The Paradox of the Diffusion of Innovations Research: Creating More Communication Bottlenecks Than Breaking Them.

ERIC Educational Resources Information Center

Melkote, Srinivas R.; Babbili, Anantha S.

The paradox of the diffusion of innovations research is that in its efforts to find ways and means of breaking the communication constraint in Third World countries, it has generated many bottlenecks that cumulatively constitute the major constraint: lack of an efficient system for delivering adequate and reliable information, knowledge, and…

On the importance of Task 1 and error performance measures in PRP dual-task studies.

PubMed

Strobach, Tilo; Schütz, Anja; Schubert, Torsten

2015-01-01

The psychological refractory period (PRP) paradigm is a dominant research tool in the literature on dual-task performance. In this paradigm a first and second component task (i.e., Task 1 and Task 2) are presented with variable stimulus onset asynchronies (SOAs) and priority to perform Task 1. The main indicator of dual-task impairment in PRP situations is an increasing Task 2-RT with decreasing SOAs. This impairment is typically explained with some task components being processed strictly sequentially in the context of the prominent central bottleneck theory. This assumption could implicitly suggest that processes of Task 1 are unaffected by Task 2 and bottleneck processing, i.e., decreasing SOAs do not increase reaction times (RTs) and error rates of the first task. The aim of the present review is to assess whether PRP dual-task studies included both RT and error data presentations and statistical analyses and whether studies including both data types (i.e., RTs and error rates) show data consistent with this assumption (i.e., decreasing SOAs and unaffected RTs and/or error rates in Task 1). This review demonstrates that, in contrast to RT presentations and analyses, error data is underrepresented in a substantial number of studies. Furthermore, a substantial number of studies with RT and error data showed a statistically significant impairment of Task 1 performance with decreasing SOA. Thus, these studies produced data that is not primarily consistent with the strong assumption that processes of Task 1 are unaffected by Task 2 and bottleneck processing in the context of PRP dual-task situations; this calls for a more careful report and analysis of Task 1 performance in PRP studies and for a more careful consideration of theories proposing additions to the bottleneck assumption, which are sufficiently general to explain Task 1 and Task 2 effects.

On the importance of Task 1 and error performance measures in PRP dual-task studies

PubMed Central

Strobach, Tilo; Schütz, Anja; Schubert, Torsten

2015-01-01

The psychological refractory period (PRP) paradigm is a dominant research tool in the literature on dual-task performance. In this paradigm a first and second component task (i.e., Task 1 and Task 2) are presented with variable stimulus onset asynchronies (SOAs) and priority to perform Task 1. The main indicator of dual-task impairment in PRP situations is an increasing Task 2-RT with decreasing SOAs. This impairment is typically explained with some task components being processed strictly sequentially in the context of the prominent central bottleneck theory. This assumption could implicitly suggest that processes of Task 1 are unaffected by Task 2 and bottleneck processing, i.e., decreasing SOAs do not increase reaction times (RTs) and error rates of the first task. The aim of the present review is to assess whether PRP dual-task studies included both RT and error data presentations and statistical analyses and whether studies including both data types (i.e., RTs and error rates) show data consistent with this assumption (i.e., decreasing SOAs and unaffected RTs and/or error rates in Task 1). This review demonstrates that, in contrast to RT presentations and analyses, error data is underrepresented in a substantial number of studies. Furthermore, a substantial number of studies with RT and error data showed a statistically significant impairment of Task 1 performance with decreasing SOA. Thus, these studies produced data that is not primarily consistent with the strong assumption that processes of Task 1 are unaffected by Task 2 and bottleneck processing in the context of PRP dual-task situations; this calls for a more careful report and analysis of Task 1 performance in PRP studies and for a more careful consideration of theories proposing additions to the bottleneck assumption, which are sufficiently general to explain Task 1 and Task 2 effects. PMID:25904890

Scaling up quality care for mothers and newborns around the time of birth: an overview of methods and analyses of intervention-specific bottlenecks and solutions.

PubMed

Dickson, Kim E; Kinney, Mary V; Moxon, Sarah G; Ashton, Joanne; Zaka, Nabila; Simen-Kapeu, Aline; Sharma, Gaurav; Kerber, Kate J; Daelmans, Bernadette; Gülmezoglu, A; Mathai, Matthews; Nyange, Christabel; Baye, Martina; Lawn, Joy E

2015-01-01

The Every Newborn Action Plan (ENAP) and Ending Preventable Maternal Mortality targets cannot be achieved without high quality, equitable coverage of interventions at and around the time of birth. This paper provides an overview of the methodology and findings of a nine paper series of in-depth analyses which focus on the specific challenges to scaling up high-impact interventions and improving quality of care for mothers and newborns around the time of birth, including babies born small and sick. The bottleneck analysis tool was applied in 12 countries in Africa and Asia as part of the ENAP process. Country workshops engaged technical experts to complete a tool designed to synthesise "bottlenecks" hindering the scale up of maternal-newborn intervention packages across seven health system building blocks. We used quantitative and qualitative methods and literature review to analyse the data and present priority actions relevant to different health system building blocks for skilled birth attendance, emergency obstetric care, antenatal corticosteroids (ACS), basic newborn care, kangaroo mother care (KMC), treatment of neonatal infections and inpatient care of small and sick newborns. The 12 countries included in our analysis account for the majority of global maternal (48%) and newborn (58%) deaths and stillbirths (57%). Our findings confirm previously published results that the interventions with the most perceived bottlenecks are facility-based where rapid emergency care is needed, notably inpatient care of small and sick newborns, ACS, treatment of neonatal infections and KMC. Health systems building blocks with the highest rated bottlenecks varied for different interventions. Attention needs to be paid to the context specific bottlenecks for each intervention to scale up quality care. Crosscutting findings on health information gaps inform two final papers on a roadmap for improvement of coverage data for newborns and indicate the need for leadership for effective audit systems. Achieving the Sustainable Development Goal targets for ending preventable mortality and provision of universal health coverage will require large-scale approaches to improving quality of care. These analyses inform the development of systematic, targeted approaches to strengthening of health systems, with a focus on overcoming specific bottlenecks for the highest impact interventions.

Scaling up quality care for mothers and newborns around the time of birth: an overview of methods and analyses of intervention-specific bottlenecks and solutions

PubMed Central

2015-01-01

Background The Every Newborn Action Plan (ENAP) and Ending Preventable Maternal Mortality targets cannot be achieved without high quality, equitable coverage of interventions at and around the time of birth. This paper provides an overview of the methodology and findings of a nine paper series of in-depth analyses which focus on the specific challenges to scaling up high-impact interventions and improving quality of care for mothers and newborns around the time of birth, including babies born small and sick. Methods The bottleneck analysis tool was applied in 12 countries in Africa and Asia as part of the ENAP process. Country workshops engaged technical experts to complete a tool designed to synthesise "bottlenecks" hindering the scale up of maternal-newborn intervention packages across seven health system building blocks. We used quantitative and qualitative methods and literature review to analyse the data and present priority actions relevant to different health system building blocks for skilled birth attendance, emergency obstetric care, antenatal corticosteroids (ACS), basic newborn care, kangaroo mother care (KMC), treatment of neonatal infections and inpatient care of small and sick newborns. Results The 12 countries included in our analysis account for the majority of global maternal (48%) and newborn (58%) deaths and stillbirths (57%). Our findings confirm previously published results that the interventions with the most perceived bottlenecks are facility-based where rapid emergency care is needed, notably inpatient care of small and sick newborns, ACS, treatment of neonatal infections and KMC. Health systems building blocks with the highest rated bottlenecks varied for different interventions. Attention needs to be paid to the context specific bottlenecks for each intervention to scale up quality care. Crosscutting findings on health information gaps inform two final papers on a roadmap for improvement of coverage data for newborns and indicate the need for leadership for effective audit systems. Conclusions Achieving the Sustainable Development Goal targets for ending preventable mortality and provision of universal health coverage will require large-scale approaches to improving quality of care. These analyses inform the development of systematic, targeted approaches to strengthening of health systems, with a focus on overcoming specific bottlenecks for the highest impact interventions. PMID:26390820

Self-organized phenomena of pedestrian counterflow through a wide bottleneck in a channel

NASA Astrophysics Data System (ADS)

Dong, Li-Yun; Lan, Dong-Kai; Li, Xiang

2016-09-01

The pedestrian counterflow through a bottleneck in a channel shows a variety of flow patterns due to self-organization. In order to reveal the underlying mechanism, a cellular automaton model was proposed by incorporating the floor field and the view field which reflects the global information of the studied area and local interactions with others. The presented model can well reproduce typical collective behaviors, such as lane formation. Numerical simulations were performed in the case of a wide bottleneck and typical flow patterns at different density ranges were identified as rarefied flow, laminar flow, interrupted bidirectional flow, oscillatory flow, intermittent flow, and choked flow. The effects of several parameters, such as the size of view field and the width of opening, on the bottleneck flow are also analyzed in detail. The view field plays a vital role in reproducing self-organized phenomena of pedestrian. Numerical results showed that the presented model can capture key characteristics of bottleneck flows. Project supported by the National Basic Research Program of China (Grant No. 2012CB725404) and the National Natural Science Foundation of China (Grant Nos. 11172164 and 11572184).

Antenatal corticosteroids for management of preterm birth: a multi-country analysis of health system bottlenecks and potential solutions

PubMed Central

2015-01-01

Background Preterm birth complications are the leading cause of deaths for children under five years. Antenatal corticosteroids (ACS) are effective at reducing mortality and serious morbidity amongst infants born at <34 weeks gestation. WHO guidelines strongly recommend use of ACS for women at risk of imminent preterm birth where gestational age, imminent preterm birth, and risk of maternal infection can be assessed, and appropriate maternal/newborn care provided. However, coverage remains low in high-burden countries for reasons not previously systematically investigated. Methods The bottleneck analysis tool was applied in 12 countries in Africa and Asia as part of the Every Newborn Action Plan process. Country workshops involved technical experts to complete the survey tool, which is designed to synthesise and grade health system "bottlenecks", factors that hinder the scale up, of maternal-newborn intervention packages. We used quantitative and qualitative methods to analyse the bottleneck data, combined with literature review, to present priority bottlenecks and actions relevant to different health system building blocks for ACS. Results Eleven out of twelve countries provided data in response to the ACS questionnaire. Health system building blocks most frequently reported as having significant or very major bottlenecks were health information systems (11 countries), essential medical products and technologies (9 out of 11 countries) and health service delivery (9 out of 11 countries). Bottlenecks included absence of coverage data, poor gestational age metrics, lack of national essential medicines listing, discrepancies between prescribing authority and provider cadres managing care, delays due to referral, and lack of supervision, mentoring and quality improvement systems. Conclusions Analysis centred on health system building blocks in which 9 or more countries (>75%) reported very major or significant bottlenecks. Health information systems should include improved gestational age assessment and track ACS coverage, use and outcomes. Better health service delivery requires clarified policy assigning roles by level of care and cadre of provider, dependent on capability to assess gestational age and risk of preterm birth, and the implementation of guidelines with adequate supervision, mentoring and quality improvement systems, including audit and feedback. National essential medicines lists should include dexamethasone for antenatal use, and dexamethasone should be integrated into supply logistics. PMID:26390927

An analysis of the influence of deep neural network (DNN) topology in bottleneck feature based language recognition.

PubMed

Lozano-Diez, Alicia; Zazo, Ruben; Toledano, Doroteo T; Gonzalez-Rodriguez, Joaquin

2017-01-01

Language recognition systems based on bottleneck features have recently become the state-of-the-art in this research field, showing its success in the last Language Recognition Evaluation (LRE 2015) organized by NIST (U.S. National Institute of Standards and Technology). This type of system is based on a deep neural network (DNN) trained to discriminate between phonetic units, i.e. trained for the task of automatic speech recognition (ASR). This DNN aims to compress information in one of its layers, known as bottleneck (BN) layer, which is used to obtain a new frame representation of the audio signal. This representation has been proven to be useful for the task of language identification (LID). Thus, bottleneck features are used as input to the language recognition system, instead of a classical parameterization of the signal based on cepstral feature vectors such as MFCCs (Mel Frequency Cepstral Coefficients). Despite the success of this approach in language recognition, there is a lack of studies analyzing in a systematic way how the topology of the DNN influences the performance of bottleneck feature-based language recognition systems. In this work, we try to fill-in this gap, analyzing language recognition results with different topologies for the DNN used to extract the bottleneck features, comparing them and against a reference system based on a more classical cepstral representation of the input signal with a total variability model. This way, we obtain useful knowledge about how the DNN configuration influences bottleneck feature-based language recognition systems performance.

Parallel Implementation of MAFFT on CUDA-Enabled Graphics Hardware.

PubMed

Zhu, Xiangyuan; Li, Kenli; Salah, Ahmad; Shi, Lin; Li, Keqin

2015-01-01

Multiple sequence alignment (MSA) constitutes an extremely powerful tool for many biological applications including phylogenetic tree estimation, secondary structure prediction, and critical residue identification. However, aligning large biological sequences with popular tools such as MAFFT requires long runtimes on sequential architectures. Due to the ever increasing sizes of sequence databases, there is increasing demand to accelerate this task. In this paper, we demonstrate how graphic processing units (GPUs), powered by the compute unified device architecture (CUDA), can be used as an efficient computational platform to accelerate the MAFFT algorithm. To fully exploit the GPU's capabilities for accelerating MAFFT, we have optimized the sequence data organization to eliminate the bandwidth bottleneck of memory access, designed a memory allocation and reuse strategy to make full use of limited memory of GPUs, proposed a new modified-run-length encoding (MRLE) scheme to reduce memory consumption, and used high-performance shared memory to speed up I/O operations. Our implementation tested in three NVIDIA GPUs achieves speedup up to 11.28 on a Tesla K20m GPU compared to the sequential MAFFT 7.015.

The information science of microbial ecology.

PubMed

Hahn, Aria S; Konwar, Kishori M; Louca, Stilianos; Hanson, Niels W; Hallam, Steven J

2016-06-01

A revolution is unfolding in microbial ecology where petabytes of 'multi-omics' data are produced using next generation sequencing and mass spectrometry platforms. This cornucopia of biological information has enormous potential to reveal the hidden metabolic powers of microbial communities in natural and engineered ecosystems. However, to realize this potential, the development of new technologies and interpretative frameworks grounded in ecological design principles are needed to overcome computational and analytical bottlenecks. Here we explore the relationship between microbial ecology and information science in the era of cloud-based computation. We consider microorganisms as individual information processing units implementing a distributed metabolic algorithm and describe developments in ecoinformatics and ubiquitous computing with the potential to eliminate bottlenecks and empower knowledge creation and translation. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

Fixation times in differentiation and evolution in the presence of bottlenecks, deserts, and oases.

PubMed

Chou, Tom; Wang, Yu

2015-05-07

Cellular differentiation and evolution are stochastic processes that can involve multiple types (or states) of particles moving on a complex, high-dimensional state-space or "fitness" landscape. Cells of each specific type can thus be quantified by their population at a corresponding node within a network of states. Their dynamics across the state-space network involve genotypic or phenotypic transitions that can occur upon cell division, such as during symmetric or asymmetric cell differentiation, or upon spontaneous mutation. Here, we use a general multi-type branching processes to study first passage time statistics for a single cell to appear in a specific state. Our approach readily allows for nonexponentially distributed waiting times between transitions, reflecting, e.g., the cell cycle. For simplicity, we restrict most of our detailed analysis to exponentially distributed waiting times (Poisson processes). We present results for a sequential evolutionary process in which L successive transitions propel a population from a "wild-type" state to a given "terminally differentiated," "resistant," or "cancerous" state. Analytic and numeric results are also found for first passage times across an evolutionary chain containing a node with increased death or proliferation rate, representing a desert/bottleneck or an oasis. Processes involving cell proliferation are shown to be "nonlinear" (even though mean-field equations for the expected particle numbers are linear) resulting in first passage time statistics that depend on the position of the bottleneck or oasis. Our results highlight the sensitivity of stochastic measures to cell division fate and quantify the limitations of using certain approximations (such as the fixed-population and mean-field assumptions) in evaluating fixation times. Published by Elsevier Ltd.

Optimized distributed systems achieve significant performance improvement on sorted merging of massive VCF files.

PubMed

Sun, Xiaobo; Gao, Jingjing; Jin, Peng; Eng, Celeste; Burchard, Esteban G; Beaty, Terri H; Ruczinski, Ingo; Mathias, Rasika A; Barnes, Kathleen; Wang, Fusheng; Qin, Zhaohui S

2018-06-01

Sorted merging of genomic data is a common data operation necessary in many sequencing-based studies. It involves sorting and merging genomic data from different subjects by their genomic locations. In particular, merging a large number of variant call format (VCF) files is frequently required in large-scale whole-genome sequencing or whole-exome sequencing projects. Traditional single-machine based methods become increasingly inefficient when processing large numbers of files due to the excessive computation time and Input/Output bottleneck. Distributed systems and more recent cloud-based systems offer an attractive solution. However, carefully designed and optimized workflow patterns and execution plans (schemas) are required to take full advantage of the increased computing power while overcoming bottlenecks to achieve high performance. In this study, we custom-design optimized schemas for three Apache big data platforms, Hadoop (MapReduce), HBase, and Spark, to perform sorted merging of a large number of VCF files. These schemas all adopt the divide-and-conquer strategy to split the merging job into sequential phases/stages consisting of subtasks that are conquered in an ordered, parallel, and bottleneck-free way. In two illustrating examples, we test the performance of our schemas on merging multiple VCF files into either a single TPED or a single VCF file, which are benchmarked with the traditional single/parallel multiway-merge methods, message passing interface (MPI)-based high-performance computing (HPC) implementation, and the popular VCFTools. Our experiments suggest all three schemas either deliver a significant improvement in efficiency or render much better strong and weak scalabilities over traditional methods. Our findings provide generalized scalable schemas for performing sorted merging on genetics and genomics data using these Apache distributed systems.

Optimized distributed systems achieve significant performance improvement on sorted merging of massive VCF files

PubMed Central

Gao, Jingjing; Jin, Peng; Eng, Celeste; Burchard, Esteban G; Beaty, Terri H; Ruczinski, Ingo; Mathias, Rasika A; Barnes, Kathleen; Wang, Fusheng

2018-01-01

Abstract Background Sorted merging of genomic data is a common data operation necessary in many sequencing-based studies. It involves sorting and merging genomic data from different subjects by their genomic locations. In particular, merging a large number of variant call format (VCF) files is frequently required in large-scale whole-genome sequencing or whole-exome sequencing projects. Traditional single-machine based methods become increasingly inefficient when processing large numbers of files due to the excessive computation time and Input/Output bottleneck. Distributed systems and more recent cloud-based systems offer an attractive solution. However, carefully designed and optimized workflow patterns and execution plans (schemas) are required to take full advantage of the increased computing power while overcoming bottlenecks to achieve high performance. Findings In this study, we custom-design optimized schemas for three Apache big data platforms, Hadoop (MapReduce), HBase, and Spark, to perform sorted merging of a large number of VCF files. These schemas all adopt the divide-and-conquer strategy to split the merging job into sequential phases/stages consisting of subtasks that are conquered in an ordered, parallel, and bottleneck-free way. In two illustrating examples, we test the performance of our schemas on merging multiple VCF files into either a single TPED or a single VCF file, which are benchmarked with the traditional single/parallel multiway-merge methods, message passing interface (MPI)–based high-performance computing (HPC) implementation, and the popular VCFTools. Conclusions Our experiments suggest all three schemas either deliver a significant improvement in efficiency or render much better strong and weak scalabilities over traditional methods. Our findings provide generalized scalable schemas for performing sorted merging on genetics and genomics data using these Apache distributed systems. PMID:29762754

Central as well as Peripheral Attentional Bottlenecks in Dual-Task Performance Activate Lateral Prefrontal Cortices

PubMed Central

Szameitat, André J.; Vanloo, Azonya; Müller, Hermann J.

2016-01-01

Human information processing suffers from severe limitations in parallel processing. In particular, when required to respond to two stimuli in rapid succession, processing bottlenecks may appear at central and peripheral stages of task processing. Importantly, it has been suggested that executive functions are needed to resolve the interference arising at such bottlenecks. The aims of the present study were to test whether central attentional limitations (i.e., bottleneck at the decisional response selection stage) as well as peripheral limitations (i.e., bottleneck at response initiation) both demand executive functions located in the lateral prefrontal cortex. For this, we re-analyzed two previous studies, in which a total of 33 participants performed a dual-task according to the paradigm of the psychological refractory period (PRP) during functional magnetic resonance imaging (fMRI). In one study (N = 17), the PRP task consisted of two two-choice response tasks known to suffer from a central bottleneck (CB group). In the other study (N = 16), the PRP task consisted of two simple-response tasks known to suffer from a peripheral bottleneck (PB group). Both groups showed considerable dual-task costs in form of slowing of the second response in the dual-task (PRP effect). Imaging results are based on the subtraction of both single-tasks from the dual-task within each group. In the CB group, the bilateral middle frontal gyri and inferior frontal gyri were activated. Higher activation in these areas was associated with lower dual-task costs. In the PB group, the right middle frontal and inferior frontal gyrus (IFG) were activated. Here, higher activation was associated with higher dual-task costs. In conclusion we suggest that central and peripheral bottlenecks both demand executive functions located in lateral prefrontal cortices (LPFC). Differences between the CB and PB groups with respect to the exact prefrontal areas activated and the correlational patterns suggest that the executive functions resolving interference at least partially differ between the groups. PMID:27014044

The nocturnal bottleneck and the evolution of activity patterns in mammals.

PubMed

Gerkema, Menno P; Davies, Wayne I L; Foster, Russell G; Menaker, Michael; Hut, Roelof A

2013-08-22

In 1942, Walls described the concept of a 'nocturnal bottleneck' in placental mammals, where these species could survive only by avoiding daytime activity during times in which dinosaurs were the dominant taxon. Walls based this concept of a longer episode of nocturnality in early eutherian mammals by comparing the visual systems of reptiles, birds and all three extant taxa of the mammalian lineage, namely the monotremes, marsupials (now included in the metatherians) and placentals (included in the eutherians). This review describes the status of what has become known as the nocturnal bottleneck hypothesis, giving an overview of the chronobiological patterns of activity. We review the ecological plausibility that the activity patterns of (early) eutherian mammals were restricted to the night, based on arguments relating to endothermia, energy balance, foraging and predation, taking into account recent palaeontological information. We also assess genes, relating to light detection (visual and non-visual systems) and the photolyase DNA protection system that were lost in the eutherian mammalian lineage. Our conclusion presently is that arguments in favour of the nocturnal bottleneck hypothesis in eutherians prevail.

Treatment of neonatal infections: a multi-country analysis of health system bottlenecks and potential solutions.

PubMed

Simen-Kapeu, Aline; Seale, Anna C; Wall, Steve; Nyange, Christabel; Qazi, Shamim A; Moxon, Sarah G; Young, Mark; Liu, Grace; Darmstadt, Gary L; Dickson, Kim E; Lawn, Joy E

2015-01-01

Around one-third of the world's 2.8 million neonatal deaths are caused by infections. Most of these deaths are preventable, but occur due to delays in care-seeking, and access to effective antibiotic treatment with supportive care. Understanding variation in health system bottlenecks to scale-up of case management of neonatal infections and identifying solutions is essential to reduce mortality, and also morbidity. A standardised bottleneck analysis tool was applied in 12 countries in Africa and Asia as part of the development of the Every Newborn Action Plan. Country workshops involved technical experts to complete a survey tool, to grade health system "bottlenecks" hindering scale up of maternal-newborn intervention packages. Quantitative and qualitative methods were used to analyse the data, combined with literature review, to present priority bottlenecks and synthesise actions to improve case management of newborn infections. For neonatal infections, the health system building blocks most frequently graded as major or significant bottlenecks, irrespective of mortality context and geographical region, were health workforce (11 out of 12 countries), and community ownership and partnership (11 out of 12 countries). Lack of data to inform decision making, and limited funding to increase access to quality neonatal care were also major challenges. Rapid recognition of possible serious bacterial infection and access to care is essential. Inpatient hospital care remains the first line of treatment for neonatal infections. In situations where referral is not possible, the use of simplified antibiotic regimens for outpatient management for non-critically ill young infants has recently been reported in large clinical trials; WHO is developing a guideline to treat this group of young infants. Improving quality of care through more investment in the health workforce at all levels of care is critical, in addition to ensuring development and dissemination of national guidelines. Improved information systems are needed to track coverage and adequately manage drug supply logistics for improved health outcomes. It is important to increase community ownership and partnership, for example through involvement of community groups.

Treatment of neonatal infections: a multi-country analysis of health system bottlenecks and potential solutions

PubMed Central

2015-01-01

Background Around one-third of the world's 2.8 million neonatal deaths are caused by infections. Most of these deaths are preventable, but occur due to delays in care-seeking, and access to effective antibiotic treatment with supportive care. Understanding variation in health system bottlenecks to scale-up of case management of neonatal infections and identifying solutions is essential to reduce mortality, and also morbidity. Methods A standardised bottleneck analysis tool was applied in 12 countries in Africa and Asia as part of the development of the Every Newborn Action Plan. Country workshops involved technical experts to complete a survey tool, to grade health system "bottlenecks" hindering scale up of maternal-newborn intervention packages. Quantitative and qualitative methods were used to analyse the data, combined with literature review, to present priority bottlenecks and synthesise actions to improve case management of newborn infections. Results For neonatal infections, the health system building blocks most frequently graded as major or significant bottlenecks, irrespective of mortality context and geographical region, were health workforce (11 out of 12 countries), and community ownership and partnership (11 out of 12 countries). Lack of data to inform decision making, and limited funding to increase access to quality neonatal care were also major challenges. Conclusions Rapid recognition of possible serious bacterial infection and access to care is essential. Inpatient hospital care remains the first line of treatment for neonatal infections. In situations where referral is not possible, the use of simplified antibiotic regimens for outpatient management for non-critically ill young infants has recently been reported in large clinical trials; WHO is developing a guideline to treat this group of young infants. Improving quality of care through more investment in the health workforce at all levels of care is critical, in addition to ensuring development and dissemination of national guidelines. Improved information systems are needed to track coverage and adequately manage drug supply logistics for improved health outcomes. It is important to increase community ownership and partnership, for example through involvement of community groups. PMID:26391217

Automatic choroid cells segmentation and counting in fluorescence microscopic image

NASA Astrophysics Data System (ADS)

Fei, Jianjun; Zhu, Weifang; Shi, Fei; Xiang, Dehui; Lin, Xiao; Yang, Lei; Chen, Xinjian

2016-03-01

In this paper, we proposed a method to automatically segment and count the rhesus choroid-retinal vascular endothelial cells (RF/6A) in fluorescence microscopic images which is based on shape classification, bottleneck detection and accelerated Dijkstra algorithm. The proposed method includes four main steps. First, a thresholding filter and morphological operations are applied to reduce the noise. Second, a shape classifier is used to decide whether a connected component is needed to be segmented. In this step, the AdaBoost classifier is applied with a set of shape features. Third, the bottleneck positions are found based on the contours of the connected components. Finally, the cells segmentation and counting are completed based on the accelerated Dijkstra algorithm with the gradient information between the bottleneck positions. The results show the feasibility and efficiency of the proposed method.

Mule deer and pronghorn migration in western Wyoming

USGS Publications Warehouse

Sawyer, H.; Lindzey, F.; McWhirter, D.

2005-01-01

Migratory mule deer (Odocoileus hemionus) and pronghorn (Antilocapra americana) populations rely on seasonal ranges to meet their annual nutritional and energetic requirements. Because seasonal ranges often occur great distances apart and across a mix of vegetation types and land ownership, maintaining migration corridors to and from these ranges can be difficult, especially if managers do not have detailed information on mule deer and pronghorn seasonal movements. We captured, radiomarked, and monitored mule deer (n = 171) and pronghorn (n = 34) in western Wyoming to document seasonal distribution patterns and migration routes. Mule deer and pronghorn migrated 20-158 km and 116-258 km, respectively, between seasonal ranges. These distances represented the longest recorded migrations for either species. We identified a number of bottlenecks along the migration routes of mule deer and pronghorn, but the most critical appeared to be the 1.6-km-wide Trapper's Point bottleneck, which was used by both mule deer and pronghorn during their spring and autumn migrations. Housing developments and roadways apparently have reduced the effective width of this bottleneck to <0.8 km. We estimate 2,500-3,500 mule deer and 1,500-2,000 pronghorn move through the bottleneck twice a year during spring and autumn migrations. Identification and protection of migration corridors and bottlenecks will be necessary to maintain mule deer and pronghorn populations throughout their range.

DNA as a digital information storage device: hope or hype?

PubMed

Panda, Darshan; Molla, Kutubuddin Ali; Baig, Mirza Jainul; Swain, Alaka; Behera, Deeptirekha; Dash, Manaswini

2018-05-01

The total digital information today amounts to 3.52 × 10 22 bits globally, and at its consistent exponential rate of growth is expected to reach 3 × 10 24 bits by 2040. Data storage density of silicon chips is limited, and magnetic tapes used to maintain large-scale permanent archives begin to deteriorate within 20 years. Since silicon has limited data storage ability and serious limitations, such as human health hazards and environmental pollution, researchers across the world are intently searching for an appropriate alternative. Deoxyribonucleic acid (DNA) is an appealing option for such a purpose due to its endurance, a higher degree of compaction, and similarity to the sequential code of 0's and 1's as found in a computer. This emerging field of DNA as means of data storage has the potential to transform science fiction into reality, wherein a device that can fit in our palms can accommodate the information of the entire world, as latest research has revealed that just four grams of DNA could store the annual global digital information. DNA has all the properties to supersede the conventional hard disk, as it is capable of retaining ten times more data, has a thousandfold storage density, and consumes 10 8 times less power to store a similar amount of data. Although DNA has an enormous potential as a data storage device of the future, multiple bottlenecks such as exorbitant costs, excruciatingly slow writing and reading mechanisms, and vulnerability to mutations or errors need to be resolved. In this review, we have critically analyzed the emergence of DNA as a molecular storage device for the future, its ability to address the future digital data crunch, potential challenges in achieving this objective, various current industrial initiatives, and major breakthroughs.

Policing the Information Highway.

ERIC Educational Resources Information Center

McClure, Ben

1996-01-01

Although broadband Asynchronous Transfer Mode (ATM) can deliver much greater amounts of information than narrow-band Integrated Services Digital Networks (ISDN), in reality bottlenecks place severe constraints on its performance. This article discusses shortfalls in Internet services, technology and user behavior, and describes efforts in the…

Environment construction and bottleneck breakthrough in the improvement of wisdom exhibition

NASA Astrophysics Data System (ADS)

Zhang, Jiankang

2017-08-01

Wisdom exhibition is an inexorable trend in convention and exhibition industry in China. Information technology must be utilized by exhibition industry to achieve intelligent application and wisdom management, breaking the limitation of time as well as space, which raise the quality of exhibition service and level of operation to a totally new standard. Accordingly, exhibition industry should optimize mobile internet, a fundamental technology platform, during the advancing process of wisdom exhibition and consummate the combination among three plates including wisdom connection of information, wisdom exhibition environment and wisdom application of technology. Besides, the industry should realize the wisdom of external environment including wisdom of exhibition city, exhibition place, exhibition resource deal etc and break through bottle-neck in construction of wisdom exhibition industry, which includes construction of big data center, development of Mobile Internet application platform, promotion of information construction, innovative design of application scenarios.

Distinguishing Positive Selection From Neutral Evolution: Boosting the Performance of Summary Statistics

PubMed Central

Lin, Kao; Li, Haipeng; Schlötterer, Christian; Futschik, Andreas

2011-01-01

Summary statistics are widely used in population genetics, but they suffer from the drawback that no simple sufficient summary statistic exists, which captures all information required to distinguish different evolutionary hypotheses. Here, we apply boosting, a recent statistical method that combines simple classification rules to maximize their joint predictive performance. We show that our implementation of boosting has a high power to detect selective sweeps. Demographic events, such as bottlenecks, do not result in a large excess of false positives. A comparison to other neutrality tests shows that our boosting implementation performs well compared to other neutrality tests. Furthermore, we evaluated the relative contribution of different summary statistics to the identification of selection and found that for recent sweeps integrated haplotype homozygosity is very informative whereas older sweeps are better detected by Tajima's π. Overall, Watterson's θ was found to contribute the most information for distinguishing between bottlenecks and selection. PMID:21041556

The effect of a sequential structure of practice for the training of perceptual-cognitive skills in tennis

PubMed Central

2017-01-01

Objective Anticipation of opponent actions, through the use of advanced (i.e., pre-event) kinematic information, can be trained using video-based temporal occlusion. Typically, this involves isolated opponent skills/shots presented as trials in a random order. However, two different areas of research concerning representative task design and contextual (non-kinematic) information, suggest this structure of practice restricts expert performance. The aim of this study was to examine the effect of a sequential structure of practice during video-based training of anticipatory behavior in tennis, as well as the transfer of these skills to the performance environment. Methods In a pre-practice-retention-transfer design, participants viewed life-sized video of tennis rallies across practice in either a sequential order (sequential group), in which participants were exposed to opponent skills/shots in the order they occur in the sport, or a non-sequential (non-sequential group) random order. Results In the video-based retention test, the sequential group was significantly more accurate in their anticipatory judgments when the retention condition replicated the sequential structure compared to the non-sequential group. In the non-sequential retention condition, the non-sequential group was more accurate than the sequential group. In the field-based transfer test, overall decision time was significantly faster in the sequential group compared to the non-sequential group. Conclusion Findings highlight the benefits of a sequential structure of practice for the transfer of anticipatory behavior in tennis. We discuss the role of contextual information, and the importance of representative task design, for the testing and training of perceptual-cognitive skills in sport. PMID:28355263

Damming the genomic data flood using a comprehensive analysis and storage data structure

PubMed Central

Bouffard, Marc; Phillips, Michael S.; Brown, Andrew M.K.; Marsh, Sharon; Tardif, Jean-Claude; van Rooij, Tibor

2010-01-01

Data generation, driven by rapid advances in genomic technologies, is fast outpacing our analysis capabilities. Faced with this flood of data, more hardware and software resources are added to accommodate data sets whose structure has not specifically been designed for analysis. This leads to unnecessarily lengthy processing times and excessive data handling and storage costs. Current efforts to address this have centered on developing new indexing schemas and analysis algorithms, whereas the root of the problem lies in the format of the data itself. We have developed a new data structure for storing and analyzing genotype and phenotype data. By leveraging data normalization techniques, database management system capabilities and the use of a novel multi-table, multidimensional database structure we have eliminated the following: (i) unnecessarily large data set size due to high levels of redundancy, (ii) sequential access to these data sets and (iii) common bottlenecks in analysis times. The resulting novel data structure horizontally divides the data to circumvent traditional problems associated with the use of databases for very large genomic data sets. The resulting data set required 86% less disk space and performed analytical calculations 6248 times faster compared to a standard approach without any loss of information. Database URL: http://castor.pharmacogenomics.ca PMID:21159730

Research on Production Scheduling System with Bottleneck Based on Multi-agent

NASA Astrophysics Data System (ADS)

Zhenqiang, Bao; Weiye, Wang; Peng, Wang; Pan, Quanke

Aimed at the imbalance problem of resource capacity in Production Scheduling System, this paper uses Production Scheduling System based on multi-agent which has been constructed, and combines the dynamic and autonomous of Agent; the bottleneck problem in the scheduling is solved dynamically. Firstly, this paper uses Bottleneck Resource Agent to find out the bottleneck resource in the production line, analyses the inherent mechanism of bottleneck, and describes the production scheduling process based on bottleneck resource. Bottleneck Decomposition Agent harmonizes the relationship of job's arrival time and transfer time in Bottleneck Resource Agent and Non-Bottleneck Resource Agents, therefore, the dynamic scheduling problem is simplified as the single machine scheduling of each resource which takes part in the scheduling. Finally, the dynamic real-time scheduling problem is effectively solved in Production Scheduling System.

Impacts of moving bottlenecks on traffic flow

NASA Astrophysics Data System (ADS)

Ou, Hui; Tang, Tie-Qiao

2018-06-01

Bottleneck (especially the moving bottleneck) widely exists in the urban traffic system. However, little effort has been made to study the impacts of the moving bottleneck on traffic flow (especially the evolution and propagation of traffic flow). In this article, we introduce the speed of a moving bottleneck into a traffic flow model, then propose an extended macro traffic flow with a moving bottleneck, and finally use the proposed model to study the effects of a moving bottleneck on the evolution and propagation of traffic flow under uniform flow and a small perturbation. The numerical results indicate that the moving bottleneck has prominent influences on the evolution of traffic flow under the two typical traffic situations and that the impacts are dependent on the initial density.

Using Coarrays to Parallelize Legacy Fortran Applications: Strategy and Case Study

DOE PAGES

Radhakrishnan, Hari; Rouson, Damian W. I.; Morris, Karla; ...

2015-01-01

This paper summarizes a strategy for parallelizing a legacy Fortran 77 program using the object-oriented (OO) and coarray features that entered Fortran in the 2003 and 2008 standards, respectively. OO programming (OOP) facilitates the construction of an extensible suite of model-verification and performance tests that drive the development. Coarray parallel programming facilitates a rapid evolution from a serial application to a parallel application capable of running on multicore processors and many-core accelerators in shared and distributed memory. We delineate 17 code modernization steps used to refactor and parallelize the program and study the resulting performance. Our initial studies were donemore » using the Intel Fortran compiler on a 32-core shared memory server. Scaling behavior was very poor, and profile analysis using TAU showed that the bottleneck in the performance was due to our implementation of a collective, sequential summation procedure. We were able to improve the scalability and achieve nearly linear speedup by replacing the sequential summation with a parallel, binary tree algorithm. We also tested the Cray compiler, which provides its own collective summation procedure. Intel provides no collective reductions. With Cray, the program shows linear speedup even in distributed-memory execution. We anticipate similar results with other compilers once they support the new collective procedures proposed for Fortran 2015.« less

Aging and Attentional Control

PubMed Central

Tsang, Pamela S.

