear in an ever broadening range of examples including random lasers, non-Gaussian kinetics, or foraging strategies. The penalizing or reinforcing effect of the environment, however, has been little explored so far. We report a new phenomenon which manifests as a qualitative transition in the spatial decay behavior of the stationary measure of a jump process under an external potential, occurring on a combined change in the characteristics of the process and the lowest eigenvalue resulting from the effect of the potential. This also provides insight into the fundamental question of what is the mechanism of the spatial decay of a ground state.

Rapid evolution in insect pests: the importance of space and time in population genomics studies.

PubMed

Pélissié, Benjamin; Crossley, Michael S; Cohen, Zachary Paul; Schoville, Sean D

2018-04-01

Pest species in agroecosystems often exhibit patterns of rapid evolution to environmental and human-imposed selection pressures. Although the role of adaptive processes is well accepted, few insect pests have been studied in detail and most research has focused on selection at insecticide resistance candidate genes. Emerging genomic datasets provide opportunities to detect and quantify selection in insect pest populations, and address long-standing questions about mechanisms underlying rapid evolutionary change. We examine the strengths of recent studies that stratify population samples both in space (along environmental gradients and comparing ancestral vs. derived populations) and in time (using chronological sampling, museum specimens and comparative phylogenomics), resulting in critical insights on evolutionary processes, and providing new directions for studying pests in agroecosystems. Copyright © 2018 Elsevier Inc. All rights reserved.

Investigation of phase matching for third-harmonic generation in silicon slow light photonic crystal waveguides using Fourier optics.

PubMed

Monat, Christelle; Grillet, Christian; Corcoran, Bill; Moss, David J; Eggleton, Benjamin J; White, Thomas P; Krauss, Thomas F

2010-03-29

Using Fourier optics, we retrieve the wavevector dependence of the third-harmonic (green) light generated in a slow light silicon photonic crystal waveguide. We show that quasi-phase matching between the third-harmonic signal and the fundamental mode is provided in this geometry by coupling to the continuum of radiation modes above the light line. This process sustains third-harmonic generation with a relatively high efficiency and a substantial bandwidth limited only by the slow light window of the fundamental mode. The results give us insights into the physics of this nonlinear process in the presence of strong absorption and dispersion at visible wavelengths where bandstructure calculations are problematic. Since the characteristics (e.g. angular pattern) of the third-harmonic light primarily depend on the fundamental mode dispersion, they could be readily engineered.

Intuition and Insight: Two Processes That Build on Each Other or Fundamentally Differ?

PubMed

Zander, Thea; Öllinger, Michael; Volz, Kirsten G

2016-01-01

Intuition and insight are intriguing phenomena of non-analytical mental functioning: whereas intuition denotes ideas that have been reached by sensing the solution without any explicit representation of it, insight has been understood as the sudden and unexpected apprehension of the solution by recombining the single elements of a problem. By face validity, the two processes appear similar; according to a lay perspective, it is assumed that intuition precedes insight. Yet, predominant scientific conceptualizations of intuition and insight consider the two processes to differ with regard to their (dis-)continuous unfolding. That is, intuition has been understood as an experience-based and gradual process, whereas insight is regarded as a genuinely discontinuous phenomenon. Unfortunately, both processes have been investigated differently and without much reference to each other. In this contribution, we therefore set out to fill this lacuna by examining the conceptualizations of the assumed underlying cognitive processes of both phenomena, and by also referring to the research traditions and paradigms of the respective field. Based on early work put forward by Bowers et al. (1990, 1995), we referred to semantic coherence tasks consisting of convergent word triads (i.e., the solution has the same meaning to all three clue words) and/or divergent word triads (i.e., the solution means something different with respect to each clue word) as an excellent kind of paradigm that may be used in the future to disentangle intuition and insight experimentally. By scrutinizing the underlying mechanisms of intuition and insight, with this theoretical contribution, we hope to launch lacking but needed experimental studies and to initiate scientific cooperation between the research fields of intuition and insight that are currently still separated from each other.

Intuition and Insight: Two Processes That Build on Each Other or Fundamentally Differ?

PubMed Central

Zander, Thea; Öllinger, Michael; Volz, Kirsten G.

2016-01-01

Intuition and insight are intriguing phenomena of non-analytical mental functioning: whereas intuition denotes ideas that have been reached by sensing the solution without any explicit representation of it, insight has been understood as the sudden and unexpected apprehension of the solution by recombining the single elements of a problem. By face validity, the two processes appear similar; according to a lay perspective, it is assumed that intuition precedes insight. Yet, predominant scientific conceptualizations of intuition and insight consider the two processes to differ with regard to their (dis-)continuous unfolding. That is, intuition has been understood as an experience-based and gradual process, whereas insight is regarded as a genuinely discontinuous phenomenon. Unfortunately, both processes have been investigated differently and without much reference to each other. In this contribution, we therefore set out to fill this lacuna by examining the conceptualizations of the assumed underlying cognitive processes of both phenomena, and by also referring to the research traditions and paradigms of the respective field. Based on early work put forward by Bowers et al. (1990, 1995), we referred to semantic coherence tasks consisting of convergent word triads (i.e., the solution has the same meaning to all three clue words) and/or divergent word triads (i.e., the solution means something different with respect to each clue word) as an excellent kind of paradigm that may be used in the future to disentangle intuition and insight experimentally. By scrutinizing the underlying mechanisms of intuition and insight, with this theoretical contribution, we hope to launch lacking but needed experimental studies and to initiate scientific cooperation between the research fields of intuition and insight that are currently still separated from each other. PMID:27679592

Microarray analysis of gene expression patterns in the leaf during potato tuberization in the potato somatic hybrid Solanum tuberosum and Solanum etuberosum.

PubMed

Tiwari, Jagesh Kumar; Devi, Sapna; Sundaresha, S; Chandel, Poonam; Ali, Nilofer; Singh, Brajesh; Bhardwaj, Vinay; Singh, Bir Pal

2015-06-01

Genes involved in photoassimilate partitioning and changes in hormonal balance are important for potato tuberization. In the present study, we investigated gene expression patterns in the tuber-bearing potato somatic hybrid (E1-3) and control non-tuberous wild species Solanum etuberosum (Etb) by microarray. Plants were grown under controlled conditions and leaves were collected at eight tuber developmental stages for microarray analysis. A t-test analysis identified a total of 468 genes (94 up-regulated and 374 down-regulated) that were statistically significant (p ≤ 0.05) and differentially expressed in E1-3 and Etb. Gene Ontology (GO) characterization of the 468 genes revealed that 145 were annotated and 323 were of unknown function. Further, these 145 genes were grouped based on GO biological processes followed by molecular function and (or) PGSC description into 15 gene sets, namely (1) transport, (2) metabolic process, (3) biological process, (4) photosynthesis, (5) oxidation-reduction, (6) transcription, (7) translation, (8) binding, (9) protein phosphorylation, (10) protein folding, (11) ubiquitin-dependent protein catabolic process, (12) RNA processing, (13) negative regulation of protein, (14) methylation, and (15) mitosis. RT-PCR analysis of 10 selected highly significant genes (p ≤ 0.01) confirmed the microarray results. Overall, we show that candidate genes induced in leaves of E1-3 were implicated in tuberization processes such as transport, carbohydrate metabolism, phytohormones, and transcription/translation/binding functions. Hence, our results provide an insight into the candidate genes induced in leaf tissues during tuberization in E1-3.

Diagnostic Classification of Schizophrenia Patients on the Basis of Regional Reward-Related fMRI Signal Patterns

PubMed Central

Koch, Stefan P.; Hägele, Claudia; Haynes, John-Dylan; Heinz, Andreas; Schlagenhauf, Florian; Sterzer, Philipp

2015-01-01

Functional neuroimaging has provided evidence for altered function of mesolimbic circuits implicated in reward processing, first and foremost the ventral striatum, in patients with schizophrenia. While such findings based on significant group differences in brain activations can provide important insights into the pathomechanisms of mental disorders, the use of neuroimaging results from standard univariate statistical analysis for individual diagnosis has proven difficult. In this proof of concept study, we tested whether the predictive accuracy for the diagnostic classification of schizophrenia patients vs. healthy controls could be improved using multivariate pattern analysis (MVPA) of regional functional magnetic resonance imaging (fMRI) activation patterns for the anticipation of monetary reward. With a searchlight MVPA approach using support vector machine classification, we found that the diagnostic category could be predicted from local activation patterns in frontal, temporal, occipital and midbrain regions, with a maximal cluster peak classification accuracy of 93% for the right pallidum. Region-of-interest based MVPA for the ventral striatum achieved a maximal cluster peak accuracy of 88%, whereas the classification accuracy on the basis of standard univariate analysis reached only 75%. Moreover, using support vector regression we could additionally predict the severity of negative symptoms from ventral striatal activation patterns. These results show that MVPA can be used to substantially increase the accuracy of diagnostic classification on the basis of task-related fMRI signal patterns in a regionally specific way. PMID:25799236

Exploring the Linkage between Urban Flood Risk and Spatial Patterns in Small Urbanized Catchments of Beijing, China

PubMed Central

Yao, Lei; Chen, Liding; Wei, Wei

2017-01-01

In the context of global urbanization, urban flood risk in many cities has become a serious environmental issue, threatening the health of residents and the environment. A number of hydrological studies have linked urban flooding issues closely to the spectrum of spatial patterns of urbanization, but relatively little attention has been given to small-scale catchments within the realm of urban systems. This study aims to explore the hydrological effects of small-scaled urbanized catchments assigned with various landscape patterns. Twelve typical residential catchments in Beijing were selected as the study areas. Total Impervious Area (TIA), Directly Connected Impervious Area (DCIA), and a drainage index were used as the catchment spatial metrics. Three scenarios were designed as different spatial arrangement of catchment imperviousness. Runoff variables including total and peak runoff depth (Qt and Qp) were simulated by using Strom Water Management Model (SWMM). The relationship between catchment spatial patterns and runoff variables were determined, and the results demonstrated that, spatial patterns have inherent influences on flood risks in small urbanized catchments. Specifically: (1) imperviousness acts as an effective indicator in affecting both Qt and Qp; (2) reducing the number of rainwater inlets appropriately will benefit the catchment peak flow mitigation; (3) different spatial concentrations of impervious surfaces have inherent influences on Qp. These findings provide insights into the role of urban spatial patterns in driving rainfall-runoff processes in small urbanized catchments, which is essential for urban planning and flood management. PMID:28264521

Risk attitudes in a changing environment: An evolutionary model of the fourfold pattern of risk preferences.

PubMed

Mallpress, Dave E W; Fawcett, Tim W; Houston, Alasdair I; McNamara, John M

2015-04-01

A striking feature of human decision making is the fourfold pattern of risk attitudes, involving risk-averse behavior in situations of unlikely losses and likely gains, but risk-seeking behavior in response to likely losses and unlikely gains. Current theories to explain this pattern assume particular psychological processes to reproduce empirical observations, but do not address whether it is adaptive for the decision maker to respond to risk in this way. Here, drawing on insights from behavioral ecology, we build an evolutionary model of risk-sensitive behavior, to investigate whether particular types of environmental conditions could favor a fourfold pattern of risk attitudes. We consider an individual foraging in a changing environment, where energy is needed to prevent starvation and build up reserves for reproduction. The outcome, in terms of reproductive value (a rigorous measure of evolutionary success), of a one-off choice between a risky and a safe gain, or between a risky and a safe loss, determines the risk-sensitive behavior we should expect to see in this environment. Our results show that the fourfold pattern of risk attitudes may be adaptive in an environment in which conditions vary stochastically but are autocorrelated in time. In such an environment the current options provide information about the likely environmental conditions in the future, which affect the optimal pattern of risk sensitivity. Our model predicts that risk preferences should be both path dependent and affected by the decision maker's current state. (c) 2015 APA, all rights reserved).

Exploring the Linkage between Urban Flood Risk and Spatial Patterns in Small Urbanized Catchments of Beijing, China.

PubMed

Yao, Lei; Chen, Liding; Wei, Wei

2017-02-28

In the context of global urbanization, urban flood risk in many cities has become a serious environmental issue, threatening the health of residents and the environment. A number of hydrological studies have linked urban flooding issues closely to the spectrum of spatial patterns of urbanization, but relatively little attention has been given to small-scale catchments within the realm of urban systems. This study aims to explore the hydrological effects of small-scaled urbanized catchments assigned with various landscape patterns. Twelve typical residential catchments in Beijing were selected as the study areas. Total Impervious Area ( TIA ), Directly Connected Impervious Area ( DCIA ), and a drainage index were used as the catchment spatial metrics. Three scenarios were designed as different spatial arrangement of catchment imperviousness. Runoff variables including total and peak runoff depth ( Q t and Q p ) were simulated by using Strom Water Management Model (SWMM). The relationship between catchment spatial patterns and runoff variables were determined, and the results demonstrated that, spatial patterns have inherent influences on flood risks in small urbanized catchments. Specifically: (1) imperviousness acts as an effective indicator in affecting both Q t and Q p ; (2) reducing the number of rainwater inlets appropriately will benefit the catchment peak flow mitigation; (3) different spatial concentrations of impervious surfaces have inherent influences on Q p . These findings provide insights into the role of urban spatial patterns in driving rainfall-runoff processes in small urbanized catchments, which is essential for urban planning and flood management.

Organellar proteomics reveals hundreds of novel nuclear proteins in the malaria parasite Plasmodium falciparum

PubMed Central

2012-01-01

Background The post-genomic era of malaria research provided unprecedented insights into the biology of Plasmodium parasites. Due to the large evolutionary distance to model eukaryotes, however, we lack a profound understanding of many processes in Plasmodium biology. One example is the cell nucleus, which controls the parasite genome in a development- and cell cycle-specific manner through mostly unknown mechanisms. To study this important organelle in detail, we conducted an integrative analysis of the P. falciparum nuclear proteome. Results We combined high accuracy mass spectrometry and bioinformatic approaches to present for the first time an experimentally determined core nuclear proteome for P. falciparum. Besides a large number of factors implicated in known nuclear processes, one-third of all detected proteins carry no functional annotation, including many phylum- or genus-specific factors. Importantly, extensive experimental validation using 30 transgenic cell lines confirmed the high specificity of this inventory, and revealed distinct nuclear localization patterns of hitherto uncharacterized proteins. Further, our detailed analysis identified novel protein domains potentially implicated in gene transcription pathways, and sheds important new light on nuclear compartments and processes including regulatory complexes, the nucleolus, nuclear pores, and nuclear import pathways. Conclusion Our study provides comprehensive new insight into the biology of the Plasmodium nucleus and will serve as an important platform for dissecting general and parasite-specific nuclear processes in malaria parasites. Moreover, as the first nuclear proteome characterized in any protist organism, it will provide an important resource for studying evolutionary aspects of nuclear biology. PMID:23181666

PANTHER. Pattern ANalytics To support High-performance Exploitation and Reasoning.

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

Czuchlewski, Kristina Rodriguez; Hart, William E.

Sandia has approached the analysis of big datasets with an integrated methodology that uses computer science, image processing, and human factors to exploit critical patterns and relationships in large datasets despite the variety and rapidity of information. The work is part of a three-year LDRD Grand Challenge called PANTHER (Pattern ANalytics To support High-performance Exploitation and Reasoning). To maximize data analysis capability, Sandia pursued scientific advances across three key technical domains: (1) geospatial-temporal feature extraction via image segmentation and classification; (2) geospatial-temporal analysis capabilities tailored to identify and process new signatures more efficiently; and (3) domain- relevant models of humanmore » perception and cognition informing the design of analytic systems. Our integrated results include advances in geographical information systems (GIS) in which we discover activity patterns in noisy, spatial-temporal datasets using geospatial-temporal semantic graphs. We employed computational geometry and machine learning to allow us to extract and predict spatial-temporal patterns and outliers from large aircraft and maritime trajectory datasets. We automatically extracted static and ephemeral features from real, noisy synthetic aperture radar imagery for ingestion into a geospatial-temporal semantic graph. We worked with analysts and investigated analytic workflows to (1) determine how experiential knowledge evolves and is deployed in high-demand, high-throughput visual search workflows, and (2) better understand visual search performance and attention. Through PANTHER, Sandia's fundamental rethinking of key aspects of geospatial data analysis permits the extraction of much richer information from large amounts of data. The project results enable analysts to examine mountains of historical and current data that would otherwise go untouched, while also gaining meaningful, measurable, and defensible insights into overlooked relationships and patterns. The capability is directly relevant to the nation's nonproliferation remote-sensing activities and has broad national security applications for military and intelligence- gathering organizations.« less

Espousal of Undergraduate Teaching Normative Patterns of First-Year Teaching Assistants

ERIC Educational Resources Information Center

Helland, Patricia A.

2010-01-01

This study focuses on the espousal of undergraduate teaching normative patterns. Results showed that entering teaching assistants had higher levels of disdain than Research I faculty. The country in which students received their undergraduate degrees and gender variables also showed differences in espousal levels. The results give insight into…

Patterns of Changing Knowledge Orders: Insights from German and British Labour Market Policy

ERIC Educational Resources Information Center

Krapp, Max-Christopher; Pannowitsch, Sylvia

2017-01-01

Following an interpretative approach this paper investigates the role of knowledge orders, understood as settings which attribute relevance to specific expertise. The changing patterns of incorporation of expertise in policy formulation as well as public justification are analysed for German and British labour market policy. From a comparative…

Arts and Earning a Living.

ERIC Educational Resources Information Center

Packer, Arnold

The arts deserve a place in education, provided they are properly taught. Humans need art to make their world sensible, find patterns in their experiences, and gain insights into the future. Art, like life, rewards those who grasp new patterns and act on their interpretation of reality. A good education imparts the ability to recognize patterns…

Confluence: Synthesizing the Insights of Joseph Chilton Pearce and Natural Learning Rhythms.

ERIC Educational Resources Information Center

Luvmour, Josette; Luvmour, Ba

1999-01-01

A theory of childhood development posits an unseen pattern that contains the laws and principles determining the child's nature. An environment that provides attunement to this pattern allows the child profound spiritual awareness, within the limits of the developmental moment. Four stages of development are presented with their attributes,…

Information and Complexity Measures Applied to Observed and Simulated Soil Moisture Time Series

USDA-ARS?s Scientific Manuscript database

Time series of soil moisture-related parameters provides important insights in functioning of soil water systems. Analysis of patterns within these time series has been used in several studies. The objective of this work was to compare patterns in observed and simulated soil moisture contents to u...

Big-Data RHEED analysis for understanding epitaxial film growth processes

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

Vasudevan, Rama K; Tselev, Alexander; Baddorf, Arthur P

Reflection high energy electron diffraction (RHEED) has by now become a standard tool for in-situ monitoring of film growth by pulsed laser deposition and molecular beam epitaxy. Yet despite the widespread adoption and wealth of information in RHEED image, most applications are limited to observing intensity oscillations of the specular spot, and much additional information on growth is discarded. With ease of data acquisition and increased computation speeds, statistical methods to rapidly mine the dataset are now feasible. Here, we develop such an approach to the analysis of the fundamental growth processes through multivariate statistical analysis of RHEED image sequence.more » This approach is illustrated for growth of LaxCa1-xMnO3 films grown on etched (001) SrTiO3 substrates, but is universal. The multivariate methods including principal component analysis and k-means clustering provide insight into the relevant behaviors, the timing and nature of a disordered to ordered growth change, and highlight statistically significant patterns. Fourier analysis yields the harmonic components of the signal and allows separation of the relevant components and baselines, isolating the assymetric nature of the step density function and the transmission spots from the imperfect layer-by-layer (LBL) growth. These studies show the promise of big data approaches to obtaining more insight into film properties during and after epitaxial film growth. Furthermore, these studies open the pathway to use forward prediction methods to potentially allow significantly more control over growth process and hence final film quality.« less

Right frontal gamma and beta band enhancement while solving a spatial puzzle with insight.

PubMed

Rosen, A; Reiner, M

2017-12-01

Solving a problem with an "a-ha" effect is known as insight. Unlike incremental problem solving, insight is sudden and unique, and the question about its distinct brain activity, intrigues many researchers. In this study, electroencephalogram signals were recorded from 12 right handed, human participants before (baseline) and while they solved a spatial puzzle known as the '10 coin puzzle' that could be solved incrementally or by insight. Participants responded as soon as they reached a solution and reported whether the process was incremental or by sudden insight. EEG activity was recorded from 19 scalp locations. We found significant differences between insight and incremental solvers in the Gamma and Beta 2 bands in frontal areas (F8) and in the alpha band in right temporal areas (T6). The right-frontal gamma indicates a process of restructuring which leads to an insight solution, in spatial problems, further suggesting a universal role of gamma in restructuring. These results further suggest that solving a spatial puzzle via insight requires exclusive brain areas and neurological-cognitive processes which may be important for meta-cognitive components of insight solutions, including attention and monitoring of the solution. Copyright © 2016 Elsevier B.V. All rights reserved.

Sensitometric comparisons of Insight and Ektaspeed Plus films: effects of chemical developer depletion.

PubMed

Casanova, Marcia Spinelli; Haiter-Neto, Francisco; Bóscolo, Frab Norberto; de Almeida, Solange Maria

2006-01-01

The aim of this study was to compare the sensitometric properties of Insight and Ektaspeed Plus radiographic films manually and automatically processed using fresh and depleted chemical solutions. Ten sets of each type of film were obtained (1 set = 5 films), 5 sets being manually processed and 5 sets being automatically processed. A total of 100 films (50 Ektaspeed Plus and 50 Insight film) were exposed and developed. The first two sets of each film type were developed in fresh chemicals (one set per each type of processing), on the first day of the experiment. The other sets were processed in the same progressively depleted solutions once a week until the end of experiment, which was completed within 4 weeks. Characteristic curves were constructed to compare the sensitometric properties of the films: contrast, latitude and speed. Processing solution depletion had different effects on manually and automatically developed films, which was confirmed by the changes in the form of the characteristic curves in the third week of the automatic processing and fourth week of the manual processing. Ektaspeed Plus showed 11% reduction in contrast values for manual processing and 53% for automatic processing, while Insight contrast values showed a reduction of 25% and 59%, respectively. Insight film, however, showed lesser loss of speed and lesser increase of latitude than Ektaspeed Plus. In conclusion, chemical depletion in automatic film processing was faster than in manual developing. In depleted chemicals, both types of films had an increase in latitude values and a decrease in speed and contrast. Insight was more resistant than Ektaspeed Plus to decrease in speed and latitude when processed using older chemicals, whereas contrast in Ektaspeed Plus was comparatively more stable.

Self-Processing and the Default Mode Network: Interactions with the Mirror Neuron System

PubMed Central

Molnar-Szakacs, Istvan; Uddin, Lucina Q.

2013-01-01

Recent evidence for the fractionation of the default mode network (DMN) into functionally distinguishable subdivisions with unique patterns of connectivity calls for a reconceptualization of the relationship between this network and self-referential processing. Advances in resting-state functional connectivity analyses are beginning to reveal increasingly complex patterns of organization within the key nodes of the DMN – medial prefrontal cortex and posterior cingulate cortex – as well as between these nodes and other brain systems. Here we review recent examinations of the relationships between the DMN and various aspects of self-relevant and social-cognitive processing in light of emerging evidence for heterogeneity within this network. Drawing from a rapidly evolving social-cognitive neuroscience literature, we propose that embodied simulation and mentalizing are processes which allow us to gain insight into another’s physical and mental state by providing privileged access to our own physical and mental states. Embodiment implies that the same neural systems are engaged for self- and other-understanding through a simulation mechanism, while mentalizing refers to the use of high-level conceptual information to make inferences about the mental states of self and others. These mechanisms work together to provide a coherent representation of the self and by extension, of others. Nodes of the DMN selectively interact with brain systems for embodiment and mentalizing, including the mirror neuron system, to produce appropriate mappings in the service of social-cognitive demands. PMID:24062671

Agricultural Nutrient Cycling at the Strawberry Creek Watershed: Insights Into Processes Using Stable Isotope Analysis

NASA Astrophysics Data System (ADS)

Thuss, E.; English, M. C.; Spoelstra, J.

2009-05-01

When nitrogen availability exceeds biological demand, excess nitrogen, especially nitrate, may subsequently pollute ground and surface water. Agricultural practices in Southern Ontario typically supplement soils with organic and inorganic nutrients to aid in crop development, and employ various management techniques to limit nutrient loss. Excess nitrogen has several potential fates, which are controlled by the net effects of numerous nitrogen cycling reactions in the soil that are often difficult to measure directly. Nitrogen cycling in soils is controlled in large part by soil moisture, as it affects microbial activity and soil redox conditions. Stable isotope geochemistry is a powerful tool that provides information on nitrogen sources and processes. This study uses crop nitrogen and carbon isotope ratios to provide insights into the net effects of soil nitrogen cycling and nitrogen fate. This research was conducted at the Strawberry Creek Watershed (SCW), an agricultural research watershed located between Kitchener-Waterloo and Guelph, Ontario. The SCW exhibits elevated nitrate concentrations in groundwater, tile discharge, and the stream itself. Previous isotopic work revealed that this nitrate is largely derived from chemical fertilizer and manure applications. Field-scale hydrological processes lead to areas where the fate of applied nitrogen differs, which has an isotopic effect on the residual nitrogen that is available to plants. Results of this study indicate significant patterns in the isotopic signature of plant tissue, in both temporal and spatial scales. At the plot-scale where soil conditions are similar, there is little to no variation in foliar isotope values, but at the field-scale there appears to be a significant amount of variability related to soil moisture and nitrogen loss. This relationship can potentially provide insight into ideal conditions for nitrogen uptake efficiency. Reducing agricultural nitrogen leaching to ground and surface water requires a better understanding of nitrogen fate in the soil zone, and will result in more effective agricultural nutrient management.

Outcome dependency alters the neural substrates of impression formation

PubMed Central

Ames, Daniel L.; Fiske, Susan T.

2015-01-01

How do people maintain consistent impressions of other people when other people are often inconsistent? The present research addresses this question by combining recent neuroscientific insights with ecologically meaningful behavioral methods. Participants formed impressions of real people whom they met in a personally involving situation. fMRI and supporting behavioral data revealed that outcome dependency (i.e., depending on another person for a desired outcome) alters previously identified neural dynamics of impression formation. Consistent with past research, a functional localizer identified a region of dorsomedial PFC previously linked to social impression formation. In the main task, this ROI revealed the predicted patterns of activity across outcome dependency conditions: greater BOLD response when information confirmed (vs. violated) social expectations if participants were outcome-independent and the reverse pattern if participants were outcome-dependent. We suggest that, although social perceivers often discount expectancy-disconfirming information as noise, being dependent on another person for a desired outcome focuses impression-formation processing on the most diagnostic information, rather than on the most tractable information. PMID:23850465

Micron-scale channel formation by the release and bond-back of pre-stressed thin films: A finite element analysis

NASA Astrophysics Data System (ADS)

Annabattula, R. K.; Huck, W. T. S.; Onck, P. R.

2010-04-01

Buckling of thin films on a rigid substrate during use or fabrication is a well-known but unwanted phenomenon. However, this phenomenon can also be exploited to generate well-controlled patterns at the micro and nano-scale. These patterned surfaces find various technological applications such as optical gratings or micro/nano-fluidic channels. In this article, we present a numerical model that accounts for the buckling-up of pre-strained thin films by a reduction of the interface toughness and the subsequent bond-back. Channels are formed whose dimensions can be controlled by tuning the film dimensions, film thickness and stiffness, the eigenstrain in the film and the cohesive interface energy between the film and the substrate. We will show how the buckling-up and draping back processes can be captured in terms of a limited set of dimensionless parameters, providing quantitative insight on how these parameters should be tuned to generate a specified channel geometry.