2013-01-01

The research examines the structural bottleneck account and the resource account of the substantial dual-task deficits among older adults. Procedures from two common dual-task methodologies--the psychological refractory period and the relative-priority manipulation--were used to encourage maximization of the joint performance. Performance and time-sharing strategies from subjects between the ages of 20 and 70 were examined. Age-related declines in time-sharing efficiency and in the precision of the executive control process were observed. The age-related effect was larger when two manual responses were required than when one manual and one vocal response were required but no evidence for obligatory sequential processing was found. Except for the most demanding conditions, comparable practice effects were observed between the younger and older subjects, suggesting considerable cognitive plasticity in the older subjects. Implications for the two attentional accounts were discussed. PMID:23281799

Parallel-In-Time For Moving Meshes

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

Falgout, R. D.; Manteuffel, T. A.; Southworth, B.

2016-02-04

With steadily growing computational resources available, scientists must develop e ective ways to utilize the increased resources. High performance, highly parallel software has be- come a standard. However until recent years parallelism has focused primarily on the spatial domain. When solving a space-time partial di erential equation (PDE), this leads to a sequential bottleneck in the temporal dimension, particularly when taking a large number of time steps. The XBraid parallel-in-time library was developed as a practical way to add temporal parallelism to existing se- quential codes with only minor modi cations. In this work, a rezoning-type moving mesh is appliedmore » to a di usion problem and formulated in a parallel-in-time framework. Tests and scaling studies are run using XBraid and demonstrate excellent results for the simple model problem considered herein.« less

Kullback-Leibler information function and the sequential selection of experiments to discriminate among several linear models. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Sidik, S. M.

1972-01-01

A sequential adaptive experimental design procedure for a related problem is studied. It is assumed that a finite set of potential linear models relating certain controlled variables to an observed variable is postulated, and that exactly one of these models is correct. The problem is to sequentially design most informative experiments so that the correct model equation can be determined with as little experimentation as possible. Discussion includes: structure of the linear models; prerequisite distribution theory; entropy functions and the Kullback-Leibler information function; the sequential decision procedure; and computer simulation results. An example of application is given.

Bottleneck analysis and strategic planning using Tanahashi model for childhood diarrhea management in Gujarat, Western India.

PubMed

Rupani, Mihir Prafulbhai; Gaonkar, Narayan T; Bhatt, Gneyaa S

2016-10-01

In spite of continued efforts, India is still lagging behind in achieving its MDG goals. The objectives of this study were to identify stake-holders who have a role to play in childhood diarrhea management, to identify gaps in childhood diarrhea management and to propose strategic options for relieving these gaps. Bottleneck analysis exercise was carried out based on the Tanahashi model in six High Priority Districts (HPDs) of Gujarat in period between July-November 2013. The major bottlenecks identified for Childhood Diarrhea management were poor demand generation, unsafe drinking water, poor access to improved sanitation facility and lack of equitable distribution and replenishment mechanisms for Oral Rehydration Solution (ORS) packets and Zinc tablets till the front-line worker level. The main strategic options that were suggested for relieving these bottlenecks were Zinc-ORS roll out in scale-up districts, develop Information Education Communication/Behaviour Change Communication (IEC/BCC) plan for childhood diarrhea management at state/district level, use of Drug Logistics Information Management System (DLIMS) software for supply chain management of Zinc-ORS, strengthening of chlorination activity at household level, monitoring implementation of Nirmal Bharat Abhiyaan (NBA) for constructing improved sanitation facilities at household level and to develop an IEC/BCC plan for hygiene promotion and usage of sanitary latrines. Use of Zinc tablets need to be intensified through an effective scale-up. Adequate demand generation activity is needed. There is need to address safe drinking water and improved sanitation measures at household levels. Multi-sectoral engagements and ownership of Zinc-ORS program is the need of the hour. Copyright © 2016 Elsevier Ltd. All rights reserved.

Improving traffic flow at a 2-to-1 lane reduction with wirelessly connected, adaptive cruise control vehicles

NASA Astrophysics Data System (ADS)

Davis, L. C.

2016-06-01

Wirelessly connected vehicles that exchange information about traffic conditions can reduce delays caused by congestion. At a 2-to-1 lane reduction, the improvement in flow past a bottleneck due to traffic with a random mixture of 40% connected vehicles is found to be 52%. Control is based on connected-vehicle-reported velocities near the bottleneck. In response to indications of congestion the connected vehicles, which are also adaptive cruise control vehicles, reduce their speed in slowdown regions. Early lane changes of manually driven vehicles from the terminated lane to the continuous lane are induced by the slowing connected vehicles. Self-organized congestion at the bottleneck is thus delayed or eliminated, depending upon the incoming flow magnitude. For the large majority of vehicles, travel times past the bottleneck are substantially reduced. Control is responsible for delaying the onset of congestion as the incoming flow increases. Adaptive cruise control increases the flow out of the congested state at the bottleneck. The nature of the congested state, when it occurs, appears to be similar under a variety of conditions. Typically 80-100 vehicles are approximately equally distributed between the lanes in the 500 m region prior to the end of the terminated lane. Without the adaptive cruise control capability, connected vehicles can delay the onset of congestion but do not increase the asymptotic flow past the bottleneck. Calculations are done using the Kerner-Klenov three-phase theory, stochastic discrete-time model for manual vehicles. The dynamics of the connected vehicles is given by a conventional adaptive cruise control algorithm plus commanded deceleration. Because time in the model for manual vehicles is discrete (one-second intervals), it is assumed that the acceleration of any vehicle immediately in front of a connected vehicle is constant during the time interval, thereby preserving the computational simplicity and speed of a discrete-time model.

Human Cognition and Information Processing: Potential Problems for a Field Dependent Human Sequential Information Processor.

ERIC Educational Resources Information Center

Shaughnessy, M.; And Others

Numerous cognitive psychologists have validated the hypothesis, originally advanced by the Russian physician, A. Luria, that different individuals process information in two distinctly different manners: simultaneously and sequentially. The importance of recognizing the existence of these two distinct styles of processing information and selecting…

Bottlenecks in HIV-1 transmission: insights from the study of founder viruses.

PubMed

Joseph, Sarah B; Swanstrom, Ronald; Kashuba, Angela D M; Cohen, Myron S

2015-07-01

HIV-1 infection typically results from the transmission of a single viral variant, the transmitted/founder (T/F) virus. Studies of these HIV-1 variants provide critical information about the transmission bottlenecks and the selective pressures acting on the virus in the transmission fluid and in the recipient tissues. These studies reveal that T/F virus phenotypes are shaped by stochastic and selective forces that restrict transmission and may be targets for prevention strategies. In this Review, we highlight how studies of T/F viruses contribute to a better understanding of the biology of HIV-1 transmission and discuss how these findings affect HIV-1 prevention strategies.

Transmission Bottleneck Size Estimation from Pathogen Deep-Sequencing Data, with an Application to Human Influenza A Virus.

PubMed

Sobel Leonard, Ashley; Weissman, Daniel B; Greenbaum, Benjamin; Ghedin, Elodie; Koelle, Katia

2017-07-15

The bottleneck governing infectious disease transmission describes the size of the pathogen population transferred from the donor to the recipient host. Accurate quantification of the bottleneck size is particularly important for rapidly evolving pathogens such as influenza virus, as narrow bottlenecks reduce the amount of transferred viral genetic diversity and, thus, may decrease the rate of viral adaptation. Previous studies have estimated bottleneck sizes governing viral transmission by using statistical analyses of variants identified in pathogen sequencing data. These analyses, however, did not account for variant calling thresholds and stochastic viral replication dynamics within recipient hosts. Because these factors can skew bottleneck size estimates, we introduce a new method for inferring bottleneck sizes that accounts for these factors. Through the use of a simulated data set, we first show that our method, based on beta-binomial sampling, accurately recovers transmission bottleneck sizes, whereas other methods fail to do so. We then apply our method to a data set of influenza A virus (IAV) infections for which viral deep-sequencing data from transmission pairs are available. We find that the IAV transmission bottleneck size estimates in this study are highly variable across transmission pairs, while the mean bottleneck size of 196 virions is consistent with a previous estimate for this data set. Furthermore, regression analysis shows a positive association between estimated bottleneck size and donor infection severity, as measured by temperature. These results support findings from experimental transmission studies showing that bottleneck sizes across transmission events can be variable and influenced in part by epidemiological factors. IMPORTANCE The transmission bottleneck size describes the size of the pathogen population transferred from the donor to the recipient host and may affect the rate of pathogen adaptation within host populations. Recent advances in sequencing technology have enabled bottleneck size estimation from pathogen genetic data, although there is not yet a consistency in the statistical methods used. Here, we introduce a new approach to infer the bottleneck size that accounts for variant identification protocols and noise during pathogen replication. We show that failing to account for these factors leads to an underestimation of bottleneck sizes. We apply this method to an existing data set of human influenza virus infections, showing that transmission is governed by a loose, but highly variable, transmission bottleneck whose size is positively associated with the severity of infection of the donor. Beyond advancing our understanding of influenza virus transmission, we hope that this work will provide a standardized statistical approach for bottleneck size estimation for viral pathogens. Copyright © 2017 Sobel Leonard et al.

Managing microbial communities for sequentially reconstruct genomes from complex metagenomes

NASA Astrophysics Data System (ADS)

Delmont, Tom O.; Vogel, Timothy M.; Simonet, Pascal

2013-04-01

Global understanding on environmental microbial communities is currently limited by the bottleneck of genome reconstruction. Soil is a typical example where individual cells are currently mostly uncultured and metagenomic datasets unassembled. In this study, the microbial community composition of a natural grassland soil was managed under several controlled selective pressures to experiment a "multi-evenness" stratagem for sequentially attempt to reconstruct genomes from a complex metagenome. While lowly represented in the natural community, several newly dominant genomes (an enrichment attaining 105 in some cases) were successfully reconstructed under various "harsh" tested conditions. These genomes belong to several genera including (but not restricted to) Leifsonia, Rhodanobacter, Bacillus, Ktedonobacter, Xanthomonas, Streptomyces and Burkholderia. So far, from 10 to 78% of generated metagenomic datasets were reconstructed, so providing access to more than 88 000 genes of known or unknown functions and to their genetic environment. Adaptative genes directly related to selective pressures were found, mostly in large plasmids. Functions of potential industrial interest (e.g., novel polyketide synthase modules in Streptomyces) were also discovered. Furthermore, an important phage infection snapshot (>1500X of coverage for the most represented phage) was observed among the Streptomyces population (three distinct genomes reconstructed) of a particular enrichment (mercury, 0.02g/kg) during the fourth month of incubation. This "divide and conquer" strategy could be applied to other environments and using auxiliary sequencing approaches like single cell to detect, connect and mine taxa and functions of interest while creating an extensive set of reference genomes from across the planet. Next limit could turn out to become our imagination defining novel selective pressures to sequentially make dominant the 1030 cells of the biosphere.

Vanishing dual-task interference after practice: has the bottleneck been eliminated or is it merely latent?

NASA Technical Reports Server (NTRS)

Ruthruff, Eric; Johnston, James C.; Van Selst, Mark; Whitsell, Shelly; Remington, Roger

2003-01-01

Practice can, in some cases, largely eliminate measured dual-task interference. Does this absence of interference indicate the absence of a processing bottleneck (defined as an inability to carry out certain stages in parallel)? The authors show that a bottleneck need not produce any observable interference, provided that there is no temporal overlap in the demand for bottleneck stages on the 2 tasks. Such a "latent" bottleneck is especially likely after practice, when central stages are short. The authors provide new evidence that a latent bottleneck occurred for a participant who produced no interference in M. Van Selst, E. Ruthruff, and J. C. Johnston (1999). These findings demonstrate that the absence of dual-task interference does not necessarily indicate the absence of a processing bottleneck.

DISCRN: A Distributed Storytelling Framework for Intelligence Analysis.

PubMed

Shukla, Manu; Dos Santos, Raimundo; Chen, Feng; Lu, Chang-Tien

2017-09-01

Storytelling connects entities (people, organizations) using their observed relationships to establish meaningful storylines. This can be extended to spatiotemporal storytelling that incorporates locations, time, and graph computations to enhance coherence and meaning. But when performed sequentially these computations become a bottleneck because the massive number of entities make space and time complexity untenable. This article presents DISCRN, or distributed spatiotemporal ConceptSearch-based storytelling, a distributed framework for performing spatiotemporal storytelling. The framework extracts entities from microblogs and event data, and links these entities using a novel ConceptSearch to derive storylines in a distributed fashion utilizing key-value pair paradigm. Performing these operations at scale allows deeper and broader analysis of storylines. The novel parallelization techniques speed up the generation and filtering of storylines on massive datasets. Experiments with microblog posts such as Twitter data and Global Database of Events, Language, and Tone events show the efficiency of the techniques in DISCRN.

Asynchronous multilevel adaptive methods for solving partial differential equations on multiprocessors - Performance results

NASA Technical Reports Server (NTRS)

Mccormick, S.; Quinlan, D.

1989-01-01

The fast adaptive composite grid method (FAC) is an algorithm that uses various levels of uniform grids (global and local) to provide adaptive resolution and fast solution of PDEs. Like all such methods, it offers parallelism by using possibly many disconnected patches per level, but is hindered by the need to handle these levels sequentially. The finest levels must therefore wait for processing to be essentially completed on all the coarser ones. A recently developed asynchronous version of FAC, called AFAC, completely eliminates this bottleneck to parallelism. This paper describes timing results for AFAC, coupled with a simple load balancing scheme, applied to the solution of elliptic PDEs on an Intel iPSC hypercube. These tests include performance of certain processes necessary in adaptive methods, including moving grids and changing refinement. A companion paper reports on numerical and analytical results for estimating convergence factors of AFAC applied to very large scale examples.

nStudy: A System for Researching Information Problem Solving

ERIC Educational Resources Information Center

Winne, Philip H.; Nesbit, John C.; Popowich, Fred

2017-01-01

A bottleneck in gathering big data about learning is instrumentation designed to record data about processes students use to learn and information on which those processes operate. The software system nStudy fills this gap. nStudy is an extension to the Chrome web browser plus a server side database for logged trace data plus peripheral modules…

Priority Intelligence Requirements: The Operational Vacuum

DTIC Science & Technology

1990-05-16

armored vehicles , not ho!: the systems are used to achieve operational goals.34 Enemy mobilization, employment philosophy, and history are excluded in...extensive security problems create massive bottlenecks in the dissemination of intellingence information .48 Today, we sport a tremendous intelligence

Breeding nursery tissue collection for possible genomic analysis

USDA-ARS?s Scientific Manuscript database

Phenotyping is considered a major bottleneck in breeding programs. With new genomic technologies, high throughput genotype schemes are constantly being developed. However, every genomic technology requires phenotypic data to inform prediction models generated from the technology. Forage breeders con...

Bottlenecks in HIV-1 transmission: insights from the study of founder viruses

PubMed Central

Joseph, Sarah B.; Swanstrom, Ronald; Kashuba, Angela D. M.; Cohen, Myron S.

2016-01-01

HIV-1 infection typically results from the transmission of a single viral variant, the transmitted/founder (T/F) virus. Studies of these HIV-1 variants provide critical information about the transmission bottlenecks and the selective pressures acting on the virus in the transmission fluid and in the recipient tissues. These studies reveal that T/F virus phenotypes are shaped by stochastic and selective forces that restrict transmission and may be targets for prevention strategies. In this Review, we highlight how studies of T/F viruses contribute to a better understanding of the biology of HIV-1 transmission and discuss how these findings affect HIV-1 prevention strategies. PMID:26052661

Self-regulated learning of important information under sequential and simultaneous encoding conditions.

PubMed

Middlebrooks, Catherine D; Castel, Alan D

2018-05-01

Learners make a number of decisions when attempting to study efficiently: they must choose which information to study, for how long to study it, and whether to restudy it later. The current experiments examine whether documented impairments to self-regulated learning when studying information sequentially, as opposed to simultaneously, extend to the learning of and memory for valuable information. In Experiment 1, participants studied lists of words ranging in value from 1-10 points sequentially or simultaneously at a preset presentation rate; in Experiment 2, study was self-paced and participants could choose to restudy. Although participants prioritized high-value over low-value information, irrespective of presentation, those who studied the items simultaneously demonstrated superior value-based prioritization with respect to recall, study selections, and self-pacing. The results of the present experiments support the theory that devising, maintaining, and executing efficient study agendas is inherently different under sequential formatting than simultaneous. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

Neural Mechanisms Underlying Visual Short-Term Memory Gain for Temporally Distinct Objects.

PubMed

Ihssen, Niklas; Linden, David E J; Miller, Claire E; Shapiro, Kimron L

2015-08-01

Recent research has shown that visual short-term memory (VSTM) can substantially be improved when the to-be-remembered objects are split in 2 half-arrays (i.e., sequenced) or the entire array is shown twice (i.e., repeated), rather than presented simultaneously. Here we investigate the hypothesis that sequencing and repeating displays overcomes attentional "bottlenecks" during simultaneous encoding. Using functional magnetic resonance imaging, we show that sequencing and repeating displays increased brain activation in extrastriate and primary visual areas, relative to simultaneous displays (Study 1). Passively viewing identical stimuli did not increase visual activation (Study 2), ruling out a physical confound. Importantly, areas of the frontoparietal attention network showed increased activation in repetition but not in sequential trials. This dissociation suggests that repeating a display increases attentional control by allowing attention to be reallocated in a second encoding episode. In contrast, sequencing the array poses fewer demands on control, with competition from nonattended objects being reduced by the half-arrays. This idea was corroborated by a third study in which we found optimal VSTM for sequential displays minimizing attentional demands. Importantly these results provide support within the same experimental paradigm for the role of stimulus-driven and top-down attentional control aspects of biased competition theory in setting constraints on VSTM. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Update schemes of multi-velocity floor field cellular automaton for pedestrian dynamics

NASA Astrophysics Data System (ADS)

Luo, Lin; Fu, Zhijian; Cheng, Han; Yang, Lizhong

2018-02-01

Modeling pedestrian movement is an interesting problem both in statistical physics and in computational physics. Update schemes of cellular automaton (CA) models for pedestrian dynamics govern the schedule of pedestrian movement. Usually, different update schemes make the models behave in different ways, which should be carefully recalibrated. Thus, in this paper, we investigated the influence of four different update schemes, namely parallel/synchronous scheme, random scheme, order-sequential scheme and shuffled scheme, on pedestrian dynamics. The multi-velocity floor field cellular automaton (FFCA) considering the changes of pedestrians' moving properties along walking paths and heterogeneity of pedestrians' walking abilities was used. As for parallel scheme only, the collisions detection and resolution should be considered, resulting in a great difference from any other update schemes. For pedestrian evacuation, the evacuation time is enlarged, and the difference in pedestrians' walking abilities is better reflected, under parallel scheme. In face of a bottleneck, for example a exit, using a parallel scheme leads to a longer congestion period and a more dispersive density distribution. The exit flow and the space-time distribution of density and velocity have significant discrepancies under four different update schemes when we simulate pedestrian flow with high desired velocity. Update schemes may have no influence on pedestrians in simulation to create tendency to follow others, but sequential and shuffled update scheme may enhance the effect of pedestrians' familiarity with environments.

Health-system strengthening and tuberculosis control.

PubMed

Atun, Rifat; Weil, Diana E C; Eang, Mao Tan; Mwakyusa, David

2010-06-19

Weak health systems are hindering global efforts for tuberculosis care and control, but little evidence is available on effective interventions to address system bottlenecks. This report examines published evidence, programme reviews, and case studies to identify innovations in system design and tuberculosis control to resolve these bottlenecks. We outline system bottlenecks in relation to governance, financing, supply chain management, human resources, health-information systems, and service delivery; and adverse effects from rapid introduction of suboptimum system designs. This report also documents innovative solutions for disease control and system design. Solutions pursued in individual countries are specific to the nature of the tuberculosis epidemic, the underlying national health system, and the contributors engaged: no one size fits all. Findings from countries, including Bangladesh, Cambodia, India, Tanzania, Thailand, and Vietnam, suggest that advances in disease control and system strengthening are complementary. Tuberculosis care and control are essential elements of health systems, and simultaneous efforts to innovate systems and disease response are mutually reinforcing. Highly varied and context-specific responses to tuberculosis show that solutions need to be documented and compared to develop evidence-based policies and practice. Copyright 2010 Elsevier Ltd. All rights reserved.

Genetic structure and conservation of Mountain Lions in the South-Brazilian Atlantic Rain Forest.

PubMed

Castilho, Camila S; Marins-Sá, Luiz G; Benedet, Rodrigo C; Freitas, Thales R O

2012-01-01

The Brazilian Atlantic Rain Forest, one of the most endangered ecosystems worldwide, is also among the most important hotspots as regards biodiversity. Through intensive logging, the initial area has been reduced to around 12% of its original size. In this study we investigated the genetic variability and structure of the mountain lion, Puma concolor. Using 18 microsatellite loci we analyzed evidence of allele dropout, null alleles and stuttering, calculated the number of allele/locus, PIC, observed and expected heterozygosity, linkage disequilibrium, Hardy-Weinberg equilibrium, F(IS), effective population size and genetic structure (MICROCHECKER, CERVUS, GENEPOP, FSTAT, ARLEQUIN, ONESAMP, LDNe, PCAGEN, GENECLASS software), we also determine whether there was evidence of a bottleneck (HYBRIDLAB, BOTTLENECK software) that might influence the future viability of the population in south Brazil. 106 alleles were identified, with the number of alleles/locus ranging from 2 to 11. Mean observed heterozygosity, mean number of alleles and polymorphism information content were 0.609, 5.89, and 0.6255, respectively. This population presented evidence of a recent bottleneck and loss of genetic variation. Persistent regional poaching constitutes an increasing in the extinction risk.

The nocturnal bottleneck and the evolution of activity patterns in mammals

PubMed Central

Gerkema, Menno P.; Davies, Wayne I. L.; Foster, Russell G.; Menaker, Michael; Hut, Roelof A.

2013-01-01

In 1942, Walls described the concept of a ‘nocturnal bottleneck’ in placental mammals, where these species could survive only by avoiding daytime activity during times in which dinosaurs were the dominant taxon. Walls based this concept of a longer episode of nocturnality in early eutherian mammals by comparing the visual systems of reptiles, birds and all three extant taxa of the mammalian lineage, namely the monotremes, marsupials (now included in the metatherians) and placentals (included in the eutherians). This review describes the status of what has become known as the nocturnal bottleneck hypothesis, giving an overview of the chronobiological patterns of activity. We review the ecological plausibility that the activity patterns of (early) eutherian mammals were restricted to the night, based on arguments relating to endothermia, energy balance, foraging and predation, taking into account recent palaeontological information. We also assess genes, relating to light detection (visual and non-visual systems) and the photolyase DNA protection system that were lost in the eutherian mammalian lineage. Our conclusion presently is that arguments in favour of the nocturnal bottleneck hypothesis in eutherians prevail. PMID:23825205

Implementation of a web-based medication tracking system in a large academic medical center.

PubMed

Calabrese, Sam V; Williams, Jonathan P

2012-10-01

Pharmacy workflow efficiencies achieved through the use of an electronic medication-tracking system are described. Medication dispensing turnaround times at the inpatient pharmacy of a large hospital were evaluated before and after transition from manual medication tracking to a Web-based tracking process involving sequential bar-code scanning and real-time monitoring of medication status. The transition was carried out in three phases: (1) a workflow analysis, including the identification of optimal points for medication scanning with hand-held wireless devices, (2) the phased implementation of an automated solution and associated hardware at a central dispensing pharmacy and three satellite locations, and (3) postimplementation data collection to evaluate the impact of the new tracking system and areas for improvement. Relative to the manual tracking method, electronic medication tracking allowed the capture of far more data points, enabling the pharmacy team to delineate the time required for each step of the medication dispensing process and to identify the steps most likely to involve delays. A comparison of baseline and postimplementation data showed substantial reductions in overall medication turnaround times with the use of the Web-based tracking system (time reductions of 45% and 22% at the central and satellite sites, respectively). In addition to more accurate projections and documentation of turnaround times, the Web-based tracking system has facilitated quality-improvement initiatives. Implementation of an electronic tracking system for monitoring the delivery of medications provided a comprehensive mechanism for calculating turnaround times and allowed the pharmacy to identify bottlenecks within the medication distribution system. Altering processes removed these bottlenecks and decreased delivery turnaround times.

Uncertainty quantification of seabed parameters for large data volumes along survey tracks with a tempered particle filter

NASA Astrophysics Data System (ADS)

Dettmer, J.; Quijano, J. E.; Dosso, S. E.; Holland, C. W.; Mandolesi, E.

2016-12-01

Geophysical seabed properties are important for the detection and classification of unexploded ordnance. However, current surveying methods such as vertical seismic profiling, coring, or inversion are of limited use when surveying large areas with high spatial sampling density. We consider surveys based on a source and receiver array towed by an autonomous vehicle which produce large volumes of seabed reflectivity data that contain unprecedented and detailed seabed information. The data are analyzed with a particle filter, which requires efficient reflection-coefficient computation, efficient inversion algorithms and efficient use of computer resources. The filter quantifies information content of multiple sequential data sets by considering results from previous data along the survey track to inform the importance sampling at the current point. Challenges arise from environmental changes along the track where the number of sediment layers and their properties change. This is addressed by a trans-dimensional model in the filter which allows layering complexity to change along a track. Efficiency is improved by likelihood tempering of various particle subsets and including exchange moves (parallel tempering). The filter is implemented on a hybrid computer that combines central processing units (CPUs) and graphics processing units (GPUs) to exploit three levels of parallelism: (1) fine-grained parallel computation of spherical reflection coefficients with a GPU implementation of Levin integration; (2) updating particles by concurrent CPU processes which exchange information using automatic load balancing (coarse grained parallelism); (3) overlapping CPU-GPU communication (a major bottleneck) with GPU computation by staggering CPU access to the multiple GPUs. The algorithm is applied to spherical reflection coefficients for data sets along a 14-km track on the Malta Plateau, Mediterranean Sea. We demonstrate substantial efficiency gains over previous methods. [This research was supported in part by the U.S. Dept of Defense, thought the Strategic Environmental Research and Development Program (SERDP).

Genetic diversity and fitness in black-footed ferrets before and during a bottleneck.

PubMed

Wisely, S M; Buskirk, S W; Fleming, M A; McDonald, D B; Ostrander, E A

2002-01-01

The black-footed ferret (Mustela nigripes) is an endangered North American carnivore that underwent a well-documented population bottleneck in the mid-1980s. To better understand the effects of a bottleneck on a free-ranging carnivore population, we used 24 microsatellite loci to compare genetic diversity before versus during the bottleneck, and compare the last wild population to two historical populations. We also compared genetic diversity in black-footed ferrets to that of two sibling species, the steppe polecat (Mustela eversmanni) and the European polecat (Mustela putorius). Black-footed ferrets during the bottleneck had less genetic diversity than steppe polecats. The three black-footed ferret populations were well differentiated (F(ST) = 0.57 +/- 0.15; mean +/- SE). We attributed the decrease in genetic diversity in black-footed ferrets to localized extinction of these genetically distinct subpopulations and to the bottleneck in the surviving subpopulation. Although genetic diversity decreased, female fecundity and juvenile survival were not affected by the population bottleneck.

Sequential vs simultaneous encoding of spatial information: a comparison between the blind and the sighted.

PubMed

Ruotolo, Francesco; Ruggiero, Gennaro; Vinciguerra, Michela; Iachini, Tina

2012-02-01

The aim of this research is to assess whether the crucial factor in determining the characteristics of blind people's spatial mental images is concerned with the visual impairment per se or the processing style that the dominant perceptual modalities used to acquire spatial information impose, i.e. simultaneous (vision) vs sequential (kinaesthesis). Participants were asked to learn six positions in a large parking area via movement alone (congenitally blind, adventitiously blind, blindfolded sighted) or with vision plus movement (simultaneous sighted, sequential sighted), and then to mentally scan between positions in the path. The crucial manipulation concerned the sequential sighted group. Their visual exploration was made sequential by putting visual obstacles within the pathway in such a way that they could not see simultaneously the positions along the pathway. The results revealed a significant time/distance linear relation in all tested groups. However, the linear component was lower in sequential sighted and blind participants, especially congenital. Sequential sighted and congenitally blind participants showed an almost overlapping performance. Differences between groups became evident when mentally scanning farther distances (more than 5m). This threshold effect could be revealing of processing limitations due to the need of integrating and updating spatial information. Overall, the results suggest that the characteristics of the processing style rather than the visual impairment per se affect blind people's spatial mental images. Copyright © 2011 Elsevier B.V. All rights reserved.

Information Retrieval: A Sequential Learning Process.

ERIC Educational Resources Information Center

Bookstein, Abraham

1983-01-01

Presents decision-theoretic models which intrinsically include retrieval of multiple documents whereby system responds to request by presenting documents to patron in sequence, gathering feedback, and using information to modify future retrievals. Document independence model, set retrieval model, sequential retrieval model, learning model,…

Population history, gene flow, and bottlenecks in island populations of a secondary seed disperser, the southern grey shrike (Lanius meridionalis koenigi)

PubMed Central

Padilla, David P; Spurgin, Lewis G; Fairfield, Eleanor A; Illera, Juan Carlos; Richardson, David S

2015-01-01

Studying the population history and demography of organisms with important ecological roles can aid understanding of evolutionary processes at the community level and inform conservation. We screened genetic variation (mtDNA and microsatellite) across the populations of the southern grey shrike (Lanius meridionalis koenigi) in the Canary Islands, where it is an endemic subspecies and an important secondary seed disperser. We show that the Canarian subspecies is polyphyletic with L. meridionalis elegans from North Africa and that shrikes have colonized the Canary Islands from North Africa multiple times. Substantial differences in genetic diversity exist across islands, which are most likely the product of a combination of historical colonization events and recent bottlenecks. The Eastern Canary Islands had the highest overall levels of genetic diversity and have probably been most recently and/or frequently colonized from Africa. Recent or ongoing bottlenecks were detected in three of the islands and are consistent with anecdotal evidence of population declines due to human disturbance. These findings are troubling given the shrike's key ecological role in the Canary Islands, and further research is needed to understand the community-level consequences of declines in shrike populations. Finally, we found moderate genetic differentiation among populations, which largely reflected the shrike's bottleneck history; however, a significant pattern of isolation-by-distance indicated that some gene flow occurs between islands. This study is a useful first step toward understanding how secondary seed dispersal operates over broad spatial scales. PMID:25628862

Addressing Challenges in Web Accessibility for the Blind and Visually Impaired

ERIC Educational Resources Information Center

Guercio, Angela; Stirbens, Kathleen A.; Williams, Joseph; Haiber, Charles

2011-01-01

Searching for relevant information on the web is an important aspect of distance learning. This activity is a challenge for visually impaired distance learners. While sighted people have the ability to filter information in a fast and non sequential way, blind persons rely on tools that process the information in a sequential way. Learning is…

Traffic behavior at freeway bottlenecks.

DOT National Transportation Integrated Search

2014-09-01

This study examines traffic behavior in the vicinity of a freeway bottleneck, revisiting commonly held : assumptions and uncovering systematic biases that likely have distorted empirical studies of bottleneck : formation, capacity drop, and the funda...

Design of a model to predict surge capacity bottlenecks for burn mass casualties at a large academic medical center.

PubMed

Abir, Mahshid; Davis, Matthew M; Sankar, Pratap; Wong, Andrew C; Wang, Stewart C

2013-02-01

To design and test a model to predict surge capacity bottlenecks at a large academic medical center in response to a mass-casualty incident (MCI) involving multiple burn victims. Using the simulation software ProModel, a model of patient flow and anticipated resource use, according to principles of disaster management, was developed based upon historical data from the University Hospital of the University of Michigan Health System. Model inputs included: (a) age and weight distribution for casualties, and distribution of size and depth of burns; (b) rate of arrival of casualties to the hospital, and triage to ward or critical care settings; (c) eligibility for early discharge of non-MCI inpatients at time of MCI; (d) baseline occupancy of intensive care unit (ICU), surgical step-down, and ward; (e) staff availability-number of physicians, nurses, and respiratory therapists, and the expected ratio of each group to patients; (f) floor and operating room resources-anticipating the need for mechanical ventilators, burn care and surgical resources, blood products, and intravenous fluids; (g) average hospital length of stay and mortality rate for patients with inhalation injury and different size burns; and (h) average number of times that different size burns undergo surgery. Key model outputs include time to bottleneck for each limiting resource and average waiting time to hospital bed availability. Given base-case model assumptions (including 100 mass casualties with an inter-arrival rate to the hospital of one patient every three minutes), hospital utilization is constrained within the first 120 minutes to 21 casualties, due to the limited number of beds. The first bottleneck is attributable to exhausting critical care beds, followed by floor beds. Given this limitation in number of patients, the temporal order of the ensuing bottlenecks is as follows: Lactated Ringer's solution (4 h), silver sulfadiazine/Silvadene (6 h), albumin (48 h), thrombin topical (72 h), type AB packed red blood cells (76 h), silver dressing/Acticoat (100 h), bismuth tribromophenate/Xeroform (102 h), and gauze bandage rolls/Kerlix (168 h). The following items do not precipitate a bottleneck: ventilators, topical epinephrine, staplers, foams, antimicrobial non-adherent dressing/Telfa types A, B, or O blood. Nurse, respiratory therapist, and physician staffing does not induce bottlenecks. This model, and similar models for non-burn-related MCIs, can serve as a real-time estimation and management tool for hospital capacity in the setting of MCIs, and can inform supply decision support for disaster management.

Damage to white matter bottlenecks contributes to language impairments after left hemispheric stroke.

PubMed

Griffis, Joseph C; Nenert, Rodolphe; Allendorfer, Jane B; Szaflarski, Jerzy P

2017-01-01

Damage to the white matter underlying the left posterior temporal lobe leads to deficits in multiple language functions. The posterior temporal white matter may correspond to a bottleneck where both dorsal and ventral language pathways are vulnerable to simultaneous damage. Damage to a second putative white matter bottleneck in the left deep prefrontal white matter involving projections associated with ventral language pathways and thalamo-cortical projections has recently been proposed as a source of semantic deficits after stroke. Here, we first used white matter atlases to identify the previously described white matter bottlenecks in the posterior temporal and deep prefrontal white matter. We then assessed the effects of damage to each region on measures of verbal fluency, picture naming, and auditory semantic decision-making in 43 chronic left hemispheric stroke patients. Damage to the posterior temporal bottleneck predicted deficits on all tasks, while damage to the anterior bottleneck only significantly predicted deficits in verbal fluency. Importantly, the effects of damage to the bottleneck regions were not attributable to lesion volume, lesion loads on the tracts traversing the bottlenecks, or damage to nearby cortical language areas. Multivariate lesion-symptom mapping revealed additional lesion predictors of deficits. Post-hoc fiber tracking of the peak white matter lesion predictors using a publicly available tractography atlas revealed evidence consistent with the results of the bottleneck analyses. Together, our results provide support for the proposal that spatially specific white matter damage affecting bottleneck regions, particularly in the posterior temporal lobe, contributes to chronic language deficits after left hemispheric stroke. This may reflect the simultaneous disruption of signaling in dorsal and ventral language processing streams.

Forced guidance and distribution of practice in sequential information processing.

NASA Technical Reports Server (NTRS)

Decker, L. R.; Rogers, C. A., Jr.

1973-01-01

Distribution of practice and forced guidance were used in a sequential information-processing task in an attempt to increase the capacity of human information-processing mechanisms. A reaction time index of the psychological refractory period was used as the response measure. Massing of practice lengthened response times while forced guidance shortened them. Interpretation was in terms of load reduction upon the response-selection stage of the information-processing system.-

Investigation of the performance of fermentation processes using a mathematical model including effects of metabolic bottleneck and toxic product on cells.

PubMed

Sriyudthsak, Kansuporn; Shiraishi, Fumihide

2010-11-01

A number of recent research studies have focused on theoretical and experimental investigation of a bottleneck in a metabolic reaction network. However, there is no study on how the bottleneck affects the performance of a fermentation process when a product is highly toxic and remarkably influences the growth and death of cells. The present work therefore studies the effect of bottleneck on product concentrations under different product toxicity conditions. A generalized bottleneck model in a fed-batch fermentation is constructed including both the bottleneck and the product influences on cell growth and death. The simulation result reveals that when the toxic product strongly influences the cell growth and death, the final product concentration is hardly changed even if the bottleneck is removed, whereas it is markedly changed by the degree of product toxicity. The performance of an ethanol fermentation process is also discussed as a case example to validate this result. In conclusion, when the product is highly toxic, one cannot expect a significant increase in the final product concentration even if removing the bottleneck; rather, it may be more effective to somehow protect the cells so that they can continuously produce the product. Copyright © 2010 Elsevier Inc. All rights reserved.

Involvement of Working Memory in College Students' Sequential Pattern Learning and Performance

ERIC Educational Resources Information Center

Kundey, Shannon M. A.; De Los Reyes, Andres; Rowan, James D.; Lee, Bern; Delise, Justin; Molina, Sabrina; Cogdill, Lindsay

2013-01-01

When learning highly organized sequential patterns of information, humans and nonhuman animals learn rules regarding the hierarchical structures of these sequences. In three experiments, we explored the role of working memory in college students' sequential pattern learning and performance in a computerized task involving a sequential…

Trial Sequential Methods for Meta-Analysis

ERIC Educational Resources Information Center

Kulinskaya, Elena; Wood, John

2014-01-01

Statistical methods for sequential meta-analysis have applications also for the design of new trials. Existing methods are based on group sequential methods developed for single trials and start with the calculation of a required information size. This works satisfactorily within the framework of fixed effects meta-analysis, but conceptual…

Dual-task performance with ideomotor-compatible tasks: is the central processing bottleneck intact, bypassed, or shifted in locus?

NASA Technical Reports Server (NTRS)

Lien, Mei-Ching; McCann, Robert S.; Ruthruff, Eric; Proctor, Robert W.

2005-01-01

The present study examined whether the central bottleneck, assumed to be primarily responsible for the psychological refractory period (PRP) effect, is intact, bypassed, or shifted in locus with ideomotor (IM)-compatible tasks. In 4 experiments, factorial combinations of IM- and non-IM-compatible tasks were used for Task 1 and Task 2. All experiments showed substantial PRP effects, with a strong dependency between Task 1 and Task 2 response times. These findings, along with model-based simulations, indicate that the processing bottleneck was not bypassed, even with two IM-compatible tasks. Nevertheless, systematic changes in the PRP and correspondence effects across experiments suggest that IM compatibility shifted the locus of the bottleneck. The findings favor an engage-bottleneck-later hypothesis, whereby parallelism between tasks occurs deeper into the processing stream for IM- than for non-IM-compatible tasks, without the bottleneck being actually eliminated.

Trial Sequential Analysis in systematic reviews with meta-analysis.

PubMed

Wetterslev, Jørn; Jakobsen, Janus Christian; Gluud, Christian

2017-03-06

Most meta-analyses in systematic reviews, including Cochrane ones, do not have sufficient statistical power to detect or refute even large intervention effects. This is why a meta-analysis ought to be regarded as an interim analysis on its way towards a required information size. The results of the meta-analyses should relate the total number of randomised participants to the estimated required meta-analytic information size accounting for statistical diversity. When the number of participants and the corresponding number of trials in a meta-analysis are insufficient, the use of the traditional 95% confidence interval or the 5% statistical significance threshold will lead to too many false positive conclusions (type I errors) and too many false negative conclusions (type II errors). We developed a methodology for interpreting meta-analysis results, using generally accepted, valid evidence on how to adjust thresholds for significance in randomised clinical trials when the required sample size has not been reached. The Lan-DeMets trial sequential monitoring boundaries in Trial Sequential Analysis offer adjusted confidence intervals and restricted thresholds for statistical significance when the diversity-adjusted required information size and the corresponding number of required trials for the meta-analysis have not been reached. Trial Sequential Analysis provides a frequentistic approach to control both type I and type II errors. We define the required information size and the corresponding number of required trials in a meta-analysis and the diversity (D 2 ) measure of heterogeneity. We explain the reasons for using Trial Sequential Analysis of meta-analysis when the actual information size fails to reach the required information size. We present examples drawn from traditional meta-analyses using unadjusted naïve 95% confidence intervals and 5% thresholds for statistical significance. Spurious conclusions in systematic reviews with traditional meta-analyses can be reduced using Trial Sequential Analysis. Several empirical studies have demonstrated that the Trial Sequential Analysis provides better control of type I errors and of type II errors than the traditional naïve meta-analysis. Trial Sequential Analysis represents analysis of meta-analytic data, with transparent assumptions, and better control of type I and type II errors than the traditional meta-analysis using naïve unadjusted confidence intervals.

High variance in reproductive success generates a false signature of a genetic bottleneck in populations of constant size: a simulation study

PubMed Central

2013-01-01

Background Demographic bottlenecks can severely reduce the genetic variation of a population or a species. Establishing whether low genetic variation is caused by a bottleneck or a constantly low effective number of individuals is important to understand a species’ ecology and evolution, and it has implications for conservation management. Recent studies have evaluated the power of several statistical methods developed to identify bottlenecks. However, the false positive rate, i.e. the rate with which a bottleneck signal is misidentified in demographically stable populations, has received little attention. We analyse this type of error (type I) in forward computer simulations of stable populations having greater than Poisson variance in reproductive success (i.e., variance in family sizes). The assumption of Poisson variance underlies bottleneck tests, yet it is commonly violated in species with high fecundity. Results With large variance in reproductive success (Vk ≥ 40, corresponding to a ratio between effective and census size smaller than 0.1), tests based on allele frequencies, allelic sizes, and DNA sequence polymorphisms (heterozygosity excess, M-ratio, and Tajima’s D test) tend to show erroneous signals of a bottleneck. Similarly, strong evidence of population decline is erroneously detected when ancestral and current population sizes are estimated with the model based method MSVAR. Conclusions Our results suggest caution when interpreting the results of bottleneck tests in species showing high variance in reproductive success. Particularly in species with high fecundity, computer simulations are recommended to confirm the occurrence of a population bottleneck. PMID:24131797

Replantation surgery in Quebec: The bottlenecks to rapid care

PubMed Central

Borsuk, Daniel E; Zadeh, Teanoosh; Lee, Chen; Moore, Karl; Tan, Grace

2006-01-01

INTRODUCTION Time delays resulting in prolonged ischemia have a significant impact on the successful reattachment of amputated body parts. No studies have addressed the issues surrounding delays from the time of the accident to the start of replantation surgery. The present paper identifies the bottlenecks that prolong the time before patients are able to gain access to a replant team. METHODS A total of 50 patients underwent microsurgical replantation, because of traumatic amputation, at a university-based hospital from 1996 to 2003. The charts were analyzed to ascertain individual time intervals from the onset of injury until the beginning of replant surgery. RESULTS The average length of time for patients who came directly to the replant centre was 3 h 40 min before surgery began. In contrast, for those referred from outlying hospitals, the elapsed time was 6 h 21 min. CONCLUSIONS Two major bottlenecks were found. First, for patients who were referred from other health centres, delays were due to a lack of information as to where patients could receive appropriate replant surgery. Second, delays at the replant centre were primarily due to insufficient physical and human resources in the operating room. PMID:19554107

Genetic structure and conservation of Mountain Lions in the South-Brazilian Atlantic Rain Forest

PubMed Central

Castilho, Camila S.; Marins-Sá, Luiz G.; Benedet, Rodrigo C.; Freitas, Thales R.O.

2012-01-01

The Brazilian Atlantic Rain Forest, one of the most endangered ecosystems worldwide, is also among the most important hotspots as regards biodiversity. Through intensive logging, the initial area has been reduced to around 12% of its original size. In this study we investigated the genetic variability and structure of the mountain lion, Puma concolor. Using 18 microsatellite loci we analyzed evidence of allele dropout, null alleles and stuttering, calculated the number of allele/locus, PIC, observed and expected heterozygosity, linkage disequilibrium, Hardy-Weinberg equilibrium, FIS, effective population size and genetic structure (MICROCHECKER, CERVUS, GENEPOP, FSTAT, ARLEQUIN, ONESAMP, LDNe, PCAGEN, GENECLASS software), we also determine whether there was evidence of a bottleneck (HYBRIDLAB, BOTTLENECK software) that might influence the future viability of the population in south Brazil. 106 alleles were identified, with the number of alleles/locus ranging from 2 to 11. Mean observed heterozygosity, mean number of alleles and polymorphism information content were 0.609, 5.89, and 0.6255, respectively. This population presented evidence of a recent bottleneck and loss of genetic variation. Persistent regional poaching constitutes an increasing in the extinction risk. PMID:22481876

Pre-Whaling Genetic Diversity and Population Ecology in Eastern Pacific Gray Whales: Insights from Ancient DNA and Stable Isotopes

PubMed Central

Alter, S. Elizabeth; Newsome, Seth D.; Palumbi, Stephen R.

2012-01-01

Commercial whaling decimated many whale populations, including the eastern Pacific gray whale, but little is known about how population dynamics or ecology differed prior to these removals. Of particular interest is the possibility of a large population decline prior to whaling, as such a decline could explain the ∼5-fold difference between genetic estimates of prior abundance and estimates based on historical records. We analyzed genetic (mitochondrial control region) and isotopic information from modern and prehistoric gray whales using serial coalescent simulations and Bayesian skyline analyses to test for a pre-whaling decline and to examine prehistoric genetic diversity, population dynamics and ecology. Simulations demonstrate that significant genetic differences observed between ancient and modern samples could be caused by a large, recent population bottleneck, roughly concurrent with commercial whaling. Stable isotopes show minimal differences between modern and ancient gray whale foraging ecology. Using rejection-based Approximate Bayesian Computation, we estimate the size of the population bottleneck at its minimum abundance and the pre-bottleneck abundance. Our results agree with previous genetic studies suggesting the historical size of the eastern gray whale population was roughly three to five times its current size. PMID:22590499

Kangaroo mother care: a multi-country analysis of health system bottlenecks and potential solutions.

PubMed

Vesel, Linda; Bergh, Anne-Marie; Kerber, Kate J; Valsangkar, Bina; Mazia, Goldy; Moxon, Sarah G; Blencowe, Hannah; Darmstadt, Gary L; de Graft Johnson, Joseph; Dickson, Kim E; Ruiz Peláez, Juan; von Xylander, Severin; Lawn, Joy E

2015-01-01

Preterm birth is now the leading cause of under-five child deaths worldwide with one million direct deaths plus approximately another million where preterm is a risk factor for neonatal deaths due to other causes. There is strong evidence that kangaroo mother care (KMC) reduces mortality among babies with birth weight <2000 g (mostly preterm). KMC involves continuous skin-to-skin contact, breastfeeding support, and promotion of early hospital discharge with follow-up. The World Health Organization has endorsed KMC for stabilised newborns in health facilities in both high-income and low-resource settings. The objectives of this paper are to: (1) use a 12-country analysis to explore health system bottlenecks affecting the scale-up of KMC; (2) propose solutions to the most significant bottlenecks; and (3) outline priority actions for scale-up. The bottleneck analysis tool was applied in 12 countries in Africa and Asia as part of the Every Newborn Action Plan process. Country workshops involved technical experts to complete the survey tool, which is designed to synthesise and grade health system "bottlenecks", factors that hinder the scale-up, of maternal-newborn intervention packages. We used quantitative and qualitative methods to analyse the bottleneck data, combined with literature review, to present priority bottlenecks and actions relevant to different health system building blocks for KMC. Marked differences were found in the perceived severity of health system bottlenecks between Asian and African countries, with the former reporting more significant or very major bottlenecks for KMC with respect to all the health system building blocks. Community ownership and health financing bottlenecks were significant or very major bottlenecks for KMC in both low and high mortality contexts, particularly in South Asia. Significant bottlenecks were also reported for leadership and governance and health workforce building blocks. There are at least a dozen countries worldwide with national KMC programmes, and we identify three pathways to scale: (1) champion-led; (2) project-initiated; and (3) health systems designed. The combination of all three pathways may lead to more rapid scale-up. KMC has the potential to save lives, and change the face of facility-based newborn care, whilst empowering women to care for their preterm newborns.

Kangaroo mother care: a multi-country analysis of health system bottlenecks and potential solutions

PubMed Central

2015-01-01

Background Preterm birth is now the leading cause of under-five child deaths worldwide with one million direct deaths plus approximately another million where preterm is a risk factor for neonatal deaths due to other causes. There is strong evidence that kangaroo mother care (KMC) reduces mortality among babies with birth weight <2000 g (mostly preterm). KMC involves continuous skin-to-skin contact, breastfeeding support, and promotion of early hospital discharge with follow-up. The World Health Organization has endorsed KMC for stabilised newborns in health facilities in both high-income and low-resource settings. The objectives of this paper are to: (1) use a 12-country analysis to explore health system bottlenecks affecting the scale-up of KMC; (2) propose solutions to the most significant bottlenecks; and (3) outline priority actions for scale-up. Methods The bottleneck analysis tool was applied in 12 countries in Africa and Asia as part of the Every Newborn Action Plan process. Country workshops involved technical experts to complete the survey tool, which is designed to synthesise and grade health system "bottlenecks", factors that hinder the scale-up, of maternal-newborn intervention packages. We used quantitative and qualitative methods to analyse the bottleneck data, combined with literature review, to present priority bottlenecks and actions relevant to different health system building blocks for KMC. Results Marked differences were found in the perceived severity of health system bottlenecks between Asian and African countries, with the former reporting more significant or very major bottlenecks for KMC with respect to all the health system building blocks. Community ownership and health financing bottlenecks were significant or very major bottlenecks for KMC in both low and high mortality contexts, particularly in South Asia. Significant bottlenecks were also reported for leadership and governance and health workforce building blocks. Conclusions There are at least a dozen countries worldwide with national KMC programmes, and we identify three pathways to scale: (1) champion-led; (2) project-initiated; and (3) health systems designed. The combination of all three pathways may lead to more rapid scale-up. KMC has the potential to save lives, and change the face of facility-based newborn care, whilst empowering women to care for their preterm newborns. PMID:26391115

Quality care during labour and birth: a multi-country analysis of health system bottlenecks and potential solutions

PubMed Central

2015-01-01

Background Good outcomes during pregnancy and childbirth are related to availability, utilisation and effective implementation of essential interventions for labour and childbirth. The majority of the estimated 289,000 maternal deaths, 2.8 million neonatal deaths and 2.6 million stillbirths every year could be prevented by improving access to and scaling up quality care during labour and birth. Methods The bottleneck analysis tool was applied in 12 countries in Africa and Asia as part of the Every Newborn Action Plan process. Country workshops engaged technical experts to complete the survey tool, which is designed to synthesise and grade health system "bottlenecks", factors that hinder the scale up, of maternal-newborn intervention packages. We used quantitative and qualitative methods to analyse the bottleneck data, combined with literature review, to present priority bottlenecks and actions relevant to different health system building blocks for skilled birth attendance and basic and comprehensive emergency obstetric care. Results Across 12 countries the most critical bottlenecks identified by workshop participants for skilled birth attendance were health financing (10 out of 12 countries) and health workforce (9 out of 12 countries). Health service delivery bottlenecks were found to be the most critical for both basic and comprehensive emergency obstetric care (9 out of 12 countries); health financing was identified as having critical bottlenecks for comprehensive emergency obstetric care (9 out of 12 countries). Solutions to address health financing bottlenecks included strengthening national financing mechanisms and removing financial barriers to care seeking. For addressing health workforce bottlenecks, improved human resource planning is needed, including task shifting and improving training quality. For health service delivery, proposed solutions included improving quality of care and establishing public private partnerships. Conclusions Progress towards the 2030 targets for ending preventable maternal and newborn deaths is dependent on improving quality of care during birth and the immediate postnatal period. Strengthening national health systems to improve maternal and newborn health, as a cornerstone of universal health coverage, will only be possible by addressing specific health system bottlenecks during labour and birth, including those within health workforce, health financing and health service delivery. PMID:26390886

Improving Emergency Department flow through optimized bed utilization

PubMed Central

Chartier, Lucas Brien; Simoes, Licinia; Kuipers, Meredith; McGovern, Barb

2016-01-01

Over the last decade, patient volumes in the emergency department (ED) have grown disproportionately compared to the increase in staffing and resources at the Toronto Western Hospital, an academic tertiary care centre in Toronto, Canada. The resultant congestion has spilled over to the ED waiting room, where medically undifferentiated and potentially unstable patients must wait until a bed becomes available. The aim of this quality improvement project was to decrease the 90th percentile of wait time between triage and bed assignment (time-to-bed) by half, from 120 to 60 minutes, for our highest acuity patients. We engaged key stakeholders to identify barriers and potential strategies to achieve optimal flow of patients into the ED. We first identified multiple flow-interrupting challenges, including operational bottlenecks and cultural issues. We then generated change ideas to address two main underlying causes of ED congestion: unnecessary patient utilization of ED beds and communication breakdown causing bed turnaround delays. We subsequently performed seven tests of change through sequential plan-do-study-act (PDSA) cycles. The most significant gains were made by improving communication strategies: small gains were achieved through the optimization of in-house digital information management systems, while significant improvements were achieved through the implementation of a low-tech direct contact mechanism (a two-way radio or walkie-talkie). In the post-intervention phase, time-to-bed for the 90th percentile of high-acuity patients decreased from 120 minutes to 66 minutes, with special cause variation showing a significant shift in the weekly measurements. PMID:27752312

Improving Emergency Department flow through optimized bed utilization.

PubMed

Chartier, Lucas Brien; Simoes, Licinia; Kuipers, Meredith; McGovern, Barb

2016-01-01

Over the last decade, patient volumes in the emergency department (ED) have grown disproportionately compared to the increase in staffing and resources at the Toronto Western Hospital, an academic tertiary care centre in Toronto, Canada. The resultant congestion has spilled over to the ED waiting room, where medically undifferentiated and potentially unstable patients must wait until a bed becomes available. The aim of this quality improvement project was to decrease the 90th percentile of wait time between triage and bed assignment (time-to-bed) by half, from 120 to 60 minutes, for our highest acuity patients. We engaged key stakeholders to identify barriers and potential strategies to achieve optimal flow of patients into the ED. We first identified multiple flow-interrupting challenges, including operational bottlenecks and cultural issues. We then generated change ideas to address two main underlying causes of ED congestion: unnecessary patient utilization of ED beds and communication breakdown causing bed turnaround delays. We subsequently performed seven tests of change through sequential plan-do-study-act (PDSA) cycles. The most significant gains were made by improving communication strategies: small gains were achieved through the optimization of in-house digital information management systems, while significant improvements were achieved through the implementation of a low-tech direct contact mechanism (a two-way radio or walkie-talkie). In the post-intervention phase, time-to-bed for the 90th percentile of high-acuity patients decreased from 120 minutes to 66 minutes, with special cause variation showing a significant shift in the weekly measurements.

Deep Learning for Population Genetic Inference.

PubMed

Sheehan, Sara; Song, Yun S

2016-03-01

Given genomic variation data from multiple individuals, computing the likelihood of complex population genetic models is often infeasible. To circumvent this problem, we introduce a novel likelihood-free inference framework by applying deep learning, a powerful modern technique in machine learning. Deep learning makes use of multilayer neural networks to learn a feature-based function from the input (e.g., hundreds of correlated summary statistics of data) to the output (e.g., population genetic parameters of interest). We demonstrate that deep learning can be effectively employed for population genetic inference and learning informative features of data. As a concrete application, we focus on the challenging problem of jointly inferring natural selection and demography (in the form of a population size change history). Our method is able to separate the global nature of demography from the local nature of selection, without sequential steps for these two factors. Studying demography and selection jointly is motivated by Drosophila, where pervasive selection confounds demographic analysis. We apply our method to 197 African Drosophila melanogaster genomes from Zambia to infer both their overall demography, and regions of their genome under selection. We find many regions of the genome that have experienced hard sweeps, and fewer under selection on standing variation (soft sweep) or balancing selection. Interestingly, we find that soft sweeps and balancing selection occur more frequently closer to the centromere of each chromosome. In addition, our demographic inference suggests that previously estimated bottlenecks for African Drosophila melanogaster are too extreme.

Deep Learning for Population Genetic Inference

PubMed Central

Sheehan, Sara; Song, Yun S.

2016-01-01

Given genomic variation data from multiple individuals, computing the likelihood of complex population genetic models is often infeasible. To circumvent this problem, we introduce a novel likelihood-free inference framework by applying deep learning, a powerful modern technique in machine learning. Deep learning makes use of multilayer neural networks to learn a feature-based function from the input (e.g., hundreds of correlated summary statistics of data) to the output (e.g., population genetic parameters of interest). We demonstrate that deep learning can be effectively employed for population genetic inference and learning informative features of data. As a concrete application, we focus on the challenging problem of jointly inferring natural selection and demography (in the form of a population size change history). Our method is able to separate the global nature of demography from the local nature of selection, without sequential steps for these two factors. Studying demography and selection jointly is motivated by Drosophila, where pervasive selection confounds demographic analysis. We apply our method to 197 African Drosophila melanogaster genomes from Zambia to infer both their overall demography, and regions of their genome under selection. We find many regions of the genome that have experienced hard sweeps, and fewer under selection on standing variation (soft sweep) or balancing selection. Interestingly, we find that soft sweeps and balancing selection occur more frequently closer to the centromere of each chromosome. In addition, our demographic inference suggests that previously estimated bottlenecks for African Drosophila melanogaster are too extreme. PMID:27018908

Integrated quantification and identification of aldehydes and ketones in biological samples.

PubMed

Siegel, David; Meinema, Anne C; Permentier, Hjalmar; Hopfgartner, Gérard; Bischoff, Rainer

2014-05-20

The identification of unknown compounds remains to be a bottleneck of mass spectrometry (MS)-based metabolomics screening experiments. Here, we present a novel approach which facilitates the identification and quantification of analytes containing aldehyde and ketone groups in biological samples by adding chemical information to MS data. Our strategy is based on rapid autosampler-in-needle-derivatization with p-toluenesulfonylhydrazine (TSH). The resulting TSH-hydrazones are separated by ultrahigh-performance liquid chromatography (UHPLC) and detected by electrospray ionization-quadrupole-time-of-flight (ESI-QqTOF) mass spectrometry using a SWATH (Sequential Window Acquisition of all Theoretical Fragment-Ion Spectra) data-independent high-resolution mass spectrometry (HR-MS) approach. Derivatization makes small, poorly ionizable or retained analytes amenable to reversed phase chromatography and electrospray ionization in both polarities. Negatively charged TSH-hydrazone ions furthermore show a simple and predictable fragmentation pattern upon collision induced dissociation, which enables the chemo-selective screening for unknown aldehydes and ketones via a signature fragment ion (m/z 155.0172). By means of SWATH, targeted and nontargeted application scenarios of the suggested derivatization route are enabled in the frame of a single UHPLC-ESI-QqTOF-HR-MS workflow. The method's ability to simultaneously quantify and identify molecules containing aldehyde and ketone groups is demonstrated using 61 target analytes from various compound classes and a (13)C labeled yeast matrix. The identification of unknowns in biological samples is detailed using the example of indole-3-acetaldehyde.

Working Memory, Age, Crew Downsizing, System Design and Training

DTIC Science & Technology

2000-08-01

Radvansky and Zacks, 1997). As authors have noted perceived demand. Accurate "Situation Models " (Johnson- when attempting to make sense of a... models of cognitive function and workload (cf. Baddeley bodies of information to be processed or multiple results and Gathercole, 1993). The ability to...major bottleneck in human performance. Some models of multiple traces from different headings and the human information processing (Pashler, 1998) place

The Armys Bandwidth Bottleneck

DTIC Science & Technology

2003-08-01

representation requires a minimum of eight bits of information per pixel. The cinematic illusion of movement requires about 32 frames per second.3 In...Information Theory, vol. 46, no. 2 ( March 2000), pp. 388-404. 3. The development and adoption of new methods—including so- called dynamic protocols—for...Delaney, “Independent Review of Technology Maturity Assessment for Future Combat Systems Increment 1” ( March 3, 2003). The study was commissioned by the

Hydrogen gas storage in fluorinated ultramicroporous tunnel crystal

NASA Astrophysics Data System (ADS)

Kataoka, Keisuke; Katagiri, Toshimasa

2012-07-01

We report hydrogen storage at an ordinary pressure due to a bottle-neck effect of an ultramicroporous crystal. Stored hydrogen was kept at an ordinary pressure below -110 °C. The amounts of stored hydrogen gas linearly correlated with the initial pressures. These phenomena suggested the ultramicroporous tunnels worked as a molecular gas cylinder.We report hydrogen storage at an ordinary pressure due to a bottle-neck effect of an ultramicroporous crystal. Stored hydrogen was kept at an ordinary pressure below -110 °C. The amounts of stored hydrogen gas linearly correlated with the initial pressures. These phenomena suggested the ultramicroporous tunnels worked as a molecular gas cylinder. Electronic supplementary information (ESI) available. CCDC 246922. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c2nr30940h

"Bottleneck study" : transportation infrastructure and traffic management analysis of cross border bottlenecks.

DOT National Transportation Integrated Search

2004-11-01

The motivation behind the Transportation Infrastructure and Traffic Management Analysis of : Cross Border Bottlenecks study was generated by the U.S.-Mexico Border Partnership Action : Plan (Action item #2 of the 22-Point Smart Border Action Plan: De...

Probing the Non-Native H Helix Translocation in Apomyoglobin Folding Intermediates

PubMed Central

2015-01-01

Apomyoglobin folds via sequential helical intermediates that are formed by rapid collapse of the A, B, G, and H helix regions. An equilibrium molten globule with a similar structure is formed near pH 4. Previous studies suggested that the folding intermediates are kinetically trapped states in which folding is impeded by non-native packing of the G and H helices. Fluorescence spectra of mutant proteins in which cysteine residues were introduced at several positions in the G and H helices show differential quenching of W14 fluorescence, providing direct evidence of translocation of the H helix relative to helices A and G in both the kinetic and equilibrium intermediates. Förster resonance energy transfer measurements show that a 5-({2-[(acetyl)amino]ethyl}amino)naphthalene-1-sulfonic acid acceptor coupled to K140C (helix H) is closer to Trp14 (helix A) in the equilibrium molten globule than in the native state, by a distance that is consistent with sliding of the H helix in an N-terminal direction by approximately one helical turn. Formation of an S108C–L135C disulfide prevents H helix translocation in the equilibrium molten globule by locking the G and H helices into their native register. By enforcing nativelike packing of the A, G, and H helices, the disulfide resolves local energetic frustration and facilitates transient docking of the E helix region onto the hydrophobic core but has only a small effect on the refolding rate. The apomyoglobin folding landscape is highly rugged, with several energetic bottlenecks that frustrate folding; relief of any one of the major identified bottlenecks is insufficient to speed progression to the transition state. PMID:24857522

Computer-aided target tracking in motion analysis studies

NASA Astrophysics Data System (ADS)

Burdick, Dominic C.; Marcuse, M. L.; Mislan, J. D.

1990-08-01

Motion analysis studies require the precise tracking of reference objects in sequential scenes. In a typical situation, events of interest are captured at high frame rates using special cameras, and selected objects or targets are tracked on a frame by frame basis to provide necessary data for motion reconstruction. Tracking is usually done using manual methods which are slow and prone to error. A computer based image analysis system has been developed that performs tracking automatically. The objective of this work was to eliminate the bottleneck due to manual methods in high volume tracking applications such as the analysis of crash test films for the automotive industry. The system has proven to be successful in tracking standard fiducial targets and other objects in crash test scenes. Over 95 percent of target positions which could be located using manual methods can be tracked by the system, with a significant improvement in throughput over manual methods. Future work will focus on the tracking of clusters of targets and on tracking deformable objects such as airbags.

A Massively Parallel Computational Method of Reading Index Files for SOAPsnv.

PubMed

Zhu, Xiaoqian; Peng, Shaoliang; Liu, Shaojie; Cui, Yingbo; Gu, Xiang; Gao, Ming; Fang, Lin; Fang, Xiaodong

2015-12-01

SOAPsnv is the software used for identifying the single nucleotide variation in cancer genes. However, its performance is yet to match the massive amount of data to be processed. Experiments reveal that the main performance bottleneck of SOAPsnv software is the pileup algorithm. The original pileup algorithm's I/O process is time-consuming and inefficient to read input files. Moreover, the scalability of the pileup algorithm is also poor. Therefore, we designed a new algorithm, named BamPileup, aiming to improve the performance of sequential read, and the new pileup algorithm implemented a parallel read mode based on index. Using this method, each thread can directly read the data start from a specific position. The results of experiments on the Tianhe-2 supercomputer show that, when reading data in a multi-threaded parallel I/O way, the processing time of algorithm is reduced to 3.9 s and the application program can achieve a speedup up to 100×. Moreover, the scalability of the new algorithm is also satisfying.

"Bottleneck study" : transportation infrastructure and traffic management analysis of cross border bottlenecks. [Executive summary].

DOT National Transportation Integrated Search

2004-11-01

The motivation behind the Transportation Infrastructure and Traffic Management Analysis of : Cross Border Bottlenecks study was generated by the U.S.-Mexico Border Partnership Action : Plan (Action item #2 of the 22-Point Smart Border Action Plan: De...

Sequential Effects on Speeded Information Processing: A Developmental Study

ERIC Educational Resources Information Center

Smulders, S.F.A.; Notebaert, W.; Meijer, M.; Crone, E.A.; van der Molen, M.W.; Soetens, E.

2005-01-01

Two experiments were performed to assess age-related changes in sequential effects on choice reaction time (RT). Sequential effects portray the influence of previous trials on the RT to the current stimulus. In Experiment 1, three age groups (7-9, 10-12, and 18-25 years) performed a spatially compatible choice task, with response-to-stimulus…

Robust sequential working memory recall in heterogeneous cognitive networks

PubMed Central

Rabinovich, Mikhail I.; Sokolov, Yury; Kozma, Robert

2014-01-01

Psychiatric disorders are often caused by partial heterogeneous disinhibition in cognitive networks, controlling sequential and spatial working memory (SWM). Such dynamic connectivity changes suggest that the normal relationship between the neuronal components within the network deteriorates. As a result, competitive network dynamics is qualitatively altered. This dynamics defines the robust recall of the sequential information from memory and, thus, the SWM capacity. To understand pathological and non-pathological bifurcations of the sequential memory dynamics, here we investigate the model of recurrent inhibitory-excitatory networks with heterogeneous inhibition. We consider the ensemble of units with all-to-all inhibitory connections, in which the connection strengths are monotonically distributed at some interval. Based on computer experiments and studying the Lyapunov exponents, we observed and analyzed the new phenomenon—clustered sequential dynamics. The results are interpreted in the context of the winnerless competition principle. Accordingly, clustered sequential dynamics is represented in the phase space of the model by two weakly interacting quasi-attractors. One of them is similar to the sequential heteroclinic chain—the regular image of SWM, while the other is a quasi-chaotic attractor. Coexistence of these quasi-attractors means that the recall of the normal information sequence is intermittently interrupted by episodes with chaotic dynamics. We indicate potential dynamic ways for augmenting damaged working memory and other cognitive functions. PMID:25452717

Memory and decision making: Effects of sequential presentation of probabilities and outcomes in risky prospects.

PubMed

Millroth, Philip; Guath, Mona; Juslin, Peter

2018-06-07

The rationality of decision making under risk is of central concern in psychology and other behavioral sciences. In real-life, the information relevant to a decision often arrives sequentially or changes over time, implying nontrivial demands on memory. Yet, little is known about how this affects the ability to make rational decisions and a default assumption is rather that information about outcomes and probabilities are simultaneously available at the time of the decision. In 4 experiments, we show that participants receiving probability- and outcome information sequentially report substantially (29 to 83%) higher certainty equivalents than participants with simultaneous presentation. This holds also for monetary-incentivized participants with perfect recall of the information. Participants in the sequential conditions often violate stochastic dominance in the sense that they pay more for a lottery with low probability of an outcome than participants in the simultaneous condition pay for a high probability of the same outcome. Computational modeling demonstrates that Cumulative Prospect Theory (Tversky & Kahneman, 1992) fails to account for the effects of sequential presentation, but a model assuming anchoring-and adjustment constrained by memory can account for the data. By implication, established assumptions of rationality may need to be reconsidered to account for the effects of memory in many real-life tasks. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

Estimating Bottleneck Bandwidth using TCP

NASA Technical Reports Server (NTRS)

Allman, Mark

1998-01-01

Various issues associated with estimating bottleneck bandwidth using TCP are presented in viewgraph form. Specific topics include: 1) Why TCP is wanted to estimate the bottleneck bandwidth; 2) Setting ssthresh to an appropriate value to reduce loss; 3) Possible packet-pair solutions; and 4) Preliminary results: ACTS and the Internet.

C-quence: a tool for analyzing qualitative sequential data.

PubMed

Duncan, Starkey; Collier, Nicholson T

2002-02-01

C-quence is a software application that matches sequential patterns of qualitative data specified by the user and calculates the rate of occurrence of these patterns in a data set. Although it was designed to facilitate analyses of face-to-face interaction, it is applicable to any data set involving categorical data and sequential information. C-quence queries are constructed using a graphical user interface. The program does not limit the complexity of the sequential patterns specified by the user.

Bottleneck Concepts in Psychology: Exploratory First Steps

ERIC Educational Resources Information Center

Gurung, Regan A. R.; Landrum, R. Eric

2013-01-01

The authors take an initial step in identifying potential bottleneck concepts in psychology, that is, concepts that are deceptively difficult, perhaps due to student overconfidence. In order to first identify bottleneck concepts, faculty (n = 65) rated the difficulty of 91 psychological concepts from across the discipline. Students (n = 35) rated…

The Impact of Population Bottlenecks on Microbial Adaptation

NASA Astrophysics Data System (ADS)

LeClair, Joshua S.; Wahl, Lindi M.

2018-07-01

Population bottlenecks—sudden, severe reductions in population size—are ubiquitous in nature. Because of their critical implications for conservation genetics, the effects of population bottlenecks on the loss of genetic diversity have been well studied. Bottlenecks also have important implications for adaptation, however, and these effects have been addressed more recently, typically in microbial populations. In this short review, we survey both experimental and theoretical work describing the impact of population bottlenecks on microbial adaptation. Focusing on theoretical contributions, we highlight emerging insights and conclude with several open questions of interest in the field.

Bottlenecks and Waiting Points in Nucleosynthesis in X-ray bursts and Novae

NASA Astrophysics Data System (ADS)

Smith, Michael S.; Sunayama, Tomomi; Hix, W. Raphael; Lingerfelt, Eric J.; Nesaraja, Caroline D.

2010-08-01

To better understand the energy generation and element synthesis occurring in novae and X-ray bursts, we give quantitative definitions to the concepts of ``bottlenecks'' and ``waiting points'' in the thermonuclear reaction flow. We use these criteria to search for bottlenecks and waiting points in post-processing element synthesis explosion simulations. We have incorporated these into the Computational Infrastructure for Nuclear Astrophysics, a suite of nuclear astrophysics codes available online at nucastrodata.org, so that anyone may perform custom searches for bottlenecks and waiting points.

Bottlenecks and Waiting Points in Nucleosynthesis in X-ray bursts and Novae

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

Smith, Michael S.; Hix, W. Raphael; Nesaraja, Caroline D.

2010-08-12

To better understand the energy generation and element synthesis occurring in novae and X-ray bursts, we give quantitative definitions to the concepts of ''bottlenecks'' and ''waiting points'' in the thermonuclear reaction flow. We use these criteria to search for bottlenecks and waiting points in post-processing element synthesis explosion simulations. We have incorporated these into the Computational Infrastructure for Nuclear Astrophysics, a suite of nuclear astrophysics codes available online at nucastrodata.org, so that anyone may perform custom searches for bottlenecks and waiting points.

Processing bottlenecks in dual-task performance: structural limitation or strategic postponement?

NASA Technical Reports Server (NTRS)

Ruthruff, E.; Pashler, H. E.; Klaassen, A.

2001-01-01

Recent evidence indicates that a central bottleneck causes much of the slowing that occurs when two tasks are performed at the same time. This bottleneck might reflect a structural limitation inherent in the cognitive architecture. Alternatively, the bottleneck might reflect strategic (i.e., voluntary) postponement, induced by instructions to emphasize one task over the other. To distinguish structural limitations from strategic postponement, we examine a new paradigm in which subjects are told to place equal emphasis on both tasks and to emit both responses at about the same time. An experiment using this paradigm demonstrated patterns of interference that cannot easily be attributed to strategic postponement, preparation effects, or conflicts in response production. The data conform closely to the predictions of structural central bottleneck models.

Information processing in the primate visual system - An integrated systems perspective

NASA Technical Reports Server (NTRS)

Van Essen, David C.; Anderson, Charles H.; Felleman, Daniel J.

1992-01-01

The primate visual system contains dozens of distinct areas in the cerebral cortex and several major subcortical structures. These subdivisions are extensively interconnected in a distributed hierarchical network that contains several intertwined processing streams. A number of strategies are used for efficient information processing within this hierarchy. These include linear and nonlinear filtering, passage through information bottlenecks, and coordinated use of multiple types of information. In addition, dynamic regulation of information flow within and between visual areas may provide the computational flexibility needed for the visual system to perform a broad spectrum of tasks accurately and at high resolution.

A Prototype System for Retrieval of Gene Functional Information

PubMed Central

Folk, Lillian C.; Patrick, Timothy B.; Pattison, James S.; Wolfinger, Russell D.; Mitchell, Joyce A.

2003-01-01

Microarrays allow researchers to gather data about the expression patterns of thousands of genes simultaneously. Statistical analysis can reveal which genes show statistically significant results. Making biological sense of those results requires the retrieval of functional information about the genes thus identified, typically a manual gene-by-gene retrieval of information from various on-line databases. For experiments generating thousands of genes of interest, retrieval of functional information can become a significant bottleneck. To address this issue, we are currently developing a prototype system to automate the process of retrieval of functional information from multiple on-line sources. PMID:14728346

Northeast Artificial Intelligence Consortium (NAIC). Volume 12. Computer Architecture for Very Large Knowledge Bases

DTIC Science & Technology

1990-12-01

data rate to the electronics would be much lower on the average and the data much "richer" in information. Intelligent use of...system bottleneck, a high data rate should be provided by I/O systems. 2. machines with intelligent storage management specially designed for logic...management information processing, surveillance sensors, intelligence data collection and handling, solid state sciences, electromagnetics, and propagation, and electronic reliability/maintainability and compatibility.

Testing the Predictions of the Central Capacity Sharing Model

ERIC Educational Resources Information Center

Tombu, Michael; Jolicoeur, Pierre

2005-01-01

The divergent predictions of 2 models of dual-task performance are investigated. The central bottleneck and central capacity sharing models argue that a central stage of information processing is capacity limited, whereas stages before and after are capacity free. The models disagree about the nature of this central capacity limitation. The…

The Source of Execution-Related Dual-Task Interference: Motor Bottleneck or Response Monitoring?

ERIC Educational Resources Information Center

Bratzke, Daniel; Rolke, Bettina; Ulrich, Rolf

2009-01-01

The present study assessed the underlying mechanism of execution-related dual-task interference in the psychological refractory period (PRP) paradigm. The motor bottleneck hypothesis attributes this interference to a processing limitation at the motor level. By contrast, the response monitoring hypothesis attributes it to a bottleneck process that…

LBMR: Load-Balanced Multipath Routing for Wireless Data-Intensive Transmission in Real-Time Medical Monitoring.