Reflections of Low Income, Second Generation Latinas about Experiences in Depression Therapy

PubMed Central

Heilemann, MarySue V.; Pieters, Huibrie C.; Dornig, Katrina

2016-01-01

Depression is higher among second generation Latinas compared to immigrants but mental health treatment is stigmatized. Therefore, second generation Latinas were interviewed after completing an eight-session depression treatment program to gain insight on what they found valuable about their therapy experiences. Constructivist Grounded Theory guided data collection and analysis which showed that women valued treatment more when they recognized their needs were being met, the therapist was a worthy co-pilot, and the program’s structure had flexibility. Four processes were considered important to their work in therapy: understanding feelings about past events, seeing patterns, accepting self, and changing family patterns but still being “family”. Post therapy, women valued their enhanced confidence and a “toolbelt” of techniques they gained for self-treatment. These findings have implications for designing future depression treatment programs that are more likely to be desirable and effective for the growing subgroup of underserved second generation Latinas in the U.S. PMID:26825479

Analysis of Pacific oyster larval proteome and its response to high-CO2.

PubMed

Dineshram, R; Wong, Kelvin K W; Xiao, Shu; Yu, Ziniu; Qian, Pei Yuan; Thiyagarajan, Vengatesen

2012-10-01

Most calcifying organisms show depressed metabolic, growth and calcification rates as symptoms to high-CO(2) due to ocean acidification (OA) process. Analysis of the global expression pattern of proteins (proteome analysis) represents a powerful tool to examine these physiological symptoms at molecular level, but its applications are inadequate. To address this knowledge gap, 2-DE coupled with mass spectrophotometer was used to compare the global protein expression pattern of oyster larvae exposed to ambient and to high-CO(2). Exposure to OA resulted in marked reduction of global protein expression with a decrease or loss of 71 proteins (18% of the expressed proteins in control), indicating a wide-spread depression of metabolic genes expression in larvae reared under OA. This is, to our knowledge, the first proteome analysis that provides insights into the link between physiological suppression and protein down-regulation under OA in oyster larvae. Copyright © 2012 Elsevier Ltd. All rights reserved.

Notochord-derived Shh concentrates in close association with the apically positioned basal body in neural target cells and forms a dynamic gradient during neural patterning.

PubMed

Chamberlain, Chester E; Jeong, Juhee; Guo, Chaoshe; Allen, Benjamin L; McMahon, Andrew P

2008-03-01

Sonic hedgehog (Shh) ligand secreted by the notochord induces distinct ventral cell identities in the adjacent neural tube by a concentration-dependent mechanism. To study this process, we genetically engineered mice that produce bioactive, fluorescently labeled Shh from the endogenous locus. We show that Shh ligand concentrates in close association with the apically positioned basal body of neural target cells, forming a dynamic, punctate gradient in the ventral neural tube. Both ligand lipidation and target field response influence the gradient profile, but not the ability of Shh to concentrate around the basal body. Further, subcellular analysis suggests that Shh from the notochord might traffic into the neural target field by means of an apical-to-basal-oriented microtubule scaffold. This study, in which we directly observe, measure, localize and modify notochord-derived Shh ligand in the context of neural patterning, provides several new insights into mechanisms of Shh morphogen action.

Activity flow over resting-state networks shapes cognitive task activations.

PubMed

Cole, Michael W; Ito, Takuya; Bassett, Danielle S; Schultz, Douglas H

2016-12-01

Resting-state functional connectivity (FC) has helped reveal the intrinsic network organization of the human brain, yet its relevance to cognitive task activations has been unclear. Uncertainty remains despite evidence that resting-state FC patterns are highly similar to cognitive task activation patterns. Identifying the distributed processes that shape localized cognitive task activations may help reveal why resting-state FC is so strongly related to cognitive task activations. We found that estimating task-evoked activity flow (the spread of activation amplitudes) over resting-state FC networks allowed prediction of cognitive task activations in a large-scale neural network model. Applying this insight to empirical functional MRI data, we found that cognitive task activations can be predicted in held-out brain regions (and held-out individuals) via estimated activity flow over resting-state FC networks. This suggests that task-evoked activity flow over intrinsic networks is a large-scale mechanism explaining the relevance of resting-state FC to cognitive task activations.

Activity flow over resting-state networks shapes cognitive task activations

PubMed Central

Cole, Michael W.; Ito, Takuya; Bassett, Danielle S.; Schultz, Douglas H.

2016-01-01

Resting-state functional connectivity (FC) has helped reveal the intrinsic network organization of the human brain, yet its relevance to cognitive task activations has been unclear. Uncertainty remains despite evidence that resting-state FC patterns are highly similar to cognitive task activation patterns. Identifying the distributed processes that shape localized cognitive task activations may help reveal why resting-state FC is so strongly related to cognitive task activations. We found that estimating task-evoked activity flow (the spread of activation amplitudes) over resting-state FC networks allows prediction of cognitive task activations in a large-scale neural network model. Applying this insight to empirical functional MRI data, we found that cognitive task activations can be predicted in held-out brain regions (and held-out individuals) via estimated activity flow over resting-state FC networks. This suggests that task-evoked activity flow over intrinsic networks is a large-scale mechanism explaining the relevance of resting-state FC to cognitive task activations. PMID:27723746

Emerging patterns of somatic mutations in cancer

PubMed Central

Watson, Ian R.; Takahashi, Koichi; Futreal, P. Andrew; Chin, Lynda

2014-01-01

The advance in technological tools for massively parallel, high-throughput sequencing of DNA has enabled the comprehensive characterization of somatic mutations in large number of tumor samples. Here, we review recent cancer genomic studies that have assembled emerging views of the landscapes of somatic mutations through deep sequencing analyses of the coding exomes and whole genomes in various cancer types. We discuss the comparative genomics of different cancers, including mutation rates, spectrums, and roles of environmental insults that influence these processes. We highlight the developing statistical approaches used to identify significantly mutated genes, and discuss the emerging biological and clinical insights from such analyses as well as the challenges ahead translating these genomic data into clinical impacts. PMID:24022702

Radiation repair models for clinical application.

PubMed

Dale, Roger G

2018-02-28

A number of newly emerging clinical techniques involve non-conventional patterns of radiation delivery which require an appreciation of the role played by radiation repair phenomena. This review outlines the main models of radiation repair, focussing on those which are of greatest clinical usefulness and which may be incorporated into biologically effective dose assessments. The need to account for the apparent "slowing-down" of repair rates observed in some normal tissues is also examined, along with a comparison of the relative merits of the formulations which can be used to account for such phenomena. Jack Fowler brought valuable insight to the understanding of radiation repair processes and this article includes reference to his important contributions in this area.

Emerging Concepts of Data Integration in Pathogen Phylodynamics.

PubMed

Baele, Guy; Suchard, Marc A; Rambaut, Andrew; Lemey, Philippe

2017-01-01

Phylodynamics has become an increasingly popular statistical framework to extract evolutionary and epidemiological information from pathogen genomes. By harnessing such information, epidemiologists aim to shed light on the spatio-temporal patterns of spread and to test hypotheses about the underlying interaction of evolutionary and ecological dynamics in pathogen populations. Although the field has witnessed a rich development of statistical inference tools with increasing levels of sophistication, these tools initially focused on sequences as their sole primary data source. Integrating various sources of information, however, promises to deliver more precise insights in infectious diseases and to increase opportunities for statistical hypothesis testing. Here, we review how the emerging concept of data integration is stimulating new advances in Bayesian evolutionary inference methodology which formalize a marriage of statistical thinking and evolutionary biology. These approaches include connecting sequence to trait evolution, such as for host, phenotypic and geographic sampling information, but also the incorporation of covariates of evolutionary and epidemic processes in the reconstruction procedures. We highlight how a full Bayesian approach to covariate modeling and testing can generate further insights into sequence evolution, trait evolution, and population dynamics in pathogen populations. Specific examples demonstrate how such approaches can be used to test the impact of host on rabies and HIV evolutionary rates, to identify the drivers of influenza dispersal as well as the determinants of rabies cross-species transmissions, and to quantify the evolutionary dynamics of influenza antigenicity. Finally, we briefly discuss how data integration is now also permeating through the inference of transmission dynamics, leading to novel insights into tree-generative processes and detailed reconstructions of transmission trees. [Bayesian inference; birth–death models; coalescent models; continuous trait evolution; covariates; data integration; discrete trait evolution; pathogen phylodynamics.

Defining the origins of electron transfer at screen-printed graphene-like and graphite electrodes: MoO2 nanowire fabrication on edge plane sites reveals electrochemical insights.

PubMed

Rowley-Neale, Samuel J; Brownson, Dale A C; Banks, Craig E

2016-08-18

Molybdenum (di)oxide (MoO2) nanowires are fabricated onto graphene-like and graphite screen-printed electrodes (SPEs) for the first time, revealing crucial insights into the electrochemical properties of carbon/graphitic based materials. Distinctive patterns observed in the electrochemical process of nanowire decoration show that electron transfer occurs predominantly on edge plane sites when utilising SPEs fabricated/comprised of graphitic materials. Nanowire fabrication along the edge plane sites (and on edge plane like-sites/defects) of graphene/graphite is confirmed with Cyclic Voltammetry, Scanning Electron Microscopy (SEM) and Raman Spectroscopy. Comparison of the heterogeneous electron transfer (HET) rate constants (k°) at unmodified and nanowire coated SPEs show a reduction in the electrochemical reactivity of SPEs when the edge plane sites are effectively blocked/coated with MoO2. Throughout the process, the basal plane sites of the graphene/graphite electrodes remain relatively uncovered; except when the available edge plane sites have been utilised, in which case MoO2 deposition grows from the edge sites covering the entire surface of the electrode. This work clearly illustrates the distinct electron transfer properties of edge and basal plane sites on graphitic materials, indicating favourable electrochemical reactivity at the edge planes in contrast to limited reactivity at the basal plane sites. In addition to providing fundamental insights into the electron transfer properties of graphite and graphene-like SPEs, the reported simple, scalable, and cost effective formation of unique and intriguing MoO2 nanowires realised herein is of significant interest for use in both academic and commercial applications.

Emerging Concepts of Data Integration in Pathogen Phylodynamics

PubMed Central

Baele, Guy; Suchard, Marc A.; Rambaut, Andrew; Lemey, Philippe

2017-01-01

Phylodynamics has become an increasingly popular statistical framework to extract evolutionary and epidemiological information from pathogen genomes. By harnessing such information, epidemiologists aim to shed light on the spatio-temporal patterns of spread and to test hypotheses about the underlying interaction of evolutionary and ecological dynamics in pathogen populations. Although the field has witnessed a rich development of statistical inference tools with increasing levels of sophistication, these tools initially focused on sequences as their sole primary data source. Integrating various sources of information, however, promises to deliver more precise insights in infectious diseases and to increase opportunities for statistical hypothesis testing. Here, we review how the emerging concept of data integration is stimulating new advances in Bayesian evolutionary inference methodology which formalize a marriage of statistical thinking and evolutionary biology. These approaches include connecting sequence to trait evolution, such as for host, phenotypic and geographic sampling information, but also the incorporation of covariates of evolutionary and epidemic processes in the reconstruction procedures. We highlight how a full Bayesian approach to covariate modeling and testing can generate further insights into sequence evolution, trait evolution, and population dynamics in pathogen populations. Specific examples demonstrate how such approaches can be used to test the impact of host on rabies and HIV evolutionary rates, to identify the drivers of influenza dispersal as well as the determinants of rabies cross-species transmissions, and to quantify the evolutionary dynamics of influenza antigenicity. Finally, we briefly discuss how data integration is now also permeating through the inference of transmission dynamics, leading to novel insights into tree-generative processes and detailed reconstructions of transmission trees. [Bayesian inference; birth–death models; coalescent models; continuous trait evolution; covariates; data integration; discrete trait evolution; pathogen phylodynamics. PMID:28173504

Embryology of the lamprey and evolution of the vertebrate jaw: insights from molecular and developmental perspectives.

PubMed Central

Kuratani, S; Nobusada, Y; Horigome, N; Shigetani, Y

2001-01-01

Evolution of the vertebrate jaw has been reviewed and discussed based on the developmental pattern of the Japanese marine lamprey, Lampetra japonica. Though it never forms a jointed jaw apparatus, the L. japonica embryo exhibits the typical embryonic structure as well as the conserved regulatory gene expression patterns of vertebrates. The lamprey therefore shares the phylotype of vertebrates, the conserved embryonic pattern that appears at pharyngula stage, rather than representing an intermediate evolutionary state. Both gnathostomes and lampreys exhibit a tripartite configuration of the rostral-most crest-derived ectomesenchyme, each part occupying an anatomically equivalent site. Differentiated oral structure becomes apparent in post-pharyngula development. Due to the solid nasohypophyseal plate, the post-optic ectomesenchyme of the lamprey fails to grow rostromedially to form the medial nasal septum as in gnathostomes, but forms the upper lip instead. The gnathostome jaw may thus have arisen through a process of ontogenetic repatterning, in which a heterotopic shift of mesenchyme-epithelial relationships would have been involved. Further identification of shifts in tissue interaction and expression of regulatory genes are necessary to describe the evolution of the jaw fully from the standpoint of evolutionary developmental biology. PMID:11604127

Analyses of the NAC transcription factor gene family in Gossypium raimondii Ulbr.: chromosomal location, structure, phylogeny, and expression patterns.

PubMed

Shang, Haihong; Li, Wei; Zou, Changsong; Yuan, Youlu

2013-07-01

NAC domain proteins are plant-specific transcription factors known to play diverse roles in various plant developmental processes. In the present study, we performed the first comprehensive study of the NAC gene family in Gossypium raimondii Ulbr., incorporating phylogenetic, chromosomal location, gene structure, conserved motif, and expression profiling analyses. We identified 145 NAC transcription factor (NAC-TF) genes that were phylogenetically clustered into 18 distinct subfamilies. Of these, 127 NAC-TF genes were distributed across the 13 chromosomes, 80 (55%) were preferentially retained duplicates located in both duplicated regions and six were located in triplicated chromosomal regions. The majority of NAC-TF genes showed temporal-, spatial-, and tissue-specific expression patterns based on transcriptomic and qRT-PCR analyses. However, the expression patterns of several duplicate genes were partially redundant, suggesting the occurrence of sub-functionalization during their evolution. Based on their genomic organization, we concluded that genomic duplications contributed significantly to the expansion of the NAC-TF gene family in G. raimondii. Comprehensive analysis of their expression profiles could provide novel insights into the functional divergence among members of the NAC gene family in G. raimondii. © 2013 Institute of Botany, Chinese Academy of Sciences.

Altered Sleep Patterns and Physiologic Characteristics in Spontaneous Dwarf Rats

PubMed Central

Andersen, Monica L; Lee, Kil S; Guindalini, Camila; Leite, Waldemarks A; Bignotto, Magda; Tufik, Sergio

2009-01-01

Spontaneous dwarf rats are a useful experimental model for studying various biologic events associated with pituitary dwarfism. Dwarf rats occurred serendipitously in our colony of Wistar rats during experimental breeding. This study aimed to describe the sleep pattern and physiologic characteristics of these rats compared with normal-sized adult rats. Because growth hormone can attenuate the upregulation of ceruloplasmin expression caused by acute inflammation, we also assessed the basal levels of serum ceruloplasmin in these animals. At 90 d of age, body weight and length were significantly lower in dwarf rats relative to normal rats. Dwarves had lower concentrations of serum testosterone and growth hormone, but progesterone was unchanged. Corticosterone levels did not differ between groups. During the light period, the percentage of sleep time recorded and duration of slow-wave sleep did not differ between groups. However, compared with controls, dwarf rats had marked fragmentation of sleep and less paradoxical sleep. During the dark phase, sleep patterns in dwarf rats were within the normal range. Immunoblotting data showed that the levels of ceruloplasmin in serum were lower in dwarf rats. Our findings provide insight into pathologic processes related to growth hormone deficiency. PMID:19712574

Quantitative analysis of urban sprawl in Tripoli using Pearson's Chi-Square statistics and urban expansion intensity index

NASA Astrophysics Data System (ADS)

Al-sharif, Abubakr A. A.; Pradhan, Biswajeet; Zulhaidi Mohd Shafri, Helmi; Mansor, Shattri

2014-06-01

Urban expansion is a spatial phenomenon that reflects the increased level of importance of metropolises. The remotely sensed data and GIS have been widely used to study and analyze the process of urban expansions and their patterns. The capital of Libya (Tripoli) was selected to perform this study and to examine its urban growth patterns. Four satellite imageries of the study area in different dates (1984, 1996, 2002 and 2010) were used to conduct this research. The main goal of this work is identification and analyzes the urban sprawl of Tripoli metropolitan area. Urban expansion intensity index (UEII) and degree of freedom test were used to analyze and assess urban expansions in the area of study. The results show that Tripoli has sprawled urban expansion patterns; high urban expansion intensity index; and its urban development had high degree of freedom according to its urban expansion history during the time period (1984-2010). However, the novel proposed hypothesis used for zones division resulted in very good insight understanding of urban expansion direction and the effect of the distance from central business of district (CBD).

PRINCIPLES AND PATTERNS OF BAT MOVEMENTS: FROM AERODYNAMICS TO ECOLOGY

PubMed Central

Voigt, Christian C.; Frick, Winifred F.; Holderied, Marc W.; Holland, Richard; Kerth, Gerald; Mello, Marco A. R.; Plowright, Raina K.; Swartz, Sharon; Yovel, Yossi

2018-01-01

Movement ecology as an integrative discipline has advanced associated fields because it presents not only a conceptual framework for understanding movement principles but also helps formulate predictions about the consequences of movements for animals and their environments. Here, we synthesize recent studies on principles and patterns of bat movements in context of the movement ecology paradigm. The motion capacity of bats is defined by their highly articulated, flexible wings. Power production during flight follows a U-shaped curve in relation to speed in bats yet, in contrast to birds, bats use mostly exogenous nutrients for sustained flight. The navigation capacity of most bats is dominated by the echolocation system, yet other sensory modalities, including an iron-based magnetic sense, may contribute to navigation depending on a bat’s familiarity with the terrain. Patterns derived from these capacities relate to antagonistic and mutualistic interactions with food items. The navigation capacity of bats may influence their sociality, in particular, the extent of group foraging based on eavesdropping on conspecifics’ echolocation calls. We infer that understanding the movement ecology of bats within the framework of the movement ecology paradigm provides new insights into ecological processes mediated by bats, from ecosystem services to diseases. PMID:29861509

Remodeling a tissue: subtraction adds insight.

PubMed

Axelrod, Jeffrey D

2012-11-27

Sculpting a body plan requires both patterning of gene expression and translating that pattern into morphogenesis. Developmental biologists have made remarkable strides in understanding gene expression patterning, but despite a long history of fascination with the mechanics of morphogenesis, knowledge of how patterned gene expression drives the emergence of even simple shapes and forms has grown at a slower pace. The successful merging of approaches from cell biology, developmental biology, imaging, engineering, and mathematical and computational sciences is now accelerating progress toward a fuller and better integrated understanding of the forces shaping morphogenesis.

Webcams for Bird Detection and Monitoring: A Demonstration Study

PubMed Central

Verstraeten, Willem W.; Vermeulen, Bart; Stuckens, Jan; Lhermitte, Stefaan; Van der Zande, Dimitry; Van Ranst, Marc; Coppin, Pol

2010-01-01

Better insights into bird migration can be a tool for assessing the spread of avian borne infections or ecological/climatologic issues reflected in deviating migration patterns. This paper evaluates whether low budget permanent cameras such as webcams can offer a valuable contribution to the reporting of migratory birds. An experimental design was set up to study the detection capability using objects of different size, color and velocity. The results of the experiment revealed the minimum size, maximum velocity and contrast of the objects required for detection by a standard webcam. Furthermore, a modular processing scheme was proposed to track and follow migratory birds in webcam recordings. Techniques such as motion detection by background subtraction, stereo vision and lens distortion were combined to form the foundation of the bird tracking algorithm. Additional research to integrate webcam networks, however, is needed and future research should enforce the potential of the processing scheme by exploring and testing alternatives of each individual module or processing step. PMID:22319308

Epigenomics and human adaptation to high altitude.

PubMed

Julian, Colleen G

2017-11-01

Over the past decade, major technological and analytical advancements have propelled efforts toward identifying the molecular mechanisms that govern human adaptation to high altitude. Despite remarkable progress with respect to the identification of adaptive genomic signals that are strongly associated with the "hypoxia-tolerant" physiological characteristics of high-altitude populations, many questions regarding the fundamental biological processes underlying human adaptation remain unanswered. Vital to address these enduring questions will be determining the role of epigenetic processes, or non-sequence-based features of the genome, that are not only critical for the regulation of transcriptional responses to hypoxia but heritable across generations. This review proposes that epigenomic processes are involved in shaping patterns of adaptation to high altitude by influencing adaptive potential and phenotypic variability under conditions of limited oxygen supply. Improved understanding of the interaction between genetic, epigenetic, and environmental factors holds great promise to provide deeper insight into the mechanisms underlying human adaptive potential, and clarify its implications for biomedical research. Copyright © 2017 the American Physiological Society.

Webcams for bird detection and monitoring: a demonstration study.

PubMed

Verstraeten, Willem W; Vermeulen, Bart; Stuckens, Jan; Lhermitte, Stefaan; Van der Zande, Dimitry; Van Ranst, Marc; Coppin, Pol

2010-01-01

Better insights into bird migration can be a tool for assessing the spread of avian borne infections or ecological/climatologic issues reflected in deviating migration patterns. This paper evaluates whether low budget permanent cameras such as webcams can offer a valuable contribution to the reporting of migratory birds. An experimental design was set up to study the detection capability using objects of different size, color and velocity. The results of the experiment revealed the minimum size, maximum velocity and contrast of the objects required for detection by a standard webcam. Furthermore, a modular processing scheme was proposed to track and follow migratory birds in webcam recordings. Techniques such as motion detection by background subtraction, stereo vision and lens distortion were combined to form the foundation of the bird tracking algorithm. Additional research to integrate webcam networks, however, is needed and future research should enforce the potential of the processing scheme by exploring and testing alternatives of each individual module or processing step.

New insights into saline water evaporation from porous media: Complex interaction between evaporation rates, precipitation, and surface temperature

NASA Astrophysics Data System (ADS)

Shokri-Kuehni, Salomé M. S.; Vetter, Thomas; Webb, Colin; Shokri, Nima

2017-06-01

Understanding salt transport and deposition patterns during evaporation from porous media is important in many engineering and hydrological processes such as soil salinization, ecosystem functioning, and land-atmosphere interaction. As evaporation proceeds, salt concentration increases until it exceeds solubility limits, locally, and crystals precipitate. The interplay between transport processes, crystallization, and evaporation influences where crystallization occurs. During early stages, the precipitated salt creates an evolving porous structure affecting the evaporation kinetics. We conducted a comprehensive series of experiments to investigate how the salt concentration and precipitation influence evaporation dynamics. Our results illustrate the contribution of the evolving salt crust to the evaporative mass losses. High-resolution thermal imaging enabled us to investigate the complex temperature dynamics at the surface of precipitated salt, providing further confirmation of salt crust contribution to the evaporation. We identify different phases of saline water evaporation from porous media with the corresponding dominant mechanisms in each phase and extend the physical understanding of such processes.

Grasping the invisible: semantic processing of abstract words.

PubMed

Zdrazilova, Lenka; Pexman, Penny M

2013-12-01

The problem of how abstract word meanings are represented has been a challenging one. In the present study, we extended the semantic richness approach (e.g., Yap, Tan, Pexman, & Hargreaves in Psychonomic Bulletin & Review 18:742-750, 2011) to abstract words, examining the effects of six semantic richness variables on lexical-semantic processing for 207 abstract nouns. The candidate richness dimensions were context availability (CA), sensory experience rating (SER), valence, arousal, semantic neighborhood (SN), and number of associates (NoA). The behavioral tasks were lexical decision (LDT) and semantic categorization (SCT). Our results showed that the semantic richness variables were significantly related to both LDT and SCT latencies, even after lexical and orthographic factors were controlled. The patterns of richness effects varied across tasks, with CA effects in the LDT, and SER and valence effects in the SCT. These results provide new insight into how abstract meanings may be grounded, and are consistent with a dynamic, multidimensional framework for semantic processing.

Tracking and visualization of space-time activities for a micro-scale flu transmission study.

PubMed

Qi, Feng; Du, Fei

2013-02-07

Infectious diseases pose increasing threats to public health with increasing population density and more and more sophisticated social networks. While efforts continue in studying the large scale dissemination of contagious diseases, individual-based activity and behaviour study benefits not only disease transmission modelling but also the control, containment, and prevention decision making at the local scale. The potential for using tracking technologies to capture detailed space-time trajectories and model individual behaviour is increasing rapidly, as technological advances enable the manufacture of small, lightweight, highly sensitive, and affordable receivers and the routine use of location-aware devices has become widespread (e.g., smart cellular phones). The use of low-cost tracking devices in medical research has also been proved effective by more and more studies. This study describes the use of tracking devices to collect data of space-time trajectories and the spatiotemporal processing of such data to facilitate micro-scale flu transmission study. We also reports preliminary findings on activity patterns related to chances of influenza infection in a pilot study. Specifically, this study employed A-GPS tracking devices to collect data on a university campus. Spatiotemporal processing was conducted for data cleaning and segmentation. Processed data was validated with traditional activity diaries. The A-GPS data set was then used for visual explorations including density surface visualization and connection analysis to examine space-time activity patterns in relation to chances of influenza infection. When compared to diary data, the segmented tracking data demonstrated to be an effective alternative and showed greater accuracies in time as well as the details of routes taken by participants. A comparison of space-time activity patterns between participants who caught seasonal influenza and those who did not revealed interesting patterns. This study proved that tracking technology an effective technique for obtaining data for micro-scale influenza transmission research. The findings revealed micro-scale transmission hotspots on a university campus and provided insights for local control and prevention strategies.

Time-series panel analysis (TSPA): multivariate modeling of temporal associations in psychotherapy process.

PubMed

Ramseyer, Fabian; Kupper, Zeno; Caspar, Franz; Znoj, Hansjörg; Tschacher, Wolfgang

2014-10-01

Processes occurring in the course of psychotherapy are characterized by the simple fact that they unfold in time and that the multiple factors engaged in change processes vary highly between individuals (idiographic phenomena). Previous research, however, has neglected the temporal perspective by its traditional focus on static phenomena, which were mainly assessed at the group level (nomothetic phenomena). To support a temporal approach, the authors introduce time-series panel analysis (TSPA), a statistical methodology explicitly focusing on the quantification of temporal, session-to-session aspects of change in psychotherapy. TSPA-models are initially built at the level of individuals and are subsequently aggregated at the group level, thus allowing the exploration of prototypical models. TSPA is based on vector auto-regression (VAR), an extension of univariate auto-regression models to multivariate time-series data. The application of TSPA is demonstrated in a sample of 87 outpatient psychotherapy patients who were monitored by postsession questionnaires. Prototypical mechanisms of change were derived from the aggregation of individual multivariate models of psychotherapy process. In a 2nd step, the associations between mechanisms of change (TSPA) and pre- to postsymptom change were explored. TSPA allowed a prototypical process pattern to be identified, where patient's alliance and self-efficacy were linked by a temporal feedback-loop. Furthermore, therapist's stability over time in both mastery and clarification interventions was positively associated with better outcomes. TSPA is a statistical tool that sheds new light on temporal mechanisms of change. Through this approach, clinicians may gain insight into prototypical patterns of change in psychotherapy. PsycINFO Database Record (c) 2014 APA, all rights reserved.

Gaussian process based independent analysis for temporal source separation in fMRI.

PubMed

Hald, Ditte Høvenhoff; Henao, Ricardo; Winther, Ole

2017-05-15

Functional Magnetic Resonance Imaging (fMRI) gives us a unique insight into the processes of the brain, and opens up for analyzing the functional activation patterns of the underlying sources. Task-inferred supervised learning with restrictive assumptions in the regression set-up, restricts the exploratory nature of the analysis. Fully unsupervised independent component analysis (ICA) algorithms, on the other hand, can struggle to detect clear classifiable components on single-subject data. We attribute this shortcoming to inadequate modeling of the fMRI source signals by failing to incorporate its temporal nature. fMRI source signals, biological stimuli and non-stimuli-related artifacts are all smooth over a time-scale compatible with the sampling time (TR). We therefore propose Gaussian process ICA (GPICA), which facilitates temporal dependency by the use of Gaussian process source priors. On two fMRI data sets with different sampling frequency, we show that the GPICA-inferred temporal components and associated spatial maps allow for a more definite interpretation than standard temporal ICA methods. The temporal structures of the sources are controlled by the covariance of the Gaussian process, specified by a kernel function with an interpretable and controllable temporal length scale parameter. We propose a hierarchical model specification, considering both instantaneous and convolutive mixing, and we infer source spatial maps, temporal patterns and temporal length scale parameters by Markov Chain Monte Carlo. A companion implementation made as a plug-in for SPM can be downloaded from https://github.com/dittehald/GPICA. Copyright © 2017 Elsevier Inc. All rights reserved.

Dry contact transfer printing of aligned carbon nanotube patterns and characterization of their optical properties for diameter distribution and alignment.

PubMed

Pint, Cary L; Xu, Ya-Qiong; Moghazy, Sharief; Cherukuri, Tonya; Alvarez, Noe T; Haroz, Erik H; Mahzooni, Salma; Doorn, Stephen K; Kono, Junichiro; Pasquali, Matteo; Hauge, Robert H

2010-02-23

A scalable and facile approach is demonstrated where as-grown patterns of well-aligned structures composed of single-walled carbon nanotubes (SWNT) synthesized via water-assisted chemical vapor deposition (CVD) can be transferred, or printed, to any host surface in a single dry, room-temperature step using the growth substrate as a stamp. We demonstrate compatibility of this process with multiple transfers for large-scale device and specifically tailored pattern fabrication. Utilizing this transfer approach, anisotropic optical properties of the SWNT films are probed via polarized absorption, Raman, and photoluminescence spectroscopies. Using a simple model to describe optical transitions in the large SWNT species present in the aligned samples, polarized absorption data are demonstrated as an effective tool for accurate assignment of the diameter distribution from broad absorption features located in the infrared. This can be performed on either well-aligned samples or unaligned doped samples, allowing simple and rapid feedback of the SWNT diameter distribution that can be challenging and time-consuming to obtain in other optical methods. Furthermore, we discuss challenges in accurately characterizing alignment in structures of long versus short carbon nanotubes through optical techniques, where SWNT length makes a difference in the information obtained in such measurements. This work provides new insight to the efficient transfer and optical properties of an emerging class of long, large diameter SWNT species typically produced in the CVD process.

Nuclear ribosome biogenesis mediated by the DIM1A rRNA dimethylase is required for organized root growth and epidermal patterning in Arabidopsis.

PubMed

Wieckowski, Yana; Schiefelbein, John

2012-07-01

Position-dependent patterning of hair and non-hair cells in the Arabidopsis thaliana root epidermis is a powerful system to study the molecular basis of cell fate specification. Here, we report an epidermal patterning mutant affecting the ADENOSINE DIMETHYL TRANSFERASE 1A (DIM1A) rRNA dimethylase gene, predicted to participate in rRNA posttranscriptional processing and base modification. Consistent with a role in ribosome biogenesis, DIM1A is preferentially expressed in regions of rapid growth, and its product is nuclear localized with nucleolus enrichment. Furthermore, DIM1A preferentially accumulates in the developing hair cells, and the dim1A point mutant alters the cell-specific expression of the transcriptional regulators GLABRA2, CAPRICE, and WEREWOLF. Together, these findings suggest that establishment of cell-specific gene expression during root epidermis development is dependent upon proper ribosome biogenesis, possibly due to the sensitivity of the cell fate decision to relatively small differences in gene regulatory activities. Consistent with its effect on the predicted S-adenosyl-l-Met binding site, dim1A plants lack the two 18S rRNA base modifications but exhibit normal pre-rRNA processing. In addition to root epidermal defects, the dim1A mutant exhibits abnormal root meristem division, leaf development, and trichome branching. Together, these findings provide new insights into the importance of rRNA base modifications and translation regulation for plant growth and development.

Nuclear Ribosome Biogenesis Mediated by the DIM1A rRNA Dimethylase Is Required for Organized Root Growth and Epidermal Patterning in Arabidopsis[C][W

PubMed Central

Wieckowski, Yana; Schiefelbein, John

2012-01-01

Position-dependent patterning of hair and non-hair cells in the Arabidopsis thaliana root epidermis is a powerful system to study the molecular basis of cell fate specification. Here, we report an epidermal patterning mutant affecting the ADENOSINE DIMETHYL TRANSFERASE 1A (DIM1A) rRNA dimethylase gene, predicted to participate in rRNA posttranscriptional processing and base modification. Consistent with a role in ribosome biogenesis, DIM1A is preferentially expressed in regions of rapid growth, and its product is nuclear localized with nucleolus enrichment. Furthermore, DIM1A preferentially accumulates in the developing hair cells, and the dim1A point mutant alters the cell-specific expression of the transcriptional regulators GLABRA2, CAPRICE, and WEREWOLF. Together, these findings suggest that establishment of cell-specific gene expression during root epidermis development is dependent upon proper ribosome biogenesis, possibly due to the sensitivity of the cell fate decision to relatively small differences in gene regulatory activities. Consistent with its effect on the predicted S-adenosyl-l-Met binding site, dim1A plants lack the two 18S rRNA base modifications but exhibit normal pre-rRNA processing. In addition to root epidermal defects, the dim1A mutant exhibits abnormal root meristem division, leaf development, and trichome branching. Together, these findings provide new insights into the importance of rRNA base modifications and translation regulation for plant growth and development. PMID:22829145

Genetic diversity and differentiation in a wide ranging anadromous fish, American shad (Alosa sapidissima), is correlated with latitude.

PubMed

Hasselman, Daniel J; Ricard, Daniel; Bentzen, Paul

2013-03-01

Studies that span entire species ranges can provide insight into the relative roles of historical contingency and contemporary factors that influence population structure and can reveal patterns of genetic variation that might otherwise go undetected. American shad is a wide ranging anadromous clupeid fish that exhibits variation in demographic histories and reproductive strategies (both semelparity and iteroparity) and provides a unique perspective on the evolutionary processes that govern the genetic architecture of anadromous fishes. Using 13 microsatellite loci, we examined the magnitude and spatial distribution of genetic variation among 33 populations across the species' range to (i) determine whether signals of historical demography persist among contemporary populations and (ii) assess the effect of different reproductive strategies on population structure. Patterns of genetic diversity and differentiation among populations varied widely and reflect the differential influences of historical demography, microevolutionary processes and anthropogenic factors across the species' range. Sequential reductions of diversity with latitude among formerly glaciated rivers are consistent with stepwise postglacial colonization and successive population founder events. Weak differentiation among U.S. iteroparous populations may be a consequence of human-mediated gene flow, while weak differentiation among semelparous populations probably reflects natural gene flow. Evidence for an effect of reproductive strategy on population structure suggests an important role for environmental variation and suggests that the factors that are responsible for shaping American shad life history patterns may also influence population genetic structure. © 2013 Blackwell Publishing Ltd.

Insights into the three-dimensional Lagrangian geometry of the Antarctic polar vortex

NASA Astrophysics Data System (ADS)

Curbelo, Jezabel; José García-Garrido, Víctor; Mechoso, Carlos Roberto; Mancho, Ana Maria; Wiggins, Stephen; Niang, Coumba

2017-07-01

In this paper we study the three-dimensional (3-D) Lagrangian structures in the stratospheric polar vortex (SPV) above Antarctica. We analyse and visualize these structures using Lagrangian descriptor function M. The procedure for calculation with reanalysis data is explained. Benchmarks are computed and analysed that allow us to compare 2-D and 3-D aspects of Lagrangian transport. Dynamical systems concepts appropriate to 3-D, such as normally hyperbolic invariant curves, are discussed and applied. In order to illustrate our approach we select an interval of time in which the SPV is relatively undisturbed (August 1979) and an interval of rapid SPV changes (October 1979). Our results provide new insights into the Lagrangian structure of the vertical extension of the stratospheric polar vortex and its evolution. Our results also show complex Lagrangian patterns indicative of strong mixing processes in the upper troposphere and lower stratosphere. Finally, during the transition to summer in the late spring, we illustrate the vertical structure of two counterrotating vortices, one the polar and the other an emerging one, and the invariant separatrix that divides them.

Effects of trophic ecology and habitat use on maternal transfer of contaminants in four species of young of the year lamniform sharks.

PubMed

Lyons, Kady; Carlisle, Aaron; Preti, Antonella; Mull, Christopher; Blasius, Mary; O'Sullivan, John; Winkler, Chuck; Lowe, Christopher G

2013-09-01

Organic contaminant and total mercury concentrations were compared in four species of lamniform sharks over several age classes to examine bioaccumulation patterns and gain insights into trophic ecology. Contaminants found in young of the year (YOY) sharks were assumed to be derived from maternal sources and used as a proxy to investigate factors that influence maternal offloading processes. YOY white (Carcharodon carcharias) and mako (Isurus oxyrinchus) sharks had comparable and significantly higher concentrations of PCBs, DDTs, pesticides, and mercury than YOY thresher (Alopias vulpinus) or salmon (Lamna ditropis) sharks. A significant positive relationship was found between YOY contaminant loads and maternal trophic position, suggesting that trophic ecology is one factor that plays an important role in maternal offloading. Differences in organic contaminant signatures and contaminant concentration magnitudes among species corroborated what is known about species habitat use and may be used to provide insights into the feeding ecology of these animals. Copyright © 2013 The Authors. Published by Elsevier Ltd.. All rights reserved.

Low Mitochondrial DNA Diversity in an Ancient Population from China: Insight into Social Organization at the Fujia Site.

PubMed

Dong, Yu; Li, Chunxiang; Luan, Fengshi; Li, Zhenguang; Li, Hongjie; Cui, Yinqiu; Zhou, Hui; Malhi, Ripan S

2015-01-01

To gain insight into the social organization of a population associated with the Dawenkou period, we performed ancient DNA analysis of 18 individuals from human remains from the Fujia site in Shandong Province, China. Directly radiocarbon dated to 4800-4500 cal BP, the Fujia site is assumed to be associated with a transitional phase from matrilineal clans to patrilineal monogamous families. Our results reveal a low mitochondrial DNA diversity from the site and population. Combined with Y chromosome data, the pattern observed at the Fujia site is most consistent with a matrilineal community. The patterns also suggest that the bond of marriage was de-emphasized compared with the bonds of descent at Fujia.

InSight Spacecraft Arrival

NASA Image and Video Library

2018-02-28

At Vandenberg Air Force Base in California, NASA's Interior Exploration using Seismic Investigations, Geodesy and Heat Transport, or InSight, spacecraft arrives at the Astrotech processing facility. InSight was developed and built by Lockheed-Martin Space Systems in Denver, Colorado, and is scheduled for liftoff is May 5, 2018. InSight is the first mission to land on Mars and explore the Red Planet's deep interior. It will investigate processes that shaped the rocky planets of the inner solar system including Earth.

What Do Citation Patterns Reveal about the Outdoor Education Field? A Snapshot 2000-2013

ERIC Educational Resources Information Center

Brookes, Andrew; Stewart, Alistair

2016-01-01

This study considered what insights into outdoor education (OE) research and scholarship could be gleaned from citation indices and patterns. Citation indices have long been used as ranking tools in the physical sciences, and more recently have been used in humanities and social sciences. High citation measures indicate high research impact,…

Pause Time Patterns in Writing Narrative and Expository Texts by Children and Adults

ERIC Educational Resources Information Center

van Hell, Janet G.; Verhoeven, Ludo; van Beijsterveldt, Liesbeth M.

2008-01-01

How do beginning and skilled writers compose a text in the course of time? To gain insight into the temporal aspects of planning and translating activities during writing, this article examined writing in real time and analyzed pause time patterns in writing in relation to linguistic characteristics of the written product. Fourth-grade children…

How Did Agricultural Patterns Change in Serbia after the Fall of Yugoslavia?

ERIC Educational Resources Information Center

Sibinovic, Mikica

2018-01-01

In this lesson plan that takes one class period to complete, high school students explore how political systems influence economic activity by comparing 1991 and 2012 agricultural patterns around the Serbian capital of Belgrade. This lesson provides an insight into the model of transformation of agriculture in Serbia, but a comparison of the…

Tests of species-specific models reveal the importance of drought in postglacial range shifts of a Mediterranean-climate tree: insights from integrative distributional, demographic and coalescent modelling and ABC model selection.

PubMed

Bemmels, Jordan B; Title, Pascal O; Ortego, Joaquín; Knowles, L Lacey

2016-10-01

Past climate change has caused shifts in species distributions and undoubtedly impacted patterns of genetic variation, but the biological processes mediating responses to climate change, and their genetic signatures, are often poorly understood. We test six species-specific biologically informed hypotheses about such processes in canyon live oak (Quercus chrysolepis) from the California Floristic Province. These hypotheses encompass the potential roles of climatic niche, niche multidimensionality, physiological trade-offs in functional traits, and local-scale factors (microsites and local adaptation within ecoregions) in structuring genetic variation. Specifically, we use ecological niche models (ENMs) to construct temporally dynamic landscapes where the processes invoked by each hypothesis are reflected by differences in local habitat suitabilities. These landscapes are used to simulate expected patterns of genetic variation under each model and evaluate the fit of empirical data from 13 microsatellite loci genotyped in 226 individuals from across the species range. Using approximate Bayesian computation (ABC), we obtain very strong support for two statistically indistinguishable models: a trade-off model in which growth rate and drought tolerance drive habitat suitability and genetic structure, and a model based on the climatic niche estimated from a generic ENM, in which the variables found to make the most important contribution to the ENM have strong conceptual links to drought stress. The two most probable models for explaining the patterns of genetic variation thus share a common component, highlighting the potential importance of seasonal drought in driving historical range shifts in a temperate tree from a Mediterranean climate where summer drought is common. © 2016 John Wiley & Sons Ltd.

Woody-Herbaceous Species Coexistence in Mulga Hillslopes: Modelling Structure and Function

NASA Astrophysics Data System (ADS)

Soltanjalili, M. J.; Saco, P. M.; Willgoose, G. R.

2016-12-01

The fundamental processes underlying the coexistence of woody and herbaceous species in arid and semi-arid areas have been a topic of intense research during the last few decades. Experimental and modelling studies have both supported and disputed alternative hypotheses explaining this phenomenon. Vegetation models including the key processes that drive coexistence can be used to understand vegetation pattern dynamics and structure under current climate conditions, and to predict changes under future conditions. Here we present work done towards linking the observations to modelling. The model captures woody-herbaceous coexistence along a rainfall gradient characteristic of typical conditions on Mulga ecosystems in Australia. The dynamic vegetation model simulates the spatial dynamics of overland flow, soil moisture and vegetation growth of two species. It incorporates key mechanisms for coexistence and pattern formation, including facilitation by evaporation reduction through shading, and infiltration feedbacks, local and non-local seed dispersal, competition for water uptake. Model outcomes, obtained including diflerent mechanisms, are qualitatively compared to typical vegetation cover patterns in the Australian Mulga bioregion where bush fire is very infrequent and the fate of vegetation cover is mostly determined by intra- and interspecies interactions. Through these comparisons, and by drawing on the large number of recent studies that have delivered new insights into the dynamics of such ecosystems, we identify main mechanisms that need an improved representation in the dynamic vegetation models. We show that a realistic parameterization of the model leads to results which are aligned with the observations reported in the literature. At the lower end of the rainfall gradient woody species coexist with herbaceous species within a sparse banded pattern, while at higher rainfall woody species tend to dominate the landscape.

Methods for assessing movement path recursion with application to African buffalo in South Africa

USGS Publications Warehouse

Bar-David, S.; Bar-David, I.; Cross, P.C.; Ryan, S.J.; Knechtel, C.U.; Getz, W.M.

2009-01-01

Recent developments of automated methods for monitoring animal movement, e.g., global positioning systems (GPS) technology, yield high-resolution spatiotemporal data. To gain insights into the processes creating movement patterns, we present two new techniques for extracting information from these data on repeated visits to a particular site or patch ("recursions"). Identification of such patches and quantification of recursion pathways, when combined with patch-related ecological data, should contribute to our understanding of the habitat requirements of large herbivores, of factors governing their space-use patterns, and their interactions with the ecosystem. We begin by presenting output from a simple spatial model that simulates movements of large-herbivore groups based on minimal parameters: resource availability and rates of resource recovery after a local depletion. We then present the details of our new techniques of analyses (recursion analysis and circle analysis) and apply them to data generated by our model, as well as two sets of empirical data on movements of African buffalo (Syncerus coffer): the first collected in Klaserie Private Nature Reserve and the second in Kruger National Park, South Africa. Our recursion analyses of model outputs provide us with a basis for inferring aspects of the processes governing the production of buffalo recursion patterns, particularly the potential influence of resource recovery rate. Although the focus of our simulations was a comparison of movement patterns produced by different resource recovery rates, we conclude our paper with a comprehensive discussion of how recursion analyses can be used when appropriate ecological data are available to elucidate various factors influencing movement. Inter alia, these include the various limiting and preferred resources, parasites, and topographical and landscape factors. ?? 2009 by the Ecological Society of America.

Extremely selective attention: eye-tracking studies of the dynamic allocation of attention to stimulus features in categorization.

PubMed

Blair, Mark R; Watson, Marcus R; Walshe, R Calen; Maj, Fillip

2009-09-01

Humans have an extremely flexible ability to categorize regularities in their environment, in part because of attentional systems that allow them to focus on important perceptual information. In formal theories of categorization, attention is typically modeled with weights that selectively bias the processing of stimulus features. These theories make differing predictions about the degree of flexibility with which attention can be deployed in response to stimulus properties. Results from 2 eye-tracking studies show that humans can rapidly learn to differently allocate attention to members of different categories. These results provide the first unequivocal demonstration of stimulus-responsive attention in a categorization task. Furthermore, the authors found clear temporal patterns in the shifting of attention within trials that follow from the informativeness of particular stimulus features. These data provide new insights into the attention processes involved in categorization. (c) 2009 APA, all rights reserved.

Detecting spatial patterns of rivermouth processes using a geostatistical framework for near-real-time analysis

USGS Publications Warehouse

Xu, Wenzhao; Collingsworth, Paris D.; Bailey, Barbara; Carlson Mazur, Martha L.; Schaeffer, Jeff; Minsker, Barbara

2017-01-01

This paper proposes a geospatial analysis framework and software to interpret water-quality sampling data from towed undulating vehicles in near-real time. The framework includes data quality assurance and quality control processes, automated kriging interpolation along undulating paths, and local hotspot and cluster analyses. These methods are implemented in an interactive Web application developed using the Shiny package in the R programming environment to support near-real time analysis along with 2- and 3-D visualizations. The approach is demonstrated using historical sampling data from an undulating vehicle deployed at three rivermouth sites in Lake Michigan during 2011. The normalized root-mean-square error (NRMSE) of the interpolation averages approximately 10% in 3-fold cross validation. The results show that the framework can be used to track river plume dynamics and provide insights on mixing, which could be related to wind and seiche events.

Suppressing Ice Nucleation of Supercooled Condensate with Biphilic Topography

NASA Astrophysics Data System (ADS)

Hou, Youmin; Yu, Miao; Shang, Yuhe; Zhou, Peng; Song, Ruyuan; Xu, Xiaonan; Chen, Xuemei; Wang, Zuankai; Yao, Shuhuai

2018-02-01

Preventing or minimizing ice formation in supercooled water is of prominent importance in many infrastructures, transportation, and cooling systems. The overall phase change heat transfer on icephobic surfaces, in general, is intentionally sacrificed to suppress the nucleation of water and ice. However, in a condensation frosting process, inhibiting freezing without compromising the water condensation has been an unsolved challenge. Here we show that this conflict between anti-icing and efficient condensation cooling can be resolved by utilizing biphilic topography with patterned high-contrast wettability. By creating a varying interfacial thermal barrier underneath the supercooled condensate, the biphilic structures tune the nucleation rates of water and ice in the sequential condensation-to-freezing process. Our experimental and theoretical investigation of condensate freezing dynamics further unravels the correlation between the onset of droplet freezing and its characteristic radius, offering a new insight for controlling the multiphase transitions among vapor, water, and ice in supercooled conditions.

Suppressing Ice Nucleation of Supercooled Condensate with Biphilic Topography.

PubMed

Hou, Youmin; Yu, Miao; Shang, Yuhe; Zhou, Peng; Song, Ruyuan; Xu, Xiaonan; Chen, Xuemei; Wang, Zuankai; Yao, Shuhuai

2018-02-16

Preventing or minimizing ice formation in supercooled water is of prominent importance in many infrastructures, transportation, and cooling systems. The overall phase change heat transfer on icephobic surfaces, in general, is intentionally sacrificed to suppress the nucleation of water and ice. However, in a condensation frosting process, inhibiting freezing without compromising the water condensation has been an unsolved challenge. Here we show that this conflict between anti-icing and efficient condensation cooling can be resolved by utilizing biphilic topography with patterned high-contrast wettability. By creating a varying interfacial thermal barrier underneath the supercooled condensate, the biphilic structures tune the nucleation rates of water and ice in the sequential condensation-to-freezing process. Our experimental and theoretical investigation of condensate freezing dynamics further unravels the correlation between the onset of droplet freezing and its characteristic radius, offering a new insight for controlling the multiphase transitions among vapor, water, and ice in supercooled conditions.

Modeling Demic and Cultural Diffusion: An Introduction.

PubMed

Fort, Joaquim; Crema, Enrico R; Madella, Marco

2015-07-01

Identifying the processes by which human cultures spread across different populations is one of the most topical objectives shared among different fields of study. Seminal works have analyzed a variety of data and attempted to determine whether empirically observed patterns are the result of demic and/or cultural diffusion. This special issue collects articles exploring several themes (from modes of cultural transmission to drivers of dispersal mechanisms) and contexts (from the Neolithic in Europe to the spread of computer programming languages), which offer new insights that will augment the theoretical and empirical basis for the study of demic and cultural diffusion. In this introduction we outline the state of art in the modeling of these processes, briefly discuss the pros and cons of two of the most commonly used frameworks (equation-based models and agent-based models), and summarize the significance of each article in this special issue.

Altered topology of neural circuits in congenital prosopagnosia.

PubMed

Rosenthal, Gideon; Tanzer, Michal; Simony, Erez; Hasson, Uri; Behrmann, Marlene; Avidan, Galia

2017-08-21

Using a novel, fMRI-based inter-subject functional correlation (ISFC) approach, which isolates stimulus-locked inter-regional correlation patterns, we compared the cortical topology of the neural circuit for face processing in participants with an impairment in face recognition, congenital prosopagnosia (CP), and matched controls. Whereas the anterior temporal lobe served as the major network hub for face processing in controls, this was not the case for the CPs. Instead, this group evinced hyper-connectivity in posterior regions of the visual cortex, mostly associated with the lateral occipital and the inferior temporal cortices. Moreover, the extent of this hyper-connectivity was correlated with the face recognition deficit. These results offer new insights into the perturbed cortical topology in CP, which may serve as the underlying neural basis of the behavioral deficits typical of this disorder. The approach adopted here has the potential to uncover altered topologies in other neurodevelopmental disorders, as well.

Temporal dynamics reveal atypical brain response to social exclusion in autism.

PubMed

McPartland, James C; Crowley, Michael J; Perszyk, Danielle R; Naples, Adam; Mukerji, Cora E; Wu, Jia; Molfese, Peter; Bolling, Danielle Z; Pelphrey, Kevin A; Mayes, Linda C

2011-07-01

Despite significant social difficulties, children with autism spectrum disorder (ASD) are vulnerable to the effects of social exclusion. We recorded EEG while children with ASD and typical peers played a computerized game involving peer rejection. Children with ASD reported ostracism-related distress comparable to typically developing children. Event-related potentials (ERPs) indicated a distinct pattern of temporal processing of rejection events in children with ASD. While typically developing children showed enhanced response to rejection at a late slow wave indexing emotional arousal and regulation, those with autism showed attenuation at an early component, suggesting reduced engagement of attentional resources in the aversive social context. Results emphasize the importance of studying the time course of social information processing in ASD; they suggest distinct mechanisms subserving similar overt behavior and yield insights relevant to development and implementation of targeted treatment approaches and objective measures of response to treatment.

Towards oscillations-based simulation of social systems: a neurodynamic approach

NASA Astrophysics Data System (ADS)

Plikynas, Darius; Basinskas, Gytis; Laukaitis, Algirdas

2015-04-01

This multidisciplinary work presents synopsis of theories in the search for common field-like fundamental principles of self-organisation and communication existing on quantum, cellular, and even social levels. Based on these fundamental principles, we formulate conceptually novel social neuroscience paradigm (OSIMAS), which envisages social systems emerging from the coherent neurodynamical processes taking place in the individual mind-fields. In this way, societies are understood as global processes emerging from the superposition of the conscious and subconscious mind-fields of individual members of society. For the experimental validation of the biologically inspired OSIMAS paradigm, we have designed a framework of EEG-based experiments. Initial baseline individual tests of spectral cross-correlations of EEG-recorded brainwave patterns for some mental states have been provided in this paper. Preliminary experimental results do not refute the main OSIMAS postulates. This paper also provides some insights for the construction of OSIMAS-based simulation models.

Homogenization techniques for population dynamics in strongly heterogeneous landscapes.

PubMed

Yurk, Brian P; Cobbold, Christina A

2018-12-01

An important problem in spatial ecology is to understand how population-scale patterns emerge from individual-level birth, death, and movement processes. These processes, which depend on local landscape characteristics, vary spatially and may exhibit sharp transitions through behavioural responses to habitat edges, leading to discontinuous population densities. Such systems can be modelled using reaction-diffusion equations with interface conditions that capture local behaviour at patch boundaries. In this work we develop a novel homogenization technique to approximate the large-scale dynamics of the system. We illustrate our approach, which also generalizes to multiple species, with an example of logistic growth within a periodic environment. We find that population persistence and the large-scale population carrying capacity is influenced by patch residence times that depend on patch preference, as well as movement rates in adjacent patches. The forms of the homogenized coefficients yield key theoretical insights into how large-scale dynamics arise from the small-scale features.

Computer-mediated interdisciplinary teams: theory and reality.

PubMed

Vroman, Kerryellen; Kovacich, Joann

2002-05-01

The benefit of experience, tempered with the wisdom of hindsight and 5 years of text-based, asynchronous, computer-mediated, interdisciplinary team communications, provides the energy, insights and data shared in this article. Through the theoretical lens of group dynamics and the epistemology of interdisciplinary teaming, we analyze the interactions of a virtual interdisciplinary team to provide an understanding and appreciation of collaborative interdisciplinary communication in the context of interactive technologies. Whilst interactive technologies may require new patterns of language similar to that of learning a foreign language, what is communicated in the interdisciplinary team process does not change. Most important is the recognition that virtual teams, similar to their face-to-face counterparts, undergo the same challenges of interdisciplinary teaming and group developmental processes of formation: forming, storming, norming, performing, and transforming. After examining these dynamics of communication and collaboration in the context of the virtual team, the article concludes with guidelines facilitating interdisciplinary team computer-mediated communication.

Experimental Measurements of Heat Transfer through a Lunar Regolith Simulant in a Vibro-Fluidized Reactor Oven

NASA Technical Reports Server (NTRS)

Nayagam, Vedha; Berger, Gordon M.; Sacksteder, Kurt R.; Paz, Aaron

2012-01-01

Extraction of mission consumable resources such as water and oxygen from the planetary environment provides valuable reduction in launch-mass and potentially extends the mission duration. Processing of lunar regolith for resource extraction necessarily involves heating and chemical reaction of solid material with processing gases. Vibrofluidization is known to produce effective mixing and control of flow within granular media. In this study we present experimental results for vibrofluidized heat transfer in lunar regolith simulants (JSC-1 and JSC-1A) heated up to 900 C. The results show that the simulant bed height has a significant influence on the vibration induced flow field and heat transfer rates. A taller bed height leads to a two-cell circulation pattern whereas a single-cell circulation was observed for a shorter height. Lessons learned from these test results should provide insight into efficient design of future robotic missions involving In-Situ Resource Utilization.