PubMed

Tseng, Chinyang Henry

2016-05-31

In wireless networks, low-power Zigbee is an excellent network solution for wireless medical monitoring systems. Medical monitoring generally involves transmission of a large amount of data and easily causes bottleneck problems. Although Zigbee's AODV mesh routing provides extensible multi-hop data transmission to extend network coverage, it originally does not, and needs to support some form of load balancing mechanism to avoid bottlenecks. To guarantee a more reliable multi-hop data transmission for life-critical medical applications, we have developed a multipath solution, called Load-Balanced Multipath Routing (LBMR) to replace Zigbee's routing mechanism. LBMR consists of three main parts: Layer Routing Construction (LRC), a Load Estimation Algorithm (LEA), and a Route Maintenance (RM) mechanism. LRC assigns nodes into different layers based on the node's distance to the medical data gateway. Nodes can have multiple next-hops delivering medical data toward the gateway. All neighboring layer-nodes exchange flow information containing current load, which is the used by the LEA to estimate future load of next-hops to the gateway. With LBMR, nodes can choose the neighbors with the least load as the next-hops and thus can achieve load balancing and avoid bottlenecks. Furthermore, RM can detect route failures in real-time and perform route redirection to ensure routing robustness. Since LRC and LEA prevent bottlenecks while RM ensures routing fault tolerance, LBMR provides a highly reliable routing service for medical monitoring. To evaluate these accomplishments, we compare LBMR with Zigbee's AODV and another multipath protocol, AOMDV. The simulation results demonstrate LBMR achieves better load balancing, less unreachable nodes, and better packet delivery ratio than either AODV or AOMDV.

LBMR: Load-Balanced Multipath Routing for Wireless Data-Intensive Transmission in Real-Time Medical Monitoring

PubMed Central

Tseng, Chinyang Henry

2016-01-01

In wireless networks, low-power Zigbee is an excellent network solution for wireless medical monitoring systems. Medical monitoring generally involves transmission of a large amount of data and easily causes bottleneck problems. Although Zigbee’s AODV mesh routing provides extensible multi-hop data transmission to extend network coverage, it originally does not, and needs to support some form of load balancing mechanism to avoid bottlenecks. To guarantee a more reliable multi-hop data transmission for life-critical medical applications, we have developed a multipath solution, called Load-Balanced Multipath Routing (LBMR) to replace Zigbee’s routing mechanism. LBMR consists of three main parts: Layer Routing Construction (LRC), a Load Estimation Algorithm (LEA), and a Route Maintenance (RM) mechanism. LRC assigns nodes into different layers based on the node’s distance to the medical data gateway. Nodes can have multiple next-hops delivering medical data toward the gateway. All neighboring layer-nodes exchange flow information containing current load, which is the used by the LEA to estimate future load of next-hops to the gateway. With LBMR, nodes can choose the neighbors with the least load as the next-hops and thus can achieve load balancing and avoid bottlenecks. Furthermore, RM can detect route failures in real-time and perform route redirection to ensure routing robustness. Since LRC and LEA prevent bottlenecks while RM ensures routing fault tolerance, LBMR provides a highly reliable routing service for medical monitoring. To evaluate these accomplishments, we compare LBMR with Zigbee’s AODV and another multipath protocol, AOMDV. The simulation results demonstrate LBMR achieves better load balancing, less unreachable nodes, and better packet delivery ratio than either AODV or AOMDV. PMID:27258297

Irredundant Sequential Machines Via Optimal Logic Synthesis

DTIC Science & Technology

1989-10-01

1989 Irredundant Sequential Machines Via Optimal Logic Synthesis NSrinivas Devadas , Hi-Keung Tony Ma, A. Richard Newton, and Alberto Sangiovanni- S...Agency under contract N00014-87-K-0825, and a grant from AT & T Bell Laboratories. Author Information Devadas : Department of Electrical Engineering...Sequential Machines Via Optimal Logic Synthesis Srinivas Devadas * Hi-Keung Tony ha. A. Richard Newton and Alberto Sangiovanni-Viucentelli Department of

Boolean Minimization and Algebraic Factorization Procedures for Fully Testable Sequential Machines

DTIC Science & Technology

1989-09-01

Boolean Minimization and Algebraic Factorization Procedures for Fully Testable Sequential Machines Srinivas Devadas and Kurt Keutzer F ( Abstract In this...Projects Agency under contract number N00014-87-K-0825. Author Information Devadas : Department of Electrical Engineering and Computer Science, Room 36...MA 02139; (617) 253-0292. 0 * Boolean Minimization and Algebraic Factorization Procedures for Fully Testable Sequential Machines Siivas Devadas

Distributed Immune Systems for Wireless Network Information Assurance

DTIC Science & Technology

2010-04-26

ratio test (SPRT), where the goal is to optimize a hypothesis testing problem given a trade-off between the probability of errors and the...using cumulative sum (CUSUM) and Girshik-Rubin-Shiryaev (GRSh) statistics. In sequential versions of the problem the sequential probability ratio ...the more complicated problems, in particular those where no clear mean can be established. We developed algorithms based on the sequential probability

How Strategic Is the Central Bottleneck: Can It Be Overcome by Trying Harder?

ERIC Educational Resources Information Center

Ruthruff, Eric; Johnston, James C.; Remington, Roger W.

2009-01-01

Recent dual-task studies suggest that a bottleneck prevents central mental operations from working on more than one task at a time, especially at relatively low practice levels. It remains highly controversial, however, whether this bottleneck is structural (inherent to human cognitive architecture) or merely a strategic choice. If the strategic…

Anatomy of a bottleneck: diagnosing factors limiting population growth in the Puerto Rican Parrot

Treesearch

S.R. Beissinger; Jr Wunderle; J.M. Meyers; B.E. Saether; S. Engen

2008-01-01

The relative importance of genetic, demographic, environmental, and catastrophic processes that maintain population bottlenecks has received little consideration. We evaluate the role of these factors in maintaining the Puerto Rican Parrot (Amazona vittata) in a prolonged bottleneck from 1973 through 2000 despite intensive conservation efforts. We first conduct a risk...

Design of the Hospital Integrated Information Management System Based on Cloud Platform.

PubMed

Aijing, L; Jin, Y

2015-12-01

At present, the outdated information management style cannot meet the needs of hospital management, and has become the bottleneck of hospital's management and development. In order to improve the integrated management of information, hospitals have increased their investment in integrated information management systems. On account of the lack of reasonable and scientific design, some hospital integrated information management systems have common problems, such as unfriendly interface, poor portability and maintainability, low security and efficiency, lack of interactivity and information sharing. To solve the problem, this paper carries out the research and design of a hospital information management system based on cloud platform, which can realize the optimized integration of hospital information resources and save money.

The genetic rescue of two bottlenecked South Island robin populations using translocations of inbred donors.

PubMed

Heber, S; Varsani, A; Kuhn, S; Girg, A; Kempenaers, B; Briskie, J

2013-02-07

Populations forced through bottlenecks typically lose genetic variation and exhibit inbreeding depression. 'Genetic rescue' techniques that introduce individuals from outbred populations can be highly effective in reversing the deleterious effects of inbreeding, but have limited application for the majority of endangered species, which survive only in a few bottlenecked populations. We tested the effectiveness of using highly inbred populations as donors to rescue two isolated and bottlenecked populations of the South Island robin (Petroica australis). Reciprocal translocations significantly increased heterozygosity and allelic diversity. Increased genetic diversity was accompanied by increased juvenile survival and recruitment, sperm quality, and immunocompetence of hybrid individuals (crosses between the two populations) compared with inbred control individuals (crosses within each population). Our results confirm that the implementation of 'genetic rescue' using bottlenecked populations as donors provides a way of preserving endangered species and restoring their viability when outbred donor populations no longer exist.

X-ray scattering data and structural genomics

NASA Astrophysics Data System (ADS)

Doniach, Sebastian

2003-03-01

High throughput structural genomics has the ambitious goal of determining the structure of all, or a very large number of protein folds using the high-resolution techniques of protein crystallography and NMR. However, the program is facing significant bottlenecks in reaching this goal, which include problems of protein expression and crystallization. In this talk, some preliminary results on how the low-resolution technique of small-angle X-ray solution scattering (SAXS) can help ameliorate some of these bottlenecks will be presented. One of the most significant bottlenecks arises from the difficulty of crystallizing integral membrane proteins, where only a handful of structures are available compared to thousands of structures for soluble proteins. By 3-dimensional reconstruction from SAXS data, the size and shape of detergent-solubilized integral membrane proteins can be characterized. This information can then be used to classify membrane proteins which constitute some 25% of all genomes. SAXS may also be used to study the dependence of interparticle interference scattering on solvent conditions so that regions of the protein solution phase diagram which favor crystallization can be elucidated. As a further application, SAXS may be used to provide physical constraints on computational methods for protein structure prediction based on primary sequence information. This in turn can help in identifying structural homologs of a given protein, which can then give clues to its function. D. Walther, F. Cohen and S. Doniach. "Reconstruction of low resolution three-dimensional density maps from one-dimensional small angle x-ray scattering data for biomolecules." J. Appl. Cryst. 33(2):350-363 (2000). Protein structure prediction constrained by solution X-ray scattering data and structural homology identification Zheng WJ, Doniach S JOURNAL OF MOLECULAR BIOLOGY , v. 316(#1) pp. 173-187 FEB 8, 2002

Multitasking or Continuous Partial Attention: A Critical Bottleneck for Digital Natives

ERIC Educational Resources Information Center

Firat, Mehmet

2013-01-01

With the beginning of the second half of the past century, advances in Information and Communication Technologies had unprecedented influence deeply felt in all social structures. The effects were so much widespread that the differences in technology use have created a huge gap between generations in terms of everyday life and lifestyle. As a…

Language processing is not a race against time.

PubMed

Baggio, Giosuè; Vicario, Carmelo M

2016-01-01

We agree with Christiansen & Chater (C&C) that language processing and acquisition are tightly constrained by the limits of sensory and memory systems. However, the human brain supports a range of cognitive functions that mitigate the effects of information processing bottlenecks. The language system is partly organised around these moderating factors, not just around restrictions on storage and computation.

Study on traffic characteristics for a typical expressway on-ramp bottleneck considering various merging behaviors

NASA Astrophysics Data System (ADS)

Sun, Jie; Li, Zhipeng; Sun, Jian

2015-12-01

Recurring bottlenecks at freeway/expressway are considered as the main cause of traffic congestion in urban traffic system while on-ramp bottlenecks are the most significant sites that may result in congestion. In this paper, the traffic bottleneck characteristics for a simple and typical expressway on-ramp are investigated by the means of simulation modeling under the open boundary condition. In simulations, the running behaviors of each vehicle are described by a car-following model with a calibrated optimal velocity function, and lane changing actions at the merging section are modeled by a novel set of rules. We numerically derive the traffic volume of on-ramp bottleneck under different upstream arrival rates of mainline and ramp flows. It is found that the vehicles from the ramp strongly affect the pass of mainline vehicles and the merging ratio changes with the increasing of ramp vehicle, when the arrival rate of mainline flow is greater than a critical value. In addition, we clarify the dependence of the merging ratio of on-ramp bottleneck on the probability of lane changing and the length of the merging section, and some corresponding intelligent control strategies are proposed in actual traffic application.

A Unified Approach to the Synthesis of Fully Testable Sequential Machines

DTIC Science & Technology

1989-10-01

N A Unified Approach to the Synthesis of Fully Testable Sequential Machines Srinivas Devadas and Kurt Keutzer Abstract • In this paper we attempt to...research was supported in part by the Defense Advanced Research Projects Agency under contract N00014-87-K-0825. Author Information Devadas : Department...Fully Testable Sequential Maine(S P Sritiivas Devadas Departinent of Electrical Engineerinig anid Comivi Sciec Massachusetts Institute of Technology

Estimation of the size of genetic bottlenecks in cell-to-cell movement of soil-borne wheat mosaic virus and the possible role of the bottlenecks in speeding up selection of variations in trans-acting genes or elements.

PubMed

Miyashita, Shuhei; Kishino, Hirohisa

2010-02-01

Genetic bottlenecks facilitate the fixation and extinction of variants in populations, and viral populations are no exception to this theory. To examine the existence of genetic bottlenecks in cell-to-cell movement of plant RNA viruses, we prepared constructs for Soil-borne wheat mosaic virus RNA2 vectors carrying two different fluorescent proteins, yellow fluorescent protein (YFP) and cyan fluorescent protein (CFP). Coinoculation of host plant leaves with the two RNA2 vectors and the wild-type RNA1 showed separation of the two vector RNA2s, mostly within seven to nine cell-to-cell movements from individual initially coinfected cells. Our statistical analysis showed that the number of viral RNA genomes establishing infection in adjacent cells after the first cell-to-cell movement from an initially infected cell was 5.97 +/- 0.22 on average and 5.02 +/- 0.29 after the second cell-to-cell movement. These results indicate that plant RNA viruses may generally face narrow genetic bottlenecks in every cell-to-cell movement. Furthermore, our model suggests that, rather than suffering from fitness losses caused by the bottlenecks, the plant RNA viruses are utilizing the repeated genetic bottlenecks as an essential element of rapid selection of their adaptive variants in trans-acting genes or elements to respond to host shifting and changes in the growth conditions of the hosts.

The source of dual-task limitations: Serial or parallel processing of multiple response selections?

PubMed Central

Marois, René

2014-01-01

Although it is generally recognized that the concurrent performance of two tasks incurs costs, the sources of these dual-task costs remain controversial. The serial bottleneck model suggests that serial postponement of task performance in dual-task conditions results from a central stage of response selection that can only process one task at a time. Cognitive-control models, by contrast, propose that multiple response selections can proceed in parallel, but that serial processing of task performance is predominantly adopted because its processing efficiency is higher than that of parallel processing. In the present study, we empirically tested this proposition by examining whether parallel processing would occur when it was more efficient and financially rewarded. The results indicated that even when parallel processing was more efficient and was incentivized by financial reward, participants still failed to process tasks in parallel. We conclude that central information processing is limited by a serial bottleneck. PMID:23864266

Computationally inexpensive identification of noninformative model parameters by sequential screening

NASA Astrophysics Data System (ADS)

Cuntz, Matthias; Mai, Juliane; Zink, Matthias; Thober, Stephan; Kumar, Rohini; Schäfer, David; Schrön, Martin; Craven, John; Rakovec, Oldrich; Spieler, Diana; Prykhodko, Vladyslav; Dalmasso, Giovanni; Musuuza, Jude; Langenberg, Ben; Attinger, Sabine; Samaniego, Luis

2015-08-01

Environmental models tend to require increasing computational time and resources as physical process descriptions are improved or new descriptions are incorporated. Many-query applications such as sensitivity analysis or model calibration usually require a large number of model evaluations leading to high computational demand. This often limits the feasibility of rigorous analyses. Here we present a fully automated sequential screening method that selects only informative parameters for a given model output. The method requires a number of model evaluations that is approximately 10 times the number of model parameters. It was tested using the mesoscale hydrologic model mHM in three hydrologically unique European river catchments. It identified around 20 informative parameters out of 52, with different informative parameters in each catchment. The screening method was evaluated with subsequent analyses using all 52 as well as only the informative parameters. Subsequent Sobol's global sensitivity analysis led to almost identical results yet required 40% fewer model evaluations after screening. mHM was calibrated with all and with only informative parameters in the three catchments. Model performances for daily discharge were equally high in both cases with Nash-Sutcliffe efficiencies above 0.82. Calibration using only the informative parameters needed just one third of the number of model evaluations. The universality of the sequential screening method was demonstrated using several general test functions from the literature. We therefore recommend the use of the computationally inexpensive sequential screening method prior to rigorous analyses on complex environmental models.

Computationally inexpensive identification of noninformative model parameters by sequential screening

NASA Astrophysics Data System (ADS)

Mai, Juliane; Cuntz, Matthias; Zink, Matthias; Thober, Stephan; Kumar, Rohini; Schäfer, David; Schrön, Martin; Craven, John; Rakovec, Oldrich; Spieler, Diana; Prykhodko, Vladyslav; Dalmasso, Giovanni; Musuuza, Jude; Langenberg, Ben; Attinger, Sabine; Samaniego, Luis

2016-04-01

Environmental models tend to require increasing computational time and resources as physical process descriptions are improved or new descriptions are incorporated. Many-query applications such as sensitivity analysis or model calibration usually require a large number of model evaluations leading to high computational demand. This often limits the feasibility of rigorous analyses. Here we present a fully automated sequential screening method that selects only informative parameters for a given model output. The method requires a number of model evaluations that is approximately 10 times the number of model parameters. It was tested using the mesoscale hydrologic model mHM in three hydrologically unique European river catchments. It identified around 20 informative parameters out of 52, with different informative parameters in each catchment. The screening method was evaluated with subsequent analyses using all 52 as well as only the informative parameters. Subsequent Sobol's global sensitivity analysis led to almost identical results yet required 40% fewer model evaluations after screening. mHM was calibrated with all and with only informative parameters in the three catchments. Model performances for daily discharge were equally high in both cases with Nash-Sutcliffe efficiencies above 0.82. Calibration using only the informative parameters needed just one third of the number of model evaluations. The universality of the sequential screening method was demonstrated using several general test functions from the literature. We therefore recommend the use of the computationally inexpensive sequential screening method prior to rigorous analyses on complex environmental models.

Auctions with Dynamic Populations: Efficiency and Revenue Maximization

NASA Astrophysics Data System (ADS)

Said, Maher

We study a stochastic sequential allocation problem with a dynamic population of privately-informed buyers. We characterize the set of efficient allocation rules and show that a dynamic VCG mechanism is both efficient and periodic ex post incentive compatible; we also show that the revenue-maximizing direct mechanism is a pivot mechanism with a reserve price. We then consider sequential ascending auctions in this setting, both with and without a reserve price. We construct equilibrium bidding strategies in this indirect mechanism where bidders reveal their private information in every period, yielding the same outcomes as the direct mechanisms. Thus, the sequential ascending auction is a natural institution for achieving either efficient or optimal outcomes.

An integrated multiscale river basin observing system in the Heihe River Basin, northwest China

NASA Astrophysics Data System (ADS)

Li, X.; Liu, S.; Xiao, Q.; Ma, M.; Jin, R.; Che, T.

2015-12-01

Using the watershed as the unit to establish an integrated watershed observing system has been an important trend in integrated eco-hydrologic studies in the past ten years. Thus far, a relatively comprehensive watershed observing system has been established in the Heihe River Basin, northwest China. In addition, two comprehensive remote sensing hydrology experiments have been conducted sequentially in the Heihe River Basin, including the Watershed Allied Telemetry Experimental Research (WATER) (2007-2010) and the Heihe Watershed Allied Telemetry Experimental Research (HiWATER) (2012-2015). Among these two experiments, an important result of WATER has been the generation of some multi-scale, high-quality comprehensive datasets, which have greatly supported the development, improvement and validation of a series of ecological, hydrological and quantitative remote-sensing models. The goal of a breakthrough for solving the "data bottleneck" problem has been achieved. HiWATER was initiated in 2012. This project has established a world-class hydrological and meteorological observation network, a flux measurement matrix and an eco-hydrological wireless sensor network. A set of super high-resolution airborne remote-sensing data has also been obtained. In addition, there has been important progress with regard to the scaling research. Furthermore, the automatic acquisition, transmission, quality control and remote control of the observational data has been realized through the use of wireless sensor network technology. The observation and information systems have been highly integrated, which will provide a solid foundation for establishing a research platform that integrates observation, data management, model simulation, scenario analysis and decision-making support to foster 21st-century watershed science in China.

When good is stickier than bad: Understanding gain/loss asymmetries in sequential framing effects.

PubMed

Sparks, Jehan; Ledgerwood, Alison

2017-08-01

Considerable research has demonstrated the power of the current positive or negative frame to shape people's current judgments. But humans must often learn about positive and negative information as they encounter that information sequentially over time. It is therefore crucial to consider the potential importance of sequencing when developing an understanding of how humans think about valenced information. Indeed, recent work looking at sequentially encountered frames suggests that some frames can linger outside the context in which they are first encountered, sticking in the mind so that subsequent frames have a muted effect. The present research builds a comprehensive account of sequential framing effects in both the loss and the gain domains. After seeing information about a potential gain or loss framed in positive terms or negative terms, participants saw the same issue reframed in the opposing way. Across 5 studies and 1566 participants, we find accumulating evidence for the notion that in the gain domain, positive frames are stickier than negative frames for novel but not familiar scenarios, whereas in the loss domain, negative frames are always stickier than positive frames. Integrating regulatory focus theory with the literatures on negativity dominance and positivity offset, we develop a new and comprehensive account of sequential framing effects that emphasizes the adaptive value of positivity and negativity biases in specific contexts. Our findings highlight the fact that research conducted solely in the loss domain risks painting an incomplete and oversimplified picture of human bias and suggest new directions for future research. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

The Case for a Gaian Bottleneck: The Biology of Habitability.

PubMed

Chopra, Aditya; Lineweaver, Charles H

2016-01-01

The prerequisites and ingredients for life seem to be abundantly available in the Universe. However, the Universe does not seem to be teeming with life. The most common explanation for this is a low probability for the emergence of life (an emergence bottleneck), notionally due to the intricacies of the molecular recipe. Here, we present an alternative Gaian bottleneck explanation: If life emerges on a planet, it only rarely evolves quickly enough to regulate greenhouse gases and albedo, thereby maintaining surface temperatures compatible with liquid water and habitability. Such a Gaian bottleneck suggests that (i) extinction is the cosmic default for most life that has ever emerged on the surfaces of wet rocky planets in the Universe and (ii) rocky planets need to be inhabited to remain habitable. In the Gaian bottleneck model, the maintenance of planetary habitability is a property more associated with an unusually rapid evolution of biological regulation of surface volatiles than with the luminosity and distance to the host star.

System to improve the Understanding of Collected Logistic Data, to Optimize Cycle-Time and Delivery Performance

NASA Astrophysics Data System (ADS)

van Rooijen, Wim-Jan; Rodriguez, Ben

2002-12-01

A complex production mask-house faces the issue of handling and understanding the logistics information from the production process of the masks. We managed to control key performance indicators like cycle-time, flow-factor, line-speed, WIP, etc. To improve the line flow, we set-up rules for optimising batching at operations and forbid batching between operations, we defined maximum and minimum WIP at the operations, scheduled urgency of the different lots and built rules for bottleneck management. Also we restricted the number of "hot lots". By migrating to the modern MES (manufacturing execution system) MaTISSe, which manages the shopfloor control, and a reporting database, we are able to eliminate the time deviations within our data, caused by data-extraction for different reports at different moments. This gives us a better understanding of our fixed bottleneck and a faster recognition of the temporarily bottlenecks caused by missing availability of machines or men. In this paper we describe the features and advantages of our new MES, as well as the migration process. We have already achieved considerable benefits. Our plan is to extend decision support within the MES, to help both managers and operators to make the right decisions. The project behind this paper reaped major benefits described here and we are looking forward to further challenges and successes.

The Now-or-Never bottleneck: A fundamental constraint on language.

PubMed

Christiansen, Morten H; Chater, Nick

2016-01-01

Memory is fleeting. New material rapidly obliterates previous material. How, then, can the brain deal successfully with the continual deluge of linguistic input? We argue that, to deal with this "Now-or-Never" bottleneck, the brain must compress and recode linguistic input as rapidly as possible. This observation has strong implications for the nature of language processing: (1) the language system must "eagerly" recode and compress linguistic input; (2) as the bottleneck recurs at each new representational level, the language system must build a multilevel linguistic representation; and (3) the language system must deploy all available information predictively to ensure that local linguistic ambiguities are dealt with "Right-First-Time"; once the original input is lost, there is no way for the language system to recover. This is "Chunk-and-Pass" processing. Similarly, language learning must also occur in the here and now, which implies that language acquisition is learning to process, rather than inducing, a grammar. Moreover, this perspective provides a cognitive foundation for grammaticalization and other aspects of language change. Chunk-and-Pass processing also helps explain a variety of core properties of language, including its multilevel representational structure and duality of patterning. This approach promises to create a direct relationship between psycholinguistics and linguistic theory. More generally, we outline a framework within which to integrate often disconnected inquiries into language processing, language acquisition, and language change and evolution.

Design of the Hospital Integrated Information Management System Based on Cloud Platform

PubMed Central

Aijing, L; Jin, Y

2015-01-01

ABSTRACT At present, the outdated information management style cannot meet the needs of hospital management, and has become the bottleneck of hospital's management and development. In order to improve the integrated management of information, hospitals have increased their investment in integrated information management systems. On account of the lack of reasonable and scientific design, some hospital integrated information management systems have common problems, such as unfriendly interface, poor portability and maintainability, low security and efficiency, lack of interactivity and information sharing. To solve the problem, this paper carries out the research and design of a hospital information management system based on cloud platform, which can realize the optimized integration of hospital information resources and save money. PMID:27399033

Genome-wide signatures of population bottlenecks and diversifying selection in European wolves

PubMed Central

Pilot, M; Greco, C; vonHoldt, B M; Jędrzejewska, B; Randi, E; Jędrzejewski, W; Sidorovich, V E; Ostrander, E A; Wayne, R K

2014-01-01

Genomic resources developed for domesticated species provide powerful tools for studying the evolutionary history of their wild relatives. Here we use 61K single-nucleotide polymorphisms (SNPs) evenly spaced throughout the canine nuclear genome to analyse evolutionary relationships among the three largest European populations of grey wolves in comparison with other populations worldwide, and investigate genome-wide effects of demographic bottlenecks and signatures of selection. European wolves have a discontinuous range, with large and connected populations in Eastern Europe and relatively smaller, isolated populations in Italy and the Iberian Peninsula. Our results suggest a continuous decline in wolf numbers in Europe since the Late Pleistocene, and long-term isolation and bottlenecks in the Italian and Iberian populations following their divergence from the Eastern European population. The Italian and Iberian populations have low genetic variability and high linkage disequilibrium, but relatively few autozygous segments across the genome. This last characteristic clearly distinguishes them from populations that underwent recent drastic demographic declines or founder events, and implies long-term bottlenecks in these two populations. Although genetic drift due to spatial isolation and bottlenecks seems to be a major evolutionary force diversifying the European populations, we detected 35 loci that are putatively under diversifying selection. Two of these loci flank the canine platelet-derived growth factor gene, which affects bone growth and may influence differences in body size between wolf populations. This study demonstrates the power of population genomics for identifying genetic signals of demographic bottlenecks and detecting signatures of directional selection in bottlenecked populations, despite their low background variability. PMID:24346500

Encoding Sequential Information in Semantic Space Models: Comparing Holographic Reduced Representation and Random Permutation

PubMed Central

Recchia, Gabriel; Sahlgren, Magnus; Kanerva, Pentti; Jones, Michael N.

2015-01-01

Circular convolution and random permutation have each been proposed as neurally plausible binding operators capable of encoding sequential information in semantic memory. We perform several controlled comparisons of circular convolution and random permutation as means of encoding paired associates as well as encoding sequential information. Random permutations outperformed convolution with respect to the number of paired associates that can be reliably stored in a single memory trace. Performance was equal on semantic tasks when using a small corpus, but random permutations were ultimately capable of achieving superior performance due to their higher scalability to large corpora. Finally, “noisy” permutations in which units are mapped to other units arbitrarily (no one-to-one mapping) perform nearly as well as true permutations. These findings increase the neurological plausibility of random permutations and highlight their utility in vector space models of semantics. PMID:25954306

Lessons from acute HIV infection.

PubMed

Robb, Merlin L; Ananworanich, Jintanat

2016-11-01

Understanding the characteristics of transmission during acute HIV infection (AHI) may inform targets for vaccine-induced immune interdiction. Individuals treated in AHI with a small HIV reservoir size may be ideal candidates for therapeutic HIV vaccines aiming for HIV remission (i.e. viremic control after treatment interruption). The AHI period is brief and peak viremia predicts a viral set point that occurs 4-5 weeks following infection. Robust HIV-specific CD8 T-cell responses lower viral set points. Phylogenetic analyses of founder viruses demonstrated unique bottleneck selections and specific genetic signatures to optimize for high-fitness variants and successful transmission events. HIV clades, route of transmission and the presence of minor variants may affect vaccine protection. Antiretroviral treatment in AHI results in smaller HIV reservoir size, better CD4 T-cell recovery and fewer virus escapes. The knowledge of untreated and treated AHI informs the development of vaccines, in that preventive vaccines will require broad coverage for multiple clades and antigenic variants associated with unique bottleneck selections. Vaccines that help the host to control viremia could minimize onward transmission. Therapeutic HIV vaccines aimed at HIV remission should be studied in early-treated individuals who have few or no viral escape mutants and a more preserved immune system.

Museum DNA reveals the demographic history of the endangered Seychelles warbler.

PubMed

Spurgin, Lewis G; Wright, David J; van der Velde, Marco; Collar, Nigel J; Komdeur, Jan; Burke, Terry; Richardson, David S

2014-11-01

The importance of evolutionary conservation - how understanding evolutionary forces can help guide conservation decisions - is widely recognized. However, the historical demography of many endangered species is unknown, despite the fact that this can have important implications for contemporary ecological processes and for extinction risk. Here, we reconstruct the population history of the Seychelles warbler (Acrocephalus sechellensis) - an ecological model species. By the 1960s, this species was on the brink of extinction, but its previous history is unknown. We used DNA samples from contemporary and museum specimens spanning 140 years to reconstruct bottleneck history. We found a 25% reduction in genetic diversity between museum and contemporary populations, and strong genetic structure. Simulations indicate that the Seychelles warbler was bottlenecked from a large population, with an ancestral N e of several thousands falling to <50 within the last century. Such a rapid decline, due to anthropogenic factors, has important implications for extinction risk in the Seychelles warbler, and our results will inform conservation practices. Reconstructing the population history of this species also allows us to better understand patterns of genetic diversity, inbreeding and promiscuity in the contemporary populations. Our approaches can be applied across species to test ecological hypotheses and inform conservation.

A Novel Ship-Tracking Method for GF-4 Satellite Sequential Images.

PubMed

Yao, Libo; Liu, Yong; He, You

2018-06-22

The geostationary remote sensing satellite has the capability of wide scanning, persistent observation and operational response, and has tremendous potential for maritime target surveillance. The GF-4 satellite is the first geostationary orbit (GEO) optical remote sensing satellite with medium resolution in China. In this paper, a novel ship-tracking method in GF-4 satellite sequential imagery is proposed. The algorithm has three stages. First, a local visual saliency map based on local peak signal-to-noise ratio (PSNR) is used to detect ships in a single frame of GF-4 satellite sequential images. Second, the accuracy positioning of each potential target is realized by a dynamic correction using the rational polynomial coefficients (RPCs) and automatic identification system (AIS) data of ships. Finally, an improved multiple hypotheses tracking (MHT) algorithm with amplitude information is used to track ships by further removing the false targets, and to estimate ships’ motion parameters. The algorithm has been tested using GF-4 sequential images and AIS data. The results of the experiment demonstrate that the algorithm achieves good tracking performance in GF-4 satellite sequential images and estimates the motion information of ships accurately.

Reverse preferential spread in complex networks

NASA Astrophysics Data System (ADS)

Toyoizumi, Hiroshi; Tani, Seiichi; Miyoshi, Naoto; Okamoto, Yoshio

2012-08-01

Large-degree nodes may have a larger influence on the network, but they can be bottlenecks for spreading information since spreading attempts tend to concentrate on these nodes and become redundant. We discuss that the reverse preferential spread (distributing information inversely proportional to the degree of the receiving node) has an advantage over other spread mechanisms. In large uncorrelated networks, we show that the mean number of nodes that receive information under the reverse preferential spread is an upper bound among any other weight-based spread mechanisms, and this upper bound is indeed a logistic growth independent of the degree distribution.

Genetic variation in westslope cutthroat trout Oncorhynchusclarkii lewisi: implications for conservation

USGS Publications Warehouse

Daniel P. Drinan,; Kalinowski, Steven T.; Vu, Ninh V.; Shepard, Bradley B.; Muhlfeld, Clint C.; Campbell, Matthew R.

2011-01-01

Twenty-five populations of westslope cutthroat trout from throughout their native range were genotyped at 20 microsatellite loci to describe the genetic structure of westslope cutthroat trout. The most genetic diversity (heterozygosity, allelic richness, and private alleles) existed in populations from the Snake River drainage, while populations from the Missouri River drainage had the least. Neighbor-joining trees grouped populations according to major river drainages. A great amount of genetic differentiation was present among and within all drainages. Based on Nei’s DS, populations in the Snake River were the most differentiated, while populations in the Missouri River were the least. This pattern of differentiation is consistent with a history of sequential founding events through which westslope cutthroat trout may have experienced a genetic bottleneck as they colonized each river basin from the Snake to the Clark Fork to the Missouri river. These data should serve as a starting point for a discussion on management units and possible distinct population segments. Given the current threats to the persistence of westslope cutthroat trout, and the substantial genetic differentiation between populations, these topics warrant attention.

Integrating Cache Performance Modeling and Tuning Support in Parallelization Tools

NASA Technical Reports Server (NTRS)

Waheed, Abdul; Yan, Jerry; Saini, Subhash (Technical Monitor)

1998-01-01

With the resurgence of distributed shared memory (DSM) systems based on cache-coherent Non Uniform Memory Access (ccNUMA) architectures and increasing disparity between memory and processors speeds, data locality overheads are becoming the greatest bottlenecks in the way of realizing potential high performance of these systems. While parallelization tools and compilers facilitate the users in porting their sequential applications to a DSM system, a lot of time and effort is needed to tune the memory performance of these applications to achieve reasonable speedup. In this paper, we show that integrating cache performance modeling and tuning support within a parallelization environment can alleviate this problem. The Cache Performance Modeling and Prediction Tool (CPMP), employs trace-driven simulation techniques without the overhead of generating and managing detailed address traces. CPMP predicts the cache performance impact of source code level "what-if" modifications in a program to assist a user in the tuning process. CPMP is built on top of a customized version of the Computer Aided Parallelization Tools (CAPTools) environment. Finally, we demonstrate how CPMP can be applied to tune a real Computational Fluid Dynamics (CFD) application.

iHADAMAC: A complementary tool for sequential resonance assignment of globular and highly disordered proteins

NASA Astrophysics Data System (ADS)

Feuerstein, Sophie; Plevin, Michael J.; Willbold, Dieter; Brutscher, Bernhard

2012-01-01

An experiment, iHADAMAC, is presented that yields information on the amino-acid type of individual residues in a protein by editing the 1H- 15N correlations into seven different 2D spectra, each corresponding to a different class of amino-acid types. Amino-acid type discrimination is realized via a Hadamard encoding scheme based on four different spin manipulations as recently introduced in the context of the sequential HADAMAC experiment. Both sequential and intra-residue HADAMAC experiments yield highly complementary information that greatly facilitate resonance assignment of proteins with high frequency degeneracy, as demonstrated here for a 188-residue intrinsically disordered protein fragment of the hepatitis C virus protein NS5A.

Sequential-Simultaneous Processing and Reading Skills in Primary Grade Children.

ERIC Educational Resources Information Center

McRae, Sandra G.

1986-01-01

The study examined relationships between two modes of information processing, simultaneous and sequential, and two sets of reading skills, word recognition and comprehension, among 40 second and third grade students. Results indicated there is a relationship between simultaneous processing and reading comprehension. (Author)

Spatial versus sequential correlations for random access coding

NASA Astrophysics Data System (ADS)

Tavakoli, Armin; Marques, Breno; Pawłowski, Marcin; Bourennane, Mohamed

2016-03-01

Random access codes are important for a wide range of applications in quantum information. However, their implementation with quantum theory can be made in two very different ways: (i) by distributing data with strong spatial correlations violating a Bell inequality or (ii) using quantum communication channels to create stronger-than-classical sequential correlations between state preparation and measurement outcome. Here we study this duality of the quantum realization. We present a family of Bell inequalities tailored to the task at hand and study their quantum violations. Remarkably, we show that the use of spatial and sequential quantum correlations imposes different limitations on the performance of quantum random access codes: Sequential correlations can outperform spatial correlations. We discuss the physics behind the observed discrepancy between spatial and sequential quantum correlations.

Sequential lineup presentation promotes less-biased criterion setting but does not improve discriminability.

PubMed

Palmer, Matthew A; Brewer, Neil

2012-06-01

When compared with simultaneous lineup presentation, sequential presentation has been shown to reduce false identifications to a greater extent than it reduces correct identifications. However, there has been much debate about whether this difference in identification performance represents improved discriminability or more conservative responding. In this research, data from 22 experiments that compared sequential and simultaneous lineups were analyzed using a compound signal-detection model, which is specifically designed to describe decision-making performance on tasks such as eyewitness identification tests. Sequential (cf. simultaneous) presentation did not influence discriminability, but produced a conservative shift in response bias that resulted in less-biased choosing for sequential than simultaneous lineups. These results inform understanding of the effects of lineup presentation mode on eyewitness identification decisions.

Accumulation of evidence during sequential decision making: the importance of top-down factors.

PubMed

de Lange, Floris P; Jensen, Ole; Dehaene, Stanislas

2010-01-13

In the last decade, great progress has been made in characterizing the accumulation of neural information during simple unitary perceptual decisions. However, much less is known about how sequentially presented evidence is integrated over time for successful decision making. The aim of this study was to study the mechanisms of sequential decision making in humans. In a magnetoencephalography (MEG) study, we presented healthy volunteers with sequences of centrally presented arrows. Sequence length varied between one and five arrows, and the accumulated directions of the arrows informed the subject about which hand to use for a button press at the end of the sequence (e.g., LRLRR should result in a right-hand press). Mathematical modeling suggested that nonlinear accumulation was the rational strategy for performing this task in the presence of no or little noise, whereas quasilinear accumulation was optimal in the presence of substantial noise. MEG recordings showed a correlate of evidence integration over parietal and central cortex that was inversely related to the amount of accumulated evidence (i.e., when more evidence was accumulated, neural activity for new stimuli was attenuated). This modulation of activity likely reflects a top-down influence on sensory processing, effectively constraining the influence of sensory information on the decision variable over time. The results indicate that, when making decisions on the basis of sequential information, the human nervous system integrates evidence in a nonlinear manner, using the amount of previously accumulated information to constrain the accumulation of additional evidence.

Land Ahoy! Understanding Submarine Command and Control During the Completion of Inshore Operations.