A two-step patterning process increases the robustness of periodic patterning in the fly eye.

PubMed

Gavish, Avishai; Barkai, Naama

2016-06-01

Complex periodic patterns can self-organize through dynamic interactions between diffusible activators and inhibitors. In the biological context, self-organized patterning is challenged by spatial heterogeneities ('noise') inherent to biological systems. How spatial variability impacts the periodic patterning mechanism and how it can be buffered to ensure precise patterning is not well understood. We examine the effect of spatial heterogeneity on the periodic patterning of the fruit fly eye, an organ composed of ∼800 miniature eye units (ommatidia) whose periodic arrangement along a hexagonal lattice self-organizes during early stages of fly development. The patterning follows a two-step process, with an initial formation of evenly spaced clusters of ∼10 cells followed by a subsequent refinement of each cluster into a single selected cell. Using a probabilistic approach, we calculate the rate of patterning errors resulting from spatial heterogeneities in cell size, position and biosynthetic capacity. Notably, error rates were largely independent of the desired cluster size but followed the distributions of signaling speeds. Pre-formation of large clusters therefore greatly increases the reproducibility of the overall periodic arrangement, suggesting that the two-stage patterning process functions to guard the pattern against errors caused by spatial heterogeneities. Our results emphasize the constraints imposed on self-organized patterning mechanisms by the need to buffer stochastic effects. Author summary Complex periodic patterns are common in nature and are observed in physical, chemical and biological systems. Understanding how these patterns are generated in a precise manner is a key challenge. Biological patterns are especially intriguing, as they are generated in a noisy environment; cell position and cell size, for example, are subject to stochastic variations, as are the strengths of the chemical signals mediating cell-to-cell communication. The need to generate a precise and robust pattern in this 'noisy' environment restricts the space of patterning mechanisms that can function in the biological setting. Mathematical modeling is useful in comparing the sensitivity of different mechanisms to such variations, thereby highlighting key aspects of their design.We use mathematical modeling to study the periodic patterning of the fruit fly eye. In this system, a highly ordered lattice of differentiated cells is generated in a two-dimensional cell epithelium. The pattern is first observed by the appearance of evenly spaced clusters of ∼10 cells that express specific genes. Each cluster is subsequently refined into a single cell, which initiates the formation and differentiation of a miniature eye unit, the ommatidium. We formulate a mathematical model based on the known molecular properties of the patterning mechanism, and use a probabilistic approach to calculate the errors in cluster formation and refinement resulting from stochastic cell-to-cell variations ('noise') in different quantitative parameters. This enables us to define the parameters most influencing noise sensitivity. Notably, we find that this error is roughly independent of the desired cluster size, suggesting that large clusters are beneficial for ensuring the overall reproducibility of the periodic cluster arrangement. For the stage of cluster refinement, we find that rapid communication between cells is critical for reducing error. Our work provides new insights into the constraints imposed on mechanisms generating periodic patterning in a realistic, noisy environment, and in particular, discusses the different considerations in achieving optimal design of the patterning network.

A Case of Error Disclosure: A Communication Privacy Management Analysis

PubMed Central

Petronio, Sandra; Helft, Paul R.; Child, Jeffrey T.

2013-01-01

To better understand the process of disclosing medical errors to patients, this research offers a case analysis using Petronios’s theoretical frame of Communication Privacy Management (CPM). Given the resistance clinicians often feel about error disclosure, insights into the way choices are made by the clinicians in telling patients about the mistake has the potential to address reasons for resistance. Applying the evidenced-based CPM theory, developed over the last 35 years and dedicated to studying disclosure phenomenon, to disclosing medical mistakes potentially has the ability to reshape thinking about the error disclosure process. Using a composite case representing a surgical mistake, analysis based on CPM theory is offered to gain insights into conversational routines and disclosure management choices of revealing a medical error. The results of this analysis show that an underlying assumption of health information ownership by the patient and family can be at odds with the way the clinician tends to control disclosure about the error. In addition, the case analysis illustrates that there are embedded patterns of disclosure that emerge out of conversations the clinician has with the patient and the patient’s family members. These patterns unfold privacy management decisions on the part of the clinician that impact how the patient is told about the error and the way that patients interpret the meaning of the disclosure. These findings suggest the need for a better understanding of how patients manage their private health information in relationship to their expectations for the way they see the clinician caring for or controlling their health information about errors. Significance for public health Much of the mission central to public health sits squarely on the ability to communicate effectively. This case analysis offers an in-depth assessment of how error disclosure is complicated by misunderstandings, assuming ownership and control over information, unwittingly following conversational scripts that convey misleading messages, and the difficulty in regulating privacy boundaries in the stressful circumstances that occur with error disclosures. As a consequence, the potential contribution to public health is the ability to more clearly see the significance of the disclosure process that has implications for many public health issues. PMID:25170501

Inhibition of Shh signalling in the chick wing gives insights into digit patterning and evolution.

PubMed

Pickering, Joseph; Towers, Matthew

2016-10-01

In an influential model of pattern formation, a gradient of Sonic hedgehog (Shh) signalling in the chick wing bud specifies cells with three antero-posterior positional values, which give rise to three morphologically different digits by a self-organizing mechanism with Turing-like properties. However, as four of the five digits of the mouse limb are morphologically similar in terms of phalangeal pattern, it has been suggested that self-organization alone could be sufficient. Here, we show that inhibition of Shh signalling at a specific stage of chick wing development results in a pattern of four digits, three of which can have the same number of phalanges. These patterning changes are dependent on a posterior extension of the apical ectodermal ridge, and this also allows the additional digit to arise from the Shh-producing cells of the polarizing region - an ability lost in ancestral theropod dinosaurs. Our analyses reveal that, if the specification of antero-posterior positional values is curtailed, self-organization can then produce several digits with the same number of phalanges. We present a model that may give important insights into how the number of digits and phalanges has diverged during the evolution of avian and mammalian limbs. © 2016. Published by The Company of Biologists Ltd.

Circulation patterns in active lava lakes

NASA Astrophysics Data System (ADS)

Redmond, T. C.; Lev, E.

2014-12-01

Active lava lakes provide a unique window into magmatic conduit processes. We investigated circulation patterns of 4 active lava lakes: Kilauea's Halemaumau crater, Mount Erebus, Erta Ale and Nyiragongo, and in an artificial "lava lake" constructed at the Syracuse University Lava Lab. We employed visual and thermal video recordings collected at these volcanoes and use computer vision techniques to extract time-dependent, two-dimensional surface velocity maps. The large amount of data available from Halemaumau enabled us to identify several characteristic circulation patterns. One such pattern is a rapid acceleration followed by rapid deceleration, often to a level lower than the pre-acceleration level, and then a slow recovery. Another pattern is periodic asymmetric peaks of gradual acceleration and rapid deceleration, or vice versa, previously explained by gas pistoning. Using spectral analysis, we find that the dominant period of circulation cycles at approximately 30 minutes, 3 times longer than the dominant period identified previously for Mount Erebus. Measuring a complete surface velocity field allowed us to map and follow locations of divergence and convergence, therefore upwelling and downwelling, thus connecting the surface flow with that at depth. At Nyiragongo, the location of main upwelling shifts gradually, yet is usually at the interior of the lake, for Erebus it is usually along the perimeter yet often there is catastrophic downwelling at the interior; For Halemaumau upwelling/downwelling position is almost always on the perimeter. In addition to velocity fields, we developed an automated tool for counting crustal plates at the surface of the lava lakes, and found a correlation, and a lag time, between changes if circulation vigor and the average size of crustal plates. Circulation in the artificial basaltic lava "lake" was limited by its size and degree of foaming, yet we measured surface velocities and identify patterns. Maximum surface velocity showed symmetrical peaks of acceleration and deceleration. In summary, extended observations at lava lakes reveal patterns of circulations at different time scales, yielding insight into different processes controlling the exchange of gas and fluids between the magma chamber and conduit, and the surface and atmosphere.

Working in Dyads and Alone: Examining Process Variables in Solving Insight Problems

ERIC Educational Resources Information Center

Tidikis, Viktoria; Ash, Ivan K.

2013-01-01

This study investigated the effects of working in dyads and their associated gender composition on performance (solution rate and time) and process variables (number of impasses, number of passed solutions, and number of problem solving suggestions and interactions) in a set of classic insight problem solving tasks. Two types of insight problems…

Process engineering with planetary ball mills.

PubMed

Burmeister, Christine Friederike; Kwade, Arno

2013-09-21

Planetary ball mills are well known and used for particle size reduction on laboratory and pilot scales for decades while during the last few years the application of planetary ball mills has extended to mechanochemical approaches. Processes inside planetary ball mills are complex and strongly depend on the processed material and synthesis and, thus, the optimum milling conditions have to be assessed for each individual system. The present review focuses on the insight into several parameters like properties of grinding balls, the filling ratio or revolution speed. It gives examples of the aspects of grinding and illustrates some general guidelines to follow for modelling processes in planetary ball mills in terms of refinement, synthesis' yield and contamination from wear. The amount of energy transferred from the milling tools to the powder is significant and hardly measurable for processes in planetary ball mills. Thus numerical simulations based on a discrete-element-method are used to describe the energy transfer to give an adequate description of the process by correlation with experiments. The simulations illustrate the effect of the geometry of planetary ball mills on the energy entry. In addition the imaging of motion patterns inside a planetary ball mill from simulations and video recordings is shown.

Genome structure drives patterns of gene family evolution in ciliates, a case study using Chilodonella uncinata (Protista, Ciliophora, Phyllopharyngea)

PubMed Central

Gao, Feng; Song, Weibo; Katz, Laura A.

2014-01-01

In most lineages, diversity among gene family members results from gene duplication followed by sequence divergence. Because of the genome rearrangements during the development of somatic nuclei, gene family evolution in ciliates involves more complex processes. Previous work on the ciliate Chilodonella uncinata revealed that macronuclear β-tubulin gene family members are generated by alternative processing, in which germline regions are alternatively used in multiple macronuclear chromosomes. To further study genome evolution in this ciliate, we analyzed its transcriptome and found that: 1) alternative processing is extensive among gene families; and 2) such gene families are likely to be C. uncinata-specific. We characterized additional macronuclear and micronuclear copies of one candidate alternatively processed gene family -- a protein kinase domain containing protein (PKc) -- from two C. uncinata strains. Analysis of the PKc sequences reveals: 1) multiple PKc gene family members in the macronucleus share some identical regions flanked by divergent regions; and 2) the shared identical regions are processed from a single micronuclear chromosome. We discuss analogous processes in lineages across the eukaryotic tree of life to provide further insights on the impact of genome structure on gene family evolution in eukaryotes. PMID:24749903

The use of the picture–word interference paradigm to examine naming abilities in aphasic individuals

PubMed Central

Hashimoto, Naomi; Thompson, Cynthia K.

2015-01-01

Background Although naming deficits are well documented in aphasia, on-line measures of naming processes have been little investigated. The use of on-line measures may offer further insight into the nature of aphasic naming deficits that would otherwise be difficult to interpret when using off-line measures. Aims The temporal activation of semantic and phonological processes was tracked in older normal control and aphasic individuals using a picture–word interference paradigm. The purpose of the study was to examine how word interference results can augment and/or corroborate standard language testing in the aphasic group, as well as to examine temporal patterns of activation in the aphasic group when compared to a normal control group. Methods & Procedures A total of 20 older normal individuals and 11 aphasic individuals participated. Detailed measures of each aphasic individual's language and naming skills were obtained. A visual picture–word interference paradigm was used in which the words bore either a semantic, phonological, or no relationship to 25 pictures. These competitor words were presented at stimulus onset asynchronies of −300 ms, +300 ms, and 0 ms. Outcomes & Results Analyses of naming RTs in both groups revealed significant early semantic interference effects, mid-semantic interference effects, and mid-phonological facilitation effects. A matched control-aphasic group comparison revealed no differences in the temporal activation of effects during the course of naming. Partial support for this RT pattern was found in the aphasic naming error pattern. The aphasic group also demonstrated greater SIEs and PFEs compared to the matched control group, which indicated disruptions of the phonological processing stage. Analyses of behavioural performances of the aphasic group corroborated this finding. Conclusions The aphasic naming RTs results were unexpected given the results from the priming literature, which has supported the idea of slowed or reduced patterns of activation in aphasic individuals. However, analyses of naming RTs also confirmed the behavioural finding of a disruption surrounding phonological processes; thus, the analyses of naming latencies offers another potential means of pinpointing breakdowns of lexical access in individuals with aphasia. PMID:26166927

Label-free proteome profiling reveals developmental-dependent patterns in young barley grains.

PubMed

Kaspar-Schoenefeld, Stephanie; Merx, Kathleen; Jozefowicz, Anna Maria; Hartmann, Anja; Seiffert, Udo; Weschke, Winfriede; Matros, Andrea; Mock, Hans-Peter

2016-06-30

Due to its importance as a cereal crop worldwide, high interest in the determination of factors influencing barley grain quality exists. This study focusses on the elucidation of protein networks affecting early grain developmental processes. NanoLC-based separation coupled to label-free MS detection was applied to gain insights into biochemical processes during five different grain developmental phases (pre-storage until storage phase, 3days to 16days after flowering). Multivariate statistics revealed two distinct developmental patterns during the analysed grain developmental phases: proteins showed either highest abundance in the middle phase of development - in the transition phase - or at later developmental stages - within the storage phase. Verification of developmental patterns observed by proteomic analysis was done by applying hypothesis-driven approaches, namely Western Blot analysis and enzyme assays. High general metabolic activity of the grain with regard to protein synthesis, cell cycle regulation, defence against oxidative stress, and energy production via photosynthesis was observed in the transition phase. Proteins upregulated in the storage phase are related towards storage protein accumulation, and interestingly to the defence of storage reserves against pathogens. A mixed regulatory pattern for most enzymes detected in our study points to regulatory mechanisms at the level of protein isoforms. In-depth understanding of early grain developmental processes of cereal caryopses is of high importance as they influence final grain weight and quality. Our knowledge about these processes is still limited, especially on proteome level. To identify key mechanisms in early barley grain development, a label-free data-independent proteomics acquisition approach has been applied. Our data clearly show, that proteins either exhibit highest expression during cellularization and the switch to the storage phase (transition phase, 5-7 DAF), or during storage product accumulation (10-16 DAF). The results highlight versatile cellular metabolic activity in the transition phase and strong convergence towards storage product accumulation in the storage phase. Notably, both phases are characterized by particular protective mechanism, such as scavenging of oxidative stress and defence against pathogens, during the transition and the storage phase, respectively. Copyright © 2016 Elsevier B.V. All rights reserved.

Evidence of territoriality and species interactions from spatial point-pattern analyses of subarctic-nesting geese

USGS Publications Warehouse

Reiter, Matthew E.; Andersen, David E.

2013-01-01

Quantifying spatial patterns of bird nests and nest fate provides insights into processes influencing a species’ distribution. At Cape Churchill, Manitoba, Canada, recent declines in breeding Eastern Prairie Population Canada geese (Branta canadensis interior) has coincided with increasing populations of nesting lesser snow geese (Chen caerulescens caerulescens) and Ross’s geese (Chen rossii). We conducted a spatial analysis of point patterns using Canada goose nest locations and nest fate, and lesser snow goose nest locations at two study areas in northern Manitoba with different densities and temporal durations of sympatric nesting Canada and lesser snow geese. Specifically, we assessed (1) whether Canada geese exhibited territoriality and at what scale and nest density; and (2) whether spatial patterns of Canada goose nest fate were associated with the density of nesting lesser snow geese as predicted by the protective-association hypothesis. Between 2001 and 2007, our data suggest that Canada geese were territorial at the scale of nearest neighbors, but were aggregated when considering overall density of conspecifics at slightly broader spatial scales. The spatial distribution of nest fates indicated that lesser snow goose nest proximity and density likely influence Canada goose nest fate. Our analyses of spatial point patterns suggested that continued changes in the distribution and abundance of breeding lesser snow geese on the Hudson Bay Lowlands may have impacts on the reproductive performance of Canada geese, and subsequently the spatial distribution of Canada goose nests.

Dual spinal lesion paradigm in the cat: evolution of the kinematic locomotor pattern.

PubMed

Barrière, Grégory; Frigon, Alain; Leblond, Hugues; Provencher, Janyne; Rossignol, Serge

2010-08-01

The recovery of voluntary quadrupedal locomotion after an incomplete spinal cord injury can involve different levels of the CNS, including the spinal locomotor circuitry. The latter conclusion was reached using a dual spinal lesion paradigm in which a low thoracic partial spinal lesion is followed, several weeks later, by a complete spinal transection (i.e., spinalization). In this dual spinal lesion paradigm, cats can express hindlimb walking 1 day after spinalization, a process that normally takes several weeks, suggesting that the locomotor circuitry within the lumbosacral spinal cord had been modified after the partial lesion. Here we detail the evolution of the kinematic locomotor pattern throughout the dual spinal lesion paradigm in five cats to gain further insight into putative neurophysiological mechanisms involved in locomotor recovery after a partial spinal lesion. All cats recovered voluntary quadrupedal locomotion with treadmill training (3-5 days/wk) over several weeks. After the partial lesion, the locomotor pattern was characterized by several left/right asymmetries in various kinematic parameters, such as homolateral and homologous interlimb coupling, cycle duration, and swing/stance durations. When no further locomotor improvement was observed, cats were spinalized. After spinalization, the hindlimb locomotor pattern rapidly reappeared, but left/right asymmetries in swing/stance durations observed after the partial lesion could disappear or reverse. It is concluded that, after a partial spinal lesion, the hindlimb locomotor pattern was actively maintained by new dynamic interactions between spinal and supraspinal levels but also by intrinsic changes within the spinal cord.

Geostatistics and spatial analysis in biological anthropology.

PubMed

Relethford, John H

2008-05-01

A variety of methods have been used to make evolutionary inferences based on the spatial distribution of biological data, including reconstructing population history and detection of the geographic pattern of natural selection. This article provides an examination of geostatistical analysis, a method used widely in geology but which has not often been applied in biological anthropology. Geostatistical analysis begins with the examination of a variogram, a plot showing the relationship between a biological distance measure and the geographic distance between data points and which provides information on the extent and pattern of spatial correlation. The results of variogram analysis are used for interpolating values of unknown data points in order to construct a contour map, a process known as kriging. The methods of geostatistical analysis and discussion of potential problems are applied to a large data set of anthropometric measures for 197 populations in Ireland. The geostatistical analysis reveals two major sources of spatial variation. One pattern, seen for overall body and craniofacial size, shows an east-west cline most likely reflecting the combined effects of past population dispersal and settlement. The second pattern is seen for craniofacial height and shows an isolation by distance pattern reflecting rapid spatial changes in the midlands region of Ireland, perhaps attributable to the genetic impact of the Vikings. The correspondence of these results with other analyses of these data and the additional insights generated from variogram analysis and kriging illustrate the potential utility of geostatistical analysis in biological anthropology. (c) 2008 Wiley-Liss, Inc.

Citizen science: A new perspective to advance spatial pattern evaluation in hydrology

PubMed Central

Stisen, Simon

2017-01-01

Citizen science opens new pathways that can complement traditional scientific practice. Intuition and reasoning often make humans more effective than computer algorithms in various realms of problem solving. In particular, a simple visual comparison of spatial patterns is a task where humans are often considered to be more reliable than computer algorithms. However, in practice, science still largely depends on computer based solutions, which inevitably gives benefits such as speed and the possibility to automatize processes. However, the human vision can be harnessed to evaluate the reliability of algorithms which are tailored to quantify similarity in spatial patterns. We established a citizen science project to employ the human perception to rate similarity and dissimilarity between simulated spatial patterns of several scenarios of a hydrological catchment model. In total, the turnout counts more than 2500 volunteers that provided over 43000 classifications of 1095 individual subjects. We investigate the capability of a set of advanced statistical performance metrics to mimic the human perception to distinguish between similarity and dissimilarity. Results suggest that more complex metrics are not necessarily better at emulating the human perception, but clearly provide auxiliary information that is valuable for model diagnostics. The metrics clearly differ in their ability to unambiguously distinguish between similar and dissimilar patterns which is regarded a key feature of a reliable metric. The obtained dataset can provide an insightful benchmark to the community to test novel spatial metrics. PMID:28558050

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

DOE PAGES

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

2016-07-05

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

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

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

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

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

InSight Spacecraft Arrival

NASA Image and Video Library

2018-02-28

After arrival at Vandenberg Air Force Base in California, ground crews prepare NASA's Interior Exploration using Seismic Investigations, Geodesy and Heat Transport, or InSight, spacecraft for transportation to the Astrotech processing facility. InSight was developed and built by Lockheed-Martin Space Systems in Denver, Colorado, and is scheduled for liftoff is May 5, 2018. InSight is the first mission to explore the deep interior of Mars. It will investigate processes that shaped the rocky planets of the inner solar system including Earth.

InSight Spacecraft Uncrating, Removal from Container, Lift Heat

NASA Image and Video Library

2018-03-01

At Vandenberg Air Force Base in California, NASA's Interior Exploration using Seismic Investigations, Geodesy and Heat Transport, or InSight, spacecraft is uncrated inside the Astrotech processing facility. InSight was developed and built by Lockheed-Martin Space Systems in Denver, Colorado, and is scheduled for liftoff is May 5, 2018. InSight is the first mission to land on Mars and explore the Red Planet's deep interior. It will investigate processes that shaped the rocky planets of the inner solar system including Earth.

Neural processing of food and emotional stimuli in adolescent and adult anorexia nervosa patients.

PubMed

Horndasch, Stefanie; Roesch, Julie; Forster, Clemens; Dörfler, Arnd; Lindsiepe, Silja; Heinrich, Hartmut; Graap, Holmer; Moll, Gunther H; Kratz, Oliver

2018-01-01

A constant preoccupation with food and restrictive eating are main symptoms of anorexia nervosa (AN). Imaging studies revealed aberrant neural activation patterns in brain regions processing hedonic and reward reactions as well as-potentially aversive-emotions. An imbalance between so called "bottom-up" and "top-down" control areas is discussed. The present study is focusing on neural processing of disease-specific food stimuli and emotional stimuli and its developmental course in adolescent and adult AN patients and could offer new insight into differential mechanisms underlying shorter or more chronic disease. 33 adolescents aged 12-18 years (15 AN patients, 18 control participants) and 32 adult women (16 AN patients, 16 control participants) underwent functional magnetic resonance imaging (fMRI, 3T high-field scanner) while watching pictures of high and low-calorie food and affective stimuli. Afterwards, they rated subjective valence of each picture. FMRI data analysis was performed using a region of interest based approach. Pictures of high-calorie food items were rated more negatively by AN patients. Differences in activation between patients and controls were found in "bottom up" and "top down" control areas for food stimuli and in several emotion processing regions for affective stimuli which were more pronounced in adolescents than in adults. A differential pattern was seen for food stimuli compared to generally emotion eliciting stimuli. Adolescents with AN show reduced processing of affective stimuli and enhanced activation of regions involved in "bottom up" reward processing and "top down" control as well as the insula with regard to food stimuli with a focus on brain regions which underlie changes during adolescent development. In adults less clear and less specific activation differences were present, pointing towards a high impact that regions undergoing maturation might have on AN symptoms.

Determination of dominant biogeochemical processes in a contaminated aquifer-wetland system using multivariate statistical analysis

USGS Publications Warehouse

Baez-Cazull, S. E.; McGuire, J.T.; Cozzarelli, I.M.; Voytek, M.A.

2008-01-01

Determining the processes governing aqueous biogeochemistry in a wetland hydrologically linked to an underlying contaminated aquifer is challenging due to the complex exchange between the systems and their distinct responses to changes in precipitation, recharge, and biological activities. To evaluate temporal and spatial processes in the wetland-aquifer system, water samples were collected using cm-scale multichambered passive diffusion samplers (peepers) to span the wetland-aquifer interface over a period of 3 yr. Samples were analyzed for major cations and anions, methane, and a suite of organic acids resulting in a large dataset of over 8000 points, which was evaluated using multivariate statistics. Principal component analysis (PCA) was chosen with the purpose of exploring the sources of variation in the dataset to expose related variables and provide insight into the biogeochemical processes that control the water chemistry of the system. Factor scores computed from PCA were mapped by date and depth. Patterns observed suggest that (i) fermentation is the process controlling the greatest variability in the dataset and it peaks in May; (ii) iron and sulfate reduction were the dominant terminal electron-accepting processes in the system and were associated with fermentation but had more complex seasonal variability than fermentation; (iii) methanogenesis was also important and associated with bacterial utilization of minerals as a source of electron acceptors (e.g., barite BaSO4); and (iv) seasonal hydrological patterns (wet and dry periods) control the availability of electron acceptors through the reoxidation of reduced iron-sulfur species enhancing iron and sulfate reduction. Copyright ?? 2008 by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America. All rights reserved.

Screening mosaic F1 females for mutations affecting zebrafish heart induction and patterning.

PubMed

Alexander, J; Stainier, D Y; Yelon, D

1998-01-01

The genetic pathways underlying the induction and anterior-posterior patterning of the heart are poorly understood. The recent emergence of the zebrafish model system now allows a classical genetic approach to such challenging problems in vertebrate development. Two large-scale screens for mutations affecting zebrafish embryonic development have recently been completed; among the hundreds of mutations identified were several that affect specific aspects of cardiac morphogenesis, differentiation, and function. However, very few mutations affecting induction and/or anterior-posterior patterning of the heart were identified. We hypothesize that a directed approach utilizing molecular markers to examine these particular steps of heart development will uncover additional such mutations. To test this hypothesis, we are conducting two parallel screens for mutations that affect either the induction or the anterior-posterior patterning of the zebrafish heart. As an indicator of cardiac induction, we examine expression of nkx2.5, the earliest known marker of precardiac mesoderm; to assess anterior-posterior patterning, we distinguish ventricle from atrium with antibodies that recognize different myosin heavy chain isoforms. In order to expedite the examination of a large number of mutations, we are screening the haploid progeny of mosaic F1 females. In these ongoing screens, we have identified four mutations that affect nkx2.5 expression as well as 21 that disrupt either ventricular or atrial development and thus far have recovered several of these mutations, demonstrating the value of our approach. Future analysis of these and other cardiac mutations will provide further insight into the processes of induction and anterior-posterior patterning of the heart.

Assortativity Patterns in Multi-dimensional Inter-organizational Networks: A Case Study of the Humanitarian Relief Sector

NASA Astrophysics Data System (ADS)

Zhao, Kang; Ngamassi, Louis-Marie; Yen, John; Maitland, Carleen; Tapia, Andrea

We use computational tools to study assortativity patterns in multi-dimensional inter-organizational networks on the basis of different node attributes. In the case study of an inter-organizational network in the humanitarian relief sector, we consider not only macro-level topological patterns, but also assortativity on the basis of micro-level organizational attributes. Unlike assortative social networks, this inter-organizational network exhibits disassortative or random patterns on three node attributes. We believe organizations' seek of complementarity is one of the main reasons for the special patterns. Our analysis also provides insights on how to promote collaborations among the humanitarian relief organizations.

Abiotic and biotic controls over biogeochemical cycles in drylands: Insights from climate change and nitrogen deposition experiments on the Colorado Plateau

NASA Astrophysics Data System (ADS)

Reed, S.; Ferrenberg, S.; Tucker, C.; Rutherford, W. A.; Wertin, T. M.; McHugh, T. A.; Morrissey, E.; Kuske, C.; Mueller, R.; Belnap, J.