PubMed

Roberts, Aaron P J; Stanton, Neville A; Fay, Daniel

2017-12-01

The aim of this study was to use multiple command teams to provide empirical evidence for understanding communication flow, information pertinence, and tasks undertaken in a submarine control room when completing higher- and lower-demand inshore operation (INSO) scenarios. The focus of submarine operations has changed, and submarines are increasingly required to operate in costal littoral zones. However, submarine command team performance during INSO is not well understood, particularly from a sociotechnical systems perspective. A submarine control-room simulator was built. The creation of networked workstations allowed a team of nine operators to perform tasks completed by submarine command teams during INSO. The Event Analysis of Systematic Teamwork method was used to model the social, task, and information networks and to describe command team performance. Ten teams were recruited for the study, affording statistical comparisons of how command-team roles and level of demand affected performance. Results indicated that the submarine command-team members are required to rapidly integrate sonar and visual data as the periscope is used, periodically, in a "duck-and-run" fashion, to maintain covertness. The fusion of such information is primarily completed by the operations officer (OPSO), with this operator experiencing significantly greater demand than any other operator. The OPSO was a bottleneck in the command team when completing INSO, experiencing similar load in both scenarios, suggesting that the command team may benefit from data synthesis tasks being more evenly distributed within the command team. The work can inform future control-room design and command-team ways of working by identifying bottlenecks in terms of information and task flow between operators.

Sequential ensemble-based optimal design for parameter estimation: SEQUENTIAL ENSEMBLE-BASED OPTIMAL DESIGN

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

Man, Jun; Zhang, Jiangjiang; Li, Weixuan

2016-10-01

The ensemble Kalman filter (EnKF) has been widely used in parameter estimation for hydrological models. The focus of most previous studies was to develop more efficient analysis (estimation) algorithms. On the other hand, it is intuitively understandable that a well-designed sampling (data-collection) strategy should provide more informative measurements and subsequently improve the parameter estimation. In this work, a Sequential Ensemble-based Optimal Design (SEOD) method, coupled with EnKF, information theory and sequential optimal design, is proposed to improve the performance of parameter estimation. Based on the first-order and second-order statistics, different information metrics including the Shannon entropy difference (SD), degrees ofmore » freedom for signal (DFS) and relative entropy (RE) are used to design the optimal sampling strategy, respectively. The effectiveness of the proposed method is illustrated by synthetic one-dimensional and two-dimensional unsaturated flow case studies. It is shown that the designed sampling strategies can provide more accurate parameter estimation and state prediction compared with conventional sampling strategies. Optimal sampling designs based on various information metrics perform similarly in our cases. The effect of ensemble size on the optimal design is also investigated. Overall, larger ensemble size improves the parameter estimation and convergence of optimal sampling strategy. Although the proposed method is applied to unsaturated flow problems in this study, it can be equally applied in any other hydrological problems.« less

Basic newborn care and neonatal resuscitation: a multi-country analysis of health system bottlenecks and potential solutions

PubMed Central

2015-01-01

Background An estimated two-thirds of the world's 2.7 million newborn deaths could be prevented with quality care at birth and during the postnatal period. Basic Newborn Care (BNC) is part of the solution and includes hygienic birth and newborn care practices including cord care, thermal care, and early and exclusive breastfeeding. Timely provision of resuscitation if needed is also critical to newborn survival. This paper describes health system barriers to BNC and neonatal resuscitation and proposes solutions to scale up evidence-based strategies. Methods The maternal and newborn bottleneck analysis tool was applied by 12 countries in Africa and Asia as part of the Every Newborn Action Plan process. Country workshops engaged technical experts to complete the survey tool, which is designed to synthesise and grade health system "bottlenecks" that hinder the scale up of maternal-newborn intervention packages. We used quantitative and qualitative methods to analyse the bottleneck data, combined with literature review, to present priority bottlenecks and actions relevant to different health system building blocks for BNC and neonatal resuscitation. Results Eleven of the 12 countries provided grading data. Overall, bottlenecks were graded more severely for resuscitation. The most severely graded bottlenecks for BNC were health workforce (8 of 11 countries), health financing (9 out of 11) and service delivery (7 out of 9); and for neonatal resuscitation, workforce (9 out of 10), essential commodities (9 out of 10) and service delivery (8 out of 10). Country teams from Africa graded bottlenecks overall more severely. Improving workforce performance, availability of essential commodities, and well-integrated health service delivery were the key solutions proposed. Conclusions BNC was perceived to have the least health system challenges among the seven maternal and newborn intervention packages assessed. Although neonatal resuscitation bottlenecks were graded more severe than for BNC, similarities particularly in the workforce and service delivery building blocks highlight the inextricable link between the two interventions and the need to equip birth attendants with requisite skills and commodities to assess and care for every newborn. Solutions highlighted by country teams include ensuring more investment to improve workforce performance and distribution, especially numbers of skilled birth attendants, incentives for placement in challenging settings, and skills-based training particularly for neonatal resuscitation. PMID:26391000

A Systematic Approach to Subgroup Classification in Intellectual Disability

ERIC Educational Resources Information Center

Schalock, Robert L.; Luckasson, Ruth

2015-01-01

This article describes a systematic approach to subgroup classification based on a classification framework and sequential steps involved in the subgrouping process. The sequential steps are stating the purpose of the classification, identifying the classification elements, using relevant information, and using clearly stated and purposeful…

A Metacognitive Visuospatial Working Memory Training for Children

ERIC Educational Resources Information Center

Caviola, Sara; Mammarella, Irene C.; Cornoldi, Cesare; Lucangeli, Daniela

2009-01-01

The paper studies whether visuospatial working memory (VSWM) and, specifically, recall of sequential-spatial information, can be improved by metacognitive training. Twenty-two fourth-grade children were involved in seven sessions of sequential-spatial memory training, while twenty-four children attended lessons given by their teacher. The…

Probabilistic physical characteristics of phase transitions at highway bottlenecks: incommensurability of three-phase and two-phase traffic-flow theories.

PubMed

Kerner, Boris S; Klenov, Sergey L; Schreckenberg, Michael

2014-05-01

Physical features of induced phase transitions in a metastable free flow at an on-ramp bottleneck in three-phase and two-phase cellular automaton (CA) traffic-flow models have been revealed. It turns out that at given flow rates at the bottleneck, to induce a moving jam (F → J transition) in the metastable free flow through the application of a time-limited on-ramp inflow impulse, in both two-phase and three-phase CA models the same critical amplitude of the impulse is required. If a smaller impulse than this critical one is applied, neither F → J transition nor other phase transitions can occur in the two-phase CA model. We have found that in contrast with the two-phase CA model, in the three-phase CA model, if the same smaller impulse is applied, then a phase transition from free flow to synchronized flow (F → S transition) can be induced at the bottleneck. This explains why rather than the F → J transition, in the three-phase theory traffic breakdown at a highway bottleneck is governed by an F → S transition, as observed in real measured traffic data. None of two-phase traffic-flow theories incorporates an F → S transition in a metastable free flow at the bottleneck that is the main feature of the three-phase theory. On the one hand, this shows the incommensurability of three-phase and two-phase traffic-flow theories. On the other hand, this clarifies why none of the two-phase traffic-flow theories can explain the set of fundamental empirical features of traffic breakdown at highway bottlenecks.

Budget process bottlenecks for immunization financing in the Democratic Republic of the Congo (DRC).

PubMed

Le Gargasson, Jean-Bernard; Mibulumukini, Benoît; Gessner, Bradford D; Colombini, Anaïs

2014-02-19

In Democratic Republic of the Congo (DRC), the availability of domestic resources for the immunization program is limited and relies mostly on external donor support. DRC has introduced a series of reforms to move the country toward performance-based management and program budgets. The objectives of the study were to: (i) describe the budget process norm, (ii) analyze the budget process in practice and associated bottlenecks at each of its phases, and (iii) collect suggestions made by the actors involved to improve the situation. Quantitative and qualitative data were collected through: a review of published and gray literature, and individual interviews. Bottlenecks in the budget process and disbursement of funds for immunization are one of the causes of limited domestic resources for the program. Critical bottlenecks include: excessive use of off-budget procedures; limited human resources and capacity; lack of motivation; interference from ministries with the standard budget process; dependency toward the development partner's disbursements schedule; and lack of budget implementation tracking. Results show that the health sector's mobilization rate was 59% in 2011. For the credit line specific to immunization program activities, the mobilization rate for the national Expanded Program for Immunization (EPI) was 26% in 2011 and 43% for vaccines (2010). The main bottleneck for the EPI budget line (2011) and vaccine budget line (2011) occurs at the authorization phase. Budget process bottlenecks identified in the analysis lead to a low mobilization rate for the immunization program. The bottlenecks identified show that a poor flow of funds causes an insufficient percentage of already allocated resources to reach various health system levels. Copyright © 2014 Elsevier Ltd. All rights reserved.

Concordance of nuclear and mitochondrial DNA markers in detecting a founder event in Lake Clark sockeye salmon

USGS Publications Warehouse

Ramstad, Kristina M.; Woody, Carol Ann; Habicht, Chris; Sage, G. Kevin; Seeb, James E.; Allendorf, Fred W.

2007-01-01

Genetic bottleneck effects can reduce genetic variation, persistence probability, and evolutionary potential of populations. Previous microsatellite analysis suggested a bottleneck associated with a common founding of sock-eye salmon Oncorhynchus nerka populations of Lake Clark, Alaska, about 100 to 400 generations ago. The common foundingevent occurred after the last glacial recession and resulted in reduced allelic diversity and strong divergence of Lake Clarksockeye salmon relative to neighboring Six Mile Lake and LakeIliamna populations. Here we used two additional genetic marker types (allozymes and mtDNA) to examine these patterns further. Allozyme and mtDNA results were congruent with the microsatellite data in suggesting a common founder event in LakeClark sockeye salmon and confirmed the divergence of Lake Clarkpopulations from neighboring Six Mile Lake and Lake Iliamna populations. The use of multiple marker types provided better understanding of the bottleneck in Lake Clark. For example, the Sucker Bay Lake population had an exceptionally severe reduction in allelic diversity at microsatellite loci, but not at mtDNA. This suggests that the reduced microsatellite variation in Sucker Bay Lake fish is due to consistently smaller effective population size than other Lake Clark populations, rather than a more acute or additional bottleneck since founding. Caution is urged in using reduced heterozygosity as a measure of genetic bottleneck effects because stochastic variance among loci resulted in an overall increase in allozyme heterozygosity within bottlenecked Lake Clark populations. However, heterozygosity excess, which assesses heterozygosity relative to allelic variation, detected genetic bottleneck effects in both allozyme and microsatellite loci. 

Re-constructing nutritional history of Serengeti wildebeest from stable isotopes in tail hair: seasonal starvation patterns in an obligate grazer.

PubMed

Rysava, K; McGill, R A R; Matthiopoulos, J; Hopcraft, J G C

2016-07-15

Nutritional bottlenecks often limit the abundance of animal populations and alter individual behaviours; however, establishing animal condition over extended periods of time using non-invasive techniques has been a major limitation in population ecology. We test if the sequential measurement of δ(15) N values in a continually growing tissue, such as hair, can be used as a natural bio-logger akin to tree rings or ice cores to provide insights into nutritional stress. Nitrogen stable isotope ratios were measured by continuous-flow isotope-ratio mass spectrometry (IRMS) from 20 sequential segments along the tail hairs of 15 migratory wildebeest. Generalized Linear Models were used to test for variation between concurrent segments of hair from the same individual, and to compare the δ(15) N values of starved and non-starved animals. Correlations between δ(15) N values in the hair and periods of above-average energy demand during the annual cycle were tested using Generalized Additive Mixed Models. The time series of nitrogen isotope ratios in the tail hair are comparable between strands from the same individual. The most likely explanation for the pattern of (15) N enrichment between individuals is determined by life phase, and especially the energetic demands associated with reproduction. The mean δ(15) N value of starved animals was greater than that of non-starved animals, suggesting that higher δ(15) N values correlate with periods of nutritional stress. High δ(15) N values in the tail hair of wildebeest are correlated with periods of negative energy balance, suggesting they may be used as a reliable indicator of the animal's nutritional history. This technique might be applicable to other obligate grazers. Most importantly, the sequential isotopic analysis of hair offers a continuous record of the chronic condition of wildebeest (effectively converting point data into time series) and allows researchers to establish the animal's nutritional diary. © 2016 The Authors. Rapid Communications in Mass Spectrometry Published by John Wiley & Sons Ltd.

Sequential contrast-enhanced MR imaging of the penis.

PubMed

Kaneko, K; De Mouy, E H; Lee, B E

1994-04-01

To determine the enhancement patterns of the penis at magnetic resonance (MR) imaging. Sequential contrast material-enhanced MR images of the penis in a flaccid state were obtained in 16 volunteers (12 with normal penile function and four with erectile dysfunction). Subjects with normal erectile function showed gradual and centrifugal enhancement of the corpora cavernosa, while those with erectile dysfunction showed poor enhancement with abnormal progression. Sequential contrast-enhanced MR imaging provides additional morphologic information for the evaluation of erectile dysfunction.

Linkage Disequilibrium Under Recurrent Bottlenecks

PubMed Central

Schaper, E.; Eriksson, A.; Rafajlovic, M.; Sagitov, S.; Mehlig, B.

2012-01-01

To model deviations from selectively neutral genetic variation caused by different forms of selection, it is necessary to first understand patterns of neutral variation. Best understood is neutral genetic variation at a single locus. But, as is well known, additional insights can be gained by investigating multiple loci. The resulting patterns reflect the degree of association (linkage) between loci and provide information about the underlying multilocus gene genealogies. The statistical properties of two-locus gene genealogies have been intensively studied for populations of constant size, as well as for simple demographic histories such as exponential population growth and single bottlenecks. By contrast, the combined effect of recombination and sustained demographic fluctuations is poorly understood. Addressing this issue, we study a two-locus Wright–Fisher model of a population subject to recurrent bottlenecks. We derive coalescent approximations for the covariance of the times to the most recent common ancestor at two loci in samples of two chromosomes. This covariance reflects the degree of association and thus linkage disequilibrium between these loci. We find, first, that an effective population-size approximation describes the numerically observed association between two loci provided that recombination occurs either much faster or much more slowly than the population-size fluctuations. Second, when recombination occurs frequently between but rarely within bottlenecks, we observe that the association of gene histories becomes independent of physical distance over a certain range of distances. Third, we show that in this case, a commonly used measure of linkage disequilibrium, σd2 (closely related to r^2), fails to capture the long-range association between two loci. The reason is that constituent terms, each reflecting the long-range association, cancel. Fourth, we analyze a limiting case in which the long-range association can be described in terms of a Xi coalescent allowing for simultaneous multiple mergers of ancestral lines. PMID:22048021

Brown world forests: increased ungulate browsing keeps temperate trees in recruitment bottlenecks in resource hotspots.

PubMed

Churski, Marcin; Bubnicki, Jakub W; Jędrzejewska, Bogumiła; Kuijper, Dries P J; Cromsigt, Joris P G M

2017-04-01

Plant biomass consumers (mammalian herbivory and fire) are increasingly seen as major drivers of ecosystem structure and function but the prevailing paradigm in temperate forest ecology is still that their dynamics are mainly bottom-up resource-controlled. Using conceptual advances from savanna ecology, particularly the demographic bottleneck model, we present a novel view on temperate forest dynamics that integrates consumer and resource control. We used a fully factorial experiment, with varying levels of ungulate herbivory and resource (light) availability, to investigate how these factors shape recruitment of five temperate tree species. We ran simulations to project how inter- and intraspecific differences in height increment under the different experimental scenarios influence long-term recruitment of tree species. Strong herbivore-driven demographic bottlenecks occurred in our temperate forest system, and bottlenecks were as strong under resource-rich as under resource-poor conditions. Increased browsing by herbivores in resource-rich patches strongly counteracted the increased escape strength of saplings in these patches. This finding is a crucial extension of the demographic bottleneck model which assumes that increased resource availability allows plants to more easily escape consumer-driven bottlenecks. Our study demonstrates that a more dynamic understanding of consumer-resource interactions is necessary, where consumers and plants both respond to resource availability. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

Of cuts and cracks: data analytics on constrained graphs for early prediction of failure in cementitious materials

NASA Astrophysics Data System (ADS)

Kahagalage, Sanath; Tordesillas, Antoinette; Nitka, Michał; Tejchman, Jacek

2017-06-01

Using data from discrete element simulations, we develop a data analytics approach using network flow theory to study force transmission and failure in a `dog-bone' concrete specimen submitted to uniaxial tension. With this approach, we establish the extent to which the bottlenecks, i.e., a subset of contacts that impedes flow and are prone to becoming overloaded, can predict the location of the ultimate macro-crack. At the heart of this analysis is a capacity function that quantifies, in relative terms, the maximum force that can be transmitted through the different contacts or edges in the network. Here we set this function to be solely governed by the size of the contact area between the deformable spherical grains. During all the initial stages of the loading history, when no bonds are broken, we find the bottlenecks coincide consistently with, and therefore predict, the location of the crack that later forms in the failure regime after peak force. When bonds do start to break, they are spread throughout the specimen: in, near, and far from, the bottlenecks. In one stage leading up to peak force, bonds collectively break in the lower portion of the specimen, momentarily shifting the bottlenecks to this location. Just before and around peak force, however, the bottlenecks return to their original location and remain there until the macro-crack emerges right along the bottlenecks.

Flow Analysis Tool White Paper

NASA Technical Reports Server (NTRS)

Boscia, Nichole K.

2012-01-01

Faster networks are continually being built to accommodate larger data transfers. While it is intuitive to think that implementing faster networks will result in higher throughput rates, this is often not the case. There are many elements involved in data transfer, many of which are beyond the scope of the network itself. Although networks may get bigger and support faster technologies, the presence of other legacy components, such as older application software or kernel parameters, can often cause bottlenecks. Engineers must be able to identify when data flows are reaching a bottleneck that is not imposed by the network and then troubleshoot it using the tools available to them. The current best practice is to collect as much information as possible on the network traffic flows so that analysis is quick and easy. Unfortunately, no single method of collecting this information can sufficiently capture the whole endto- end picture. This becomes even more of a hurdle when large, multi-user systems are involved. In order to capture all the necessary information, multiple data sources are required. This paper presents a method for developing a flow analysis tool to effectively collect network flow data from multiple sources and provide that information to engineers in a clear, concise way for analysis. The purpose of this method is to collect enough information to quickly (and automatically) identify poorly performing flows along with the cause of the problem. The method involves the development of a set of database tables that can be populated with flow data from multiple sources, along with an easyto- use, web-based front-end interface to help network engineers access, organize, analyze, and manage all the information.

On the Inefficiency of Equilibria in Linear Bottleneck Congestion Games

NASA Astrophysics Data System (ADS)

de Keijzer, Bart; Schäfer, Guido; Telelis, Orestis A.

We study the inefficiency of equilibrium outcomes in bottleneck congestion games. These games model situations in which strategic players compete for a limited number of facilities. Each player allocates his weight to a (feasible) subset of the facilities with the goal to minimize the maximum (weight-dependent) latency that he experiences on any of these facilities. We derive upper and (asymptotically) matching lower bounds on the (strong) price of anarchy of linear bottleneck congestion games for a natural load balancing social cost objective (i.e., minimize the maximum latency of a facility). We restrict our studies to linear latency functions. Linear bottleneck congestion games still constitute a rich class of games and generalize, for example, load balancing games with identical or uniformly related machines with or without restricted assignments.

Individuation of Pairs of Objects in Infancy

ERIC Educational Resources Information Center

Leslie, Alan M.; Chen, Marian L.

2007-01-01

Looking-time studies examined whether 11-month-old infants can individuate two pairs of objects using only shape information. In order to test individuation, the object pairs were presented sequentially. Infants were familiarized either with the sequential pairs, disk-triangle/disk-triangle (XY/XY), whose shapes differed within but not across…

Demographic Divergence History of Pied Flycatcher and Collared Flycatcher Inferred from Whole-Genome Re-sequencing Data

PubMed Central

Nadachowska-Brzyska, Krystyna; Burri, Reto; Olason, Pall I.; Kawakami, Takeshi; Smeds, Linnéa; Ellegren, Hans

2013-01-01

Profound knowledge of demographic history is a prerequisite for the understanding and inference of processes involved in the evolution of population differentiation and speciation. Together with new coalescent-based methods, the recent availability of genome-wide data enables investigation of differentiation and divergence processes at unprecedented depth. We combined two powerful approaches, full Approximate Bayesian Computation analysis (ABC) and pairwise sequentially Markovian coalescent modeling (PSMC), to reconstruct the demographic history of the split between two avian speciation model species, the pied flycatcher and collared flycatcher. Using whole-genome re-sequencing data from 20 individuals, we investigated 15 demographic models including different levels and patterns of gene flow, and changes in effective population size over time. ABC provided high support for recent (mode 0.3 my, range <0.7 my) species divergence, declines in effective population size of both species since their initial divergence, and unidirectional recent gene flow from pied flycatcher into collared flycatcher. The estimated divergence time and population size changes, supported by PSMC results, suggest that the ancestral species persisted through one of the glacial periods of middle Pleistocene and then split into two large populations that first increased in size before going through severe bottlenecks and expanding into their current ranges. Secondary contact appears to have been established after the last glacial maximum. The severity of the bottlenecks at the last glacial maximum is indicated by the discrepancy between current effective population sizes (20,000–80,000) and census sizes (5–50 million birds) of the two species. The recent divergence time challenges the supposition that avian speciation is a relatively slow process with extended times for intrinsic postzygotic reproductive barriers to evolve. Our study emphasizes the importance of using genome-wide data to unravel tangled demographic histories. Moreover, it constitutes one of the first examples of the inference of divergence history from genome-wide data in non-model species. PMID:24244198

Demographic divergence history of pied flycatcher and collared flycatcher inferred from whole-genome re-sequencing data.

PubMed

Nadachowska-Brzyska, Krystyna; Burri, Reto; Olason, Pall I; Kawakami, Takeshi; Smeds, Linnéa; Ellegren, Hans

2013-11-01

Profound knowledge of demographic history is a prerequisite for the understanding and inference of processes involved in the evolution of population differentiation and speciation. Together with new coalescent-based methods, the recent availability of genome-wide data enables investigation of differentiation and divergence processes at unprecedented depth. We combined two powerful approaches, full Approximate Bayesian Computation analysis (ABC) and pairwise sequentially Markovian coalescent modeling (PSMC), to reconstruct the demographic history of the split between two avian speciation model species, the pied flycatcher and collared flycatcher. Using whole-genome re-sequencing data from 20 individuals, we investigated 15 demographic models including different levels and patterns of gene flow, and changes in effective population size over time. ABC provided high support for recent (mode 0.3 my, range <0.7 my) species divergence, declines in effective population size of both species since their initial divergence, and unidirectional recent gene flow from pied flycatcher into collared flycatcher. The estimated divergence time and population size changes, supported by PSMC results, suggest that the ancestral species persisted through one of the glacial periods of middle Pleistocene and then split into two large populations that first increased in size before going through severe bottlenecks and expanding into their current ranges. Secondary contact appears to have been established after the last glacial maximum. The severity of the bottlenecks at the last glacial maximum is indicated by the discrepancy between current effective population sizes (20,000-80,000) and census sizes (5-50 million birds) of the two species. The recent divergence time challenges the supposition that avian speciation is a relatively slow process with extended times for intrinsic postzygotic reproductive barriers to evolve. Our study emphasizes the importance of using genome-wide data to unravel tangled demographic histories. Moreover, it constitutes one of the first examples of the inference of divergence history from genome-wide data in non-model species.

Dana-Farber Cancer Institute: Discovery of Resistance Mechanisms | Office of Cancer Genomics

Cancer.gov

Resistance to targeted therapy is emerging as a bottleneck to achieving durable drug responses in cancer. The goal of the CTD2 Center at Dana Farber Cancer Institute is to identify mechanisms of resistance for both existing therapeutics as well as for emerging targets even prior to the identification of lead compounds. They aim to use this information to inform combinatorial treatments. In representative examples they have found that YAP1 leads to resistance after KRAS targeting and that PRKACA mediates resistance to HER2 therapy.

Analysis of Optimal Sequential State Discrimination for Linearly Independent Pure Quantum States.

PubMed

Namkung, Min; Kwon, Younghun

2018-04-25

Recently, J. A. Bergou et al. proposed sequential state discrimination as a new quantum state discrimination scheme. In the scheme, by the successful sequential discrimination of a qubit state, receivers Bob and Charlie can share the information of the qubit prepared by a sender Alice. A merit of the scheme is that a quantum channel is established between Bob and Charlie, but a classical communication is not allowed. In this report, we present a method for extending the original sequential state discrimination of two qubit states to a scheme of N linearly independent pure quantum states. Specifically, we obtain the conditions for the sequential state discrimination of N = 3 pure quantum states. We can analytically provide conditions when there is a special symmetry among N = 3 linearly independent pure quantum states. Additionally, we show that the scenario proposed in this study can be applied to quantum key distribution. Furthermore, we show that the sequential state discrimination of three qutrit states performs better than the strategy of probabilistic quantum cloning.

Wind River subbasin restoration: U.S. Geological Survey annual report November 2012 through December 2013

USGS Publications Warehouse

Jezorek, Ian G.; Connolly, Patrick J.

2014-01-01

Evaluating restoration efforts is of interest to many managers and agencies so that funding and time are allocated for best results. The evaluation of various life-histories of Lower Columbia River steelhead within the Wind River subbasin will provide information to better track populations, and to direct habitat restoration and water allocation planning. Increasingly detailed Viable Salmonid Population information, such as that provided by PIT-tagging and instream PTISs networks like those we are building and operating in the Wind River subbasin, will provide data to inform policy and management, as life-history strategies and production bottlenecks are identified and understood.

Nonlinear dimensionality reduction of electroencephalogram (EEG) for Brain Computer interfaces.

PubMed

Teli, Mohammad Nayeem; Anderson, Charles

2009-01-01

Patterns in electroencephalogram (EEG) signals are analyzed for a Brain Computer Interface (BCI). An important aspect of this analysis is the work on transformations of high dimensional EEG data to low dimensional spaces in which we can classify the data according to mental tasks being performed. In this research we investigate how a Neural Network (NN) in an auto-encoder with bottleneck configuration can find such a transformation. We implemented two approximate second-order methods to optimize the weights of these networks, because the more common first-order methods are very slow to converge for networks like these with more than three layers of computational units. The resulting non-linear projections of time embedded EEG signals show interesting separations that are related to tasks. The bottleneck networks do indeed discover nonlinear transformations to low-dimensional spaces that capture much of the information present in EEG signals. However, the resulting low-dimensional representations do not improve classification rates beyond what is possible using Quadratic Discriminant Analysis (QDA) on the original time-lagged EEG.

Algorithm and Architecture Independent Benchmarking with SEAK

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

Tallent, Nathan R.; Manzano Franco, Joseph B.; Gawande, Nitin A.

2016-05-23

Many applications of high performance embedded computing are limited by performance or power bottlenecks. We have designed the Suite for Embedded Applications & Kernels (SEAK), a new benchmark suite, (a) to capture these bottlenecks in a way that encourages creative solutions; and (b) to facilitate rigorous, objective, end-user evaluation for their solutions. To avoid biasing solutions toward existing algorithms, SEAK benchmarks use a mission-centric (abstracted from a particular algorithm) and goal-oriented (functional) specification. To encourage solutions that are any combination of software or hardware, we use an end-user black-box evaluation that can capture tradeoffs between performance, power, accuracy, size, andmore » weight. The tradeoffs are especially informative for procurement decisions. We call our benchmarks future proof because each mission-centric interface and evaluation remains useful despite shifting algorithmic preferences. It is challenging to create both concise and precise goal-oriented specifications for mission-centric problems. This paper describes the SEAK benchmark suite and presents an evaluation of sample solutions that highlights power and performance tradeoffs.« less

The use of polyoxometalates in protein crystallography – An attempt to widen a well-known bottleneck

PubMed Central

Bijelic, Aleksandar; Rompel, Annette

2015-01-01

Polyoxometalates (POMs) are discrete polynuclear metal-oxo anions with a fascinating variety of structures and unique chemical and physical properties. Their application in various fields is well covered in the literature, however little information about their usage in protein crystallization is available. This review summarizes the impact of the vast class of POMs on the formation of protein crystals, a well-known (frustrating) bottleneck in macromolecular crystallography, with the associated structure elucidation and a particular emphasis focused on POM's potential as a powerful crystallization additive for future research. The Protein Data Bank (PDB) was scanned for protein structures with incorporated POMs which were assigned a PDB ligand ID resulting in 30 PDB entries. These structures have been analyzed with regard to (i) the structure of POM itself in the immediate protein environment, (ii) the kind of interaction and position of the POM within the protein structure and (iii) the beneficial effects of POM on protein crystallography apparent so far. PMID:26339074

Modeling cooperative driving behavior in freeway merges.

DOT National Transportation Integrated Search

2011-11-01

Merging locations are major sources of freeway bottlenecks and are therefore important for freeway operations analysis. Microscopic simulation tools have been successfully used to analyze merging bottlenecks and to design optimum geometric configurat...

Cloud Technology May Widen Genomic Bottleneck - TCGA

Cancer.gov

Computational biologist Dr. Ilya Shmulevich suggests that renting cloud computing power might widen the bottleneck for analyzing genomic data. Learn more about his experience with the Cloud in this TCGA in Action Case Study.

Potential performance bottleneck in Linux TCP

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

Wu, Wenji; Crawford, Matt; /Fermilab

2006-12-01

TCP is the most widely used transport protocol on the Internet today. Over the years, especially recently, due to requirements of high bandwidth transmission, various approaches have been proposed to improve TCP performance. The Linux 2.6 kernel is now preemptible. It can be interrupted mid-task, making the system more responsive and interactive. However, we have noticed that Linux kernel preemption can interact badly with the performance of the networking subsystem. In this paper we investigate the performance bottleneck in Linux TCP. We systematically describe the trip of a TCP packet from its ingress into a Linux network end system tomore » its final delivery to the application; we study the performance bottleneck in Linux TCP through mathematical modeling and practical experiments; finally we propose and test one possible solution to resolve this performance bottleneck in Linux TCP.« less

Effect of a Phonon Bottleneck on Exciton and Spin Generation in Self-Assembled In1 -xGaxAs Quantum Dots

NASA Astrophysics Data System (ADS)

Huang, Y. Q.; Buyanova, I. A.; Yang, X. J.; Murayama, A.; Chen, W. M.

2018-04-01

We provide direct experimental evidence for the effect of a phonon bottleneck on exciton and spin generation in self-assembled In0.5Ga0.5As quantum dots (QDs). With the aid of tunable laser spectroscopy, we resolve and identify efficient exciton generation channels in the QDs mediated by longitudinal-optical (LO) phonons from an otherwise inhomogeneously broadened QD emission background that suffers from the phonon bottleneck effect in exciton generation. Spin-generation efficiency is found to be enhanced under the LO-assisted excitation condition due to suppressed spin relaxation accompanying accelerated exciton generation. These findings underline the importance of fine-tuning QD energy levels that will benefit potential spin-optoelectronic applications of QDs by reducing spin loss due to the phonon bottleneck.

Interference of two codirectional exclusion processes in the presence of a static bottleneck: A biologically motivated model

NASA Astrophysics Data System (ADS)

Mishra, Bhavya; Chowdhury, Debashish

2017-06-01

We develop a two-species exclusion process with a distinct pair of entry and exit sites for each species of rigid rods. The relatively slower forward stepping of the rods in an extended bottleneck region, located in between the two entry sites, controls the extent of interference of the codirectional flow of the two species of rods. The relative positions of the sites of entry of the two species of rods with respect to the location of the bottleneck are motivated by a biological phenomenon. However, the primary focus of the study here is to explore the effects of the interference of the flow of the two species of rods on their spatiotemporal organization and the regulations of this interference by the extended bottleneck. By a combination of mean-field theory and computer simulation, we calculate the flux of both species of rods and their density profiles as well as the composite phase diagrams of the system. If the bottleneck is sufficiently stringent, then some of the phases become practically unrealizable, although not ruled out on the basis of any fundamental physical principle. Moreover, the extent of suppression of flow of the downstream entrants by the flow of the upstream entrants can also be regulated by the strength of the bottleneck. We speculate on the possible implications of the results in the context of the biological phenomenon that motivated the formulation of the theoretical model.

Unveiling CO2 heterogeneous freezing plumes during champagne cork popping.

PubMed

Liger-Belair, Gérard; Cordier, Daniel; Honvault, Jacques; Cilindre, Clara

2017-09-14

Cork popping from clear transparent bottles of champagne stored at different temperatures (namely, 6, 12, and 20 °C) was filmed through high-speed video imaging in the visible light spectrum. During the cork popping process, a plume mainly composed of gaseous CO 2 with traces of water vapour freely expands out of the bottleneck through ambient air. Most interestingly, for the bottles stored at 20 °C, the characteristic grey-white cloud of fog classically observed above the bottlenecks of champagne stored at lower temperatures simply disappeared. It is replaced by a more evanescent plume, surprisingly blue, starting from the bottleneck. We suggest that heterogeneous freezing of CO 2 occurs on ice water clusters homogeneously nucleated in the bottlenecks, depending on the saturation ratio experienced by gas-phase CO 2 after adiabatic expansion (indeed highly bottle temperature dependent). Moreover, and as observed for the bottles stored at 20 °C, we show that the freezing of only a small portion of all the available CO 2 is able to pump the energy released through adiabatic expansion, thus completely inhibiting the condensation of water vapour found in air packages adjacent to the gas volume gushing out of the bottleneck.

About the Role of the Bottleneck/Cork Interface on Oxygen Transfer.

PubMed

Lagorce-Tachon, Aurélie; Karbowiak, Thomas; Paulin, Christian; Simon, Jean-Marc; Gougeon, Régis D; Bellat, Jean-Pierre

2016-09-07

The transfer of oxygen through a corked bottleneck was investigated using a manometric technique. First, the effect of cork compression on oxygen transfer was evaluated without considering the glass/cork interface. No significant effect of cork compression (at 23% strain, corresponding to the compression level of cork in a bottleneck for still wines) was noticeable on the effective diffusion coefficient of oxygen. The mean value of the effective diffusion coefficient is equal to 10(-8) m(2) s(-1), with a statistical distribution ranging from 10(-10) to 10(-7) m(2) s(-1), which is of the same order of magnitude as for the non-compressed cork. Then, oxygen transfer through cork compressed in a glass bottleneck was determined to assess the effect of the glass/cork interface. In the particular case of a gradient-imposed diffusion of oxygen through our model corked bottleneck system (dry cork without surface treatment; 200 and ∼0 hPa of oxygen on both sides of the sample), the mean effective diffusion coefficient is of 5 × 10(-7) m(2) s(-1), thus revealing the possible importance of the role of the glass/stopper interface in the oxygen transfer.

Intermodal freight capacity box : intermodal freight bottleneck measures

DOT National Transportation Integrated Search

2000-09-01

The Bureau of Transportation Statistics in partnership with the U.S. Department of Transportation's Office of Intermodalism and the Federal Highway Administration sponsored the development of an Intermodal Bottleneck Evaluation Tool (IBET) to provide...

The development of algorithms for the deployment of new version of GEM-detector-based acquisition system

NASA Astrophysics Data System (ADS)

Krawczyk, Rafał D.; Czarski, Tomasz; Kolasiński, Piotr; Linczuk, Paweł; Poźniak, Krzysztof T.; Chernyshova, Maryna; Kasprowicz, Grzegorz; Wojeński, Andrzej; Zabolotny, Wojciech; Zienkiewicz, Paweł

2016-09-01

This article is an overview of what has been implemented in the process of development and testing the GEM detector based acquisition system in terms of post-processing algorithms. Information is given on mex functions for extended statistics collection, unified hex topology and optimized S-DAQ algorithm for splitting overlapped signals. Additional discussion on bottlenecks and major factors concerning optimization is presented.

Police Communications

NASA Astrophysics Data System (ADS)

1981-01-01

Oklahoma City Police Department developed a computerized communications system, based on Johnson Space Center's (JSC's) 1960-mission control knowledge. JSC furnished information on lighting and other fatigue reducing measures, and provided specifications for equipment and design layouts. JSC also advised OCPD how to avoid communications bottlenecks associated with simultaneous handling of telephone, radio and inner-office transmissions. Oklahoma City saved money in reduced design and engineering costs by utilizing the already developed NASA technology.

Short-term memory for spatial, sequential and duration information.

PubMed

Manohar, Sanjay G; Pertzov, Yoni; Husain, Masud

2017-10-01

Space and time appear to play key roles in the way that information is organized in short-term memory (STM). Some argue that they are crucial contexts within which other stored features are embedded, allowing binding of information that belongs together within STM. Here we review recent behavioral, neurophysiological and imaging studies that have sought to investigate the nature of spatial, sequential and duration representations in STM, and how these might break down in disease. Findings from these studies point to an important role of the hippocampus and other medial temporal lobe structures in aspects of STM, challenging conventional accounts of involvement of these regions in only long-term memory.

RIEMS: a software pipeline for sensitive and comprehensive taxonomic classification of reads from metagenomics datasets.

PubMed

Scheuch, Matthias; Höper, Dirk; Beer, Martin

2015-03-03

Fuelled by the advent and subsequent development of next generation sequencing technologies, metagenomics became a powerful tool for the analysis of microbial communities both scientifically and diagnostically. The biggest challenge is the extraction of relevant information from the huge sequence datasets generated for metagenomics studies. Although a plethora of tools are available, data analysis is still a bottleneck. To overcome the bottleneck of data analysis, we developed an automated computational workflow called RIEMS - Reliable Information Extraction from Metagenomic Sequence datasets. RIEMS assigns every individual read sequence within a dataset taxonomically by cascading different sequence analyses with decreasing stringency of the assignments using various software applications. After completion of the analyses, the results are summarised in a clearly structured result protocol organised taxonomically. The high accuracy and performance of RIEMS analyses were proven in comparison with other tools for metagenomics data analysis using simulated sequencing read datasets. RIEMS has the potential to fill the gap that still exists with regard to data analysis for metagenomics studies. The usefulness and power of RIEMS for the analysis of genuine sequencing datasets was demonstrated with an early version of RIEMS in 2011 when it was used to detect the orthobunyavirus sequences leading to the discovery of Schmallenberg virus.