2016-12-01

As for all ecosystems, biogeochemical cycling in drylands represents numerous intricate connections between biotic and abiotic controls. However, patterns of many fundamental ecosystem processes that generally hold across global gradients fall apart at the arid and semiarid end of the spectrum, and data point to an exceptionally strong role for abiotic controls in explaining these patterns. Further, there are multiple dryland characteristics - such as extreme aridity and high UV radiation, as well as specialized biological communities - which can point to a conclusion that "drylands are different". Indeed, drylands are often characterized by their harsh environment, by the diverse classes of biota representing a range of traits aimed at surviving such harsh conditions, and, more recently, by the suggestion of dramatic biotic responses to seemingly subtle changes in abiotic factors. In this talk, we will explore a range of biotic and abiotic controls over fundamental biogeochemical cycling in drylands using data from a suite of manipulation experiments on the Colorado Plateau, USA. We will present results from field treatments that speak to the effects of increasing temperature, altered precipitation regimes, increased nitrogen availability via deposition, and the effects of altered litterfall inputs. Biogeochemical processes we explore will include plant photosynthesis, soil photosynthesis and respiration (with a focus on biological soil crusts), litter decomposition, and nutrient cycling. In addition, we will assess how treatments alter dryland community composition, as well as the resultant feedbacks of community shifts to environmental change. Taken together we will use these diverse datasets to ask questions about what makes drylands different or, instead, if a holistic joining of biotic and abiotic perspectives suggests they are not so different after all. These data will not only lend insight into the partitioning of and balance between biotic and abiotic controls, but will also provide perspective on how a changing world may shift this balance.

Cognitive inflexibility in Obsessive-Compulsive Disorder.

PubMed

Gruner, Patricia; Pittenger, Christopher

2017-03-14

Obsessive-Compulsive Disorder (OCD) is characterized by maladaptive patterns of repetitive, inflexible cognition and behavior that suggest a lack of cognitive flexibility. Consistent with this clinical observation, many neurocognitive studies suggest behavioral and neurobiological abnormalities in cognitive flexibility in individuals with OCD. Meta-analytic reviews support a pattern of cognitive inflexibility, with effect sizes generally in the medium range. Heterogeneity in assessments and the way underlying constructs have been operationalized point to the need for better standardization across studies, as well as more refined overarching models of cognitive flexibility and executive function (EF). Neuropsychological assessments of cognitive flexibility include measures of attentional set shifting, reversal and alternation, cued task-switching paradigms, cognitive control measures such as the Trail-Making and Stroop tasks, and several measures of motor inhibition. Differences in the cognitive constructs and neural substrates associated with these measures suggest that performance within these different domains should be examined separately. Additional factors, such as the number of consistent trials prior to a shift and whether a shift is explicitly signaled or must be inferred from a change in reward contingencies, may influence performance, and thus mask or accentuate deficits. Several studies have described abnormalities in neural activation in the absence of differences in behavioral performance, suggesting that our behavioral probes may not be adequately sensitive, but also offering important insights into potential compensatory processes. The fact that deficits of moderate effect size are seen across a broad range of classic neuropsychological tests in OCD presents a conceptual challenge, as clinical symptomatology suggests greater specificity. Traditional cognitive probes may not be sufficient to delineate specific domains of deficit in this and other neuropsychiatric disorders; a new generation of behavioral tasks that test more specific underlying constructs, supplemented by neuroimaging to provide insight into the underlying processes, may be needed. Copyright © 2016 IBRO. Published by Elsevier Ltd. All rights reserved.

Selection of stable reference genes for quantitative rt-PCR comparisons of mouse embryonic and extra-embryonic stem cells.

PubMed

Veazey, Kylee J; Golding, Michael C

2011-01-01

Isolation and culture of both embryonic and tissue specific stem cells provide an enormous opportunity to study the molecular processes driving development. To gain insight into the initial events underpinning mammalian embryogenesis, pluripotent stem cells from each of the three distinct lineages present within the preimplantation blastocyst have been derived. Embryonic (ES), trophectoderm (TS) and extraembryonic endoderm (XEN) stem cells possess the developmental potential of their founding lineages and seemingly utilize distinct epigenetic modalities to program gene expression. However, the basis for these differing cellular identities and epigenetic properties remain poorly defined.Quantitative reverse transcription-polymerase chain reaction (qPCR) is a powerful and efficient means of rapidly comparing patterns of gene expression between different developmental stages and experimental conditions. However, careful, empirical selection of appropriate reference genes is essential to accurately measuring transcriptional differences. Here we report the quantitation and evaluation of fourteen commonly used references genes between ES, TS and XEN stem cells. These included: Actb, B2m, Hsp70, Gapdh, Gusb, H2afz, Hk2, Hprt, Pgk1, Ppia, Rn7sk, Sdha, Tbp and Ywhaz. Utilizing three independent statistical analysis, we identify Pgk1, Sdha and Tbp as the most stable reference genes between each of these stem cell types. Furthermore, we identify Sdha, Tbp and Ywhaz as well as Ywhaz, Pgk1 and Hk2 as the three most stable reference genes through the in vitro differentiation of embryonic and trophectoderm stem cells respectively.Understanding the transcriptional and epigenetic regulatory mechanisms controlling cellular identity within these distinct stem cell types provides essential insight into cellular processes controlling both embryogenesis and stem cell biology. Normalizing quantitative RT-PCR measurements using the geometric mean CT values obtained for the identified mRNAs, offers a reliable method to assess differing patterns of gene expression between the three founding stem cell lineages present within the mammalian preimplantation embryo.

Tracking the Reorganization of Module Structure in Time-Varying Weighted Brain Functional Connectivity Networks.

PubMed

Schmidt, Christoph; Piper, Diana; Pester, Britta; Mierau, Andreas; Witte, Herbert

2018-05-01

Identification of module structure in brain functional networks is a promising way to obtain novel insights into neural information processing, as modules correspond to delineated brain regions in which interactions are strongly increased. Tracking of network modules in time-varying brain functional networks is not yet commonly considered in neuroscience despite its potential for gaining an understanding of the time evolution of functional interaction patterns and associated changing degrees of functional segregation and integration. We introduce a general computational framework for extracting consensus partitions from defined time windows in sequences of weighted directed edge-complete networks and show how the temporal reorganization of the module structure can be tracked and visualized. Part of the framework is a new approach for computing edge weight thresholds for individual networks based on multiobjective optimization of module structure quality criteria as well as an approach for matching modules across time steps. By testing our framework using synthetic network sequences and applying it to brain functional networks computed from electroencephalographic recordings of healthy subjects that were exposed to a major balance perturbation, we demonstrate the framework's potential for gaining meaningful insights into dynamic brain function in the form of evolving network modules. The precise chronology of the neural processing inferred with our framework and its interpretation helps to improve the currently incomplete understanding of the cortical contribution for the compensation of such balance perturbations.

Healing of the landscape after Gorkha earthquake, insights from seismic interferometry

NASA Astrophysics Data System (ADS)

Illien, Luc; Sens-Schönfelder, Christoph; Hovius, Niels; Andermann, Christoff; Turowski, Jens Martin

2017-04-01

It has been shown that earthquakes trigger transient effects in the landscape that can last from several days (enhanced river discharge) to several years (enhanced landslides rates) or even decades (e.g. river bedload). These observations are geomorphic expressions of physical changes in shallow subsurface that are yet poorly understood. To gain insights in the underlying physical processes, we appeal to exploratory geophysical methods that allow us to monitor the variation of rock strength over time. Thanks to a seismic dense array deployed in the Bhote Koshi catchment following the April 2015 7.8 Mw Gorkha (Nepal) earthquake we can apply noise correlation monitoring the evolution of the seismic wave velocities at a high spatial resolution in the landscape. Our results show that the observed velocity changes are spatially heterogeneous after ground shaking events. We attribute these velocity changes to coseismic damage that is followed by a recovery in rock strength in the sampled medium. We suggest that these results directly reflect the state of the most fractured layer in the landscape, in the shallow sub-surface. These findings allow us to discuss where erosion patterns such as landslide-prone areas cluster but also mechanisms responsible for hillslope healing after large earthquakes. Finally, this study highlights the value of seismometers for the investigation of near-surface processes in the context of natural hazards.

[Electrophysiological bases of semantic processing of objects].

PubMed

Kahlaoui, Karima; Baccino, Thierry; Joanette, Yves; Magnié, Marie-Noële

2007-02-01

How pictures and words are stored and processed in the human brain constitute a long-standing question in cognitive psychology. Behavioral studies have yielded a large amount of data addressing this issue. Generally speaking, these data show that there are some interactions between the semantic processing of pictures and words. However, behavioral methods can provide only limited insight into certain findings. Fortunately, Event-Related Potential (ERP) provides on-line cues about the temporal nature of cognitive processes and contributes to the exploration of their neural substrates. ERPs have been used in order to better understand semantic processing of words and pictures. The main objective of this article is to offer an overview of the electrophysiologic bases of semantic processing of words and pictures. Studies presented in this article showed that the processing of words is associated with an N 400 component, whereas pictures elicited both N 300 and N 400 components. Topographical analysis of the N 400 distribution over the scalp is compatible with the idea that both image-mediated concrete words and pictures access an amodal semantic system. However, given the distinctive N 300 patterns, observed only during picture processing, it appears that picture and word processing rely upon distinct neuronal networks, even if they end up activating more or less similar semantic representations.

Self-stigma, insight, and family burden among Israeli mothers of people with serious mental illness: Ethno-national considerations.

PubMed

Zisman-Ilani, Yaara; Hasson-Ohayon, Ilanit; Levy-Frank, Itamar; Tuval-Mashiach, Rivka; Roe, David

2017-06-01

The current cross-sectional study investigated and compared the associations between insight, self-stigma, and family burden among Jewish and Arab mothers of an adult son or daughter with serious mental illness (SMI) in Israel. A total of 162 Israeli mothers of a person with SMI participated in the study; 95 were Jewish (58.6%), and 67 were Arab (41.4%). Insight, self-stigma, and family burden scales were administered. Jewish mothers reported higher levels of insight into their son's or daughter's illness and reported greater family burden compared to Arab mothers. No significant differences in self-stigma scores were found between Jewish and Arab mothers. The pattern of associations between insight, self-stigma, and burden differed between Jewish and Arab mothers. Self-stigma was found to mediate the relationship between insight and burden among Jewish mothers but not among Arab mothers. Ethno-national affiliation should be taken into consideration regarding how family members conceptualize and experience mental illness, as this might affect care.

Sediment-hosted contaminants and distribution patterns in the Mississippi and Atchafalaya River Deltas

USGS Publications Warehouse

Flocks, James G.; Kindinger, Jack G.; Ferina, Nicholas; Dreher, Chandra

2002-01-01

The Mississippi and Atchafalaya Rivers transport very large amounts of bedload and suspended sediments to the deltaic and coastal environments of the northern Gulf of Mexico. Absorbed onto these sediments are contaminants that may be detrimental to the environment. To adequately assess the impact of these contaminants it is first necessary to develop an understanding of sediment distribution patterns in these deltaic systems. The distribution patterns are defined by deltaic progradational cycles. Once these patterns are identified, the natural and industrial contaminant inventories and their depositional histories can be reconstructed. Delta progradation is a function of sediment discharge, as well as channel and receiving-basin dimensions. Fluvial energy controls the sediment distribution pattern, resulting in a coarse grained or sandy framework, infilled with finer grained material occupying the overbank, interdistributary bays, wetlands and abandoned channels. It has been shown that these fine-grained sediments can carry contaminants through absorption and intern them in the sediment column or redistribute them depending on progradation or degradation of the delta deposit. Sediment distribution patterns in delta complexes can be determined through high-resolution geophysical surveys and groundtruthed with direct sampling. In the Atchafalaya and Mississippi deltas, remote sensing using High-Resolution Single-Channel Seismic Profiling (HRSP) and Sidescan Sonar was correlated to 20-ft vibracores to develop a near-surface geologic framework that identifies variability in recent sediment distribution patterns. The surveys identified bedload sand waves, abandoned-channel back-fill, prodelta and distributary mouth bars within the most recently active portions of the deltas. These depositional features respond to changes in deltaic processes and through their response may intern or transport absorbed contaminants. Characterizing these features provides insight into the fate of sediment-hosted contaminants.

New insights on Ba overabundance in open clusters. Evidence for the intermediate neutron-capture process at play?

NASA Astrophysics Data System (ADS)

Mishenina, T.; Pignatari, M.; Carraro, G.; Kovtyukh, V.; Monaco, L.; Korotin, S.; Shereta, E.; Yegorova, I.; Herwig, F.

2015-02-01

Recently, an increasing number of studies were devoted to measure the abundances of neutron-capture elements heavier than iron in stars belonging to Galactic Open Clusters (OCs). OCs span a sizeable range in metallicity (-0.6 ≤ [Fe/H] ≤ +0.4), and they show abundances of light elements similar to disc stars of the same age. A different pattern is observed for heavy elements. A large scatter is observed for Ba, with most OCs showing [Ba/Fe] and [Ba/La] overabundant with respect to the Sun. The origin of this overabundance is not clearly understood. With the goal of providing new observational insights, we determined radial velocities, atmospheric parameters and chemical composition of 27 giant stars members of five OCs: Cr 110, Cr 261, NGC 2477, NGC 2506 and NGC 5822. We used high-resolution spectra obtained with the UVES spectrograph at European Southern Observatory Paranal. We perform a detailed spectroscopic analysis of these stars to measure the abundance of up to 22 elements per star. We study the dependence of element abundance on metallicity and age with unprecedented detail, complementing our analysis with data culled from the literature. We confirm the trend of Ba overabundance in OCs, and show its large dispersion for clusters younger than ˜4 Gyr. Finally, the implications of our results for stellar nucleosynthesis are discussed. We show in this work that the Ba enrichment compared to other neutron-capture elements in OCs cannot be explained by the contributions from the slow neutron-capture process and the rapid neutron-capture process. Instead, we argue that this anomalous signature can be explained by assuming an additional contribution by the intermediate neutron-capture process.

Ocean Carbon States: Data Mining in Observations and Numerical Simulations Results

NASA Astrophysics Data System (ADS)

Latto, R.; Romanou, A.

2017-12-01

Advanced data mining techniques are rapidly becoming widely used in Climate and Earth Sciences with the purpose of extracting new meaningful information from increasingly larger and more complex datasets. This is particularly important in studies of the global carbon cycle, where any lack of understanding of its combined physical and biogeochemical drivers is detrimental to our ability to accurately describe, understand, and predict CO2 concentrations and their changes in the major carbon reservoirs. The analysis presented here evaluates the use of cluster analysis as a means of identifying and comparing spatial and temporal patterns extracted from observational and model datasets. As the observational data is organized into various regimes, which we will call "ocean carbon states", we gain insight into the physical and/or biogeochemical processes controlling the ocean carbon cycle as well as how well these processes are simulated by a state-of-the-art climate model. We find that cluster analysis effectively produces realistic, dynamic regimes that can be associated with specific processes at different temporal scales for both observations and the model. In addition, we show how these regimes can be used to illustrate and characterize the model biases in the model air-sea flux of CO2. These biases are attributed to biases in salinity, sea surface temperature, wind speed, and nitrate, which are then used to identify the physical processes that are inaccurately reproduced by the model. In this presentation, we provide a proof-of-concept application using simple datasets, and we expand to more complex ones, using several physical and biogeochemical variable pairs, thus providing considerable insight into the mechanisms and phases of the ocean carbon cycle over different temporal and spatial scales.

Comparable Dietary Patterns Describe Dietary Behavior across Ethnic Groups in the Netherlands, but Different Elements in the Diet Are Associated with Glycated Hemoglobin and Fasting Glucose Concentrations.

PubMed

Dekker, Louise H; van Dam, Rob M; Snijder, Marieke B; Peters, Ron J G; Dekker, Jacqueline M; de Vries, Jeanne H M; de Boer, Evelien J; Schulze, Matthias B; Stronks, Karien; Nicolaou, Mary

2015-08-01

Ethnic minority populations in Western societies suffer from a disproportionate burden of type 2 diabetes (T2D). Insight into the role of dietary patterns in T2D may assist public health nutrition efforts in addressing these health disparities. We explored the association between dietary patterns and biomarkers of T2D in 5 ethnic groups living in Amsterdam, Netherlands. A total of 3776 men and women aged 18-70 y of Dutch, South Asian Surinamese, African-Surinamese, Turkish, and Moroccan origin from the HELIUS (HEalthy LIfe in an Urban Setting) study were included. Diet was assessed by using a food-frequency questionnaire, and dietary patterns were derived separately per ethnic group. First, food group-based dietary patterns were derived by using principal components analysis and the association with glycated hemoglobin (HbA1c) and plasma fasting glucose was assessed by using multivariable linear regression. Second, biomarker-driven dietary patterns based on HbA1c and fasting glucose concentrations were derived by applying reduced rank regression. Two comparable food group-based dietary patterns were identified in each ethnic group: a "meat and snack" pattern and a "vegetable" pattern. The meat-and-snack pattern derived within the Dutch origin population was significantly associated with HbA1c (β = 0.09; 95% CI: 0.00, 0.19) and fasting glucose (β = 0.18; 95% CI: 0.09, 0.26) concentrations. A biomarker-derived pattern characterized by red and processed meat was observed among Dutch-origin participants; however, among ethnic minority groups, this pattern was characterized by other foods including ethnicity-specific foods (e.g., roti, couscous). Although similar food group dietary patterns were derived within 5 ethnic groups, the association of the meat-and-snack pattern with fasting glucose concentrations differed by ethnicity. Taken together with the finding of ethnic differences in biomarker-driven dietary patterns, our results imply that addressing T2D risk in multiethnic populations requires ethnicity-specific approaches. © 2015 American Society for Nutrition.

Knowledge discovery and nonlinear modeling can complement climate model simulations for predictive insights about climate extremes and their impacts

NASA Astrophysics Data System (ADS)

Ganguly, A. R.; Steinbach, M.; Kumar, V.

2009-12-01

The IPCC AR4 not only provided conclusive evidence about anticipated global warming at century scales, but also indicated with a high level of certainty that the warming is caused by anthropogenic emissions. However, an outstanding knowledge-gap is to develop credible projections of climate extremes and their impacts. Climate extremes are defined in this context as extreme weather and hydrological events, as well as changes in regional hydro-meteorological patterns, especially at decadal scales. While temperature extremes from climate models have relatively better skills, hydrological variables and their extremes have significant shortcomings. Credible projections about tropical storms, sea level rise, coastal storm surge, land glacier melts, and landslides remain elusive. The next generation of climate models is expected to have higher precision. However, their ability to provide more accurate projections of climate extremes remains to be tested. Projections of observed trends into the future may not be reliable in non-stationary environments like climate change, even though functional relationships derived from physics may hold. On the other hand, assessments of climate change impacts which are useful for stakeholders and policy makers depend critically on regional and decadal scale projections of climate extremes. Thus, climate impacts scientists often need to develop qualitative inferences about the not so-well predicted climate extremes based on insights from observations (e.g., increased hurricane intensity) or conceptual understanding (e.g., relation of wildfires to regional warming or drying and hurricanes to SST). However, neither conceptual understanding nor observed trends may be reliable when extrapolating in a non-stationary environment. These urgent societal priorities offer fertile grounds for nonlinear modeling and knowledge discovery approaches. Thus, qualitative inferences on climate extremes and impacts may be transformed into quantitative predictive insights based on a combination of hypothesis-guided data analysis and relatively hypothesis-free but data-guided discovery processes. The analysis and discovery approaches need to be cognizant of climate data characteristics like nonlinear processes, low-frequency variability, long-range spatial dependence and long-memory temporal processes; the value of physically-motivated conceptual understanding and functional associations; as well as possible thresholds and tipping points in the impacted natural, engineered or human systems. Case studies focusing on new methodologies as well as novel climate insights are discussed with a focus on stakeholder requirements.

History, ocean channels, and distance determine phylogeographic patterns in three widespread Philippine fruit bats (Pteropodidae).

PubMed

Roberts, Trina E

2006-07-01

The comparative phylogeography of widespread, codistributed species provides unique insights into regional biodiversity and diversification patterns. I used partial DNA sequences of the mitochondrial genes ND2 and cyt b to investigate phylogeographic structure in three widespread Philippine fruit bats. Ptenochirus jagori is endemic to the oceanic region of the Philippines and is most abundant in lowland primary forest. Macroglossus minimus and Cynopterus brachyotis are most common in disturbed and open habitats and are not endemic. In all three, genetic differentiation is present at multiple spatial scales and is associated to some degree with Pleistocene landbridge island groups. In P. jagori and C. brachyotis, genetic distance is correlated with geographic distance; in C. brachyotis and M. minimus, it is correlated with the sea-crossing distance between islands. P. jagori has the least overall genetic structure of these three species, whereas C. brachyotis and M. minimus have more geographic association among haplotypes, suggesting that phylogeographic patterns are linked to ecology and habitat preference. However, contrary to expectation, the two widespread, disturbed habitat species have more structure than the endemic species. Mismatch distributions suggest rapid changes in effective population size in C. brachyotis and P. jagori, whereas M. minimus appears to be demographically more stable. Geologic and geographic history are important in structuring variation, and phylogeographic patterns are the result of dynamic long-term processes rather than simply reflecting current conditions.

Health care and social service providers' descriptions of pacific islander mothers' breastfeeding patterns.

PubMed

Flood, Jeanie L; Dodgson, Joan E

2010-01-01

Despite recommendations and numerous health benefits attributed to breastfeeding, rates in the United States are below desired levels, particularly within vulnerable populations. In Hawaií, breastfeeding rates are higher than national averages except in Native Hawaiian and other Pacific Islander populations. Health care and social service providers are integral to successful breastfeeding promotion efforts. They are in an ideal position to reflect on the context in which their clients live and on its relationship to breastfeeding activities. The aim of this study was to describe health care and social service providers' perceptions of the influences on the breastfeeding patterns of Pacific Islander women. Focus ethnographic methods were used to collect interview data from health care and social service providers (N=20) serving Native Hawaiian and Pacific Islander women in one rural community. An iterative analysis process of coding and categorizing, followed by conceptual abstraction into patterns, was completed. Four patterns emerged: shaped by connections, lived unfamiliarity, stressed by circumstance, and missed opportunities. Participants' insights concerning the needs of this population yielded population-specific issues and health care system issues affecting breastfeeding promotion. A number of gaps in breastfeeding services were identified. Sociocultural, maternal knowledge, and workload barriers to successful breastfeeding predominated providers' perspectives. Broader system and community level issues were implied, but not directly addressed. The nature of successful breastfeeding support and promotion requires inclusion of this broader level perspective.

The walking behaviour of pedestrian social groups and its impact on crowd dynamics.

PubMed

Moussaïd, Mehdi; Perozo, Niriaska; Garnier, Simon; Helbing, Dirk; Theraulaz, Guy

2010-04-07

Human crowd motion is mainly driven by self-organized processes based on local interactions among pedestrians. While most studies of crowd behaviour consider only interactions among isolated individuals, it turns out that up to 70% of people in a crowd are actually moving in groups, such as friends, couples, or families walking together. These groups constitute medium-scale aggregated structures and their impact on crowd dynamics is still largely unknown. In this work, we analyze the motion of approximately 1500 pedestrian groups under natural condition, and show that social interactions among group members generate typical group walking patterns that influence crowd dynamics. At low density, group members tend to walk side by side, forming a line perpendicular to the walking direction. As the density increases, however, the linear walking formation is bent forward, turning it into a V-like pattern. These spatial patterns can be well described by a model based on social communication between group members. We show that the V-like walking pattern facilitates social interactions within the group, but reduces the flow because of its "non-aerodynamic" shape. Therefore, when crowd density increases, the group organization results from a trade-off between walking faster and facilitating social exchange. These insights demonstrate that crowd dynamics is not only determined by physical constraints induced by other pedestrians and the environment, but also significantly by communicative, social interactions among individuals.

Molecular and Functional Characterization of Broccoli EMBRYONIC FLOWER 2 Genes

PubMed Central

Chen, Long-Fang O.; Lin, Chun-Hung; Lai, Ying-Mi; Huang, Jia-Yuan; Sung, Zinmay Renee

2012-01-01

Polycomb group (PcG) proteins regulate major developmental processes in Arabidopsis. EMBRYONIC FLOWER 2 (EMF2), the VEFS domain-containing PcG gene, regulates diverse genetic pathways and is required for vegetative development and plant survival. Despite widespread EMF2-like sequences in plants, little is known about their function other than in Arabidopsis and rice. To study the role of EMF2 in broccoli (Brassica oleracea var. italica cv. Elegance) development, we identified two broccoli EMF2 (BoEMF2) genes with sequence homology to and a similar gene expression pattern to that in Arabidopsis (AtEMF2). Reducing their expression in broccoli resulted in aberrant phenotypes and gene expression patterns. BoEMF2 regulates genes involved in diverse developmental and stress programs similar to AtEMF2 in Arabidopsis. However, BoEMF2 differs from AtEMF2 in the regulation of flower organ identity, cell proliferation and elongation, and death-related genes, which may explain the distinct phenotypes. The expression of BoEMF2.1 in the Arabidopsis emf2 mutant (Rescued emf2) partially rescued the mutant phenotype and restored the gene expression pattern to that of the wild type. Many EMF2-mediated molecular and developmental functions are conserved in broccoli and Arabidopsis. Furthermore, the restored gene expression pattern in Rescued emf2 provides insights into the molecular basis of PcG-mediated growth and development. PMID:22537758

Analyzing engagement in a web-based intervention platform through visualizing log-data.

PubMed

Morrison, Cecily; Doherty, Gavin

2014-11-13

Engagement has emerged as a significant cross-cutting concern within the development of Web-based interventions. There have been calls to institute a more rigorous approach to the design of Web-based interventions, to increase both the quantity and quality of engagement. One approach would be to use log-data to better understand the process of engagement and patterns of use. However, an important challenge lies in organizing log-data for productive analysis. Our aim was to conduct an initial exploration of the use of visualizations of log-data to enhance understanding of engagement with Web-based interventions. We applied exploratory sequential data analysis to highlight sequential aspects of the log data, such as time or module number, to provide insights into engagement. After applying a number of processing steps, a range of visualizations were generated from the log-data. We then examined the usefulness of these visualizations for understanding the engagement of individual users and the engagement of cohorts of users. The visualizations created are illustrated with two datasets drawn from studies using the SilverCloud Platform: (1) a small, detailed dataset with interviews (n=19) and (2) a large dataset (n=326) with 44,838 logged events. We present four exploratory visualizations of user engagement with a Web-based intervention, including Navigation Graph, Stripe Graph, Start-Finish Graph, and Next Action Heat Map. The first represents individual usage and the last three, specific aspects of cohort usage. We provide examples of each with a discussion of salient features. Log-data analysis through data visualization is an alternative way of exploring user engagement with Web-based interventions, which can yield different insights than more commonly used summative measures. We describe how understanding the process of engagement through visualizations can support the development and evaluation of Web-based interventions. Specifically, we show how visualizations can (1) allow inspection of content or feature usage in a temporal relationship to the overall program at different levels of granularity, (2) detect different patterns of use to consider personalization in the design process, (3) detect usability issues, (4) enable exploratory analysis to support the design of statistical queries to summarize the data, (5) provide new opportunities for real-time evaluation, and (6) examine assumptions about interactivity that underlie many summative measures in this field.

Analyzing Engagement in a Web-Based Intervention Platform Through Visualizing Log-Data

PubMed Central

2014-01-01

Background Engagement has emerged as a significant cross-cutting concern within the development of Web-based interventions. There have been calls to institute a more rigorous approach to the design of Web-based interventions, to increase both the quantity and quality of engagement. One approach would be to use log-data to better understand the process of engagement and patterns of use. However, an important challenge lies in organizing log-data for productive analysis. Objective Our aim was to conduct an initial exploration of the use of visualizations of log-data to enhance understanding of engagement with Web-based interventions. Methods We applied exploratory sequential data analysis to highlight sequential aspects of the log data, such as time or module number, to provide insights into engagement. After applying a number of processing steps, a range of visualizations were generated from the log-data. We then examined the usefulness of these visualizations for understanding the engagement of individual users and the engagement of cohorts of users. The visualizations created are illustrated with two datasets drawn from studies using the SilverCloud Platform: (1) a small, detailed dataset with interviews (n=19) and (2) a large dataset (n=326) with 44,838 logged events. Results We present four exploratory visualizations of user engagement with a Web-based intervention, including Navigation Graph, Stripe Graph, Start–Finish Graph, and Next Action Heat Map. The first represents individual usage and the last three, specific aspects of cohort usage. We provide examples of each with a discussion of salient features. Conclusions Log-data analysis through data visualization is an alternative way of exploring user engagement with Web-based interventions, which can yield different insights than more commonly used summative measures. We describe how understanding the process of engagement through visualizations can support the development and evaluation of Web-based interventions. Specifically, we show how visualizations can (1) allow inspection of content or feature usage in a temporal relationship to the overall program at different levels of granularity, (2) detect different patterns of use to consider personalization in the design process, (3) detect usability issues, (4) enable exploratory analysis to support the design of statistical queries to summarize the data, (5) provide new opportunities for real-time evaluation, and (6) examine assumptions about interactivity that underlie many summative measures in this field. PMID:25406097

Towards a Theory of Vernacularisation: Insights from Written Chinese Vernaculars

ERIC Educational Resources Information Center

Snow, Don

2013-01-01

This paper examines the history of four Chinese vernaculars which have developed written forms, and argues that five of the patterns Hanan identifies in the early development of Bai Hua can also be found in the early development of written Wu, Cantonese, and Minnan. In each of the cases studied, there is a clear pattern of early use of the…

Understanding Individual Patterns of Learning: Implications for the Well-Being of Students

ERIC Educational Resources Information Center

O'Toole, Linda

2008-01-01

This article analyses the link between learning and well-being from the perspective that it is important to take into account the individual patterns of how young people learn and to encourage ways in which they can learn how they learn. Consideration is first given to recent insights and research in education and the cognitive and natural…

Integrated Warfighter Biodefense Program (IWBP)

DTIC Science & Technology

2011-05-26

empower the non-statistical subject matter expert to rapidly obtain insight into their data for discovery, forecasting and decision making. LeapWorks...Support for Time Series Pattern discovery in temporal data environments is important for many forecasting types of applications. For example, does the...as well as the forecasting horizon for the purposes of patterns discovery. Beta Testing During the period of performance for this report

Genes involved in Beauveria bassiana infection to Galleria mellonella.

PubMed

Chen, Anhui; Wang, Yulong; Shao, Ying; Zhou, Qiumei; Chen, Shanglong; Wu, Yonghua; Chen, Hongwei; Liu, Enqi

2018-05-01

The ascomycete fungus Beauveria bassiana is a natural pathogen of hundreds of insect species and is commercially produced as an environmentally friendly mycoinsecticide. Many genes involved in fungal insecticide infection have been identified but few have been further explored. In this study, we constructed three transcriptomes of B. bassiana at 24, 48 and 72 h post infection of insect pests (BbI) or control (BbC). There were 3148, 3613 and 4922 genes differentially expressed at 24, 48 and 72 h post BbI/BbC infection, respectively. A large number of genes and pathways involved in infection were identified. To further analyze those genes, expression patterns across different infection stages (0, 12, 24, 36, 48, 60, 72 and 84 h) were studied using quantitative RT-PCR. This analysis showed that the infection-related genes could be divided into four patterns: highly expressed throughout the whole infection process (thioredoxin 1); highly expressed during early stages of infection but lowly expressed after the insect death (adhesin protein Mad1); lowly expressed during early infection but highly expressed after insect death (cation transporter, OpS13); or lowly expressed across the entire infection process (catalase protein). The data provide novel insights into the insect-pathogen interaction and help to uncover the molecular mechanisms involved in fungal infection of insect pests.

The role of mechanics during brain development

NASA Astrophysics Data System (ADS)

Budday, Silvia; Steinmann, Paul; Kuhl, Ellen

2014-12-01

Convolutions are a classical hallmark of most mammalian brains. Brain surface morphology is often associated with intelligence and closely correlated with neurological dysfunction. Yet, we know surprisingly little about the underlying mechanisms of cortical folding. Here we identify the role of the key anatomic players during the folding process: cortical thickness, stiffness, and growth. To establish estimates for the critical time, pressure, and the wavelength at the onset of folding, we derive an analytical model using the Föppl-von Kármán theory. Analytical modeling provides a quick first insight into the critical conditions at the onset of folding, yet it fails to predict the evolution of complex instability patterns in the post-critical regime. To predict realistic surface morphologies, we establish a computational model using the continuum theory of finite growth. Computational modeling not only confirms our analytical estimates, but is also capable of predicting the formation of complex surface morphologies with asymmetric patterns and secondary folds. Taken together, our analytical and computational models explain why larger mammalian brains tend to be more convoluted than smaller brains. Both models provide mechanistic interpretations of the classical malformations of lissencephaly and polymicrogyria. Understanding the process of cortical folding in the mammalian brain has direct implications on the diagnostics of neurological disorders including severe retardation, epilepsy, schizophrenia, and autism.

Current perspectives and the future of domestication studies

PubMed Central

Larson, Greger; Piperno, Dolores R.; Allaby, Robin G.; Purugganan, Michael D.; Andersson, Leif; Arroyo-Kalin, Manuel; Barton, Loukas; Climer Vigueira, Cynthia; Denham, Tim; Dobney, Keith; Doust, Andrew N.; Gepts, Paul; Gilbert, M. Thomas P.; Gremillion, Kristen J.; Lucas, Leilani; Lukens, Lewis; Marshall, Fiona B.; Olsen, Kenneth M.; Pires, J. Chris; Richerson, Peter J.; Rubio de Casas, Rafael; Sanjur, Oris I.; Thomas, Mark G.; Fuller, Dorian Q.

2014-01-01

It is difficult to overstate the cultural and biological impacts that the domestication of plants and animals has had on our species. Fundamental questions regarding where, when, and how many times domestication took place have been of primary interest within a wide range of academic disciplines. Within the last two decades, the advent of new archaeological and genetic techniques has revolutionized our understanding of the pattern and process of domestication and agricultural origins that led to our modern way of life. In the spring of 2011, 25 scholars with a central interest in domestication representing the fields of genetics, archaeobotany, zooarchaeology, geoarchaeology, and archaeology met at the National Evolutionary Synthesis Center to discuss recent domestication research progress and identify challenges for the future. In this introduction to the resulting Special Feature, we present the state of the art in the field by discussing what is known about the spatial and temporal patterns of domestication, and controversies surrounding the speed, intentionality, and evolutionary aspects of the domestication process. We then highlight three key challenges for future research. We conclude by arguing that although recent progress has been impressive, the next decade will yield even more substantial insights not only into how domestication took place, but also when and where it did, and where and why it did not. PMID:24757054

The role of mechanics during brain development

PubMed Central

Budday, Silvia; Steinmann, Paul; Kuhl, Ellen

2014-01-01

Convolutions are a classical hallmark of most mammalian brains. Brain surface morphology is often associated with intelligence and closely correlated to neurological dysfunction. Yet, we know surprisingly little about the underlying mechanisms of cortical folding. Here we identify the role of the key anatomic players during the folding process: cortical thickness, stiffness, and growth. To establish estimates for the critical time, pressure, and the wavelength at the onset of folding, we derive an analytical model using the Föppl-von-Kármán theory. Analytical modeling provides a quick first insight into the critical conditions at the onset of folding, yet it fails to predict the evolution of complex instability patterns in the post-critical regime. To predict realistic surface morphologies, we establish a computational model using the continuum theory of finite growth. Computational modeling not only confirms our analytical estimates, but is also capable of predicting the formation of complex surface morphologies with asymmetric patterns and secondary folds. Taken together, our analytical and computational models explain why larger mammalian brains tend to be more convoluted than smaller brains. Both models provide mechanistic interpretations of the classical malformations of lissencephaly and polymicrogyria. Understanding the process of cortical folding in the mammalian brain has direct implications on the diagnostics of neurological disorders including severe retardation, epilepsy, schizophrenia, and autism. PMID:25202162

Modeling spatial variation in avian survival and residency probabilities

USGS Publications Warehouse

Saracco, James F.; Royle, J. Andrew; DeSante, David F.; Gardner, Beth

2010-01-01

The importance of understanding spatial variation in processes driving animal population dynamics is widely recognized. Yet little attention has been paid to spatial modeling of vital rates. Here we describe a hierarchical spatial autoregressive model to provide spatially explicit year-specific estimates of apparent survival (phi) and residency (pi) probabilities from capture-recapture data. We apply the model to data collected on a declining bird species, Wood Thrush (Hylocichla mustelina), as part of a broad-scale bird-banding network, the Monitoring Avian Productivity and Survivorship (MAPS) program. The Wood Thrush analysis showed variability in both phi and pi among years and across space. Spatial heterogeneity in residency probability was particularly striking, suggesting the importance of understanding the role of transients in local populations. We found broad-scale spatial patterning in Wood Thrush phi and pi that lend insight into population trends and can direct conservation and research. The spatial model developed here represents a significant advance over approaches to investigating spatial pattern in vital rates that aggregate data at coarse spatial scales and do not explicitly incorporate spatial information in the model. Further development and application of hierarchical capture-recapture models offers the opportunity to more fully investigate spatiotemporal variation in the processes that drive population changes.

Insight on how fishing bats discern prey and adjust their mechanic and sensorial features during the attack sequence

PubMed Central

Aizpurua, Ostaizka; Alberdi, Antton; Aihartza, Joxerra; Garin, Inazio

2015-01-01

Several insectivorous bats have included fish in their diet, yet little is known about the processes underlying this trophic shift. We performed three field experiments with wild fishing bats to address how they manage to discern fish from insects and adapt their hunting technique to capture fish. We show that bats react only to targets protruding above the water and discern fish from insects based on prey disappearance patterns. Stationary fish trigger short and shallow dips and a terminal echolocation pattern with an important component of the narrowband and low frequency calls. When the fish disappears during the attack process, bats regulate their attack increasing the number of broadband and high frequency calls in the last phase of the echolocation as well as by lengthening and deepening their dips. These adjustments may allow bats to obtain more valuable sensorial information and to perform dips adjusted to the level of uncertainty on the location of the submerged prey. The observed ultrafast regulation may be essential for enabling fishing to become cost-effective in bats, and demonstrates the ability of bats to rapidly modify and synchronise their sensorial and motor features as a response to last minute stimulus variations. PMID:26196094

Range-wide parallel climate-associated genomic clines in Atlantic salmon

PubMed Central

Stanley, Ryan R. E.; Wringe, Brendan F.; Guijarro-Sabaniel, Javier; Bourret, Vincent; Bernatchez, Louis; Bentzen, Paul; Beiko, Robert G.; Gilbey, John; Clément, Marie; Bradbury, Ian R.

2017-01-01

Clinal variation across replicated environmental gradients can reveal evidence of local adaptation, providing insight into the demographic and evolutionary processes that shape intraspecific diversity. Using 1773 genome-wide single nucleotide polymorphisms we evaluated latitudinal variation in allele frequency for 134 populations of North American and European Atlantic salmon (Salmo salar). We detected 84 (4.74%) and 195 (11%) loci showing clinal patterns in North America and Europe, respectively, with 12 clinal loci in common between continents. Clinal single nucleotide polymorphisms were evenly distributed across the salmon genome and logistic regression revealed significant associations with latitude and seasonal temperatures, particularly average spring temperature in both continents. Loci displaying parallel clines were associated with several metabolic and immune functions, suggesting a potential basis for climate-associated adaptive differentiation. These climate-based clines collectively suggest evidence of large-scale environmental associated differences on either side of the North Atlantic. Our results support patterns of parallel evolution on both sides of the North Atlantic, with evidence of both similar and divergent underlying genetic architecture. The identification of climate-associated genomic clines illuminates the role of selection and demographic processes on intraspecific diversity in this species and provides a context in which to evaluate the impacts of climate change. PMID:29291123

Algal Turf Sediments and Sediment Production by Parrotfishes across the Continental Shelf of the Northern Great Barrier Reef

PubMed Central

Goatley, Christopher H. R.; Bellwood, David R.

2017-01-01

Sediments are found in the epilithic algal matrix (EAM) of all coral reefs and play important roles in ecological processes. Although we have some understanding of patterns of EAM sediments across individual reefs, our knowledge of patterns across broader spatial scales is limited. We used an underwater vacuum sampler to quantify patterns in two of the most ecologically relevant factors of EAM sediments across the Great Barrier Reef: total load and grain size distribution. We compare these patterns with rates of sediment production and reworking by parrotfishes to gain insights into the potential contribution of parrotfishes to EAM sediments. Inner-shelf reef EAMs had the highest sediment loads with a mean of 864.1 g m-2, compared to 126.8 g m-2 and 287.4 g m-2 on mid- and outer-shelf reefs, respectively. High sediment loads were expected on inner-shelf reefs due to their proximity to the mainland, however, terrigenous siliceous sediments only accounted for 13–24% of total mass. On inner-shelf reef crests parrotfishes would take three months to produce the equivalent mass of sediment found in the EAM. On the outer-shelf it would take just three days, suggesting that inner-shelf EAMs are characterised by low rates of sediment turnover. By contrast, on-reef sediment production by parrotfishes is high on outer-shelf crests. However, exposure to oceanic swells means that much of this production is likely to be lost. Hydrodynamic activity also appears to structure sediment patterns at within-reef scales, with coarser sediments (> 250 μm) typifying exposed reef crest EAMs, and finer sediments (< 250 μm) typifying sheltered back-reef EAMs. As both the load and grain size of EAM sediments mediate a number of important ecological processes on coral reefs, the observed sediment gradients are likely to play a key role in the structure and function of the associated coral reef communities. PMID:28122042

Sequential Pattern Mining of Electronic Healthcare Reimbursement Claims: Experiences and Challenges in Uncovering How Patients are Treated by Physicians

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

Pullum, Laura L; Ramanathan, Arvind; Hobson, Tanner C

We examine the use of electronic healthcare reimbursement claims (EHRC) for analyzing healthcare delivery and practice patterns across the United States (US). We show that EHRCs are correlated with disease incidence estimates published by the Centers for Disease Control. Further, by analyzing over 1 billion EHRCs, we track patterns of clinical procedures administered to patients with autism spectrum disorder (ASD), heart disease (HD) and breast cancer (BC) using sequential pattern mining algorithms. Our analyses reveal that in contrast to treating HD and BC, clinical procedures for ASD diagnoses are highly varied leading up to and after the ASD diagnoses. Themore » discovered clinical procedure sequences also reveal significant differences in the overall costs incurred across different parts of the US, indicating a lack of consensus amongst practitioners in treating ASD patients. We show that a data-driven approach to understand clinical trajectories using EHRC can provide quantitative insights into how to better manage and treat patients. Based on our experience, we also discuss emerging challenges in using EHRC datasets for gaining insights into the state of contemporary healthcare delivery and practice in the US.« less

Temporal changes of spatial soil moisture patterns: controlling factors explained with a multidisciplinary approach

NASA Astrophysics Data System (ADS)

Martini, Edoardo; Wollschläger, Ute; Kögler, Simon; Behrens, Thorsten; Dietrich, Peter; Reinstorf, Frido; Schmidt, Karsten; Weiler, Markus; Werban, Ulrike; Zacharias, Steffen

2016-04-01

Characterizing the spatial patterns of soil moisture is critical for hydrological and meteorological models, as soil moisture is a key variable that controls matter and energy fluxes and soil-vegetation-atmosphere exchange processes. Deriving detailed process understanding at the hillslope scale is not trivial, because of the temporal variability of local soil moisture dynamics. Nevertheless, it remains a challenge to provide adequate information on the temporal variability of soil moisture and its controlling factors. Recent advances in wireless sensor technology allow monitoring of soil moisture dynamics with high temporal resolution at varying scales. In addition, mobile geophysical methods such as electromagnetic induction (EMI) have been widely used for mapping soil water content at the field scale with high spatial resolution, as being related to soil apparent electrical conductivity (ECa). The objective of this study was to characterize the spatial and temporal pattern of soil moisture at the hillslope scale and to infer the controlling hydrological processes, integrating well established and innovative sensing techniques, as well as new statistical methods. We combined soil hydrological and pedological expertise with geophysical measurements and methods from digital soil mapping for designing a wireless soil moisture monitoring network. For a hillslope site within the Schäfertal catchment (Central Germany), soil water dynamics were observed during 14 months, and soil ECa was mapped on seven occasions whithin this period of time using an EM38-DD device. Using the Spearman rank correlation coefficient, we described the temporal persistence of a dry and a wet characteristic state of soil moisture as well as the switching mechanisms, inferring the local properties that control the observed spatial patterns and the hydrological processes driving the transitions. Based on this, we evaluated the use of EMI for mapping the spatial pattern of soil moisture under different hydrologic conditions and the factors controlling the temporal variability of the ECa-soil moisture relationship. The approach provided valuable insight into the time-varying contribution of local and nonlocal factors to the characteristic spatial patterns of soil moisture and the transition mechanisms. The spatial organization of soil moisture was controlled by different processes in different soil horizons, and the topsoil's moisture did not mirror processes that take place within the soil profile. Results show that, for the Schäfertal hillslope site which is presumed to be representative for non-intensively managed soils with moderate clay content, local soil properties (e.g., soil texture and porosity) are the major control on the spatial pattern of ECa. In contrast, the ECa-soil moisture relationship is small and varies over time indicating that ECa is not a good proxy for soil moisture estimation at the investigated site.Occasionally observed stronger correlations between ECa and soil moisture may be explained by background dependencies of ECa to other state variables such as pore water electrical conductivity. The results will help to improve conceptual understanding for hydrological model studies at similar or smaller scales, and to transfer observation concepts and process understanding to larger or less instrumented sites, as well as to constrain the use of EMI-based ECa data for hydrological applications.

Patterns of cetacean vaginal folds yield insights into functionality

PubMed Central

Orbach, Dara N.; Marshall, Christopher D.; Mesnick, Sarah L.; Würsig, Bernd

2017-01-01

Complex foldings of the vaginal wall are unique to some cetaceans and artiodactyls and are of unknown function(s). The patterns of vaginal length and cumulative vaginal fold length were assessed in relation to body length and to each other in a phylogenetic context to derive insights into functionality. The reproductive tracts of 59 female cetaceans (20 species, 6 families) were dissected. Phylogenetically-controlled reduced major axis regressions were used to establish a scaling trend for the female genitalia of cetaceans. An unparalleled level of vaginal diversity within a mammalian order was found. Vaginal folds varied in number and size across species, and vaginal fold length was positively allometric with body length. Vaginal length was not a significant predictor of vaginal fold length. Functional hypotheses regarding the role of vaginal folds and the potential selection pressures that could lead to evolution of these structures are discussed. Vaginal folds may present physical barriers, which obscure the pathway of seawater and/or sperm travelling through the vagina. This study contributes broad insights to the evolution of reproductive morphology and aquatic adaptations and lays the foundation for future functional morphology analyses. PMID:28362830

Phylogeography of endemic Xantus' hummingbird (Hylocharis xantusii) shows a different history of vicariance in the Baja California Peninsula.

PubMed

González-Rubio, Cristina; García-De León, Francisco J; Rodríguez-Estrella, Ricardo

2016-09-01

Studies of phylogeographic patterns provide insight into the processes driving lineage divergence in a particular region. To identify the processes that caused phylogeographic breaks, it is necessary to use historical information and a set of appropriate molecular data to explain current patterns. To understand the influence of geological or ecological processes on the phylogeography of the only species of hummingbird endemic to the Baja California Peninsula, Hylocharis xantusii, mitochondrial DNA sequences of three concatenated genes (Cyt-b, COI and ND2; 2297bp in total) in 100 individuals were analyzed. The spatial analyses of genetic variation showed phylogeographic structure consisting of a north, central and south regions. According to estimated divergence times, two vicariant events are supported, permanent separation of the peninsula and formation of the Gulf of California at 5mya and temporary isolation of the southern region at the Isthmus of La Paz at 3mya. The temporal frame of genetic differentiation of intraspecific haplotypes indicates that 90% of haplotypes diverged within the last 500,000years, with a population expansion 80,000years ago. Only four haplotypes diverged ∼2.2 my and occurred in the south (Hxan_36, 38 and 45), and north (Hxan_45 and 56) regions; only haplotype 45 is shared between south and north populations. These regions also have the most recent haplotypes from 12,500 to 16,200years ago, and together with high levels of genetic diversity, we suggest two refuge areas, the Northern and Southern regions. Our results indicate that the phylogeographic pattern first results from vicariance processes, then is followed by historical and recent climate fluctuations that influenced conditions on the peninsula, and it is also related to oases distribution. This study presents the first investigation of phylogeography of the peninsular' endemic Xantus' hummingbird. Copyright © 2016 Elsevier Inc. All rights reserved.

Mechanical Model of Geometric Cell and Topological Algorithm for Cell Dynamics from Single-Cell to Formation of Monolayered Tissues with Pattern

PubMed Central

Kachalo, Sëma; Naveed, Hammad; Cao, Youfang; Zhao, Jieling; Liang, Jie

2015-01-01

Geometric and mechanical properties of individual cells and interactions among neighboring cells are the basis of formation of tissue patterns. Understanding the complex interplay of cells is essential for gaining insight into embryogenesis, tissue development, and other emerging behavior. Here we describe a cell model and an efficient geometric algorithm for studying the dynamic process of tissue formation in 2D (e.g. epithelial tissues). Our approach improves upon previous methods by incorporating properties of individual cells as well as detailed description of the dynamic growth process, with all topological changes accounted for. Cell size, shape, and division plane orientation are modeled realistically. In addition, cell birth, cell growth, cell shrinkage, cell death, cell division, cell collision, and cell rearrangements are now fully accounted for. Different models of cell-cell interactions, such as lateral inhibition during the process of growth, can be studied in detail. Cellular pattern formation for monolayered tissues from arbitrary initial conditions, including that of a single cell, can also be studied in detail. Computational efficiency is achieved through the employment of a special data structure that ensures access to neighboring cells in constant time, without additional space requirement. We have successfully generated tissues consisting of more than 20,000 cells starting from 2 cells within 1 hour. We show that our model can be used to study embryogenesis, tissue fusion, and cell apoptosis. We give detailed study of the classical developmental process of bristle formation on the epidermis of D. melanogaster and the fundamental problem of homeostatic size control in epithelial tissues. Simulation results reveal significant roles of solubility of secreted factors in both the bristle formation and the homeostatic control of tissue size. Our method can be used to study broad problems in monolayered tissue formation. Our software is publicly available. PMID:25974182

Feedback Limiting the Coastal Response to Irregularities in Shelf Bathymetry

NASA Astrophysics Data System (ADS)

List, J. H.; Benedet, L.

2007-12-01

Observations and engineering studies have shown that non-uniform inner shelf bathymetry can influence longshore sediment transport gradients and create patterns of shoreline change. One classic example is from Grand Isle, Louisiana, where two offshore borrow pits caused two zones of shoreline accretion landward of the pits. In addition to anthropogenic cases, many natural situations exist in which irregularities in coastal planform are thought to result from offshore shoals or depressions. Recent studies using the hydrodynamic model Delft3D have successfully simulated the observed nearshore erosion and accretion patterns landward of an inner shelf borrow pit. An analysis of the momentum balance in a steady-state simulation has demonstrated that both alongshore pressure gradients (due to alongshore variations in wave setup) and radiation stress gradients (terms relevant to alongshore forcing) are important for forcing the initial pattern of nearshore sedimentation in response to the borrow pit. The response of the coast to non-uniform inner shelf bathymetry appears to be limited, however, because observed shoreline undulations are often rather subtle. (An exception may exist in the case of a very high angle wave climate.) Therefore, feedbacks in processes must exist such that growth of the shoreline salient itself modifies the transport processes in a way that limits further growth (assuming the perturbation in inner shelf bathymetry itself remains unchanged). Examination of the Delft3D momentum balance for an inner shelf pit test case demonstrates that after a certain degree of morphologic development the forcing associated with the well-known shoreline smoothing process (a.k.a., diffusion) counteracts the forcing associated with the inner shelf pit, producing a negative feedback which arrests further growth of the shoreline salient. These results provide insights into the physical processes that control shoreline changes behind inner shelf bathymetric anomalies (i.e. man-made dredge pits and natural bathymetric features) and are therefore relevant to the understanding and prediction of shoreline change on many coasts.

Insight and recovery from acute psychotic episodes: the effects of cognitive behavior therapy and premature termination of treatment.

PubMed

Startup, Mike; Jackson, Mike C; Startup, Sue

2006-10-01

Research suggests that insight in schizophrenia is only weakly responsive to targeted psychosocial interventions. One of the aims of the present study was to examine the effects on insight of cognitive behavior therapy (CBT) for acutely psychotic patients. A second aim was to test predictions drawn from research on recovery styles that patients who reject psychological assistance will show a reduction in insight while those who continue to accept psychological assistance will show increases in insight over time. Patients with acute schizophrenia-spectrum disorders were assigned at random to treatment-as-usual (TAU) or TAU plus CBT. The latter were also divided into those who terminated treatment prematurely (dropouts) and those who did not (stay-ins). Insight was assessed at baseline and three follow-up assessments. Insight increased over the follow-up period, but there were no differences between the CBT and TAU groups. Within the CBT group, dropouts showed a reduction in insight at the 6-month assessment before returning to their baseline level, while the stay-ins showed linear improvement up to 12 months. Possible explanations for these contrasting patterns, in terms of resilience, attachment styles, and an insecure sense of self, are discussed.

Molecular-level insights into aging processes of skin elastin.

PubMed

Mora Huertas, Angela C; Schmelzer, Christian E H; Hoehenwarter, Wolfgang; Heyroth, Frank; Heinz, Andrea

2016-01-01

Skin aging is characterized by different features including wrinkling, atrophy of the dermis and loss of elasticity associated with damage to the extracellular matrix protein elastin. The aim of this study was to investigate the aging process of skin elastin at the molecular level by evaluating the influence of intrinsic (chronological aging) and extrinsic factors (sun exposure) on the morphology and susceptibility of elastin towards enzymatic degradation. Elastin was isolated from biopsies derived from sun-protected or sun-exposed skin of differently aged individuals. The morphology of the elastin fibers was characterized by scanning electron microscopy. Mass spectrometric analysis and label-free quantification allowed identifying differences in the cleavage patterns of the elastin samples after enzymatic digestion. Principal component analysis and hierarchical cluster analysis were used to visualize differences between the samples and to determine the contribution of extrinsic and intrinsic aging to the proteolytic susceptibility of elastin. Moreover, the release of potentially bioactive peptides was studied. Skin aging is associated with the decomposition of elastin fibers, which is more pronounced in sun-exposed tissue. Marker peptides were identified, which showed an age-related increase or decrease in their abundances and provide insights into the progression of the aging process of elastin fibers. Strong age-related cleavage occurs in hydrophobic tropoelastin domains 18, 20, 24 and 26. Photoaging makes the N-terminal and central parts of the tropoelastin molecules more susceptible towards enzymatic cleavage and, hence, accelerates the age-related degradation of elastin. Copyright © 2016 Elsevier B.V. and Société Française de Biochimie et Biologie Moléculaire (SFBBM). All rights reserved.

Big-data reflection high energy electron diffraction analysis for understanding epitaxial film growth processes.

PubMed

Vasudevan, Rama K; Tselev, Alexander; Baddorf, Arthur P; Kalinin, Sergei V

2014-10-28

Reflection high energy electron diffraction (RHEED) has by now become a standard tool for in situ monitoring of film growth by pulsed laser deposition and molecular beam epitaxy. Yet despite the widespread adoption and wealth of information in RHEED images, most applications are limited to observing intensity oscillations of the specular spot, and much additional information on growth is discarded. With ease of data acquisition and increased computation speeds, statistical methods to rapidly mine the data set are now feasible. Here, we develop such an approach to the analysis of the fundamental growth processes through multivariate statistical analysis of a RHEED image sequence. This approach is illustrated for growth of La(x)Ca(1-x)MnO(3) films grown on etched (001) SrTiO(3) substrates, but is universal. The multivariate methods including principal component analysis and k-means clustering provide insight into the relevant behaviors, the timing and nature of a disordered to ordered growth change, and highlight statistically significant patterns. Fourier analysis yields the harmonic components of the signal and allows separation of the relevant components and baselines, isolating the asymmetric nature of the step density function and the transmission spots from the imperfect layer-by-layer (LBL) growth. These studies show the promise of big data approaches to obtaining more insight into film properties during and after epitaxial film growth. Furthermore, these studies open the pathway to use forward prediction methods to potentially allow significantly more control over growth process and hence final film quality.