Museum DNA reveals the demographic history of the endangered Seychelles warbler

PubMed Central

Spurgin, Lewis G; Wright, David J; van der Velde, Marco; Collar, Nigel J; Komdeur, Jan; Burke, Terry; Richardson, David S

2014-01-01

The importance of evolutionary conservation – how understanding evolutionary forces can help guide conservation decisions – is widely recognized. However, the historical demography of many endangered species is unknown, despite the fact that this can have important implications for contemporary ecological processes and for extinction risk. Here, we reconstruct the population history of the Seychelles warbler (Acrocephalus sechellensis) – an ecological model species. By the 1960s, this species was on the brink of extinction, but its previous history is unknown. We used DNA samples from contemporary and museum specimens spanning 140 years to reconstruct bottleneck history. We found a 25% reduction in genetic diversity between museum and contemporary populations, and strong genetic structure. Simulations indicate that the Seychelles warbler was bottlenecked from a large population, with an ancestral Ne of several thousands falling to <50 within the last century. Such a rapid decline, due to anthropogenic factors, has important implications for extinction risk in the Seychelles warbler, and our results will inform conservation practices. Reconstructing the population history of this species also allows us to better understand patterns of genetic diversity, inbreeding and promiscuity in the contemporary populations. Our approaches can be applied across species to test ecological hypotheses and inform conservation. PMID:25553073

Sequential state discrimination and requirement of quantum dissonance

NASA Astrophysics Data System (ADS)

Pang, Chao-Qian; Zhang, Fu-Lin; Xu, Li-Fang; Liang, Mai-Lin; Chen, Jing-Ling

2013-11-01

We study the procedure for sequential unambiguous state discrimination. A qubit is prepared in one of two possible states and measured by two observers Bob and Charlie sequentially. A necessary condition for the state to be unambiguously discriminated by Charlie is the absence of entanglement between the principal qubit, prepared by Alice, and Bob's auxiliary system. In general, the procedure for both Bob and Charlie to recognize between two nonorthogonal states conclusively relies on the availability of quantum discord which is precisely the quantum dissonance when the entanglement is absent. In Bob's measurement, the left discord is positively correlated with the information extracted by Bob, and the right discord enhances the information left to Charlie. When their product achieves its maximum the probability for both Bob and Charlie to identify the state achieves its optimal value.

Advances and bottlenecks in microbial hydrogen production.

PubMed

Stephen, Alan J; Archer, Sophie A; Orozco, Rafael L; Macaskie, Lynne E

2017-09-01

Biological production of hydrogen is poised to become a significant player in the future energy mix. This review highlights recent advances and bottlenecks in various approaches to biohydrogen processes, often in concert with management of organic wastes or waste CO 2 . Some key bottlenecks are highlighted in terms of the overall energy balance of the process and highlighting the need for economic and environmental life cycle analyses with regard also to socio-economic and geographical issues. © 2017 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

Identifying, anticipating, and mitigating freight bottlenecks on Alabama interstates.

DOT National Transportation Integrated Search

2011-07-31

"This project established a framework for the creation and maintenance of a statewide strategy for identifying, : anticipating, and mitigating freight bottlenecks on interstate highways in the state of Alabama. It used : methodology developed by Camb...

Genetic bottlenecks during systemic movement of Cucumber mosaic virus vary in different host plants

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

Ali, Akhtar; Roossinck, Marilyn J., E-mail: mroossinck@noble.or

2010-09-01

Genetic bottlenecks are stochastic events that narrow variation in a population. We compared bottlenecks during the systemic infection of Cucumber mosaic virus (CMV) in four host plants. We mechanically inoculated an artificial population of twelve CMV mutants to young leaves of tomato, pepper, Nicotiana benthamiana, and squash. The inoculated leaves and primary and secondary systemically infected leaves were sampled at 2, 10, and 15 days post-inoculation. All twelve mutants were detected in all of the inoculated leaves. The number of mutants recovered from the systemically infected leaves of all host species was reduced significantly, indicating bottlenecks in systemic movement. Themore » recovery frequencies of a few of the mutants were significantly different in each host probably due to host-specific selective forces. These results have implications for the differences in virus population variation that is seen in different host plants.« less

A recent bottleneck of Y chromosome diversity coincides with a global change in culture

PubMed Central

Saag, Lauri; Vicente, Mário; Sayres, Melissa A. Wilson; Järve, Mari; Talas, Ulvi Gerst; Rootsi, Siiri; Ilumäe, Anne-Mai; Mägi, Reedik; Mitt, Mario; Pagani, Luca; Puurand, Tarmo; Faltyskova, Zuzana; Clemente, Florian; Cardona, Alexia; Metspalu, Ene; Sahakyan, Hovhannes; Yunusbayev, Bayazit; Hudjashov, Georgi; DeGiorgio, Michael; Loogväli, Eva-Liis; Eichstaedt, Christina; Eelmets, Mikk; Chaubey, Gyaneshwer; Tambets, Kristiina; Litvinov, Sergei; Mormina, Maru; Xue, Yali; Ayub, Qasim; Zoraqi, Grigor; Korneliussen, Thorfinn Sand; Akhatova, Farida; Lachance, Joseph; Tishkoff, Sarah; Momynaliev, Kuvat; Ricaut, François-Xavier; Kusuma, Pradiptajati; Razafindrazaka, Harilanto; Pierron, Denis; Cox, Murray P.; Sultana, Gazi Nurun Nahar; Willerslev, Rane; Muller, Craig; Westaway, Michael; Lambert, David; Skaro, Vedrana; Kovačevic´, Lejla; Turdikulova, Shahlo; Dalimova, Dilbar; Khusainova, Rita; Trofimova, Natalya; Akhmetova, Vita; Khidiyatova, Irina; Lichman, Daria V.; Isakova, Jainagul; Pocheshkhova, Elvira; Sabitov, Zhaxylyk; Barashkov, Nikolay A.; Nymadawa, Pagbajabyn; Mihailov, Evelin; Seng, Joseph Wee Tien; Evseeva, Irina; Migliano, Andrea Bamberg; Abdullah, Syafiq; Andriadze, George; Primorac, Dragan; Atramentova, Lubov; Utevska, Olga; Yepiskoposyan, Levon; Marjanovic´, Damir; Kushniarevich, Alena; Behar, Doron M.; Gilissen, Christian; Vissers, Lisenka; Veltman, Joris A.; Balanovska, Elena; Derenko, Miroslava; Malyarchuk, Boris; Metspalu, Andres; Fedorova, Sardana; Eriksson, Anders; Manica, Andrea; Mendez, Fernando L.; Karafet, Tatiana M.; Veeramah, Krishna R.; Bradman, Neil; Hammer, Michael F.; Osipova, Ludmila P.; Balanovsky, Oleg; Khusnutdinova, Elza K.; Johnsen, Knut; Remm, Maido; Thomas, Mark G.; Tyler-Smith, Chris; Underhill, Peter A.; Willerslev, Eske; Nielsen, Rasmus; Metspalu, Mait; Villems, Richard

2015-01-01

It is commonly thought that human genetic diversity in non-African populations was shaped primarily by an out-of-Africa dispersal 50–100 thousand yr ago (kya). Here, we present a study of 456 geographically diverse high-coverage Y chromosome sequences, including 299 newly reported samples. Applying ancient DNA calibration, we date the Y-chromosomal most recent common ancestor (MRCA) in Africa at 254 (95% CI 192–307) kya and detect a cluster of major non-African founder haplogroups in a narrow time interval at 47–52 kya, consistent with a rapid initial colonization model of Eurasia and Oceania after the out-of-Africa bottleneck. In contrast to demographic reconstructions based on mtDNA, we infer a second strong bottleneck in Y-chromosome lineages dating to the last 10 ky. We hypothesize that this bottleneck is caused by cultural changes affecting variance of reproductive success among males. PMID:25770088

Saccadic eye movements impose a natural bottleneck on visual short-term memory.

PubMed

Ohl, Sven; Rolfs, Martin

2017-05-01

Visual short-term memory (VSTM) is a crucial repository of information when events unfold rapidly before our eyes, yet it maintains only a fraction of the sensory information encoded by the visual system. Here, we tested the hypothesis that saccadic eye movements provide a natural bottleneck for the transition of fragile content in sensory memory to VSTM. In 4 experiments, we show that saccades, planned and executed after the disappearance of a memory array, markedly bias visual memory performance. First, items that had appeared at the saccade target were more readily remembered than items that had appeared elsewhere, even though the saccade was irrelevant to the memory task (Experiment 1). Second, this influence was strongest for saccades elicited right after the disappearance of the memory array and gradually declined over the course of a second (Experiment 2). Third, the saccade stabilized memory representations: The imposed bias persisted even several seconds after saccade execution (Experiment 3). Finally, the advantage for stimuli congruent with the saccade target occurred even when that stimulus was far less likely to be probed in the memory test than any other stimulus in the array, ruling out a strategic effort of observers to memorize information presented at the saccade target (Experiment 4). Together, these results make a strong case that saccades inadvertently determine the content of VSTM, and highlight the key role of actions for the fundamental building blocks of cognition. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Reversible logic gates on Physarum Polycephalum

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

Schumann, Andrew

2015-03-10

In this paper, we consider possibilities how to implement asynchronous sequential logic gates and quantum-style reversible logic gates on Physarum polycephalum motions. We show that in asynchronous sequential logic gates we can erase information because of uncertainty in the direction of plasmodium propagation. Therefore quantum-style reversible logic gates are more preferable for designing logic circuits on Physarum polycephalum.

Genetic diversity in Malus ×domestica (Rosaceae) through time in response to domestication.

PubMed

Gross, Briana L; Henk, Adam D; Richards, Christopher M; Fazio, Gennaro; Volk, Gayle M

2014-10-01

• Patterns of genetic diversity in domesticated plants are affected by geographic region of origin and cultivation, intentional artificial selection, and unintentional genetic bottlenecks. While bottlenecks are mainly associated with the initial domestication process, they can also affect diversity during crop improvement. Here, we investigate the impact of the improvement process on the genetic diversity of domesticated apple in comparison with other perennial and annual fruit crops.• Apple cultivars that were developed at various times (ranging from the 13th through the 20th century) and 11 of the 15 apple cultivars that are used for 90% of the apple production in the United States were surveyed for genetic diversity based on either 9 or 19 simple sequence repeats (SSRs). Diversity was compared using standard metrics and model-based approaches based on expected heterozygosity (He) at equilibrium. Improvement bottleneck data for fruit crops were also collected from the literature.• Domesticated apples showed no significant reduction in genetic diversity through time across the last eight centuries. Diversity was generally high, with an average He > 0.7 for apples from all centuries. However, diversity of the apples currently used for the bulk of commercial production was lower.• The improvement bottleneck in domesticated apples appears to be mild or nonexistent, in contrast to improvement bottlenecks in many annual and perennial fruit crops, as documented from the literature survey. The low diversity of the subset of cultivars used for commercial production, however, indicates that an improvement bottleneck may be in progress for this perennial crop. © 2014 Botanical Society of America, Inc.

Description and effects of sequential behavior practice in teacher education.

PubMed

Sharpe, T; Lounsbery, M; Bahls, V

1997-09-01

This study examined the effects of a sequential behavior feedback protocol on the practice-teaching experiences of undergraduate teacher trainees. The performance competencies of teacher trainees were analyzed using an alternative opportunities for appropriate action measure. Data support the added utility of sequential (Sharpe, 1997a, 1997b) behavior analysis information in systematic observation approaches to teacher education. One field-based undergraduate practicum using sequential behavior (i.e., field systems analysis) principles was monitored. Summarized are the key elements of the (a) classroom instruction provided as a precursor to the practice teaching experience, (b) practice teaching experience, and (c) field systems observation tool used for evaluation and feedback, including multiple-baseline data (N = 4) to support this approach to teacher education. Results point to (a) the strong relationship between sequential behavior feedback and the positive change in four preservice teachers' day-to-day teaching practices in challenging situational contexts, and (b) the relationship between changes in teacher practices and positive changes in the behavioral practices of gymnasium pupils. Sequential behavior feedback was also socially validated by the undergraduate participants and Professional Development School teacher supervisors in the study.

The franchise bottleneck

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

Fairman, J.F.

Franchise terms can shape the structure and direction for much of the electricity industry`s future. The electricity distribution franchise can become a wide-mouth jar quenching the large retail customers` thirst for low-cost, reliable energy - or a bottleneck for captive customers.

Unclogging America's arteries : prescriptions for healthier highways

DOT National Transportation Integrated Search

1999-11-01

This first-of-its-kind study examines a significant cause of traffic congestion - America's worst bottlenecks - from three perspectives. First, it examines how much worse the gridlock will become at each of the 18 worst bottlenecks in the United Stat...

Saving Time, Saving Money: The Economics of Unclogging America's Worst Bottlenecks

DOT National Transportation Integrated Search

2000-01-01

A 1999 study by the American Highway Users Alliance entitled "Unclogging America's Arteries: Prescriptions for Healthier Highways" identified the 166 worst bottlenecks in the country and evaluated the benefits of removing them. By assigning monetary ...

Overcoming gaps and bottlenecks to advance precision agriculture

USDA-ARS?s Scientific Manuscript database

Maintaining a clear understanding of the technology gaps, knowledge needs, and training bottlenecks is required for improving adoption of precision agriculture. As an industry, precision agriculture embraces tools, methods, and practices that are constantly changing, requiring industry, education, a...

Inpatient care of small and sick newborns: a multi-country analysis of health system bottlenecks and potential solutions

PubMed Central

2015-01-01

Background Preterm birth is the leading cause of child death worldwide. Small and sick newborns require timely, high-quality inpatient care to survive. This includes provision of warmth, feeding support, safe oxygen therapy and effective phototherapy with prevention and treatment of infections. Inpatient care for newborns requires dedicated ward space, staffed by health workers with specialist training and skills. Many of the estimated 2.8 million newborns that die every year do not have access to such specialised care. Methods The bottleneck analysis tool was applied in 12 countries in Africa and Asia as part of the Every Newborn Action Plan process. Country workshops involved technical experts to complete the survey tool, which is designed to synthesise and grade health system "bottlenecks" (or factors that hinder the scale up) of maternal-newborn intervention packages. For this paper, we used quantitative and qualitative methods to analyse the bottleneck data, and combined these with literature review, to present priority bottlenecks and actions relevant to different health system building blocks for inpatient care of small and sick newborns. Results Inpatient care of small and sick newborns is an intervention package highlighted by all country workshop participants as having critical health system challenges. Health system building blocks with the highest graded (significant or major) bottlenecks were health workforce (10 out of 12 countries) and health financing (10 out of 12 countries), followed by community ownership and partnership (9 out of 12 countries). Priority actions based on solution themes for these bottlenecks are discussed. Conclusions Whilst major bottlenecks to the scale-up of quality inpatient newborn care are present, effective solutions exist. For all countries included, there is a critical need for a neonatal nursing cadre. Small and sick newborns require increased, sustained funding with specific insurance schemes to cover inpatient care and avoid catastrophic out-of-pocket payments. Core competencies, by level of care, should be defined for monitoring of newborn inpatient care, as with emergency obstetric care. Rather than fatalism that small and sick newborns will die, community interventions need to create demand for accessible, high-quality, family-centred inpatient care, including kangaroo mother care, so that every newborn can survive and thrive. PMID:26391335

Lexical Access and Dual-Task Performance: Determining the Locus of the Bottleneck

NASA Technical Reports Server (NTRS)

Allen, Phil

2004-01-01

During the two years of funding for NASA Grant "NCC21325, Lexical access and dual-task performance: Determining the locus of the bottleneck," we completed three experiments involving the psychological refractory period (PRP) and word frequency.

Management of Knowledge Representation Standards Activities

NASA Technical Reports Server (NTRS)

Patil, Ramesh S. (Principal Investigator)

1993-01-01

This report describes the efforts undertaken over the last two years to identify the issues underlying the current difficulties in sharing and reuse, and a community wide initiative to overcome them. First, we discuss four bottlenecks to sharing and reuse, present a vision of a future in which these bottlenecks have been ameliorated, and describe the efforts of the initiative's four working groups to address these bottlenecks. We then address the supporting technology and infrastructure that is critical to enabling the vision of the future. Finally, we consider topics of longer-range interest by reviewing some of the research issues raised by our vision.

Using Modeling and Simulation to Examine the Benefits of a Network Tasking Order

DTIC Science & Technology

2010-01-01

Without careful planning, the topolo- gies that form can suffer from poor Quality of Service (QoS). The networks could have bottlenecks, or worse, be... quality of service Report Documentation Page Form ApprovedOMB No. 0704-0188 Public reporting burden for the collection of information is estimated to...mission type include: • expected communications partners; • type of data transmitted; • bandwidth required (average, burst); • quality of service

Two retrievals from a single cue: A bottleneck persists across episodic and semantic memory.

PubMed

Orscheschek, Franziska; Strobach, Tilo; Schubert, Torsten; Rickard, Timothy

2018-05-01

There is evidence in the literature that two retrievals from long-term memory cannot occur in parallel. To date, however, that work has explored only the case of two retrievals from newly acquired episodic memory. These studies demonstrated a retrieval bottleneck even after dual-retrieval practice. That retrieval bottleneck may be a global property of long-term memory retrieval, or it may apply only to the case of two retrievals from episodic memory. In the current experiments, we explored whether that apparent dual-retrieval bottleneck applies to the case of one retrieval from episodic memory and one retrieval from highly overlearned semantic memory. Across three experiments, subjects learned to retrieve a left or right keypress response form a set of 14 unique word cues (e.g., black-right keypress). In addition, they learned a verbal response which involved retrieving the antonym of the presented cue (e.g., black-"white"). In the dual-retrieval condition, subjects had to retrieve both the keypress response and the antonym word. The results suggest that the retrieval bottleneck is superordinate to specific long-term memory systems and holds across different memory components. In addition, the results support the assumption of a cue-level response chunking account of learned retrieval parallelism.

Mutational Effects and Population Dynamics During Viral Adaptation Challenge Current Models

PubMed Central

Miller, Craig R.; Joyce, Paul; Wichman, Holly A.

2011-01-01

Adaptation in haploid organisms has been extensively modeled but little tested. Using a microvirid bacteriophage (ID11), we conducted serial passage adaptations at two bottleneck sizes (104 and 106), followed by fitness assays and whole-genome sequencing of 631 individual isolates. Extensive genetic variation was observed including 22 beneficial, several nearly neutral, and several deleterious mutations. In the three large bottleneck lines, up to eight different haplotypes were observed in samples of 23 genomes from the final time point. The small bottleneck lines were less diverse. The small bottleneck lines appeared to operate near the transition between isolated selective sweeps and conditions of complex dynamics (e.g., clonal interference). The large bottleneck lines exhibited extensive interference and less stochasticity, with multiple beneficial mutations establishing on a variety of backgrounds. Several leapfrog events occurred. The distribution of first-step adaptive mutations differed significantly from the distribution of second-steps, and a surprisingly large number of second-step beneficial mutations were observed on a highly fit first-step background. Furthermore, few first-step mutations appeared as second-steps and second-steps had substantially smaller selection coefficients. Collectively, the results indicate that the fitness landscape falls between the extremes of smooth and fully uncorrelated, violating the assumptions of many current mutational landscape models. PMID:21041559

Wind River subbasin restoration: Annual report of U.S. Geological Survey activities January 2014 through December 2014

USGS Publications Warehouse

Jezorek, Ian G.; Connolly, Patrick J.

2015-01-01

Evaluating restoration efforts is of interest to many managers and agencies so that funding and time are allocated for best results. The evaluation of various life-histories of Lower Columbia River steelhead within the Wind River subbasin provides information to better track populations, and more effectively direct habitat restoration and water allocation planning. Increasingly detailed Viable Salmonid Population information (Crawford and Rumsey 2009), such as that provided by PIT-tagging and instream PTISs networks like those we build and operate in the Wind River subbasin, provide data to better inform policy and management, as life-history strategies and production bottlenecks are identified and understood.

The specificity of learned parallelism in dual-memory retrieval.

PubMed

Strobach, Tilo; Schubert, Torsten; Pashler, Harold; Rickard, Timothy

2014-05-01

Retrieval of two responses from one visually presented cue occurs sequentially at the outset of dual-retrieval practice. Exclusively for subjects who adopt a mode of grouping (i.e., synchronizing) their response execution, however, reaction times after dual-retrieval practice indicate a shift to learned retrieval parallelism (e.g., Nino & Rickard, in Journal of Experimental Psychology: Learning, Memory, and Cognition, 29, 373-388, 2003). In the present study, we investigated how this learned parallelism is achieved and why it appears to occur only for subjects who group their responses. Two main accounts were considered: a task-level versus a cue-level account. The task-level account assumes that learned retrieval parallelism occurs at the level of the task as a whole and is not limited to practiced cues. Grouping response execution may thus promote a general shift to parallel retrieval following practice. The cue-level account states that learned retrieval parallelism is specific to practiced cues. This type of parallelism may result from cue-specific response chunking that occurs uniquely as a consequence of grouped response execution. The results of two experiments favored the second account and were best interpreted in terms of a structural bottleneck model.

Hydrogen production by the naked active site of the di-iron hydrogenases in water.

PubMed

Zipoli, Federico; Car, Roberto; Cohen, Morrel H; Selloni, Annabella

2009-10-01

We explored the reactivity of the active center of the [FeFe]-hydrogenases detached from the enzyme and immersed in acidified water by first-principles Car-Parrinello molecular-dynamics simulations. We focused on the identification of the structures that are stable and metastable in acidified water and on their activity for hydrogen production. Our calculations revealed that the naked active center could be an efficient catalyst provided that electrons are transferred to the cluster. We found that both bridging and terminal isomers are present at equilibrium and that the bridging configuration is essential for efficient hydrogen production. The formation of the hydrogen molecule occurs via sequential protonations of the distal iron and of the N-atom of the S-CH(2)-NH-CH(2)-S chelating group. H(2) desorption does not involve a significant energy barrier, making the process very efficient at room temperature. We established that the bottleneck in the reaction is the direct proton transfer from water to the vacant site of the distal iron. Moreover, we found that even if the terminal isomer is present at the equilibrium, its strong local hydrophobicity prevents poisoning of the cluster.

Genetic variation in westslope cutthroat trout Oncorhynchus clarkii lewisi: Implications for conservation

USGS Publications Warehouse

Drinan, D.P.; Kalinowski, S.T.; Vu, N.V.; Shepard, B.B.; Muhlfeld, C.C.; Campbell, M.R.

2011-01-01

Twenty-five populations of westslope cutthroat trout from throughout their native range were genotyped at 20 microsatellite loci to describe the genetic structure of westslope cutthroat trout. The most genetic diversity (heterozygosity, allelic richness, and private alleles) existed in populations from the Snake River drainage, while populations from the Missouri River drainage had the least. Neighbor-joining trees grouped populations according to major river drainages. A great amount of genetic differentiation was present among and within all drainages. Based on Nei's DS, populations in the Snake River were the most differentiated, while populations in the Missouri River were the least. This pattern of differentiation is consistent with a history of sequential founding events through which westslope cutthroat trout may have experienced a genetic bottleneck as they colonized each river basin from the Snake to the Clark Fork to the Missouri river. These data should serve as a starting point for a discussion on management units and possible distinct population segments. Given the current threats to the persistence of westslope cutthroat trout, and the substantial genetic differentiation between populations, these topics warrant attention. ?? 2011 Springer Science+Business Media B.V.

Ecology and Evolution of the Human Microbiota: Fire, Farming and Antibiotics

PubMed Central

Gillings, Michael R.; Paulsen, Ian T.; Tetu, Sasha G.

2015-01-01

Human activities significantly affect all ecosystems on the planet, including the assemblages that comprise our own microbiota. Over the last five million years, various evolutionary and ecological drivers have altered the composition of the human microbiota, including the use of fire, the invention of agriculture, and the increasing availability of processed foods after the Industrial Revolution. However, no factor has had a faster or more direct effect than antimicrobial agents. Biocides, disinfectants and antibiotics select for individual cells that carry resistance genes, immediately reducing both overall microbial diversity and within-species genetic diversity. Treated individuals may never recover their original diversity, and repeated treatments lead to a series of genetic bottlenecks. The sequential introduction of diverse antimicrobial agents has selected for increasingly complex DNA elements that carry multiple resistance genes, and has fostered their spread through the human microbiota. Practices that interfere with microbial colonization, such as sanitation, Caesarian births and bottle-feeding, exacerbate the effects of antimicrobials, generating species-poor and less resilient microbial assemblages in the developed world. More and more evidence is accumulating that these perturbations to our internal ecosystems lie at the heart of many diseases whose frequency has shown a dramatic increase over the last half century. PMID:26371047

Ecology and Evolution of the Human Microbiota: Fire, Farming and Antibiotics.

PubMed

Gillings, Michael R; Paulsen, Ian T; Tetu, Sasha G

2015-09-08

Human activities significantly affect all ecosystems on the planet, including the assemblages that comprise our own microbiota. Over the last five million years, various evolutionary and ecological drivers have altered the composition of the human microbiota, including the use of fire, the invention of agriculture, and the increasing availability of processed foods after the Industrial Revolution. However, no factor has had a faster or more direct effect than antimicrobial agents. Biocides, disinfectants and antibiotics select for individual cells that carry resistance genes, immediately reducing both overall microbial diversity and within-species genetic diversity. Treated individuals may never recover their original diversity, and repeated treatments lead to a series of genetic bottlenecks. The sequential introduction of diverse antimicrobial agents has selected for increasingly complex DNA elements that carry multiple resistance genes, and has fostered their spread through the human microbiota. Practices that interfere with microbial colonization, such as sanitation, Caesarian births and bottle-feeding, exacerbate the effects of antimicrobials, generating species-poor and less resilient microbial assemblages in the developed world. More and more evidence is accumulating that these perturbations to our internal ecosystems lie at the heart of many diseases whose frequency has shown a dramatic increase over the last half century.

P-HARP: A parallel dynamic spectral partitioner

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

Sohn, A.; Biswas, R.; Simon, H.D.

1997-05-01

Partitioning unstructured graphs is central to the parallel solution of problems in computational science and engineering. The authors have introduced earlier the sequential version of an inertial spectral partitioner called HARP which maintains the quality of recursive spectral bisection (RSB) while forming the partitions an order of magnitude faster than RSB. The serial HARP is known to be the fastest spectral partitioner to date, three to four times faster than similar partitioners on a variety of meshes. This paper presents a parallel version of HARP, called P-HARP. Two types of parallelism have been exploited: loop level parallelism and recursive parallelism.more » P-HARP has been implemented in MPI on the SGI/Cray T3E and the IBM SP2. Experimental results demonstrate that P-HARP can partition a mesh of over 100,000 vertices into 256 partitions in 0.25 seconds on a 64-processor T3E. Experimental results further show that P-HARP can give nearly a 20-fold speedup on 64 processors. These results indicate that graph partitioning is no longer a major bottleneck that hinders the advancement of computational science and engineering for dynamically-changing real-world applications.« less

Contraception supply chain challenges: a review of evidence from low- and middle-income countries.

PubMed

Mukasa, Bakali; Ali, Moazzam; Farron, Madeline; Van de Weerdt, Renee

2017-10-01

To identify and assess factors determining the functioning of supply chain systems for modern contraception in low- and middle-income countries (LMICs), and to identify challenges contributing to contraception stockouts that may lead to unmet need. Scientific databases and grey literature were searched including Database of Abstracts of Reviews of Effectiveness (DARE), PubMed, MEDLINE, POPLINE, CINAHL, Academic Search Complete, Science Direct, Web of Science, Cochrane Central, Google Scholar, WHO databases and websites of key international organisations. Studies indicated that supply chain system inefficiencies significantly affect availability of modern FP and contraception commodities in LMICs, especially in rural public facilities where distribution barriers may be acute. Supply chain failures or bottlenecks may be attributed to: weak and poorly institutionalized logistic management information systems (LMIS), poor physical infrastructures in LMICs, lack of trained and dedicated staff for supply chain management, inadequate funding, and rigid government policies on task sharing. However, there is evidence that implementing effective LMISs and involving public and private providers will distribution channels resulted in reduction in medical commodities' stockout rates. Supply chain bottlenecks contribute significantly to persistent high stockout rates for modern contraceptives in LMICs. Interventions aimed at enhancing uptake of contraceptives to reduce the problem of unmet need in LMICs should make strong commitments towards strengthening these countries' health commodities supply chain management systems. Current evidence is limited and additional, and well-designed implementation research on contraception supply chain systems is warranted to gain further understanding and insights on the determinants of supply chain bottlenecks and their impact on stockouts of contraception commodities.

Nonlinear analysis and synthesis of video images using deep dynamic bottleneck neural networks for face recognition.

PubMed

Moghadam, Saeed Montazeri; Seyyedsalehi, Seyyed Ali

2018-05-31

Nonlinear components extracted from deep structures of bottleneck neural networks exhibit a great ability to express input space in a low-dimensional manifold. Sharing and combining the components boost the capability of the neural networks to synthesize and interpolate new and imaginary data. This synthesis is possibly a simple model of imaginations in human brain where the components are expressed in a nonlinear low dimensional manifold. The current paper introduces a novel Dynamic Deep Bottleneck Neural Network to analyze and extract three main features of videos regarding the expression of emotions on the face. These main features are identity, emotion and expression intensity that are laid in three different sub-manifolds of one nonlinear general manifold. The proposed model enjoying the advantages of recurrent networks was used to analyze the sequence and dynamics of information in videos. It is noteworthy to mention that this model also has also the potential to synthesize new videos showing variations of one specific emotion on the face of unknown subjects. Experiments on discrimination and recognition ability of extracted components showed that the proposed model has an average of 97.77% accuracy in recognition of six prominent emotions (Fear, Surprise, Sadness, Anger, Disgust, and Happiness), and 78.17% accuracy in the recognition of intensity. The produced videos revealed variations from neutral to the apex of an emotion on the face of the unfamiliar test subject which is on average 0.8 similar to reference videos in the scale of the SSIM method. Copyright © 2018 Elsevier Ltd. All rights reserved.

Microsatellite variation and rare alleles in a bottlenecked Hawaiian Islands endemic: implications for reintroductions

USGS Publications Warehouse

Reynolds, Michelle H.; Pearce, John M.; Lavretsky, Philip; Seixas, Pedro P.; Courtot, Karen

2015-01-01

Conservation of genetic biodiversity in endangered wildlife populations is an important challenge to address since the loss of alleles and genetic drift may influence future adaptability. Reintroduction aims to re-establish species to restored or protected ecosystems; however, moving a subset of individuals may result in loss of gene variants during the management-induced bottleneck (i.e. translocation). The endangered Laysan teal Anas laysanensis was once widespread across the Hawaiian archipelago, but became isolated on Laysan Island (415 ha) from the mid-1800s until 2004 when a translocation to Midway Atoll (596 ha) was undertaken to reduce extinction risks. We compared genetic diversity and quantified variation at microsatellite loci sampled from 230 individuals from the wild populations at Laysan (1999 to 2009) and Midway (2007 to 2010; n = 133 Laysan, n = 96 Midway birds). We identified polymorphic markers by screening nuclear microsatellites (N = 83). Low nuclear variation was detected, consistent with the species’ insular isolation and historical bottleneck. Six of 83 microsatellites were polymorphic. We found limited but similar estimates of allelic richness (2.58 alleles per locus) and heterozygosity within populations. However, 2 rare alleles found in the Laysan source population were not present in Midway’s reintroduced population, and a unique allele was discovered in an individual on Midway. Differentiation between island populations was low (FST = 0.6%), but statistically significant. Our results indicate that genetic drift had little effect on offspring generations 3 to 6 yr post-release and demonstrate the utility of using known founder events to help quantify genetic capture during translocations and to inform management decisions.

Reducing Bottlenecks to Improve the Efficiency of the Lung Cancer Care Delivery Process: A Process Engineering Modeling Approach to Patient-Centered Care.

PubMed

Ju, Feng; Lee, Hyo Kyung; Yu, Xinhua; Faris, Nicholas R; Rugless, Fedoria; Jiang, Shan; Li, Jingshan; Osarogiagbon, Raymond U

2017-12-01

The process of lung cancer care from initial lesion detection to treatment is complex, involving multiple steps, each introducing the potential for substantial delays. Identifying the steps with the greatest delays enables a focused effort to improve the timeliness of care-delivery, without sacrificing quality. We retrospectively reviewed clinical events from initial detection, through histologic diagnosis, radiologic and invasive staging, and medical clearance, to surgery for all patients who had an attempted resection of a suspected lung cancer in a community healthcare system. We used a computer process modeling approach to evaluate delays in care delivery, in order to identify potential 'bottlenecks' in waiting time, the reduction of which could produce greater care efficiency. We also conducted 'what-if' analyses to predict the relative impact of simulated changes in the care delivery process to determine the most efficient pathways to surgery. The waiting time between radiologic lesion detection and diagnostic biopsy, and the waiting time from radiologic staging to surgery were the two most critical bottlenecks impeding efficient care delivery (more than 3 times larger compared to reducing other waiting times). Additionally, instituting surgical consultation prior to cardiac consultation for medical clearance and decreasing the waiting time between CT scans and diagnostic biopsies, were potentially the most impactful measures to reduce care delays before surgery. Rigorous computer simulation modeling, using clinical data, can provide useful information to identify areas for improving the efficiency of care delivery by process engineering, for patients who receive surgery for lung cancer.

Standardization of Freeze Frame TV Codecs

DTIC Science & Technology

1990-06-01

Kodak SV9600 Still Video Transceiver Colorado Video, Inc.286 Digital Transceiver Image Data Corp. CP-200 Photophone Interand Corp. DISCON Imagephone...error recovery Proprietary Proprby retransmission errorIMAGE BUILD-UP Sequential Sequential PHOTOPHONE Video Teleconferenc- DISCON Imaqephone GENERIC...and information transfer is effected among terminals. An indication of the function and power of these commands can be obtained by reviewing Table

A Prospective Sequential Analysis of the Relation between Physical Aggression and Peer Rejection Acts in a High-Risk Preschool Sample

ERIC Educational Resources Information Center

Chen, Chin-Chih; McComas, Jennifer J.; Hartman, Ellie; Symons, Frank J.

2011-01-01

Research Findings: In early childhood education, the social ecology of the child is considered critical for healthy behavioral development. There is, however, relatively little information based on directly observing what children do that describes the moment-by-moment (i.e., sequential) relation between physical aggression and peer rejection acts…

An initial assessment of freight bottlenecks on highways.

DOT National Transportation Integrated Search

2005-10-01

This white paper is an initial effort to identify and quantify, on a national basis, highway bottlenecks that delay trucks and increase costs to businesses and consumers. The paper is the first to look specifically at the impacts and costs of highway...

The sequential structure of brain activation predicts skill.

PubMed

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

2016-01-29

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

Staphylococcus aureus infection dynamics.

PubMed

Pollitt, Eric J G; Szkuta, Piotr T; Burns, Nicola; Foster, Simon J

2018-06-01

Staphylococcus aureus is a human commensal that can also cause systemic infections. This transition requires evasion of the immune response and the ability to exploit different niches within the host. However, the disease mechanisms and the dominant immune mediators against infection are poorly understood. Previously it has been shown that the infecting S. aureus population goes through a population bottleneck, from which very few bacteria escape to establish the abscesses that are characteristic of many infections. Here we examine the host factors underlying the population bottleneck and subsequent clonal expansion in S. aureus infection models, to identify underpinning principles of infection. The bottleneck is a common feature between models and is independent of S. aureus strain. Interestingly, the high doses of S. aureus required for the widely used "survival" model results in a reduced population bottleneck, suggesting that host defences have been simply overloaded. This brings into question the applicability of the survival model. Depletion of immune mediators revealed key breakpoints and the dynamics of systemic infection. Loss of macrophages, including the liver Kupffer cells, led to increased sensitivity to infection as expected but also loss of the population bottleneck and the spread to other organs still occurred. Conversely, neutrophil depletion led to greater susceptibility to disease but with a concomitant maintenance of the bottleneck and lack of systemic spread. We also used a novel microscopy approach to examine abscess architecture and distribution within organs. From these observations we developed a conceptual model for S. aureus disease from initial infection to mature abscess. This work highlights the need to understand the complexities of the infectious process to be able to assign functions for host and bacterial components, and why S. aureus disease requires a seemingly high infectious dose and how interventions such as a vaccine may be more rationally developed.

Microscopic theory of traffic-flow instability governing traffic breakdown at highway bottlenecks: Growing wave of increase in speed in synchronized flow.

PubMed

Kerner, Boris S

2015-12-01

We have revealed a growing local speed wave of increase in speed that can randomly occur in synchronized flow (S) at a highway bottleneck. The development of such a traffic flow instability leads to free flow (F) at the bottleneck; therefore, we call this instability an S→F instability. Whereas the S→F instability leads to a local increase in speed (growing acceleration wave), in contrast, the classical traffic flow instability introduced in the 1950s-1960s and incorporated later in a huge number of traffic flow models leads to a growing wave of a local decrease in speed (growing deceleration wave). We have found that the S→F instability can occur only if there is a finite time delay in driver overacceleration. The initial speed disturbance of increase in speed (called "speed peak") that initiates the S→F instability occurs usually at the downstream front of synchronized flow at the bottleneck. There can be many speed peaks with random amplitudes that occur randomly over time. It has been found that the S→F instability exhibits a nucleation nature: Only when a speed peak amplitude is large enough can the S→F instability occur; in contrast, speed peaks of smaller amplitudes cause dissolving speed waves of a local increase in speed (dissolving acceleration waves) in synchronized flow. We have found that the S→F instability governs traffic breakdown-a phase transition from free flow to synchronized flow (F→S transition) at the bottleneck: The nucleation nature of the S→F instability explains the metastability of free flow with respect to an F→S transition at the bottleneck.

Microscopic theory of traffic-flow instability governing traffic breakdown at highway bottlenecks: Growing wave of increase in speed in synchronized flow

NASA Astrophysics Data System (ADS)

Kerner, Boris S.