The control of automatic imitation based on bottom-up and top-down cues to animacy: insights from brain and behavior.

PubMed

Klapper, André; Ramsey, Richard; Wigboldus, Daniël; Cross, Emily S

2014-11-01

Humans automatically imitate other people's actions during social interactions, building rapport and social closeness in the process. Although the behavioral consequences and neural correlates of imitation have been studied extensively, little is known about the neural mechanisms that control imitative tendencies. For example, the degree to which an agent is perceived as human-like influences automatic imitation, but it is not known how perception of animacy influences brain circuits that control imitation. In the current fMRI study, we examined how the perception and belief of animacy influence the control of automatic imitation. Using an imitation-inhibition paradigm that involves suppressing the tendency to imitate an observed action, we manipulated both bottom-up (visual input) and top-down (belief) cues to animacy. Results show divergent patterns of behavioral and neural responses. Behavioral analyses show that automatic imitation is equivalent when one or both cues to animacy are present but reduces when both are absent. By contrast, right TPJ showed sensitivity to the presence of both animacy cues. Thus, we demonstrate that right TPJ is biologically tuned to control imitative tendencies when the observed agent both looks like and is believed to be human. The results suggest that right TPJ may be involved in a specialized capacity to control automatic imitation of human agents, rather than a universal process of conflict management, which would be more consistent with generalist theories of imitative control. Evidence for specialized neural circuitry that "controls" imitation offers new insight into developmental disorders that involve atypical processing of social information, such as autism spectrum disorders.

Similar and contrasting dimensions of social cognition in schizophrenia and healthy subjects.

PubMed

Mehta, Urvakhsh Meherwan; Thirthalli, Jagadisha; Bhagyavathi, H D; Keshav Kumar, J; Subbakrishna, D K; Gangadhar, Bangalore N; Eack, Shaun M; Keshavan, Matcheri S

2014-08-01

Schizophrenia patients experience substantial impairments in social cognition (SC) and these deficits are associated with their poor functional outcome. Though SC is consistently shown to emerge as a cognitive dimension distinct from neurocognition, the dimensionality of SC is poorly understood. Moreover, comparing the components of SC between schizophrenia patients and healthy comparison subjects would provide specific insights on the construct validity of SC. We conducted principal component analyses of eight SC test scores (representing four domains of SC, namely, theory of mind, emotion processing, social perception and attributional bias) independently in 170 remitted schizophrenia patients and 111 matched healthy comparison subjects. We also conducted regression analyses to evaluate the relative contribution of individual SC components to other symptom dimensions, which are important clinical determinants of functional outcome (i.e., neurocognition, negative symptoms, motivational deficits and insight) in schizophrenia. A three-factor solution representing socio-emotional processing, social-inferential ability and external attribution components emerged in the patient group that accounted for 64.43% of the variance. In contrast, a two-factor solution representing socio-emotional processing and social-inferential ability was derived in the healthy comparison group that explained 56.5% of the variance. In the patient group, the social-inferential component predicted negative symptoms and motivational deficits. Our results suggest the presence of a multidimensional SC construct. The dimensionality of SC observed across the two groups, though not identical, displayed important parallels. Individual components also demonstrated distinct patterns of association with other symptom dimensions, thus supporting their external validity. Copyright © 2014 Elsevier B.V. All rights reserved.

Comparative transcriptome analysis reveals a global insight into molecular processes regulating citrate accumulation in sweet orange (Citrus sinensis).

PubMed

Lu, Xiaopeng; Cao, Xiongjun; Li, Feifei; Li, Jing; Xiong, Jiang; Long, Guiyou; Cao, Shangyin; Xie, Shenxi

2016-12-01

Citrate, the predominant organic acid in citrus, determines the taste of these fruits. However, little is known about the synergic molecular processes regulating citrate accumulation. Using 'Dahongtiancheng' (Citrus sinensis) and 'Bingtangcheng' (C. sinensis) with significant difference in citrate, the objectives of this study were to understand the global mechanisms of high-citrate accumulation in sweet orange. 'Dahongtiancheng' and 'Bingtangcheng' exhibit significantly different patterns in citrate accumulation throughout fruit development, with the largest differences observed at 50-70 days after full bloom (DAFB). Comparative transcriptome profiling was performed for the endocarps of both cultivars at 50 and 70 DAFB. Over 34.5 million clean reads per library were successfully mapped to the reference database and 670-2630 differentially expressed genes (DEGs) were found in four libraries. Among the genes, five transcription factors were ascertained to be the candidates regulating citrate accumulation. Functional assignments of the DEGs indicated that photosynthesis, the citrate cycle and amino acid metabolism were significantly altered in 'Dahongtiancheng'. Physiological and molecular analyses suggested that high photosynthetic efficiency and partial impairment of citrate catabolism were crucial for the high-citrate trait, and amino acid biosynthesis was one of the important directions for citrate flux. The results reveal a global insight into the gene expression changes in a high-citrate compared with a low-citrate sweet orange. High accumulating efficiency and impaired degradation of citrate may be associated with the high-citrate trait of 'Dahongtiancheng'. Findings in this study increase understanding of the molecular processes regulating citrate accumulation in sweet orange. © 2016 Scandinavian Plant Physiology Society.

A three-component hydrograph separation based on geochemical tracers in a tropical mountainous headwater catchment in northern Thailand

NASA Astrophysics Data System (ADS)

Hugenschmidt, C.; Ingwersen, J.; Sangchan, W.; Sukvanachaikul, Y.; Duffner, A.; Uhlenbrook, S.; Streck, T.

2014-02-01

Land-use change in the mountainous parts of northern Thailand is reflected by an increased application of agrochemicals, which may be lost to surface and groundwater. The close relation between flow paths and contaminant transport within hydrological systems requires recognizing and understanding the dominant hydrological processes. To date, the vast majority of studies on runoff generation have been conducted in temperate regions. Tropical regions suffer from a general lack of data, and little is known about runoff generation processes. To fill this knowledge gap, a three-component hydrograph separation based on geochemical tracers was carried out in a steep, remote and monsoon-dominated study site (7 km2) in northern Thailand. Silica and electrical conductivity (EC) were identified as useful tracers and were applied to calculate the fractions of groundwater (similar to pre-event water), shallow subsurface flow and surface runoff on stormflow. K+ was a useful indicator for surface runoff dynamics, and Ca2+ provided insights into groundwater behaviour. Nevertheless, neither measure was applicable for the quantification of runoff components. Cl- and further parameters (e.g. Na+, K+, and Mg2+) were also not helpful for flow path identification, nor were their concentrations distinguishable among the components. Groundwater contributed the largest fractions to stormflow (62-80%) throughout all events, followed by shallow subsurface flow (17-36%) and surface runoff (2-13%). Our results provide important insights into the dynamics of the runoff processes in the study area and may be used to assess the transport pattern of contaminants (i.e. agrochemicals) here.

Animal-Borne Imaging Reveals Novel Insights into the Foraging Behaviors and Diel Activity of a Large-Bodied Apex Predator, the American Alligator (Alligator mississippiensis)

PubMed Central

Nifong, James C.; Nifong, Rachel L.; Silliman, Brian R.; Lowers, Russell H.; Guillette, Louis J.; Ferguson, Jake M.; Welsh, Matthew; Abernathy, Kyler; Marshall, Greg

2014-01-01

Large-bodied, top- and apex predators (e.g., crocodilians, sharks, wolves, killer whales) can exert strong top-down effects within ecological communities through their interactions with prey. Due to inherent difficulties while studying the behavior of these often dangerous predatory species, relatively little is known regarding their feeding behaviors and activity patterns, information that is essential to understanding their role in regulating food web dynamics and ecological processes. Here we use animal-borne imaging systems (Crittercam) to study the foraging behavior and activity patterns of a cryptic, large-bodied predator, the American alligator (Alligator mississippiensis) in two estuaries of coastal Florida, USA. Using retrieved video data we examine the variation in foraging behaviors and activity patterns due to abiotic factors. We found the frequency of prey-attacks (mean = 0.49 prey attacks/hour) as well as the probability of prey-capture success (mean = 0.52 per attack) were significantly affected by time of day. Alligators attempted to capture prey most frequently during the night. Probability of prey-capture success per attack was highest during morning hours and sequentially lower during day, night, and sunset, respectively. Position in the water column also significantly affected prey-capture success, as individuals’ experienced two-fold greater success when attacking prey while submerged. These estimates are the first for wild adult American alligators and one of the few examples for any crocodilian species worldwide. More broadly, these results reveal that our understandings of crocodilian foraging behaviors are biased due to previous studies containing limited observations of cryptic and nocturnal foraging interactions. Our results can be used to inform greater understanding regarding the top-down effects of American alligators in estuarine food webs. Additionally, our results highlight the importance and power of using animal-borne imaging when studying the behavior of elusive large-bodied, apex predators, as it provides critical insights into their trophic and behavioral interactions. PMID:24454711

Forest dynamics in the U.S. indicate disproportionate attrition in western forests, rural areas and public lands

PubMed Central

2017-01-01

Forests are experiencing significant changes; studying geographic patterns in forests is critical in understanding the impact of forest dynamics to biodiversity, soil erosion, water chemistry and climate. Few studies have examined forest geographic pattern changes other than fragmentation; however, other spatial processes of forest dynamics are of equal importance. Here, we study forest attrition, the complete removal of forest patches, that can result in complete habitat loss, severe decline of population sizes and species richness, and shifts of local and regional environmental conditions. We aim to develop a simple yet insightful proximity-based spatial indicator capturing forest attrition that is independent of spatial scale and boundaries with worldwide application potential. Using this proximity indicator, we evaluate forest attrition across ecoregions, land ownership and urbanization stratifications across continental United States of America. Nationally, the total forest cover loss was approximately 90,400 km2, roughly the size of the state of Maine, constituting a decline of 2.96%. Examining the spatial arrangement of this change the average FAD was 3674m in 1992 and increased by 514m or 14.0% in 2001. Simulations of forest cover loss indicate only a 10m FAD increase suggesting that the observed FAD increase was more than an order of magnitude higher than expected. Furthermore, forest attrition is considerably higher in the western United States, in rural areas and in public lands. Our mathematical model (R2 = 0.93) supports estimation of attrition for a given forest cover. The FAD metric quantifies forest attrition across spatial scales and geographic boundaries and assesses unambiguously changes over time. The metric is applicable to any landscape and offers a new complementary insight on forest landscape patterns from local to global scales, improving future exploration of drivers and repercussions of forest cover changes and supporting more informative management of forest carbon, changing climate and species biodiversity. PMID:28225787

Animal-borne imaging reveals novel insights into the foraging behaviors and Diel activity of a large-bodied apex predator, the American alligator (Alligator mississippiensis).

PubMed

Nifong, James C; Nifong, Rachel L; Silliman, Brian R; Lowers, Russell H; Guillette, Louis J; Ferguson, Jake M; Welsh, Matthew; Abernathy, Kyler; Marshall, Greg

2014-01-01

Large-bodied, top- and apex predators (e.g., crocodilians, sharks, wolves, killer whales) can exert strong top-down effects within ecological communities through their interactions with prey. Due to inherent difficulties while studying the behavior of these often dangerous predatory species, relatively little is known regarding their feeding behaviors and activity patterns, information that is essential to understanding their role in regulating food web dynamics and ecological processes. Here we use animal-borne imaging systems (Crittercam) to study the foraging behavior and activity patterns of a cryptic, large-bodied predator, the American alligator (Alligator mississippiensis) in two estuaries of coastal Florida, USA. Using retrieved video data we examine the variation in foraging behaviors and activity patterns due to abiotic factors. We found the frequency of prey-attacks (mean = 0.49 prey attacks/hour) as well as the probability of prey-capture success (mean = 0.52 per attack) were significantly affected by time of day. Alligators attempted to capture prey most frequently during the night. Probability of prey-capture success per attack was highest during morning hours and sequentially lower during day, night, and sunset, respectively. Position in the water column also significantly affected prey-capture success, as individuals' experienced two-fold greater success when attacking prey while submerged. These estimates are the first for wild adult American alligators and one of the few examples for any crocodilian species worldwide. More broadly, these results reveal that our understandings of crocodilian foraging behaviors are biased due to previous studies containing limited observations of cryptic and nocturnal foraging interactions. Our results can be used to inform greater understanding regarding the top-down effects of American alligators in estuarine food webs. Additionally, our results highlight the importance and power of using animal-borne imaging when studying the behavior of elusive large-bodied, apex predators, as it provides critical insights into their trophic and behavioral interactions.

Wettability Control on Fluid-Fluid Displacements in Patterned Microfluidics

NASA Astrophysics Data System (ADS)

Zhao, B.; Trojer, M.; Cueto-Felgueroso, L.; Juanes, R.

2014-12-01

Two-phase flow in porous media is important in many natural and industrial processes like geologic CO2 sequestration, enhanced oil recovery, and water infiltration in soil. While it is well known that the wetting properties of porous media can vary drastically depending on the type of media and the pore fluids, the effect of wettability on fluid displacement continues to challenge our microscopic and macroscopic descriptions. Here we study this problem experimentally, starting with the classic experiment of two-phase flow in a capillary tube. We image the shape of the meniscus and measure the associated capillary pressure for a wide range of capillary numbers. We confirm that wettability exerts a fundamental control on meniscus deformation, and synthesize new observations on the dependence of the dynamic capillary pressure on wetting properties (contact angle) and flow conditions (viscosity contrast and capillary number). We compare our experiments to a macroscopic phase-field model of two-phase flow. We use the insights gained from the capillary tube experiments to explore the viscous fingering instability in the Hele-Shaw geometry in the partial-wetting regime. A key difference between a Hele-Shaw cell and a porous medium is the existence of micro-structures (i.e. pores and pore throats). To investigate how these micro-structrues impact fluid-fluid displacement, we conduct experiments on a planar microfluidic device patterned with vertical posts. We track the evolution of the fluid-fluid interface and elucidate the impact of wetting on the cooperative nature of fluid displacement during pore invasion events. We use the insights gained from the capillary tube and patterned microfluidics experiments to elucidate the effect of wetting properties on viscous fingering and capillary fingering in a Hele-Shaw cell filled with glass beads, where we observe a contact-angle-dependent stabilizing behavior for the emerging flow instabilities, as the system transitions from drainage to imbibition.

Forest dynamics in the U.S. indicate disproportionate attrition in western forests, rural areas and public lands.

PubMed

Yang, Sheng; Mountrakis, Giorgos

2017-01-01

Forests are experiencing significant changes; studying geographic patterns in forests is critical in understanding the impact of forest dynamics to biodiversity, soil erosion, water chemistry and climate. Few studies have examined forest geographic pattern changes other than fragmentation; however, other spatial processes of forest dynamics are of equal importance. Here, we study forest attrition, the complete removal of forest patches, that can result in complete habitat loss, severe decline of population sizes and species richness, and shifts of local and regional environmental conditions. We aim to develop a simple yet insightful proximity-based spatial indicator capturing forest attrition that is independent of spatial scale and boundaries with worldwide application potential. Using this proximity indicator, we evaluate forest attrition across ecoregions, land ownership and urbanization stratifications across continental United States of America. Nationally, the total forest cover loss was approximately 90,400 km2, roughly the size of the state of Maine, constituting a decline of 2.96%. Examining the spatial arrangement of this change the average FAD was 3674m in 1992 and increased by 514m or 14.0% in 2001. Simulations of forest cover loss indicate only a 10m FAD increase suggesting that the observed FAD increase was more than an order of magnitude higher than expected. Furthermore, forest attrition is considerably higher in the western United States, in rural areas and in public lands. Our mathematical model (R2 = 0.93) supports estimation of attrition for a given forest cover. The FAD metric quantifies forest attrition across spatial scales and geographic boundaries and assesses unambiguously changes over time. The metric is applicable to any landscape and offers a new complementary insight on forest landscape patterns from local to global scales, improving future exploration of drivers and repercussions of forest cover changes and supporting more informative management of forest carbon, changing climate and species biodiversity.

InSight Spacecraft Uncrating, Removal from Container, Lift Heat

NASA Image and Video Library

2018-03-01

Inside the Astrotech processing facility at Vandenberg Air Force Base in California, the heatshield for NASA's Interior Exploration using Seismic Investigations, Geodesy and Heat Transport, or InSight, spacecraft is removed from protective wrapping. InSight was developed and built by Lockheed-Martin Space Systems in Denver, Colorado, and is scheduled for liftoff is May 5, 2018. InSight is the first mission to land on Mars and explore the Red Planet's deep interior. It will investigate processes that shaped the rocky planets of the inner solar system including Earth.

InSight Spacecraft Uncrating, Removal from Container, Lift Heat

NASA Image and Video Library

2018-03-01

Inside the Astrotech processing facility at Vandenberg Air Force Base in California, technicians and engineers inspect the heatshield for NASA's Interior Exploration using Seismic Investigations, Geodesy and Heat Transport, or InSight, spacecraft. InSight was developed and built by Lockheed-Martin Space Systems in Denver, Colorado, and is scheduled for liftoff is May 5, 2018. InSight is the first mission to land on Mars and explore the Red Planet's deep interior. It will investigate processes that shaped the rocky planets of the inner solar system including Earth.

InSight Spacecraft Uncrating, Removal from Container, Lift Heat

NASA Image and Video Library

2018-03-01

Inside the Astrotech processing facility at Vandenberg Air Force Base in California, the heatshield for NASA's Interior Exploration using Seismic Investigations, Geodesy and Heat Transport, or InSight, spacecraft has been removed from protective wrapping. InSight was developed and built by Lockheed-Martin Space Systems in Denver, Colorado, and is scheduled for liftoff is May 5, 2018. InSight is the first mission to land on Mars and explore the Red Planet's deep interior. It will investigate processes that shaped the rocky planets of the inner solar system including Earth.

Executive-affective connectivity in smokers viewing anti-smoking images: an fMRI study.

PubMed

Dinh-Williams, Laurence; Mendrek, Adrianna; Dumais, Alexandre; Bourque, Josiane; Potvin, Stéphane

2014-12-30

Despite knowledge of the harmful consequences of smoking on health, tobacco users continue to smoke. Neuroimaging studies have begun to provide insight into the mechanisms underlying this response. Regions involved in executive control and affective processing/persuasion are activated when viewing the negative value of smoking, but these systems can interact in ways that promote or hinder its impact on behavior. The goal of this functional magnetic resonance imaging (fMRI) study was to examine the dynamics between these systems during the processing of images designed to elicit a negative emotional response regarding tobacco smoking in a group of current smokers. Thirty chronic smokers passively viewed aversive smoking-related, aversive nonsmoking-related and neutral images presented in a block design while being scanned. Functional connectivity analyses showed that the left inferior frontal gyrus (IFG) is negatively associated to activity in medial frontal, cingulate, limbic, subcortical and parietal regions in chronic smokers during the processing of aversive smoking-related material, a pattern that was significantly greater when stimuli were drug-related compared with when they were nondrug-related. Our results suggest that individuals with tobacco dependence present different patterns of functional connectivity depending on whether the aversive stimuli are smoking- or nonsmoking-related. Activity in the left inferior frontal gyrus may act to down-regulate corresponding activity in regions key to an affective and persuasive response during the processing of anti-smoking material. This mechanism may reduce the extent to which "feeling bad" brings about a change in behavior. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

The development of a change model of "exits" during cognitive analytic therapy for the treatment of depression.

PubMed

Sandhu, Sundeep Kaur; Kellett, Stephen; Hardy, Gillian

2017-11-01

"Exits" in cognitive analytic therapy (CAT) are methods that change unhelpful patterns or roles during the final "revision" phase of the therapy. How exits are conceived and achieved is currently poorly understood. This study focussed on the revision stage to explore and define how change is accomplished in CAT. Qualitative content analysis studied transcripts of sessions 6 and 7 of a protocol delivered 8-session CAT treatment for depression. Eight participants met the study inclusion criteria, and therefore, 16 sessions were analysed. The exit model developed contained 3 distinct (but interacting) phases: (a) developing an observing self via therapist input or client self-reflection, (b) breaking out of old patterns by creating new roles and procedures, and (c) utilisation of a range of methods to support and maintain change. Levels of interrater reliability for the exit categories that formed the model were good. The revision stage of CAT emerged as a complex and dynamic process involving 3 interacting stages. Further research is recommended to understand how exits relate to durability of change and whether change processes differ according to presenting problem. Exit work in cognitive analytic therapy is a dynamic process that requires progression through stages of insight, active change, and consolidation. Development of an "observing self" is an important foundation stone for change, and cognitive analytic therapists need to work within the client's zone of proximal development. A number of aspects appear important in facilitating change, such as attending to the process and feelings generated by change talk. Copyright © 2017 John Wiley & Sons, Ltd.

Ecohydrological interactions within "fairy circles" in the Namib Desert: Revisiting the self-organization hypothesis

NASA Astrophysics Data System (ADS)

Ravi, Sujith; Wang, Lixin; Kaseke, Kudzai Farai; Buynevich, Ilya V.; Marais, Eugene

2017-02-01

Vegetation patterns such as rings, bands, and spots are recurrent characteristics of resource-limited arid and semiarid ecosystems. One of the most recognizable vegetation patterns is the millions of circular patches, often referred to as "fairy circles," within the arid grassland matrix extending over hundreds of kilometers in the Namib Desert. Several modeling studies have highlighted the role of plant-soil interactions in the formation of these fairy circles. However, little is known about the spatial and temporal variabilities of hydrological processes inside a fairy circle. In particular, a detailed field assessment of hydrological and soil properties inside and outside the fairy circles is limited. We conducted extensive measurements of infiltration rate, soil moisture, grass biometric, and sediment grain-size distribution from multiple circles and interspaces in the Namib Desert. Our results indicate that considerable heterogeneity in hydrological processes exists within the fairy circles, resulting from the presence of coarser particles in the inner bare soil areas, whereas concentration of fine soil occurs on the vegetated edges. The trapping of aeolian and water-borne sediments by plants may result in the observed soil textural changes beneath the vegetation, which in turn, explains the heterogeneity in hydrological processes such as infiltration and runoff. Our investigation provides new insights and experimental data on the ecohydrological processes associated with fairy circles, from a less studied location devoid of sand termite activity within the circles. The results seem to provide support to the "self-organization hypothesis" of fairy circle formation attributed to the antiphase spatial biomass-water distributions.

Rapid prototyping of three-dimensional microstructures from multiwalled carbon nanotubes

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

Hung, W.H.; Kumar, Rajay; Bushmaker, Adam

The authors report a method for creating three-dimensional carbon nanotube structures, whereby a focused laser beam is used to selectively burn local regions of a dense forest of multiwalled carbon nanotubes. Raman spectroscopy and scanning electron microscopy are used to quantify the threshold for laser burnout and depth of burnout. The minimum power density for burning carbon nanotubes in air is found to be 244 {mu}W/{mu}m{sup 2}. We create various three-dimensional patterns using this method, illustrating its potential use for the rapid prototyping of carbon nanotube microstructures. Undercut profiles, changes in nanotube density, and nanoparticle formation are observed after lasermore » surface treatment and provide insight into the dynamic process of the burnout mechanism.« less

Critical insights for researchers and decision-makers.

PubMed

Tomblin, Seven

2004-01-01

Regionalization organizations are essential building blocks of health restructuring and are designed to be agents of change and integration in most provinces in Canada. Yet, despite this, most citizens seem to be unaware of regional health authorities, why they exist, the drivers and constraints involved, or whether these divergent structures and regional governance processes have influenced patterns of restructuring and health outcomes. And even when discussions have taken place, these debates have tended to be more prescriptive than analytical. All of this has complicated the task of conceptualizing and making sense of the determinants that have influenced regionalization forms of health service restructuring in Canada and how these have influenced the way resources have been allocated, decisions reached and accountability exercised.

Faunal isotope records reveal trophic and nutrient dynamics in twentieth century Yellowstone grasslands.

PubMed

Fox-Dobbs, Kena; Nelson, Abigail A; Koch, Paul L; Leonard, Jennifer A

2012-10-23

Population sizes and movement patterns of ungulate grazers and their predators have fluctuated dramatically over the past few centuries, largely owing to overharvesting, land-use change and historic management. We used δ(13)C and δ(15)N values measured from bone collagen of historic and recent gray wolves and their potential primary prey from Yellowstone National Park to gain insight into the trophic dynamics and nutrient conditions of historic and modern grasslands. The diet of reintroduced wolves closely parallels that of the historic population. We suggest that a significant shift in faunal δ(15)N values over the past century reflects impacts of anthropogenic environmental changes on grassland ecosystems, including grazer-mediated shifts in grassland nitrogen cycle processes.

Faunal isotope records reveal trophic and nutrient dynamics in twentieth century Yellowstone grasslands

PubMed Central

Fox-Dobbs, Kena; Nelson, Abigail A.; Koch, Paul L.; Leonard, Jennifer A.

2012-01-01

Population sizes and movement patterns of ungulate grazers and their predators have fluctuated dramatically over the past few centuries, largely owing to overharvesting, land-use change and historic management. We used δ13C and δ15N values measured from bone collagen of historic and recent gray wolves and their potential primary prey from Yellowstone National Park to gain insight into the trophic dynamics and nutrient conditions of historic and modern grasslands. The diet of reintroduced wolves closely parallels that of the historic population. We suggest that a significant shift in faunal δ15N values over the past century reflects impacts of anthropogenic environmental changes on grassland ecosystems, including grazer-mediated shifts in grassland nitrogen cycle processes. PMID:22675135

Oscillations, neural computations and learning during wake and sleep.

PubMed

Penagos, Hector; Varela, Carmen; Wilson, Matthew A

2017-06-01

Learning and memory theories consider sleep and the reactivation of waking hippocampal neural patterns to be crucial for the long-term consolidation of memories. Here we propose that precisely coordinated representations across brain regions allow the inference and evaluation of causal relationships to train an internal generative model of the world. This training starts during wakefulness and strongly benefits from sleep because its recurring nested oscillations may reflect compositional operations that facilitate a hierarchical processing of information, potentially including behavioral policy evaluations. This suggests that an important function of sleep activity is to provide conditions conducive to general inference, prediction and insight, which contribute to a more robust internal model that underlies generalization and adaptive behavior. Copyright © 2017 Elsevier Ltd. All rights reserved.

Creative Cognition and Brain Network Dynamics

PubMed Central

Beaty, Roger E.; Benedek, Mathias; Silvia, Paul J.; Schacter, Daniel L.

2015-01-01

Creative thinking is central to the arts, sciences, and everyday life. How does the brain produce creative thought? A series of recently published papers has begun to provide insight into this question, reporting a strikingly similar pattern of brain activity and connectivity across a range of creative tasks and domains, from divergent thinking to poetry composition to musical improvisation. This research suggests that creative thought involves dynamic interactions of large-scale brain systems, with the most compelling finding being that the default and executive control networks, which can show an antagonistic relationship, actually cooperate during creative cognition and artistic performance. These findings have implications for understanding how brain networks interact to support complex cognitive processes, particularly those involving goal-directed, self-generated thought. PMID:26553223

Deciphering Neural Codes of Memory during Sleep

PubMed Central

Chen, Zhe; Wilson, Matthew A.

2017-01-01

Memories of experiences are stored in the cerebral cortex. Sleep is critical for consolidating hippocampal memory of wake experiences into the neocortex. Understanding representations of neural codes of hippocampal-neocortical networks during sleep would reveal important circuit mechanisms on memory consolidation, and provide novel insights into memory and dreams. Although sleep-associated ensemble spike activity has been investigated, identifying the content of memory in sleep remains challenging. Here, we revisit important experimental findings on sleep-associated memory (i.e., neural activity patterns in sleep that reflect memory processing) and review computational approaches for analyzing sleep-associated neural codes (SANC). We focus on two analysis paradigms for sleep-associated memory, and propose a new unsupervised learning framework (“memory first, meaning later”) for unbiased assessment of SANC. PMID:28390699

Trends in Karyotype Evolution in Astyanax (Teleostei, Characiformes, Characidae): Insights From Molecular Data

PubMed Central

Pazza, Rubens; Dergam, Jorge A.; Kavalco, Karine F.

2018-01-01

The study of patterns and evolutionary processes in neotropical fish is not always an easy task due the wide distribution of major fish groups in large and extensive river basins. Thus, it is not always possible to detect or correlate possible effects of chromosome rearrangements in the evolution of biodiversity. In the Astyanax genus, chromosome data obtained since the 1970s have shown evidence of cryptic species, karyotypic plasticity, supernumerary chromosomes, triploidies, and minor chromosomal rearrangements. In the present work, we map and discuss the main chromosomal events compatible with the molecular evolution of the genus Astyanax (Characiformes, Characidae) using mitochondrial DNA sequence data, in the search for major chromosome evolutionary trends within this taxon. PMID:29713335

Abiotic/biotic coupling in the rhizosphere: a reactive transport modeling analysis

USGS Publications Warehouse

Lawrence, Corey R.; Steefel, Carl; Maher, Kate

2014-01-01

A new generation of models is needed to adequately simulate patterns of soil biogeochemical cycling in response changing global environmental drivers. For example, predicting the influence of climate change on soil organic matter storage and stability requires models capable of addressing complex biotic/abiotic interactions of rhizosphere and weathering processes. Reactive transport modeling provides a powerful framework simulating these interactions and the resulting influence on soil physical and chemical characteristics. Incorporation of organic reactions in an existing reactive transport model framework has yielded novel insights into soil weathering and development but much more work is required to adequately capture root and microbial dynamics in the rhizosphere. This endeavor provides many advantages over traditional soil biogeochemical models but also many challenges.

Chronobiology of epilepsy: diagnostic and therapeutic implications of chrono-epileptology.

PubMed

Loddenkemper, Tobias; Lockley, Steven W; Kaleyias, Joseph; Kothare, Sanjeev V

2011-04-01

The combination of chronobiology and epilepsy offers novel diagnostic and therapeutic management options. Knowledge of the interactions between circadian periodicity, entrainment, sleep patterns, and epilepsy may provide additional diagnostic options beyond sleep deprivation and extended release medication formulations. It may also provide novel insights into the physiologic, biochemical, and genetic regulation processes of epilepsy and the circadian clock, rendering new treatment options. Temporal fluctuations of seizure susceptibility based on sleep homeostasis and circadian phase in selected epilepsies may provide predictability based on mathematical models. Chrono-epileptology offers opportunities for individualized patient-oriented treatment paradigms based on chrono-pharmacology, differential medication dosing, chrono-drug delivery systems, and utilization of "zeitgebers" such as chronobiotics or light-therapy and desynchronization strategies among others.

Space-Use Patterns of the Asiatic Wild Ass (Equus hemionus): Complementary Insights from Displacement, Recursion Movement and Habitat Selection Analyses.

PubMed

Giotto, Nina; Gerard, Jean-François; Ziv, Alon; Bouskila, Amos; Bar-David, Shirli

2015-01-01

The way in which animals move and use the landscape is influenced by the spatial distribution of resources, and is of importance when considering species conservation. We aimed at exploring how landscape-related factors affect a large herbivore's space-use patterns by using a combined approach, integrating movement (displacement and recursions) and habitat selection analyses. We studied the endangered Asiatic wild ass (Equus hemionus) in the Negev Desert, Israel, using GPS monitoring and direct observation. We found that the main landscape-related factors affecting the species' space-use patterns, on a daily and seasonal basis, were vegetation cover, water sources and topography. Two main habitat types were selected: high-elevation sites during the day (specific microclimate: windy on warm summer days) and streambed surroundings during the night (coupled with high vegetation when the animals were active in summer). Distribution of recursion times (duration between visits) revealed a 24-hour periodicity, a pattern that could be widespread among large herbivores. Characterizing frequently revisited sites suggested that recursion movements were mainly driven by a few landscape features (water sources, vegetation patches, high-elevation points), but also by social factors, such as territoriality, which should be further explored. This study provided complementary insights into the space-use patterns of E. hemionus. Understanding of the species' space-use patterns, at both large and fine spatial scale, is required for developing appropriate conservation protocols. Our approach could be further applied for studying the space-use patterns of other species in heterogeneous landscapes.

Space-Use Patterns of the Asiatic Wild Ass (Equus hemionus): Complementary Insights from Displacement, Recursion Movement and Habitat Selection Analyses

PubMed Central

Giotto, Nina; Gerard, Jean-François; Ziv, Alon; Bouskila, Amos; Bar-David, Shirli

2015-01-01

The way in which animals move and use the landscape is influenced by the spatial distribution of resources, and is of importance when considering species conservation. We aimed at exploring how landscape-related factors affect a large herbivore’s space-use patterns by using a combined approach, integrating movement (displacement and recursions) and habitat selection analyses. We studied the endangered Asiatic wild ass (Equus hemionus) in the Negev Desert, Israel, using GPS monitoring and direct observation. We found that the main landscape-related factors affecting the species’ space-use patterns, on a daily and seasonal basis, were vegetation cover, water sources and topography. Two main habitat types were selected: high-elevation sites during the day (specific microclimate: windy on warm summer days) and streambed surroundings during the night (coupled with high vegetation when the animals were active in summer). Distribution of recursion times (duration between visits) revealed a 24-hour periodicity, a pattern that could be widespread among large herbivores. Characterizing frequently revisited sites suggested that recursion movements were mainly driven by a few landscape features (water sources, vegetation patches, high-elevation points), but also by social factors, such as territoriality, which should be further explored. This study provided complementary insights into the space-use patterns of E. hemionus. Understanding of the species’ space-use patterns, at both large and fine spatial scale, is required for developing appropriate conservation protocols. Our approach could be further applied for studying the space-use patterns of other species in heterogeneous landscapes. PMID:26630393

Understanding Insight in the Context of Q

ERIC Educational Resources Information Center

Coghlan, David

2012-01-01

In Revans' learning formula, L = P + Q, Q represents "questioning insight", by which Revans means that insight comes out of the process of questioning programmed knowledge (P) in the light of experience. We typically focus on the content of an insight rather than on the act of insight. Drawing primarily on the work of Bernard Lonergan this paper…

G-jitter Effects on Transport and Pattern Formation

NASA Technical Reports Server (NTRS)

Schatz, Michael F.

2003-01-01

The research performed under this grant has led to an number of new insights into two general categories of fluid flows in the presence of time-dependent acceleration, as outlined briefly below. These results have been widely communicated in the scientific community through seven presentations at international conferences (4 invited, 3 contributed), five published papers (4 journal articles and 1 conference proceeding), and images from the research featured on the cover of all 2003 editions of the research journal, Nonlinearity. The work performed under this proposal also contained a substantial educational component by contributed significantly to the scientific training of one postdoctoral associate, one Ph.D. student and five undergraduate researchers. One main area of focus in this research was convective flow with time-dependent acceleration. Convection is one class of behavior that can arise from g-jitter effects. Our research focused on studies of Rayleigh-Benard system, which is an important model for understanding thermal convection; studies of this problem in the presence of acceleration modulations provided insight into the nature of g-jitter induced flow and of the effects of modulation and noise on non-equilibrium pattern formation. Our experiments on vertically vibrated Rayleigh-Benard convection demonstrated the existence of two classes of pure flow patterns (synchronous & subharmonic) patterns) that had long been predicted by theory but never before observed experimentally. Detailed studies of ranges of parameters where both classes of patterns exist simultaneously led to the discovery of a new type of patterns (called superlattices) in systems driven out of thermodynamic equilibrium.

Insights from Earth Sciences into Human Evolution studies: The example of prehistoric landscape use in Africa and the Levant

NASA Astrophysics Data System (ADS)

Devès, Maud H.; Reynolds, Sally; King, Geoffrey C. P.; Kuebler, Simon; Sturdy, Derek; Godet, Nan

2015-07-01

Fossil remains are embedded in a continually evolving landscape. Earth scientists have the methods and approaches to study the processes that shape the landscape at various temporal and spatial scales. Some of these methods can generate insights that are of potential use for researchers in other fields, such as archaeology and palaeoanthropology. Here we present two case studies to illustrate how a broader landscape perspective can provide new insights into the land use by Pliocene hominins in southern Africa, and more recently, by Palaeolithic hominins in the southern Levant. Key landscape attributes can help explain why humans, hominins and the wider animal community exploit certain types of landscapes in predictable ways. Our first case study examines how active tectonics or volcanism appears to be important in creating fertile regions with reliable water sources and complex topography. While relatively easy for agile primates such as hominins to negotiate, zones of complex topography are harder for certain predators and prey animals to traverse. In the second case study, we consider that differences in soil edaphics can exert a major control on animals by supplying or failing to supply necessary trace elements, such as selenium, copper, phosphate and potassium (Henkin et al., 1995). We show that the pattern of trace element distribution can accurately map animal movements between areas of suitable grazing. This predictability could have enabled Levantine humans to ambush megafauna during these seasonal migrations. By studying the landscape attributes around fossil site locations, Earth scientists can offer new insights and perspectives into the past, particularly on the ways in which the inhabitants would have used their landscapes.

Emerging Career Experiences: A Qualitative Exploration of the Career Patterns of Early Career Professionals Living in a Southeast United States Community

ERIC Educational Resources Information Center

Simmons, Steven F.

2013-01-01

The purpose of this qualitative study was to gain insight into the career patterns of early career professionals living in Aiken County, South Carolina. Two theoretical frameworks were selected for this study; Patton and McMahon's (1999) Career Development Systems Theory and Higgins and Kram's (2001) Developmental Network Theory. The researcher…

Precipitation thresholds and drought-induced tree die-off: Insights from patterns of Pinus edulis mortality along an environmental stress gradient

Treesearch

Michael J. Clifford; Patrick D. Royer; Neil S. Cobb; David D. Breshears; Paulette L. Ford

2013-01-01

Recent regional tree die-off events appear to have been triggered by a combination of drought and heat - referred to as 'global-change-type drought'. To complement experiments focused on resolving mechanisms of drought-induced tree mortality, an evaluation of how patterns of tree die-off relate to highly spatially variable precipitation is needed....

Female-Specific Intergenerational Transmission Patterns of the Human Corticolimbic Circuitry

PubMed Central

Yamagata, Bun; Murayama, Kou; Black, Jessica M.; Hancock, Roeland; Mimura, Masaru; Yang, Tony T.; Reiss, Allan L.

2016-01-01

Parents have large genetic and environmental influences on offspring's cognition, behavior, and brain. These intergenerational effects are observed in mood disorders, with particularly robust association in depression between mothers and daughters. No studies have thus far examined the neural bases of these intergenerational effects in humans. Corticolimbic circuitry is known to be highly relevant in a wide range of processes, including mood regulation and depression. These findings suggest that corticolimbic circuitry may also show matrilineal transmission patterns. Therefore, we examined human parent–offspring association in this neurocircuitry and investigated the degree of association in gray matter volume between parent and offspring. We used voxelwise correlation analysis in a total of 35 healthy families, consisting of parents and their biological offspring. We found positive associations of regional gray matter volume in the corticolimbic circuit, including the amygdala, hippocampus, anterior cingulate cortex, and ventromedial prefrontal cortex between biological mothers and daughters. This association was significantly greater than mother–son, father–daughter, and father–son associations. The current study suggests that the corticolimbic circuitry, which has been implicated in mood regulation, shows a matrilineal-specific transmission patterns. Our preliminary findings are consistent with what has been found behaviorally in depression and may have clinical implications for disorders known to have dysfunction in mood regulation such as depression. Studies such as ours will likely bridge animal work examining gene expression in the brains and clinical symptom-based observations and provide promising ways to investigate intergenerational transmission patterns in the human brain. SIGNIFICANCE STATEMENT Parents have large genetic and environmental influences on the offspring, known as intergenerational effects. Specifically, depression has been shown to exhibit strong matrilineal transmission patterns. Although intergenerational transmission patterns in the human brain are virtually unknown, this would suggest that the corticolimbic circuitry relevant to a wide range of processes including mood regulation may also show matrilineal transmission patterns. Therefore, we examined the degree of association in corticolimbic gray matter volume (GMV) between parent and offspring in 35 healthy families. We found that positive correlations in maternal corticolimbic GMV with daughters were significantly greater than other parent–offspring dyads. Our findings provide new insight into the potential neuroanatomical basis of circuit-based female-specific intergenerational transmission patterns in depression. PMID:26818513

Spatiotemporal Patterns, Monitoring Network Design, and Environmental Justice of Air Pollution in the Phoenix Metropolitan Region: A Landscape Approach

NASA Astrophysics Data System (ADS)

Pope, Ronald L.

Air pollution is a serious problem in most urban areas around the world, which has a number of negative ecological and human health impacts. As a result, it's vitally important to detect and characterize air pollutants to protect the health of the urban environment and our citizens. An important early step in this process is ensuring that the air pollution monitoring network is properly designed to capture the patterns of pollution and that all social demographics in the urban population are represented. An important aspect in characterizing air pollution patterns is scale in space and time which, along with pattern and process relationships, is a key subject in the field of landscape ecology. Thus, using multiple landscape ecological methods, this dissertation research begins by characterizing and quantifying the multi-scalar patterns of ozone (O3) and particulate matter (PM10) in the Phoenix, Arizona, metropolitan region. Results showed that pollution patterns are scale-dependent, O3 is a regionally-scaled pollutant at longer temporal scales, and PM10 is a locally-scaled pollutant with patterns sensitive to season. Next, this dissertation examines the monitoring network within Maricopa County. Using a novel multiscale indicator-based approach, the adequacy of the network was quantified by integrating inputs from various academic and government stakeholders. Furthermore, deficiencies were spatially defined and recommendations were made on how to strengthen the design of the network. A sustainability ranking system also provided new insight into the strengths and weaknesses of the network. Lastly, the study addresses the question of whether distinct social groups were experiencing inequitable exposure to pollutants - a key issue of distributive environmental injustice. A novel interdisciplinary method using multi-scalar ambient pollution data and hierarchical multiple regression models revealed environmental inequities between air pollutants and race, ethnicity, age, and socioeconomic classes. The results indicate that changing the scale of the analysis can change the equitable relationship between pollution and demographics. The scientific findings of the scale-dependent relationships among air pollution patterns, network design, and population demographics, brought to light through this study, can help policymakers make informed decisions for protecting the human health and the urban environment in the Phoenix metropolitan region and beyond.

From Darwin's Origin of Species toward a theory of natural history.

PubMed

Boero, Ferdinando

2015-01-01

Darwin is the father of evolutionary theory because he identified evolutionary patterns and, with Natural Selection, he ascertained the exquisitely ecological ultimate processes that lead to evolution. The proximate processes of evolution he proposed, however, predated the discovery of genetics, the backbone of modern evolutionary theory. The later discovery of the laws of inheritance by Mendel and the rediscovery of Mendel in the early 20th century led to two reforms of Darwinism: Neo-Darwinism and the Modern Synthesis (and subsequent refinements). If Darwin's evolutionary thought required much refinement, his ecological insight is still very modern. In the first edition of The Origin of Species, Darwin did not use either the word "evolution" or the word "ecology". "Ecology" was not coined until after the publication of the Origin. Evolution, for him, was the origin of varieties, then species, which he referred to as well-marked varieties, whereas, instead of using ecology, he used "the economy of nature". The Origin contains a high proportion of currently accepted ecological principles. Darwin labelled himself a naturalist. His discipline (natural history) was a blend of ecology and evolution in which he investigated both the patterns and the processes that determine the organization of life. Reductionist approaches, however, often keep the two disciplines separated from each other, undermining a full understanding of natural phenomena that might be favored by blending ecology and evolution through the development of a modern Theory of Natural History based on Darwin's vision of the study of life.

Insights into mortality patterns and causes of death through a process point of view model.

PubMed

Anderson, James J; Li, Ting; Sharrow, David J

2017-02-01

Process point of view (POV) models of mortality, such as the Strehler-Mildvan and stochastic vitality models, represent death in terms of the loss of survival capacity through challenges and dissipation. Drawing on hallmarks of aging, we link these concepts to candidate biological mechanisms through a framework that defines death as challenges to vitality where distal factors defined the age-evolution of vitality and proximal factors define the probability distribution of challenges. To illustrate the process POV, we hypothesize that the immune system is a mortality nexus, characterized by two vitality streams: increasing vitality representing immune system development and immunosenescence representing vitality dissipation. Proximal challenges define three mortality partitions: juvenile and adult extrinsic mortalities and intrinsic adult mortality. Model parameters, generated from Swedish mortality data (1751-2010), exhibit biologically meaningful correspondences to economic, health and cause-of-death patterns. The model characterizes the twentieth century epidemiological transition mainly as a reduction in extrinsic mortality resulting from a shift from high magnitude disease challenges on individuals at all vitality levels to low magnitude stress challenges on low vitality individuals. Of secondary importance, intrinsic mortality was described by a gradual reduction in the rate of loss of vitality presumably resulting from reduction in the rate of immunosenescence. Extensions and limitations of a distal/proximal framework for characterizing more explicit causes of death, e.g. the young adult mortality hump or cancer in old age are discussed.

Insights into mortality patterns and causes of death through a process point of view model

PubMed Central

Anderson, James J.; Li, Ting; Sharrow, David J.

2016-01-01

Process point of view models of mortality, such as the Strehler-Mildvan and stochastic vitality models, represent death in terms of the loss of survival capacity through challenges and dissipation. Drawing on hallmarks of aging, we link these concepts to candidate biological mechanisms through a framework that defines death as challenges to vitality where distal factors defined the age-evolution of vitality and proximal factors define the probability distribution of challenges. To illustrate the process point of view, we hypothesize that the immune system is a mortality nexus, characterized by two vitality streams: increasing vitality representing immune system development and immunosenescence representing vitality dissipation. Proximal challenges define three mortality partitions: juvenile and adult extrinsic mortalities and intrinsic adult mortality. Model parameters, generated from Swedish mortality data (1751-2010), exhibit biologically meaningful correspondences to economic, health and cause-of-death patterns. The model characterizes the 20th century epidemiological transition mainly as a reduction in extrinsic mortality resulting from a shift from high magnitude disease challenges on individuals at all vitality levels to low magnitude stress challenges on low vitality individuals. Of secondary importance, intrinsic mortality was described by a gradual reduction in the rate of loss of vitality presumably resulting from reduction in the rate of immunosenescence. Extensions and limitations of a distal/proximal framework for characterizing more explicit causes of death, e.g. the young adult mortality hump or cancer in old age are discussed. PMID:27885527

Estimating replicate time shifts using Gaussian process regression

PubMed Central

Liu, Qiang; Andersen, Bogi; Smyth, Padhraic; Ihler, Alexander

2010-01-01

Motivation: Time-course gene expression datasets provide important insights into dynamic aspects of biological processes, such as circadian rhythms, cell cycle and organ development. In a typical microarray time-course experiment, measurements are obtained at each time point from multiple replicate samples. Accurately recovering the gene expression patterns from experimental observations is made challenging by both measurement noise and variation among replicates' rates of development. Prior work on this topic has focused on inference of expression patterns assuming that the replicate times are synchronized. We develop a statistical approach that simultaneously infers both (i) the underlying (hidden) expression profile for each gene, as well as (ii) the biological time for each individual replicate. Our approach is based on Gaussian process regression (GPR) combined with a probabilistic model that accounts for uncertainty about the biological development time of each replicate. Results: We apply GPR with uncertain measurement times to a microarray dataset of mRNA expression for the hair-growth cycle in mouse back skin, predicting both profile shapes and biological times for each replicate. The predicted time shifts show high consistency with independently obtained morphological estimates of relative development. We also show that the method systematically reduces prediction error on out-of-sample data, significantly reducing the mean squared error in a cross-validation study. Availability: Matlab code for GPR with uncertain time shifts is available at http://sli.ics.uci.edu/Code/GPRTimeshift/ Contact: ihler@ics.uci.edu PMID:20147305

Resource Use in Small Island States: Material Flows in Iceland and Trinidad and Tobago, 1961-2008.

PubMed

Krausmann, Fridolin; Richter, Regina; Eisenmenger, Nina

2014-04-01

Iceland and Trinidad and Tobago are small open, high-income island economies with very specific resource-use patterns. This article presents a material flow analysis (MFA) for the two countries covering a time period of nearly five decades. Both countries have a narrow domestic resource base, their economy being largely based on the exploitation of one or two key resources for export production. In the case of Trinidad and Tobago, the physical economy is dominated by oil and natural gas extraction and petrochemical industries, whereas Iceland's economy for centuries has been based on fisheries. More recently, abundant hydropower and geothermal heat were the basis for the establishment of large export-oriented metal processing industries, which fully depend on imported raw materials and make use of domestic renewable electricity. Both countries are highly dependent on these natural resources and vulnerable to overexploitation and price developments. We show how the export-oriented industries lead to high and growing levels of per capita material and energy use and carbon dioxide emissions resulting from large amounts of processing wastes and energy consumption in production processes. The example of small open economies with an industrial production system focused on few, but abundant, key resources and of comparatively low complexity provides interesting insights of how resource endowment paired with availability or absence of infrastructure and specific institutional arrangements drives domestic resource-use patterns. This also contributes to a better understanding and interpretation of MFA indicators, such as domestic material consumption.

Resource Use in Small Island States

PubMed Central

Krausmann, Fridolin; Richter, Regina; Eisenmenger, Nina

2014-01-01

Iceland and Trinidad and Tobago are small open, high-income island economies with very specific resource-use patterns. This article presents a material flow analysis (MFA) for the two countries covering a time period of nearly five decades. Both countries have a narrow domestic resource base, their economy being largely based on the exploitation of one or two key resources for export production. In the case of Trinidad and Tobago, the physical economy is dominated by oil and natural gas extraction and petrochemical industries, whereas Iceland's economy for centuries has been based on fisheries. More recently, abundant hydropower and geothermal heat were the basis for the establishment of large export-oriented metal processing industries, which fully depend on imported raw materials and make use of domestic renewable electricity. Both countries are highly dependent on these natural resources and vulnerable to overexploitation and price developments. We show how the export-oriented industries lead to high and growing levels of per capita material and energy use and carbon dioxide emissions resulting from large amounts of processing wastes and energy consumption in production processes. The example of small open economies with an industrial production system focused on few, but abundant, key resources and of comparatively low complexity provides interesting insights of how resource endowment paired with availability or absence of infrastructure and specific institutional arrangements drives domestic resource-use patterns. This also contributes to a better understanding and interpretation of MFA indicators, such as domestic material consumption. PMID:25505367

Phagocyte dynamics in a highly regenerative urochordate: insights into development and host defense.

PubMed

Lauzon, Robert J; Brown, Christina; Kerr, Louie; Tiozzo, Stefano

2013-02-15

Phagocytosis is a cellular process by which particles and foreign bodies are engulfed and degraded by specialized cells. It is functionally involved in nutrient acquisition and represents a fundamental mechanism used to remove pathogens and cellular debris. In the marine invertebrate chordate Botryllus schlosseri, cell corpse engulfment by phagocytic cells is the recurrent mechanism of programmed cell clearance and a critical process for the successful execution of asexual regeneration and colony homeostasis. In the present study, we have utilized a naturally occurring process of vascular parabiosis coupled with intravascular microinjection of fluorescent bioparticles and liposomes as tools to investigate the dynamics of phagocyte behavior in real-time during cyclical body regeneration. Our findings indicate that B. schlosseri harbors two major populations of post-mitotic phagocytes, which display distinct phagocytic specificity and homing patterns: a static population that lines the circulatory system epithelia, and a mobile population that continuously recirculates throughout the colony and exhibits a characteristic homing pattern within mesenchymal niches called ventral islands (VI). We observed that a significant proportion of ventral island phagocytes (VIP) die and are engulfed by other VIP following takeover. Selective impairment of VIP activity curtailed zooid resorption and asexual development. Together, these findings strongly suggest that ventral islands are sites of phagocyte homing and turnover. As botryllid ascidians represent invertebrate chordates capable of whole body regeneration in a non-embryonic scenario, we discuss the pivotal role that phagocytosis plays in homeostasis, tissue renewal and host defense. Copyright © 2012 Elsevier Inc. All rights reserved.

Insight and analysis problem solving in microbes to machines.

PubMed

Clark, Kevin B

2015-11-01

A key feature for obtaining solutions to difficult problems, insight is oftentimes vaguely regarded as a special discontinuous intellectual process and/or a cognitive restructuring of problem representation or goal approach. However, this nearly century-old state of art devised by the Gestalt tradition to explain the non-analytical or non-trial-and-error, goal-seeking aptitude of primate mentality tends to neglect problem-solving capabilities of lower animal phyla, Kingdoms other than Animalia, and advancing smart computational technologies built from biological, artificial, and composite media. Attempting to provide an inclusive, precise definition of insight, two major criteria of insight, discontinuous processing and problem restructuring, are here reframed using terminology and statistical mechanical properties of computational complexity classes. Discontinuous processing becomes abrupt state transitions in algorithmic/heuristic outcomes or in types of algorithms/heuristics executed by agents using classical and/or quantum computational models. And problem restructuring becomes combinatorial reorganization of resources, problem-type substitution, and/or exchange of computational models. With insight bounded by computational complexity, humans, ciliated protozoa, and complex technological networks, for example, show insight when restructuring time requirements, combinatorial complexity, and problem type to solve polynomial and nondeterministic polynomial decision problems. Similar effects are expected from other problem types, supporting the idea that insight might be an epiphenomenon of analytical problem solving and consequently a larger information processing framework. Thus, this computational complexity definition of insight improves the power, external and internal validity, and reliability of operational parameters with which to classify, investigate, and produce the phenomenon for computational agents ranging from microbes to man-made devices. Copyright © 2015 Elsevier Ltd. All rights reserved.

Using population genetic analyses to understand seed dispersal patterns

NASA Astrophysics Data System (ADS)

Hamrick, J. L.; Trapnell, Dorset W.

2011-11-01

Neutral genetic markers have been employed in several ways to understand seed dispersal patterns in natural and human modified landscapes. Genetic differentiation among spatially separated populations, using biparentally and maternally inherited genetic markers, allows determination of the relative historical effectiveness of pollen and seed dispersal. Genetic relatedness among individuals, estimated as a function of spatial separation between pairs of individuals, has also been used to indirectly infer seed dispersal distances. Patterns of genetic relatedness among plants in recently colonized populations provide insights into the role of seed dispersal in population colonization and expansion. High genetic relatedness within expanding populations indicates original colonization by a few individuals and population expansion by the recruitment of the original colonists' progeny; low relatedness should occur if population growth results primarily from continuous seed immigration from multiple sources. Parentage analysis procedures can identify maternal parents of dispersed fruits, seeds, or seedlings providing detailed descriptions of contemporary seed dispersal patterns. With standard parent-pair analyses of seeds or seedlings, problems can arise in distinguishing the maternal parent. However, the use of maternal DNA from dispersed fruits or seed coats allows direct identification of maternal individuals and, as a consequence, the distance and patterns of seed dispersal and deposition. Application of combinations of these approaches provides additional insights into the role seed dispersal plays in the genetic connectivity between populations in natural and disturbed landscapes.

Investigation of Optimal Digital Image Correlation Patterns for Deformation Measurement

NASA Technical Reports Server (NTRS)

Bomarito, G. F.; Ruggles, T. J.; Hochhalter, J. D.; Cannon, A. H.

2016-01-01

Digital image correlation (DIC) relies on the surface texture of a specimen to measure deformation. When the specimen itself has little or no texture, a pattern is applied to the surface which deforms with the specimen and acts as an artificial surface texture. Because the applied pattern has an effect on the accuracy of DIC, an ideal pattern is sought for which the error introduced into DIC measurements is minimal. In this work, a study is performed in which several DIC pattern quality metrics from the literature are correlated to DIC measurement error. The resulting correlations give insight on the optimality of DIC patterns in general. Optimizations are then performed to produce patterns which are well suited for DIC. These patterns are tested to show their relative benefits. Chief among these benefits are a reduction in error of approximately 30 with respect to a randomly generated pattern.