2015-12-01

We have revealed a growing local speed wave of increase in speed that can randomly occur in synchronized flow (S) at a highway bottleneck. The development of such a traffic flow instability leads to free flow (F) at the bottleneck; therefore, we call this instability an S →F instability. Whereas the S →F instability leads to a local increase in speed (growing acceleration wave), in contrast, the classical traffic flow instability introduced in the 1950s-1960s and incorporated later in a huge number of traffic flow models leads to a growing wave of a local decrease in speed (growing deceleration wave). We have found that the S →F instability can occur only if there is a finite time delay in driver overacceleration. The initial speed disturbance of increase in speed (called "speed peak") that initiates the S →F instability occurs usually at the downstream front of synchronized flow at the bottleneck. There can be many speed peaks with random amplitudes that occur randomly over time. It has been found that the S →F instability exhibits a nucleation nature: Only when a speed peak amplitude is large enough can the S →F instability occur; in contrast, speed peaks of smaller amplitudes cause dissolving speed waves of a local increase in speed (dissolving acceleration waves) in synchronized flow. We have found that the S →F instability governs traffic breakdown—a phase transition from free flow to synchronized flow (F →S transition) at the bottleneck: The nucleation nature of the S →F instability explains the metastability of free flow with respect to an F →S transition at the bottleneck.

Genetic diversity in Malus × domestica (Rosaceae) through time in response to domestication

USDA-ARS?s Scientific Manuscript database

Patterns of genetic diversity in domesticated plants are affected by geographic region of origin and cultivation, intentional artificial selection, and unintentional loss of diversity referred to as genetic bottlenecks. While bottlenecks are mainly associated with the initial domestication process, ...

Dynamic bottleneck elimination in mattress manufacturing line using theory of constraints.

PubMed

Gundogar, Emin; Sari, Murat; Kokcam, Abdullah H

2016-01-01

There is a tough competition in the furniture sector like other sectors. Along with the varying product range, production system should also be renewed on a regular basis and the production costs should be kept under control. In this study, spring mattress manufacturing line of a furniture manufacturing company is analyzed. The company wants to increase its production output with new investments. The objective is to find the bottlenecks in production line in order to balance the semi-finished material flow. These bottlenecks are investigated and several different scenarios are tested to improve the current manufacturing system. The problem with a main theme based on the elimination of the bottleneck is solved using Goldratt and Cox's theory of constraints with a simulation based heuristic method. Near optimal alternatives are determined by system models built in Arena 13.5 simulation software. Results show that approximately 46 % capacity enhancements with 2 buffer stocks have increased average production by 88.8 %.

Using barcoded Zika virus to assess virus population structure in vitro and in Aedes aegypti mosquitoes.

PubMed

Weger-Lucarelli, James; Garcia, Selene M; Rückert, Claudia; Byas, Alex; O'Connor, Shelby L; Aliota, Matthew T; Friedrich, Thomas C; O'Connor, David H; Ebel, Gregory D

2018-06-20

Arboviruses such as Zika virus (ZIKV, Flaviviridae; Flavivirus) must replicate in both mammalian and insect hosts possessing strong immune defenses. Accordingly, transmission between and replication within hosts involves genetic bottlenecks, during which viral population size and genetic diversity may be significantly reduced. To help quantify these bottlenecks and their effects, we constructed 4 "barcoded" ZIKV populations that theoretically contain thousands of barcodes each. After identifying the most diverse barcoded virus, we passaged this virus 3 times in 2 mammalian and mosquito cell lines and characterized the population using deep sequencing of the barcoded region of the genome. C6/36 maintain higher barcode diversity, even after 3 passages, than Vero. Additionally, field-caught mosquitoes exposed to the virus to assess bottlenecks in a natural host. A progressive reduction in barcode diversity occurred throughout systemic infection of these mosquitoes. Differences in bottlenecks during systemic spread were observed between different populations of Aedes aegypti. Copyright © 2018. Published by Elsevier Inc.

A recent bottleneck of Y chromosome diversity coincides with a global change in culture.

PubMed

Karmin, Monika; Saag, Lauri; Vicente, Mário; Wilson Sayres, Melissa A; Järve, Mari; Talas, Ulvi Gerst; Rootsi, Siiri; Ilumäe, Anne-Mai; Mägi, Reedik; Mitt, Mario; Pagani, Luca; Puurand, Tarmo; Faltyskova, Zuzana; Clemente, Florian; Cardona, Alexia; Metspalu, Ene; Sahakyan, Hovhannes; Yunusbayev, Bayazit; Hudjashov, Georgi; DeGiorgio, Michael; Loogväli, Eva-Liis; Eichstaedt, Christina; Eelmets, Mikk; Chaubey, Gyaneshwer; Tambets, Kristiina; Litvinov, Sergei; Mormina, Maru; Xue, Yali; Ayub, Qasim; Zoraqi, Grigor; Korneliussen, Thorfinn Sand; Akhatova, Farida; Lachance, Joseph; Tishkoff, Sarah; Momynaliev, Kuvat; Ricaut, François-Xavier; Kusuma, Pradiptajati; Razafindrazaka, Harilanto; Pierron, Denis; Cox, Murray P; Sultana, Gazi Nurun Nahar; Willerslev, Rane; Muller, Craig; Westaway, Michael; Lambert, David; Skaro, Vedrana; Kovačevic, Lejla; Turdikulova, Shahlo; Dalimova, Dilbar; Khusainova, Rita; Trofimova, Natalya; Akhmetova, Vita; Khidiyatova, Irina; Lichman, Daria V; Isakova, Jainagul; Pocheshkhova, Elvira; Sabitov, Zhaxylyk; Barashkov, Nikolay A; Nymadawa, Pagbajabyn; Mihailov, Evelin; Seng, Joseph Wee Tien; Evseeva, Irina; Migliano, Andrea Bamberg; Abdullah, Syafiq; Andriadze, George; Primorac, Dragan; Atramentova, Lubov; Utevska, Olga; Yepiskoposyan, Levon; Marjanovic, Damir; Kushniarevich, Alena; Behar, Doron M; Gilissen, Christian; Vissers, Lisenka; Veltman, Joris A; Balanovska, Elena; Derenko, Miroslava; Malyarchuk, Boris; Metspalu, Andres; Fedorova, Sardana; Eriksson, Anders; Manica, Andrea; Mendez, Fernando L; Karafet, Tatiana M; Veeramah, Krishna R; Bradman, Neil; Hammer, Michael F; Osipova, Ludmila P; Balanovsky, Oleg; Khusnutdinova, Elza K; Johnsen, Knut; Remm, Maido; Thomas, Mark G; Tyler-Smith, Chris; Underhill, Peter A; Willerslev, Eske; Nielsen, Rasmus; Metspalu, Mait; Villems, Richard; Kivisild, Toomas

2015-04-01

It is commonly thought that human genetic diversity in non-African populations was shaped primarily by an out-of-Africa dispersal 50-100 thousand yr ago (kya). Here, we present a study of 456 geographically diverse high-coverage Y chromosome sequences, including 299 newly reported samples. Applying ancient DNA calibration, we date the Y-chromosomal most recent common ancestor (MRCA) in Africa at 254 (95% CI 192-307) kya and detect a cluster of major non-African founder haplogroups in a narrow time interval at 47-52 kya, consistent with a rapid initial colonization model of Eurasia and Oceania after the out-of-Africa bottleneck. In contrast to demographic reconstructions based on mtDNA, we infer a second strong bottleneck in Y-chromosome lineages dating to the last 10 ky. We hypothesize that this bottleneck is caused by cultural changes affecting variance of reproductive success among males. © 2015 Karmin et al.; Published by Cold Spring Harbor Laboratory Press.

Reducing the Analytical Bottleneck for Domain Scientists: Lessons from a Climate Data Visualization Case Study

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

Dasgupta, Aritra; Poco, Jorge; Bertini, Enrico

2016-01-01

The gap between large-scale data production rate and the rate of generation of data-driven scientific insights has led to an analytical bottleneck in scientific domains like climate, biology, etc. This is primarily due to the lack of innovative analytical tools that can help scientists efficiently analyze and explore alternative hypotheses about the data, and communicate their findings effectively to a broad audience. In this paper, by reflecting on a set of successful collaborative research efforts between with a group of climate scientists and visualization researchers, we introspect how interactive visualization can help reduce the analytical bottleneck for domain scientists.

Effect of density feedback on the two-route traffic scenario with bottleneck

NASA Astrophysics Data System (ADS)

Sun, Xiao-Yan; Ding, Zhong-Jun; Huang, Guo-Hua

2016-12-01

In this paper, we investigate the effect of density feedback on the two-route scenario with a bottleneck. The simulation and theory analysis shows that there exist two critical vehicle entry probabilities αc1 and αc2. When vehicle entry probability α≤αc1, four different states, i.e. free flow state, transition state, maximum current state and congestion state are identified in the system, which correspond to three critical reference densities. However, in the interval αc1<α<αc2, the free flow and transition state disappear, and there is only congestion state when α≥αc2. According to the results, traffic control center can adjust the reference density so that the system is in maximum current state. In this case, the capacity of the traffic system reaches maximum so that drivers can make full use of the roads. We hope that the study results can provide good advice for alleviating traffic jam and be useful to traffic control center for designing advanced traveller information systems.

Inferring Demographic History Using Two-Locus Statistics.

PubMed

Ragsdale, Aaron P; Gutenkunst, Ryan N

2017-06-01

Population demographic history may be learned from contemporary genetic variation data. Methods based on aggregating the statistics of many single loci into an allele frequency spectrum (AFS) have proven powerful, but such methods ignore potentially informative patterns of linkage disequilibrium (LD) between neighboring loci. To leverage such patterns, we developed a composite-likelihood framework for inferring demographic history from aggregated statistics of pairs of loci. Using this framework, we show that two-locus statistics are more sensitive to demographic history than single-locus statistics such as the AFS. In particular, two-locus statistics escape the notorious confounding of depth and duration of a bottleneck, and they provide a means to estimate effective population size based on the recombination rather than mutation rate. We applied our approach to a Zambian population of Drosophila melanogaster Notably, using both single- and two-locus statistics, we inferred a substantially lower ancestral effective population size than previous works and did not infer a bottleneck history. Together, our results demonstrate the broad potential for two-locus statistics to enable powerful population genetic inference. Copyright © 2017 by the Genetics Society of America.

Factory approach can streamline patient accounting.

PubMed

Rands, J; Muench, M

1991-08-01

Although they may seem fundamentally different, similarities exist between operations of factories and healthcare organizations' business offices. As a result, a patient accounting approach based on manufacturing firms' management techniques may help smooth healthcare business processes. Receivables performance management incorporates the Japanese techniques of "just-in-time" and total quality management to reduce unbilled accounts and information backlog and accelerate payment. A preliminary diagnostic assessment of a patient accounting process helps identify bottlenecks and set priorities for work flow.

Concurrent Learning of Control in Multi agent Sequential Decision Tasks

DTIC Science & Technology

2018-04-17

Concurrent Learning of Control in Multi-agent Sequential Decision Tasks The overall objective of this project was to develop multi-agent reinforcement...learning (MARL) approaches for intelligent agents to autonomously learn distributed control policies in decentral- ized partially observable...shall be subject to any oenalty for failing to comply with a collection of information if it does not display a currently valid OMB control number

The bandwidth of consolidation into visual short-term memory (VSTM) depends on the visual feature

PubMed Central

Miller, James R.; Becker, Mark W.; Liu, Taosheng

2014-01-01

We investigated the nature of the bandwidth limit in the consolidation of visual information into visual short-term memory. In the first two experiments, we examined whether previous results showing differential consolidation bandwidth for color and orientation resulted from methodological differences by testing the consolidation of color information with methods used in prior orientation experiments. We briefly presented two color patches with masks, either sequentially or simultaneously, followed by a location cue indicating the target. Participants identified the target color via button-press (Experiment 1) or by clicking a location on a color wheel (Experiment 2). Although these methods have previously demonstrated that two orientations are consolidated in a strictly serial fashion, here we found equivalent performance in the sequential and simultaneous conditions, suggesting that two colors can be consolidated in parallel. To investigate whether this difference resulted from different consolidation mechanisms or a common mechanism with different features consuming different amounts of bandwidth, Experiment 3 presented a color patch and an oriented grating either sequentially or simultaneously. We found a lower performance in the simultaneous than the sequential condition, with orientation showing a larger impairment than color. These results suggest that consolidation of both features share common mechanisms. However, it seems that color requires less information to be encoded than orientation. As a result two colors can be consolidated in parallel without exceeding the bandwidth limit, whereas two orientations or an orientation and a color exceed the bandwidth and appear to be consolidated serially. PMID:25317065

Diagnostic causal reasoning with verbal information.

PubMed

Meder, Björn; Mayrhofer, Ralf

2017-08-01

In diagnostic causal reasoning, the goal is to infer the probability of causes from one or multiple observed effects. Typically, studies investigating such tasks provide subjects with precise quantitative information regarding the strength of the relations between causes and effects or sample data from which the relevant quantities can be learned. By contrast, we sought to examine people's inferences when causal information is communicated through qualitative, rather vague verbal expressions (e.g., "X occasionally causes A"). We conducted three experiments using a sequential diagnostic inference task, where multiple pieces of evidence were obtained one after the other. Quantitative predictions of different probabilistic models were derived using the numerical equivalents of the verbal terms, taken from an unrelated study with different subjects. We present a novel Bayesian model that allows for incorporating the temporal weighting of information in sequential diagnostic reasoning, which can be used to model both primacy and recency effects. On the basis of 19,848 judgments from 292 subjects, we found a remarkably close correspondence between the diagnostic inferences made by subjects who received only verbal information and those of a matched control group to whom information was presented numerically. Whether information was conveyed through verbal terms or numerical estimates, diagnostic judgments closely resembled the posterior probabilities entailed by the causes' prior probabilities and the effects' likelihoods. We observed interindividual differences regarding the temporal weighting of evidence in sequential diagnostic reasoning. Our work provides pathways for investigating judgment and decision making with verbal information within a computational modeling framework. Copyright © 2017 Elsevier Inc. All rights reserved.

Structural drift: the population dynamics of sequential learning.

PubMed

Crutchfield, James P; Whalen, Sean

2012-01-01

We introduce a theory of sequential causal inference in which learners in a chain estimate a structural model from their upstream "teacher" and then pass samples from the model to their downstream "student". It extends the population dynamics of genetic drift, recasting Kimura's selectively neutral theory as a special case of a generalized drift process using structured populations with memory. We examine the diffusion and fixation properties of several drift processes and propose applications to learning, inference, and evolution. We also demonstrate how the organization of drift process space controls fidelity, facilitates innovations, and leads to information loss in sequential learning with and without memory.

Viewer Perspective Affects Central Bottleneck Requirements in Spatial Translation Tasks

ERIC Educational Resources Information Center

Franz, Elizabeth A.; Sebastian, Alexandra; Hust, Christina; Norris, Tom

2008-01-01

A psychological refractory period (PRP) approach and the locus of slack logic were applied to examine the novel question of whether spatial translation processes can begin before the central bottleneck when effector or noneffector stimuli are processed from an egocentric (viewer-centered) perspective. In single tasks, trials requiring spatial…

Social Influences in Sequential Decision Making

PubMed Central

Schöbel, Markus; Rieskamp, Jörg; Huber, Rafael

2016-01-01

People often make decisions in a social environment. The present work examines social influence on people’s decisions in a sequential decision-making situation. In the first experimental study, we implemented an information cascade paradigm, illustrating that people infer information from decisions of others and use this information to make their own decisions. We followed a cognitive modeling approach to elicit the weight people give to social as compared to private individual information. The proposed social influence model shows that participants overweight their own private information relative to social information, contrary to the normative Bayesian account. In our second study, we embedded the abstract decision problem of Study 1 in a medical decision-making problem. We examined whether in a medical situation people also take others’ authority into account in addition to the information that their decisions convey. The social influence model illustrates that people weight social information differentially according to the authority of other decision makers. The influence of authority was strongest when an authority's decision contrasted with private information. Both studies illustrate how the social environment provides sources of information that people integrate differently for their decisions. PMID:26784448

Social Influences in Sequential Decision Making.

PubMed

Schöbel, Markus; Rieskamp, Jörg; Huber, Rafael

2016-01-01

People often make decisions in a social environment. The present work examines social influence on people's decisions in a sequential decision-making situation. In the first experimental study, we implemented an information cascade paradigm, illustrating that people infer information from decisions of others and use this information to make their own decisions. We followed a cognitive modeling approach to elicit the weight people give to social as compared to private individual information. The proposed social influence model shows that participants overweight their own private information relative to social information, contrary to the normative Bayesian account. In our second study, we embedded the abstract decision problem of Study 1 in a medical decision-making problem. We examined whether in a medical situation people also take others' authority into account in addition to the information that their decisions convey. The social influence model illustrates that people weight social information differentially according to the authority of other decision makers. The influence of authority was strongest when an authority's decision contrasted with private information. Both studies illustrate how the social environment provides sources of information that people integrate differently for their decisions.

Examining Informal Learning in Commercial Airline Pilots' Communities of Practice

ERIC Educational Resources Information Center

Corns, Kevin M.

2014-01-01

A pragmatic sequential mixed methods research methodology was used to examine commercial airline pilots' (N =156) types and frequencies of informal learning activities, perceptions of workplace informal learning, and opinions on how organizations should support workplace informal learning outside of the formal learning environment. This study…

Sequential causal inference: Application to randomized trials of adaptive treatment strategies

PubMed Central

Dawson, Ree; Lavori, Philip W.

2009-01-01

SUMMARY Clinical trials that randomize subjects to decision algorithms, which adapt treatments over time according to individual response, have gained considerable interest as investigators seek designs that directly inform clinical decision making. We consider designs in which subjects are randomized sequentially at decision points, among adaptive treatment options under evaluation. We present a sequential method to estimate the comparative effects of the randomized adaptive treatments, which are formalized as adaptive treatment strategies. Our causal estimators are derived using Bayesian predictive inference. We use analytical and empirical calculations to compare the predictive estimators to (i) the ‘standard’ approach that allocates the sequentially obtained data to separate strategy-specific groups as would arise from randomizing subjects at baseline; (ii) the semi-parametric approach of marginal mean models that, under appropriate experimental conditions, provides the same sequential estimator of causal differences as the proposed approach. Simulation studies demonstrate that sequential causal inference offers substantial efficiency gains over the standard approach to comparing treatments, because the predictive estimators can take advantage of the monotone structure of shared data among adaptive strategies. We further demonstrate that the semi-parametric asymptotic variances, which are marginal ‘one-step’ estimators, may exhibit significant bias, in contrast to the predictive variances. We show that the conditions under which the sequential method is attractive relative to the other two approaches are those most likely to occur in real studies. PMID:17914714

Urban park characteristics, genetic variation, and historical demography of white-footed mouse (Peromyscus leucopus) populations in New York City

PubMed Central

Nagy, Christopher

2014-01-01

Severe fragmentation is a typical fate of native remnant habitats in cities, and urban wildlife with limited dispersal ability are predicted to lose genetic variation in isolated urban patches. However, little information exists on the characteristics of urban green spaces required to conserve genetic variation. In this study, we examine whether isolation in New York City (NYC) parks results in genetic bottlenecks in white-footed mice (Peromyscus leucopus), and test the hypotheses that park size and time since isolation are associated with genetic variability using nonlinear regression and information-theoretic model selection. White-footed mice have previously been documented to exhibit male-biased dispersal, which may create disparities in genetic variation between males and females in urban parks. We use genotypes of 18 neutral microsatellite data and four different statistical tests to assess this prediction. Given that sex-biased dispersal may create disparities between population genetic patterns inferred from bi- vs. uni-parentally inherited markers, we also sequenced a 324 bp segment of the mitochondrial D-loop for independent inferences of historical demography in urban P. leucopus. We report that isolation in urban parks does not necessarily result in genetic bottlenecks; only three out of 14 populations in NYC parks exhibited a signature of a recent bottleneck at 18 neutral microsatellite loci. Mouse populations in larger urban parks, or parks that have been isolated for shorter periods of time, also do not generally contain greater genetic variation than populations in smaller parks. These results suggest that even small networks of green spaces may be sufficient to maintain the evolutionary potential of native species with certain characteristics. We also found that isolation in urban parks results in weak to nonexistent sex-biased dispersal in a species known to exhibit male-biased dispersal in less fragmented environments. In contrast to nuclear loci, mitochondrial D-loop haplotypes exhibited a mutational pattern of demographic expansion after a recent bottleneck or selective sweep. Estimates of the timing of this expansion suggest that it occurred concurrent with urbanization of NYC over the last few dozens to hundreds of years. Given the general non-neutrality of mtDNA in many systems and evidence of selection on related coding sequences in urban P. leucopus, we argue that the P. leucopus mitochondrial genome experienced recent negative selection against haplotypes not favored in isolated urban parks. In general, rapid adaptive evolution driven by urbanization, global climate change, and other human-caused factors is underappreciated by evolutionary biologists, but many more cases will likely be documented in the near future. PMID:24688884

Evidence of low genetic variation and rare alleles in a bottlenecked endangered island endemic, the Lasan Teal (Anas laysanensis)

USGS Publications Warehouse

Reynolds, Michelle H.; Pearce, John M.; Lavretsky, Philip; Peters Jeffrey L,; Courtot, Karen; Seixas, Pedro P.

2015-01-01

Genetic diversity is assumed to reflect the evolutionary potential and adaptability of populations, and thus quantifying the genetic diversity of endangered species is useful for recovery programs. In particular, if conservation strategies include reintroductions, periodic genetic assessments are useful to evaluate whether management efforts have resulted in the maximization or loss of genetic variation within populations over generations. In this study, we collected blood, feather, and tissue samples during 1999–2009 and quantified genetic diversity for a critically endangered waterfowl species endemic to the Hawaiian archipelago, the Laysan teal or duck (Anas laysanensis; n = 239 individual birds sampled). The last extant population of this species at Laysan Island was sourced in 2004–2005 for a ‘wild to wild’ translocation of 42 individuals for an experimental reintroduction to Midway Atoll. To inform future management strategies, we compared genetic diversity sampled from the source population (n = 133 Laysan birds) including 23 of Midway’s founders and offspring of the translocated population 2–5 years post release (n = 96 Midway birds). We attempted to identify polymorphic markers by screening nuclear microsatellite (N = 83) and intronic loci (N = 19), as well as the mitochondrial control region (mtDNA) for a subset of samples. Among 83 microsatellite loci screened, six were variable. We found low nuclear variation consistent with the species’ historical population bottlenecks and sequence variation was observed at a single intron locus. We detected no variation within the mtDNA. We found limited but similar estimates of allelic richness (2.58 alleles per locus) and heterozygosity within islands. Two rare alleles found in the Laysan Island source population were not present in the Midway translocated group, and a rare allele was discovered in an individual on Midway in 2008. We found similar genetic diversity and low, but statistically significant, levels of differentiation (0.6%) between island populations suggesting that genetic drift (as a result of translocation-induced population bottlenecking) has had a limited effect within five years post-release. Our results have utility for informing translocation and genetic management decisions.

Algorithms for the Construction of Parallel Tests by Zero-One Programming. Project Psychometric Aspects of Item Banking No. 7. Research Report 86-7.

ERIC Educational Resources Information Center

Boekkooi-Timminga, Ellen

Nine methods for automated test construction are described. All are based on the concepts of information from item response theory. Two general kinds of methods for the construction of parallel tests are presented: (1) sequential test design; and (2) simultaneous test design. Sequential design implies that the tests are constructed one after the…

NDetermin: Inferring Nondeterministic Sequential Specifications for Parallelism Correctness

DTIC Science & Technology

2011-12-16

other provision of law, no person shall be subject to a penalty for failing to comply with a collection of information if it does not display a...Lab affiliates National Instruments, NEC, Nokia , NVIDIA, and Samsung. NDetermin: Inferring Nondeterministic Sequential Specifications for Parallelism...concurrently update x, some of these CAS’s will fail and those parallel loop iterations will recompute their updates to x and try again. Consider the parallel

Algorithms for Large-Scale Astronomical Problems

DTIC Science & Technology

2013-08-01

implemented as a succession of Hadoop MapReduce jobs and sequential programs written in Java . The sampling and splitting stages are implemented as...one MapReduce job, the partitioning and clustering phases make up another job. The merging stage is implemented as a stand-alone Java program. The...Merging. The merging stage is implemented as a sequential Java program that reads the files with the shell information, which were generated by

Waste in Place. A New Sequential Curriculum Covering the Behavioral Aspects of Waste Management for Grades K-6. [Teacher Background and Seven Units].

ERIC Educational Resources Information Center

Keep America Beautiful, Inc., New York, NY.

"Waste in Place" is an interdisciplinary, sequential curriculum for kindergarten through sixth grade. The eight units in the curriculum (one offering background information for teachers and one for each grade level) offer students the opportunity to learn about proper management of solid waste and the role of the individual in determining the best…

A protein-dependent side-chain rotamer library.

PubMed

Bhuyan, Md Shariful Islam; Gao, Xin

2011-12-14

Protein side-chain packing problem has remained one of the key open problems in bioinformatics. The three main components of protein side-chain prediction methods are a rotamer library, an energy function and a search algorithm. Rotamer libraries summarize the existing knowledge of the experimentally determined structures quantitatively. Depending on how much contextual information is encoded, there are backbone-independent rotamer libraries and backbone-dependent rotamer libraries. Backbone-independent libraries only encode sequential information, whereas backbone-dependent libraries encode both sequential and locally structural information. However, side-chain conformations are determined by spatially local information, rather than sequentially local information. Since in the side-chain prediction problem, the backbone structure is given, spatially local information should ideally be encoded into the rotamer libraries. In this paper, we propose a new type of backbone-dependent rotamer library, which encodes structural information of all the spatially neighboring residues. We call it protein-dependent rotamer libraries. Given any rotamer library and a protein backbone structure, we first model the protein structure as a Markov random field. Then the marginal distributions are estimated by the inference algorithms, without doing global optimization or search. The rotamers from the given library are then re-ranked and associated with the updated probabilities. Experimental results demonstrate that the proposed protein-dependent libraries significantly outperform the widely used backbone-dependent libraries in terms of the side-chain prediction accuracy and the rotamer ranking ability. Furthermore, without global optimization/search, the side-chain prediction power of the protein-dependent library is still comparable to the global-search-based side-chain prediction methods.

Synthesis of qualitative linguistic research--a pilot review integrating and generalizing findings on doctor-patient interaction.

PubMed

Nowak, Peter

2011-03-01

There is a broad range qualitative linguistic research (sequential analysis) on doctor-patient interaction that had only a marginal impact on clinical research and practice. At least in parts this is due to the lack of qualitative research synthesis in the field. Available research summaries are not systematic in their methodology. This paper proposes a synthesis methodology for qualitative, sequential analytic research on doctor-patient interaction. The presented methodology is not new but specifies standard methodology of qualitative research synthesis for sequential analytic research. This pilot review synthesizes twelve studies on German-speaking doctor-patient interactions, identifies 45 verbal actions of doctors and structures them in a systematics of eight interaction components. Three interaction components ("Listening", "Asking for information", and "Giving information") seem to be central and cover two thirds of the identified action types. This pilot review demonstrates that sequential analytic research can be synthesized in a consistent and meaningful way, thus providing a more comprehensive and unbiased integration of research. Future synthesis of qualitative research in the area of health communication research is very much needed. Qualitative research synthesis can support the development of quantitative research and of educational materials in medical training and patient training. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

Visual short-term memory for sequential arrays.

PubMed

Kumar, Arjun; Jiang, Yuhong

2005-04-01

The capacity of visual short-term memory (VSTM) for a single visual display has been investigated in past research, but VSTM for multiple sequential arrays has been explored only recently. In this study, we investigate the capacity of VSTM across two sequential arrays separated by a variable stimulus onset asynchrony (SOA). VSTM for spatial locations (Experiment 1), colors (Experiments 2-4), orientations (Experiments 3 and 4), and conjunction of color and orientation (Experiment 4) were tested, with the SOA across the two sequential arrays varying from 100 to 1,500 msec. We find that VSTM for the trailing array is much better than VSTM for the leading array, but when averaged across the two arrays VSTM has a constant capacity independent of the SOA. We suggest that multiple displays compete for retention in VSTM and that separating information into two temporally discrete groups does not enhance the overall capacity of VSTM.

A stacked sequential learning method for investigator name recognition from web-based medical articles

NASA Astrophysics Data System (ADS)

Zhang, Xiaoli; Zou, Jie; Le, Daniel X.; Thoma, George

2010-01-01

"Investigator Names" is a newly required field in MEDLINE citations. It consists of personal names listed as members of corporate organizations in an article. Extracting investigator names automatically is necessary because of the increasing volume of articles reporting collaborative biomedical research in which a large number of investigators participate. In this paper, we present an SVM-based stacked sequential learning method in a novel application - recognizing named entities such as the first and last names of investigators from online medical journal articles. Stacked sequential learning is a meta-learning algorithm which can boost any base learner. It exploits contextual information by adding the predicted labels of the surrounding tokens as features. We apply this method to tag words in text paragraphs containing investigator names, and demonstrate that stacked sequential learning improves the performance of a nonsequential base learner such as an SVM classifier.

The architecture of visual narrative comprehension: the interaction of narrative structure and page layout in understanding comics.

PubMed

Cohn, Neil

2014-01-01

How do people make sense of the sequential images in visual narratives like comics? A growing literature of recent research has suggested that this comprehension involves the interaction of multiple systems: The creation of meaning across sequential images relies on a "narrative grammar" that packages conceptual information into categorical roles organized in hierarchic constituents. These images are encapsulated into panels arranged in the layout of a physical page. Finally, how panels frame information can impact both the narrative structure and page layout. Altogether, these systems operate in parallel to construct the Gestalt whole of comprehension of this visual language found in comics.

Sequential Sampling Models in Cognitive Neuroscience: Advantages, Applications, and Extensions.

PubMed

Forstmann, B U; Ratcliff, R; Wagenmakers, E-J

2016-01-01

Sequential sampling models assume that people make speeded decisions by gradually accumulating noisy information until a threshold of evidence is reached. In cognitive science, one such model--the diffusion decision model--is now regularly used to decompose task performance into underlying processes such as the quality of information processing, response caution, and a priori bias. In the cognitive neurosciences, the diffusion decision model has recently been adopted as a quantitative tool to study the neural basis of decision making under time pressure. We present a selective overview of several recent applications and extensions of the diffusion decision model in the cognitive neurosciences.

Kullback-Leibler information function and the sequential selection of experiments to discriminate among several linear models

NASA Technical Reports Server (NTRS)

Sidik, S. M.

1972-01-01

The error variance of the process prior multivariate normal distributions of the parameters of the models are assumed to be specified, prior probabilities of the models being correct. A rule for termination of sampling is proposed. Upon termination, the model with the largest posterior probability is chosen as correct. If sampling is not terminated, posterior probabilities of the models and posterior distributions of the parameters are computed. An experiment was chosen to maximize the expected Kullback-Leibler information function. Monte Carlo simulation experiments were performed to investigate large and small sample behavior of the sequential adaptive procedure.

Comparison of simultaneous and sequential SPECT imaging for discrimination tasks in assessment of cardiac defects.

PubMed

Trott, C M; Ouyang, J; El Fakhri, G

2010-11-21

Simultaneous rest perfusion/fatty-acid metabolism studies have the potential to replace sequential rest/stress perfusion studies for the assessment of cardiac function. Simultaneous acquisition has the benefits of increased signal and lack of need for patient stress, but is complicated by cross-talk between the two radionuclide signals. We consider a simultaneous rest (99m)Tc-sestamibi/(123)I-BMIPP imaging protocol in place of the commonly used sequential rest/stress (99m)Tc-sestamibi protocol. The theoretical precision with which the severity of a cardiac defect and the transmural extent of infarct can be measured is computed for simultaneous and sequential SPECT imaging, and their performance is compared for discriminating (1) degrees of defect severity and (2) sub-endocardial from transmural defects. We consider cardiac infarcts for which reduced perfusion and metabolism are observed. From an information perspective, simultaneous imaging is found to yield comparable or improved performance compared with sequential imaging for discriminating both severity of defect and transmural extent of infarct, for three defects of differing location and size.

76 FR 2748 - Competition in the Railroad Industry

Federal Register 2010, 2011, 2012, 2013, 2014

2011-01-14

...) (Bottleneck II), aff'd sub nom. MidAmerican Energy Co. v. STB, 169 F.3d 1099 (8th Cir. 1999). The Board also... segment-by-segment basis--can reasonably be applied in today's transportation world. In particular, we... through rates, and whether the reasoning in Great Northern Railway encompasses ``bottleneck'' situations...

Widening the Knowledge Acquisition Bottleneck for Constraint-Based Tutors

ERIC Educational Resources Information Center

Suraweera, Pramuditha; Mitrovic, Antonija; Martin, Brent

2010-01-01

Intelligent Tutoring Systems (ITS) are effective tools for education. However, developing them is a labour-intensive and time-consuming process. A major share of the effort is devoted to acquiring the domain knowledge that underlies the system's intelligence. The goal of this research is to reduce this knowledge acquisition bottleneck and better…

Civil Preparedness and Post-Attack U.S. Economic Recovery. A State-of-the-Art Assessment and Selected Annotated Bibliography.

DTIC Science & Technology

1979-10-01

Although bottlenecks have been discussed thus far in an indus- trial or microeconomic sense, national bottlenecks are possible too, with...Texas Division of Disaster Emergency Services, 1978. JThis workbook provides a detailed format for a multi-meeting workshop to enable local (city/council

What's Feeling Got to Do with It? Decoding Emotional Bottlenecks in the History Classroom

ERIC Educational Resources Information Center

Middendorf, Joan; Mickute, Jolanta; Saunders, Tara; Najar, José; Clark-Huckstep, Andrew E.; Pace, David

2015-01-01

The understandings and preconceptions students bring into the history classroom can interfere with student learning. Analyses of student and professor interviews in light of emotional bottlenecks revealed two different, though related, student preconceptions: procedural preconceptions about history as a field of study and pre-existing worldviews…

Origin of the correlations between exit times in pedestrian flows through a bottleneck

NASA Astrophysics Data System (ADS)

Nicolas, Alexandre; Touloupas, Ioannis

2018-01-01

Robust statistical features have emerged from the microscopic analysis of dense pedestrian flows through a bottleneck, notably with respect to the time gaps between successive passages. We pinpoint the mechanisms at the origin of these features thanks to simple models that we develop and analyse quantitatively. We disprove the idea that anticorrelations between successive time gaps (i.e. an alternation between shorter ones and longer ones) are a hallmark of a zipper-like intercalation of pedestrian lines and show that they simply result from the possibility that pedestrians from distinct ‘lines’ or directions cross the bottleneck within a short time interval. A second feature concerns the bursts of escapes, i.e. egresses that come in fast succession. Despite the ubiquity of exponential distributions of burst sizes, entailed by a Poisson process, we argue that anomalous (power-law) statistics arise if the bottleneck is nearly congested, albeit only in a tiny portion of parameter space. The generality of the proposed mechanisms implies that similar statistical features should also be observed for other types of particulate flows.

Percolation transition in dynamical traffic network with evolving critical bottlenecks.

PubMed

Li, Daqing; Fu, Bowen; Wang, Yunpeng; Lu, Guangquan; Berezin, Yehiel; Stanley, H Eugene; Havlin, Shlomo

2015-01-20

A critical phenomenon is an intrinsic feature of traffic dynamics, during which transition between isolated local flows and global flows occurs. However, very little attention has been given to the question of how the local flows in the roads are organized collectively into a global city flow. Here we characterize this organization process of traffic as "traffic percolation," where the giant cluster of local flows disintegrates when the second largest cluster reaches its maximum. We find in real-time data of city road traffic that global traffic is dynamically composed of clusters of local flows, which are connected by bottleneck links. This organization evolves during a day with different bottleneck links appearing in different hours, but similar in the same hours in different days. A small improvement of critical bottleneck roads is found to benefit significantly the global traffic, providing a method to improve city traffic with low cost. Our results may provide insights on the relation between traffic dynamics and percolation, which can be useful for efficient transportation, epidemic control, and emergency evacuation.

Acoustic-optical phonon up-conversion and hot-phonon bottleneck in lead-halide perovskites

PubMed Central

Yang, Jianfeng; Wen, Xiaoming; Xia, Hongze; Sheng, Rui; Ma, Qingshan; Kim, Jincheol; Tapping, Patrick; Harada, Takaaki; Kee, Tak W.; Huang, Fuzhi; Cheng, Yi-Bing; Green, Martin; Ho-Baillie, Anita; Huang, Shujuan; Shrestha, Santosh; Patterson, Robert; Conibeer, Gavin

2017-01-01

The hot-phonon bottleneck effect in lead-halide perovskites (APbX3) prolongs the cooling period of hot charge carriers, an effect that could be used in the next-generation photovoltaics devices. Using ultrafast optical characterization and first-principle calculations, four kinds of lead-halide perovskites (A=FA+/MA+/Cs+, X=I−/Br−) are compared in this study to reveal the carrier-phonon dynamics within. Here we show a stronger phonon bottleneck effect in hybrid perovskites than in their inorganic counterparts. Compared with the caesium-based system, a 10 times slower carrier-phonon relaxation rate is observed in FAPbI3. The up-conversion of low-energy phonons is proposed to be responsible for the bottleneck effect. The presence of organic cations introduces overlapping phonon branches and facilitates the up-transition of low-energy modes. The blocking of phonon propagation associated with an ultralow thermal conductivity of the material also increases the overall up-conversion efficiency. This result also suggests a new and general method for achieving long-lived hot carriers in materials. PMID:28106061

Stochastic modelling, Bayesian inference, and new in vivo measurements elucidate the debated mtDNA bottleneck mechanism

PubMed Central

Johnston, Iain G; Burgstaller, Joerg P; Havlicek, Vitezslav; Kolbe, Thomas; Rülicke, Thomas; Brem, Gottfried; Poulton, Jo; Jones, Nick S

2015-01-01

Dangerous damage to mitochondrial DNA (mtDNA) can be ameliorated during mammalian development through a highly debated mechanism called the mtDNA bottleneck. Uncertainty surrounding this process limits our ability to address inherited mtDNA diseases. We produce a new, physically motivated, generalisable theoretical model for mtDNA populations during development, allowing the first statistical comparison of proposed bottleneck mechanisms. Using approximate Bayesian computation and mouse data, we find most statistical support for a combination of binomial partitioning of mtDNAs at cell divisions and random mtDNA turnover, meaning that the debated exact magnitude of mtDNA copy number depletion is flexible. New experimental measurements from a wild-derived mtDNA pairing in mice confirm the theoretical predictions of this model. We analytically solve a mathematical description of this mechanism, computing probabilities of mtDNA disease onset, efficacy of clinical sampling strategies, and effects of potential dynamic interventions, thus developing a quantitative and experimentally-supported stochastic theory of the bottleneck. DOI: http://dx.doi.org/10.7554/eLife.07464.001 PMID:26035426

Data Base Management Systems Panel Workshop: Executive summary

NASA Technical Reports Server (NTRS)

1979-01-01

Data base management systems (DBMS) for space acquired and associated data are discussed. The full range of DBMS needs is covered including acquiring, managing, storing, archiving, accessing and dissemination of data for an application. Existing bottlenecks in DBMS operations, expected developments in the field of remote sensing, communications, and computer science are discussed, and an overview of existing conditions and expected problems is presented. The requirements for a proposed spatial information system and characteristics of a comprehensive browse facility for earth observations applications are included.

The Effect of an Extreme and Prolonged Population Bottleneck on Patterns of Deleterious Variation: Insights from the Greenlandic Inuit.

PubMed

Pedersen, Casper-Emil T; Lohmueller, Kirk E; Grarup, Niels; Bjerregaard, Peter; Hansen, Torben; Siegismund, Hans R; Moltke, Ida; Albrechtsen, Anders

2017-02-01

The genetic consequences of population bottlenecks on patterns of deleterious genetic variation in human populations are of tremendous interest. Based on exome sequencing of 18 Greenlandic Inuit we show that the Inuit have undergone a severe ∼20,000-year-long bottleneck. This has led to a markedly more extreme distribution of allele frequencies than seen for any other human population tested to date, making the Inuit the perfect population for investigating the effect of a bottleneck on patterns of deleterious variation. When comparing proxies for genetic load that assume an additive effect of deleterious alleles, the Inuit show, at most, a slight increase in load compared to European, East Asian, and African populations. Specifically, we observe <4% increase in the number of derived deleterious alleles in the Inuit. In contrast, proxies for genetic load under a recessive model suggest that the Inuit have a significantly higher load (20% increase or more) compared to other less bottlenecked human populations. Forward simulations under realistic models of demography support our empirical findings, showing up to a 6% increase in the genetic load for the Inuit population across all models of dominance. Further, the Inuit population carries fewer deleterious variants than other human populations, but those that are present tend to be at higher frequency than in other populations. Overall, our results show how recent demographic history has affected patterns of deleterious variants in human populations. Copyright © 2017 by the Genetics Society of America.

Genetics of the Shimokita macaque population suggest an ancient bottleneck.

PubMed

Kawamoto, Yoshi; Tomari, Ken-ichiro; Kawai, Shizuka; Kawamoto, Sakie

2008-01-01

The macaque population of the Shimokita Peninsula represents the northernmost distribution of this species and is isolated from other populations in the Tohoku region of Japan. A previous protein-based study revealed a high level of genetic variability in this population and considerable differentiation from other populations. In order to reassess the genetic features of the Shimokita macaques, we examined 11 autosomal microsatellite loci and three Y chromosomal microsatellite loci. We observed considerable differentiation from other Japanese populations of macaques, but in contrast to the previous results, we observed significantly lower genetic variability in this population. There was a weak indication of a population bottleneck, suggesting a decay over time from an excess of heterozygotes that might be expected in the initial stages of a bottleneck. This may indicate that an ancient bottleneck occurred during the warm period after the last glacial period rather than a recent bottleneck due to hunting in modern times. The frequencies of private alleles were exceptionally high in the Shimokita population, suggesting that the difference in variability as determined in various studies was due to accidental sampling of marker loci with low power to resolve genetic variations in the protein-based studies. The assessments of interpopulation differentiation as determined using autosomal and Y chromosomal markers were highly correlated, and using both types of markers the Shimokita population was found to be the most differentiated of the study populations, probably due to infrequent gene flow with surrounding populations.

A novel visual hardware behavioral language

NASA Technical Reports Server (NTRS)

Li, Xueqin; Cheng, H. D.

1992-01-01

Most hardware behavioral languages just use texts to describe the behavior of the desired hardware design. This is inconvenient for VLSI designers who enjoy using the schematic approach. The proposed visual hardware behavioral language has the ability to graphically express design information using visual parallel models (blocks), visual sequential models (processes) and visual data flow graphs (which consist of primitive operational icons, control icons, and Data and Synchro links). Thus, the proposed visual hardware behavioral language can not only specify hardware concurrent and sequential functionality, but can also visually expose parallelism, sequentiality, and disjointness (mutually exclusive operations) for the hardware designers. That would make the hardware designers capture the design ideas easily and explicitly using this visual hardware behavioral language.

A single origin and moderate bottleneck during domestication of soybean (Glycine max): implications from microsatellites and nucleotide sequences

PubMed Central

Guo, Juan; Wang, Yunsheng; Song, Chi; Zhou, Jianfeng; Qiu, Lijuan; Huang, Hongwen; Wang, Ying

2010-01-01

Background and Aims It is essential to illuminate the evolutionary history of crop domestication in order to understand further the origin and development of modern cultivation and agronomy; however, despite being one of the most important crops, the domestication origin and bottleneck of soybean (Glycine max) are poorly understood. In the present study, microsatellites and nucleotide sequences were employed to elucidate the domestication genetics of soybean. Methods The genomes of 79 landrace soybeans (endemic cultivated soybeans) and 231 wild soybeans (G. soja) that represented the species-wide distribution of wild soybean in East Asia were scanned with 56 microsatellites to identify the genetic structure and domestication origin of soybean. To understand better the domestication bottleneck, four nucleotide sequences were selected to simulate the domestication bottleneck. Key Results Model-based analysis revealed that most of the landrace genotypes were assigned to the inferred wild soybean cluster of south China, South Korea and Japan. Phylogeny for wild and landrace soybeans showed that all landrace soybeans formed a single cluster supporting a monophyletic origin of all the cultivars. The populations of the nearest branches which were basal to the cultivar lineage were wild soybeans from south China. The coalescent simulation detected a bottleneck severity of K′ = 2 during soybean domestication, which could be explained by a foundation population of 6000 individuals if domestication duration lasted 3000 years. Conclusions As a result of integrating geographic distribution with microsatellite genotype assignment and phylogeny between landrace and wild soybeans, a single origin of soybean in south China is proposed. The coalescent simulation revealed a moderate genetic bottleneck with an effective wild soybean population used for domestication estimated to be ≈2 % of the total number of ancestral wild soybeans. Wild soybeans in Asia, especially in south China contain tremendous genetic resources for cultivar improvement. PMID:20566681

Estimation of the bottleneck size in Florida panthers

USGS Publications Warehouse

Culver, M.; Hedrick, P.W.; Murphy, K.; O'Brien, S.; Hornocker, M.G.

2008-01-01

We have estimated the extent of genetic variation in museum (1890s) and contemporary (1980s) samples of Florida panthers Puma concolor coryi for both nuclear loci and mtDNA. The microsatellite heterozygosity in the contemporary sample was only 0.325 that in the museum samples although our sample size and number of loci are limited. Support for this estimate is provided by a sample of 84 microsatellite loci in contemporary Florida panthers and Idaho pumas Puma concolor hippolestes in which the contemporary Florida panther sample had only 0.442 the heterozygosity of Idaho pumas. The estimated diversities in mtDNA in the museum and contemporary samples were 0.600 and 0.000, respectively. Using a population genetics approach, we have estimated that to reduce either the microsatellite heterozygosity or the mtDNA diversity this much (in a period of c. 80years during the 20th century when the numbers were thought to be low) that a very small bottleneck size of c. 2 for several generations and a small effective population size in other generations is necessary. Using demographic data from Yellowstone pumas, we estimated the ratio of effective to census population size to be 0.315. Using this ratio, the census population size in the Florida panthers necessary to explain the loss of microsatellite variation was c .41 for the non-bottleneck generations and 6.2 for the two bottleneck generations. These low bottleneck population sizes and the concomitant reduced effectiveness of selection are probably responsible for the high frequency of several detrimental traits in Florida panthers, namely undescended testicles and poor sperm quality. The recent intensive monitoring both before and after the introduction of Texas pumas in 1995 will make the recovery and genetic restoration of Florida panthers a classic study of an endangered species. Our estimates of the bottleneck size responsible for the loss of genetic variation in the Florida panther completes an unknown aspect of this account. ?? 2008 The Authors. Journal compilation ?? 2008 The Zoological Society of London.

Bottlenecks to coral recovery in the Seychelles

NASA Astrophysics Data System (ADS)

Chong-Seng, K. M.; Graham, N. A. J.; Pratchett, M. S.

2014-06-01

Processes that affect recovery of coral assemblages require investigation because coral reefs are experiencing a diverse array of more frequent disturbances. Potential bottlenecks to coral recovery include limited larval supply, low rates of settlement, and high mortality of new recruits or juvenile corals. We investigated spatial variation in local abundance of scleractinian corals in the Seychelles at three distinct life history stages (recruits, juveniles, and adults) on reefs with differing benthic conditions. Following widespread coral loss due to the 1998 bleaching event, some reefs are recovering (i.e., relatively high scleractinian coral cover: `coral-dominated'), some reefs have low cover of living macrobenthos and unconsolidated rubble substrates (`rubble-dominated'), and some reefs have high cover of macroalgae (`macroalgal-dominated'). Rates of coral recruitment to artificial settlement tiles were similar across all reef conditions, suggesting that larval supply does not explain differential coral recovery across the three reef types. However, acroporid recruits were absent on macroalgal-dominated reefs (0.0 ± 0.0 recruits tile-1) in comparison to coral-dominated reefs (5.2 ± 1.6 recruits tile-1). Juvenile coral colony density was significantly lower on macroalgal-dominated reefs (2.4 ± 1.1 colonies m-2), compared to coral-dominated reefs (16.8 ± 2.4 m-2) and rubble-dominated reefs (33.1 ± 7.3 m-2), suggesting that macroalgal-dominated reefs have either a bottleneck to successful settlement on the natural substrates or a high post-settlement mortality bottleneck. Rubble-dominated reefs had very low cover of adult corals (10.0 ± 1.7 %) compared to coral-dominated reefs (33.4 ± 3.6 %) despite no statistical difference in their juvenile coral densities. A bottleneck caused by low juvenile colony survivorship on unconsolidated rubble-dominated reefs is possible, or alternatively, recruitment to rubble-dominated reefs has only recently begun. This study identified bottlenecks to recovery of coral assemblages that varied depending on post-disturbance habitat condition.

HNCA-TOCSY-CANH experiments with alternate 13C-12C labeling: a set of 3D experiment with unique supra-sequential information for mainchain resonance assignment

PubMed Central

Takeuchi, Koh; Gal, Maayan; Takahashi, Hideo; Shimada, Ichio

2011-01-01

Described here is a set of three-dimensional (3D) NMR experiments that rely on CACA-TOCSY magnetization transfer via the weak 3JCαCα coupling. These pulse sequences, which resemble recently described 13C detected CACA-TOCSY (Takeuchi et al. 2010) experiments, are recorded in 1H2O, and use 1H excitation and detection. These experiments require alternate 13C-12C labeling together with perdeuteration, which allows utilizing the small 3JCαCα scalar coupling that is otherwise masked by the stronger 1JCC couplings in uniformly 13C labeled samples. These new experiments provide a unique assignment ladder-mark that yields bidirectional supra-sequential information and can readily straddle proline residues. Unlike the conventional HNCA experiment, which contains only sequential information to the 13Cα of the preceding residue, the 3D hnCA-TOCSY-caNH experiment can yield sequential correlations to alpha carbons in positions i−1, i + 1 and i−2. Furthermore, the 3D hNca-TOCSY-caNH and Hnca-TOC-SY-caNH experiments, which share the same magnetization pathway but use a different chemical shift encoding, directly couple the 15N-1H spin pair of residue i to adjacent amide protons and nitrogens at positions i−2, i−1, i + 1 and i + 2, respectively. These new experimental features make protein backbone assignments more robust by reducing the degeneracy problem associated with the conventional 3D NMR experiments. PMID:21110064

Information processing capacity in psychopathy: Effects of anomalous attention.

PubMed

Hamilton, Rachel K B; Newman, Joseph P

2018-03-01

Hamilton and colleagues (2015) recently proposed that an integrative deficit in psychopathy restricts simultaneous processing, thereby leaving fewer resources available for information encoding, narrowing the scope of attention, and undermining associative processing. The current study evaluated this parallel processing deficit proposal using the Simultaneous-Sequential paradigm. This investigation marks the first a priori test of the Hamilton et al.'s theoretical framework. We predicted that psychopathy would be associated with inferior performance (as indexed by lower accuracy and longer response time) on trials requiring simultaneous processing of visual information relative to trials necessitating sequential processing. Results were consistent with these predictions, supporting the proposal that psychopathy is characterized by a reduced capacity to process multicomponent perceptual information concurrently. We discuss the potential implications of impaired simultaneous processing for the conceptualization of the psychopathic deficit. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

An efficient and accurate approach to MTE-MART for time-resolved tomographic PIV

NASA Astrophysics Data System (ADS)

Lynch, K. P.; Scarano, F.

2015-03-01

The motion-tracking-enhanced MART (MTE-MART; Novara et al. in Meas Sci Technol 21:035401, 2010) has demonstrated the potential to increase the accuracy of tomographic PIV by the combined use of a short sequence of non-simultaneous recordings. A clear bottleneck of the MTE-MART technique has been its computational cost. For large datasets comprising time-resolved sequences, MTE-MART becomes unaffordable and has been barely applied even for the analysis of densely seeded tomographic PIV datasets. A novel implementation is proposed for tomographic PIV image sequences, which strongly reduces the computational burden of MTE-MART, possibly below that of regular MART. The method is a sequential algorithm that produces a time-marching estimation of the object intensity field based on an enhanced guess, which is built upon the object reconstructed at the previous time instant. As the method becomes effective after a number of snapshots (typically 5-10), the sequential MTE-MART (SMTE) is most suited for time-resolved sequences. The computational cost reduction due to SMTE simply stems from the fewer MART iterations required for each time instant. Moreover, the method yields superior reconstruction quality and higher velocity field measurement precision when compared with both MART and MTE-MART. The working principle is assessed in terms of computational effort, reconstruction quality and velocity field accuracy with both synthetic time-resolved tomographic images of a turbulent boundary layer and two experimental databases documented in the literature. The first is the time-resolved data of flow past an airfoil trailing edge used in the study of Novara and Scarano (Exp Fluids 52:1027-1041, 2012); the second is a swirling jet in a water flow. In both cases, the effective elimination of ghost particles is demonstrated in number and intensity within a short temporal transient of 5-10 frames, depending on the seeding density. The increased value of the velocity space-time correlation coefficient demonstrates the increased velocity field accuracy of SMTE compared with MART.

The altitudinal mobility of wild sheep at the Epigravettian site of Kalavan 1 (Lesser Caucasus, Armenia): Evidence from a sequential isotopic analysis in tooth enamel.

PubMed

Tornero, Carlos; Balasse, Marie; Bălăşescu, Adrian; Chataigner, Christine; Gasparyan, Boris; Montoya, Cyril

2016-08-01

Kalavan 1 is an Epigravettian hunting campsite in the Aregunyats mountain chain in northeastern Armenia (Lesser Caucasus). The site lies at an elevation of 1640 m in a bottleneck that controls the descent into the Barepat Valley from the alpine meadows above. The lithic and faunal assemblages show evidence of the production of hunting weapons, the hunting and targeting of wild sheep (Ovis orientalis), and the constitution of animal product reserves. A seasonal occupation of the site was proposed within a model of occupation by Epigravettian hunter-gatherers that involved a search for obsidian resources in high altitude sources from the spring to the summer and settling at Kalavan 1 at the end of summer or during autumn to coincide with the migration of wild herds from the alpine meadows to the valley. A key parameter of this model is wild sheep ethology, with a specifically seasonal vertical mobility, based on observations from contemporary mouflon populations from the surrounding areas. In this study, the vertical mobility of Paleolithic wild sheep was directly investigated through sequential isotope analysis (δ(18)O, δ(13)C) in teeth. A marked seasonality of birth is suggested that reflects a physiological adaptation to the strong environmental constraints of this mountainous region. Most importantly, a recurrent altitudinal mobility was demonstrated on a seasonal basis, which confirms that wild sheep migrated from lowland areas that they occupied in the winter and then moved to higher altitude meadows during the summer. Last, low inter-individual variability in the stable isotope sequences favors a hypothesis of accumulation for these faunal remains over a short time period. Overall, this new dataset strengthens the previous interpretations for Kalavan 1 and contributes to an understanding of the pattern of occupation of mountain territories by Epigravettian communities. Copyright © 2016 Elsevier Ltd. All rights reserved.

Composite solvers for linear saddle point problems arising from the incompressible Stokes equations with highly heterogeneous viscosity structure

NASA Astrophysics Data System (ADS)

Sanan, P.; Schnepp, S. M.; May, D.; Schenk, O.

2014-12-01

Geophysical applications require efficient forward models for non-linear Stokes flow on high resolution spatio-temporal domains. The bottleneck in applying the forward model is solving the linearized, discretized Stokes problem which takes the form of a large, indefinite (saddle point) linear system. Due to the heterogeniety of the effective viscosity in the elliptic operator, devising effective preconditioners for saddle point problems has proven challenging and highly problem-dependent. Nevertheless, at least three approaches show promise for preconditioning these difficult systems in an algorithmically scalable way using multigrid and/or domain decomposition techniques. The first is to work with a hierarchy of coarser or smaller saddle point problems. The second is to use the Schur complement method to decouple and sequentially solve for the pressure and velocity. The third is to use the Schur decomposition to devise preconditioners for the full operator. These involve sub-solves resembling inexact versions of the sequential solve. The choice of approach and sub-methods depends crucially on the motivating physics, the discretization, and available computational resources. Here we examine the performance trade-offs for preconditioning strategies applied to idealized models of mantle convection and lithospheric dynamics, characterized by large viscosity gradients. Due to the arbitrary topological structure of the viscosity field in geodynamical simulations, we utilize low order, inf-sup stable mixed finite element spatial discretizations which are suitable when sharp viscosity variations occur in element interiors. Particular attention is paid to possibilities within the decoupled and approximate Schur complement factorization-based monolithic approaches to leverage recently-developed flexible, communication-avoiding, and communication-hiding Krylov subspace methods in combination with `heavy' smoothers, which require solutions of large per-node sub-problems, well-suited to solution on hybrid computational clusters. To manage the combinatorial explosion of solver options (which include hybridizations of all the approaches mentioned above), we leverage the modularity of the PETSc library.

Parallelization of a Fully-Distributed Hydrologic Model using Sub-basin Partitioning

NASA Astrophysics Data System (ADS)

Vivoni, E. R.; Mniszewski, S.; Fasel, P.; Springer, E.; Ivanov, V. Y.; Bras, R. L.

2005-12-01

A primary obstacle towards advances in watershed simulations has been the limited computational capacity available to most models. The growing trend of model complexity, data availability and physical representation has not been matched by adequate developments in computational efficiency. This situation has created a serious bottleneck which limits existing distributed hydrologic models to small domains and short simulations. In this study, we present novel developments in the parallelization of a fully-distributed hydrologic model. Our work is based on the TIN-based Real-time Integrated Basin Simulator (tRIBS), which provides continuous hydrologic simulation using a multiple resolution representation of complex terrain based on a triangulated irregular network (TIN). While the use of TINs reduces computational demand, the sequential version of the model is currently limited over large basins (>10,000 km2) and long simulation periods (>1 year). To address this, a parallel MPI-based version of the tRIBS model has been implemented and tested using high performance computing resources at Los Alamos National Laboratory. Our approach utilizes domain decomposition based on sub-basin partitioning of the watershed. A stream reach graph based on the channel network structure is used to guide the sub-basin partitioning. Individual sub-basins or sub-graphs of sub-basins are assigned to separate processors to carry out internal hydrologic computations (e.g. rainfall-runoff transformation). Routed streamflow from each sub-basin forms the major hydrologic data exchange along the stream reach graph. Individual sub-basins also share subsurface hydrologic fluxes across adjacent boundaries. We demonstrate how the sub-basin partitioning provides computational feasibility and efficiency for a set of test watersheds in northeastern Oklahoma. We compare the performance of the sequential and parallelized versions to highlight the efficiency gained as the number of processors increases. We also discuss how the coupled use of TINs and parallel processing can lead to feasible long-term simulations in regional watersheds while preserving basin properties at high-resolution.

Expert system for online surveillance of nuclear reactor coolant pumps

DOEpatents

Gross, Kenny C.; Singer, Ralph M.; Humenik, Keith E.

1993-01-01

An expert system for online surveillance of nuclear reactor coolant pumps. This system provides a means for early detection of pump or sensor degradation. Degradation is determined through the use of a statistical analysis technique, sequential probability ratio test, applied to information from several sensors which are responsive to differing physical parameters. The results of sequential testing of the data provide the operator with an early warning of possible sensor or pump failure.

Fair and efficient network congestion control based on minority game

NASA Astrophysics Data System (ADS)

Wang, Zuxi; Wang, Wen; Hu, Hanping; Deng, Zhaozhang

2011-12-01

Low link utility, RTT unfairness and unfairness of Multi-Bottleneck network are the existing problems in the present network congestion control algorithms at large. Through the analogy of network congestion control with the "El Farol Bar" problem, we establish a congestion control model based on minority game(MG), and then present a novel network congestion control algorithm based on the model. The result of simulations indicates that the proposed algorithm can make the achievements of link utility closing to 100%, zero packet lose rate, and small of queue size. Besides, the RTT unfairness and the unfairness of Multi-Bottleneck network can be solved, to achieve the max-min fairness in Multi-Bottleneck network, while efficiently weaken the "ping-pong" oscillation caused by the overall synchronization.

Emerging from the bottleneck: Benefits of the comparative approach to modern neuroscience

PubMed Central

Brenowitz, Eliot A.; Zakon, Harold H.

2015-01-01

Neuroscience historically exploited a wide diversity of animal taxa. Recently, however, research focused increasingly on a few model species. This trend accelerated with the genetic revolution, as genomic sequences and genetic tools became available for a few species, which formed a bottleneck. This coalescence on a small set of model species comes with several costs often not considered, especially in the current drive to use mice explicitly as models for human diseases. Comparative studies of strategically chosen non-model species can complement model species research and yield more rigorous studies. As genetic sequences and tools become available for many more species, we are poised to emerge from the bottleneck and once again exploit the rich biological diversity offered by comparative studies. PMID:25800324

Cultural hitchhiking and competition between patrilineal kin groups explain the post-Neolithic Y-chromosome bottleneck.

PubMed

Zeng, Tian Chen; Aw, Alan J; Feldman, Marcus W

2018-05-25

In human populations, changes in genetic variation are driven not only by genetic processes, but can also arise from cultural or social changes. An abrupt population bottleneck specific to human males has been inferred across several Old World (Africa, Europe, Asia) populations 5000-7000 BP. Here, bringing together anthropological theory, recent population genomic studies and mathematical models, we propose a sociocultural hypothesis, involving the formation of patrilineal kin groups and intergroup competition among these groups. Our analysis shows that this sociocultural hypothesis can explain the inference of a population bottleneck. We also show that our hypothesis is consistent with current findings from the archaeogenetics of Old World Eurasia, and is important for conceptions of cultural and social evolution in prehistory.

Forgetting the Past: Individual Differences in Recency in Subjective Valuations from Experience

ERIC Educational Resources Information Center

Ashby, Nathaniel J. S.; Rakow, Tim

2014-01-01

Recent research investigating decisions from experience suggests that not all information is treated equally in the decision process, with more recently encountered information having a greater impact. We report 2 studies investigating how this differential treatment of sequentially encountered information affects subjective valuations of risky…

Item Selection Criteria with Practical Constraints for Computerized Classification Testing

ERIC Educational Resources Information Center

Lin, Chuan-Ju

2011-01-01

This study compares four item selection criteria for a two-category computerized classification testing: (1) Fisher information (FI), (2) Kullback-Leibler information (KLI), (3) weighted log-odds ratio (WLOR), and (4) mutual information (MI), with respect to the efficiency and accuracy of classification decision using the sequential probability…

Information Structures and Pedagogic Applications.

ERIC Educational Resources Information Center

Chambers, F.

The underlying structure of meaning in a text is to a certain extent belied by the surface structure, or sequential organization, of the text. The underlying information structures (IS) organize information according to cognitive and cultural factors. It may be demonstrated that just three major IS with various subvarieties can describe any text:…

Deep bottleneck features for spoken language identification.

PubMed

Jiang, Bing; Song, Yan; Wei, Si; Liu, Jun-Hua; McLoughlin, Ian Vince; Dai, Li-Rong

2014-01-01

A key problem in spoken language identification (LID) is to design effective representations which are specific to language information. For example, in recent years, representations based on both phonotactic and acoustic features have proven their effectiveness for LID. Although advances in machine learning have led to significant improvements, LID performance is still lacking, especially for short duration speech utterances. With the hypothesis that language information is weak and represented only latently in speech, and is largely dependent on the statistical properties of the speech content, existing representations may be insufficient. Furthermore they may be susceptible to the variations caused by different speakers, specific content of the speech segments, and background noise. To address this, we propose using Deep Bottleneck Features (DBF) for spoken LID, motivated by the success of Deep Neural Networks (DNN) in speech recognition. We show that DBFs can form a low-dimensional compact representation of the original inputs with a powerful descriptive and discriminative capability. To evaluate the effectiveness of this, we design two acoustic models, termed DBF-TV and parallel DBF-TV (PDBF-TV), using a DBF based i-vector representation for each speech utterance. Results on NIST language recognition evaluation 2009 (LRE09) show significant improvements over state-of-the-art systems. By fusing the output of phonotactic and acoustic approaches, we achieve an EER of 1.08%, 1.89% and 7.01% for 30 s, 10 s and 3 s test utterances respectively. Furthermore, various DBF configurations have been extensively evaluated, and an optimal system proposed.

The influence of training on the attentional blink and psychological refractory period.

PubMed

Garner, K G; Tombu, M N; Dux, P E

2014-05-01

A growing body of research suggests that dual-task interference in sensory consolidation (e.g., the attentional blink, AB) and response selection (e.g., the psychological refractory period, PRP) stems from a common central bottleneck of information processing. With regard to response selection, it is well known that training reduces dual-task interference. We tested whether training that is known to be effective for response selection can also reduce dual-task interference in sensory consolidation. Over two experiments, performance on a PRP paradigm (Exp. 1) and on AB paradigms (differing in their stimuli and task demands, Exps. 1 and 2) was examined after participants had completed a relevant training regimen (T1 practice for both paradigms), an irrelevant training regimen (comparable sensorimotor training, not related to T1 for both tasks), a visual-search training regimen (Exp. 2 only), or after participants had been allocated to a no-training control group. Training that had shown to be effective for reducing dual-task interference in response selection was also found to be effective for reducing interference in sensory consolidation. In addition, we found some evidence that training benefits transferred to the sensory consolidation of untrained stimuli. Collectively, these findings show that training benefits can transfer across cognitive operations that draw on the central bottleneck in information processing. These findings have implications for theories of the AB and for the design of cognitive-training regimens that aim to produce transferable training benefits.

The architecture of visual narrative comprehension: the interaction of narrative structure and page layout in understanding comics

PubMed Central

Cohn, Neil

2014-01-01

How do people make sense of the sequential images in visual narratives like comics? A growing literature of recent research has suggested that this comprehension involves the interaction of multiple systems: The creation of meaning across sequential images relies on a “narrative grammar” that packages conceptual information into categorical roles organized in hierarchic constituents. These images are encapsulated into panels arranged in the layout of a physical page. Finally, how panels frame information can impact both the narrative structure and page layout. Altogether, these systems operate in parallel to construct the Gestalt whole of comprehension of this visual language found in comics. PMID:25071651

A Survey on Distributed Mobile Database and Data Mining

NASA Astrophysics Data System (ADS)

Goel, Ajay Mohan; Mangla, Neeraj; Patel, R. B.

2010-11-01

The anticipated increase in popular use of the Internet has created more opportunity in information dissemination, Ecommerce, and multimedia communication. It has also created more challenges in organizing information and facilitating its efficient retrieval. In response to this, new techniques have evolved which facilitate the creation of such applications. Certainly the most promising among the new paradigms is the use of mobile agents. In this paper, mobile agent and distributed database technologies are applied in the banking system. Many approaches have been proposed to schedule data items for broadcasting in a mobile environment. In this paper, an efficient strategy for accessing multiple data items in mobile environments and the bottleneck of current banking will be proposed.

The graphic cell method: a new look at digitizing geologic maps

USGS Publications Warehouse

Hanley, J.T.

1982-01-01

The graphic cell method is an alternative method of digitizing areal geologic information. It involves a discrete-point sampling scheme in which the computer establishes a matrix of cells over the map. Each cell and the whole cell is assigned the identity or value of the geologic information that is recognized at its center. Cell size may be changed to suit the needs of the user. The computer program resolves the matrix and identifies potential errors such as multiple assignments. Input includes the digitized boundaries of each geologic formation. This method should eliminate a primary bottleneck in the creation and testing of geomathematical models in such disciplines as resource appraisal. ?? 1982.

A new Information publishing system Based on Internet of things

NASA Astrophysics Data System (ADS)

Zhu, Li; Ma, Guoguang

2018-03-01

A new information publishing system based on Internet of things is proposed, which is composed of four level hierarchical structure, including the screen identification layer, the network transport layer, the service management layer and the publishing application layer. In the architecture, the screen identification layer has realized the internet of screens in which geographically dispersed independent screens are connected to the internet by the customized set-top boxes. The service management layer uses MQTT protocol to implement a lightweight broker-based publish/subscribe messaging mechanism in constrained environments such as internet of things to solve the bandwidth bottleneck. Meanwhile the cloud-based storage technique is used to storage and manage the promptly increasing multimedia publishing information. The paper has designed and realized a prototype SzIoScreen, and give some related test results.

Transmission of human mtDNA heteroplasmy in the Genome of the Netherlands families: support for a variable-size bottleneck

PubMed Central

Li, Mingkun; Rothwell, Rebecca; Vermaat, Martijn; Wachsmuth, Manja; Schröder, Roland; Laros, Jeroen F.J.; van Oven, Mannis; de Bakker, Paul I.W.; Bovenberg, Jasper A.; van Duijn, Cornelia M.; van Ommen, Gert-Jan B.; Slagboom, P. Eline; Swertz, Morris A.; Wijmenga, Cisca; Kayser, Manfred; Boomsma, Dorret I.; Zöllner, Sebastian; de Knijff, Peter; Stoneking, Mark

2016-01-01

Although previous studies have documented a bottleneck in the transmission of mtDNA genomes from mothers to offspring, several aspects remain unclear, including the size and nature of the bottleneck. Here, we analyze the dynamics of mtDNA heteroplasmy transmission in the Genomes of the Netherlands (GoNL) data, which consists of complete mtDNA genome sequences from 228 trios, eight dizygotic (DZ) twin quartets, and 10 monozygotic (MZ) twin quartets. Using a minor allele frequency (MAF) threshold of 2%, we identified 189 heteroplasmies in the trio mothers, of which 59% were transmitted to offspring, and 159 heteroplasmies in the trio offspring, of which 70% were inherited from the mothers. MZ twin pairs exhibited greater similarity in MAF at heteroplasmic sites than DZ twin pairs, suggesting that the heteroplasmy MAF in the oocyte is the major determinant of the heteroplasmy MAF in the offspring. We used a likelihood method to estimate the effective number of mtDNA genomes transmitted to offspring under different bottleneck models; a variable bottleneck size model provided the best fit to the data, with an estimated mean of nine individual mtDNA genomes transmitted. We also found evidence for negative selection during transmission against novel heteroplasmies (in which the minor allele has never been observed in polymorphism data). These novel heteroplasmies are enhanced for tRNA and rRNA genes, and mutations associated with mtDNA diseases frequently occur in these genes. Our results thus suggest that the female germ line is able to recognize and select against deleterious heteroplasmies. PMID:26916109

Population bottlenecks, genetic diversity and breeding ability of the three-spined stickleback (Gasterosteus aculeatus) from three polluted English Rivers.

PubMed

Santos, Eduarda M; Hamilton, Patrick B; Coe, Tobias S; Ball, Jonathan S; Cook, Alastair C; Katsiadaki, Ioanna; Tyler, Charles R

2013-10-15

Pollution is a significant environmental pressure on fish populations in both freshwater and marine environments. Populations subjected to chronic exposure to pollutants can experience impacts ranging from altered reproductive capacity to changes in population genetic structure. Few studies, however, have examined the reproductive vigor of individuals within populations inhabiting environments characterized by chronic pollution. In this study we undertook an analysis of populations of three-spined sticklebacks (Gasterosteus aculeatus) from polluted sites, to determine levels of genetic diversity, assess for evidence of historic population genetic bottlenecks and determine the reproductive competitiveness of males from these locations. The sites chosen included locations in the River Aire, the River Tees and the River Birket, English rivers that have been impacted by pollution from industrial and/or domestic effluents for over 100 years. Male reproductive competitiveness was determined via competitive breeding experiments with males and females derived from a clean water site, employing DNA microsatellites to determine parentage outcome. Populations of stickleback collected from the three historically polluted sites showed evidence of recent population bottlenecks, although only the River Aire population showed low genetic diversity. In contrast, fish collected from two relatively unpolluted sites within the River Gowy and Houghton Springs showed weak, or no evidence of such bottlenecks. Nevertheless, males derived from polluted sites were able to reproduce successfully in competition with males derived from clean water exposures, indicating that these bottlenecks have not resulted in any substantial loss of reproductive fitness in males. Copyright © 2013 Elsevier B.V. All rights reserved.

Cognitive structure, flexibility, and plasticity in human multitasking-An integrative review of dual-task and task-switching research.

PubMed

Koch, Iring; Poljac, Edita; Müller, Hermann; Kiesel, Andrea

2018-06-01

Numerous studies showed decreased performance in situations that require multiple tasks or actions relative to appropriate control conditions. Because humans often engage in such multitasking activities, it is important to understand how multitasking affects performance. In the present article, we argue that research on dual-task interference and sequential task switching has proceeded largely separately using different experimental paradigms and methodology. In our article we aim at organizing this complex set of research in terms of three complementary research perspectives on human multitasking. One perspective refers to structural accounts in terms of cognitive bottlenecks (i.e., critical processing stages). A second perspective refers to cognitive flexibility in terms of the underlying cognitive control processes. A third perspective emphasizes cognitive plasticity in terms of the influence of practice on human multitasking abilities. With our review article we aimed at highlighting the value of an integrative position that goes beyond isolated consideration of a single theoretical research perspective and that broadens the focus from single experimental paradigms (dual task and task switching) to favor instead a view that emphasizes the fundamental similarity of the underlying cognitive mechanisms across multitasking paradigms. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

EMMA: An Extensible Mammalian Modular Assembly Toolkit for the Rapid Design and Production of Diverse Expression Vectors.

PubMed

Martella, Andrea; Matjusaitis, Mantas; Auxillos, Jamie; Pollard, Steven M; Cai, Yizhi

2017-07-21

Mammalian plasmid expression vectors are critical reagents underpinning many facets of research across biology, biomedical research, and the biotechnology industry. Traditional cloning methods often require laborious manual design and assembly of plasmids using tailored sequential cloning steps. This process can be protracted, complicated, expensive, and error-prone. New tools and strategies that facilitate the efficient design and production of bespoke vectors would help relieve a current bottleneck for researchers. To address this, we have developed an extensible mammalian modular assembly kit (EMMA). This enables rapid and efficient modular assembly of mammalian expression vectors in a one-tube, one-step golden-gate cloning reaction, using a standardized library of compatible genetic parts. The high modularity, flexibility, and extensibility of EMMA provide a simple method for the production of functionally diverse mammalian expression vectors. We demonstrate the value of this toolkit by constructing and validating a range of representative vectors, such as transient and stable expression vectors (transposon based vectors), targeting vectors, inducible systems, polycistronic expression cassettes, fusion proteins, and fluorescent reporters. The method also supports simple assembly combinatorial libraries and hierarchical assembly for production of larger multigenetic cargos. In summary, EMMA is compatible with automated production, and novel genetic parts can be easily incorporated, providing new opportunities for mammalian synthetic biology.

Fractional Steps methods for transient problems on commodity computer architectures

NASA Astrophysics Data System (ADS)

Krotkiewski, M.; Dabrowski, M.; Podladchikov, Y. Y.

2008-12-01

Fractional Steps methods are suitable for modeling transient processes that are central to many geological applications. Low memory requirements and modest computational complexity facilitates calculations on high-resolution three-dimensional models. An efficient implementation of Alternating Direction Implicit/Locally One-Dimensional schemes for an Opteron-based shared memory system is presented. The memory bandwidth usage, the main bottleneck on modern computer architectures, is specially addressed. High efficiency of above 2 GFlops per CPU is sustained for problems of 1 billion degrees of freedom. The optimized sequential implementation of all 1D sweeps is comparable in execution time to copying the used data in the memory. Scalability of the parallel implementation on up to 8 CPUs is close to perfect. Performing one timestep of the Locally One-Dimensional scheme on a system of 1000 3 unknowns on 8 CPUs takes only 11 s. We validate the LOD scheme using a computational model of an isolated inclusion subject to a constant far field flux. Next, we study numerically the evolution of a diffusion front and the effective thermal conductivity of composites consisting of multiple inclusions and compare the results with predictions based on the differential effective medium approach. Finally, application of the developed parabolic solver is suggested for a real-world problem of fluid transport and reactions inside a reservoir.

Information Management: Publishing and Printing: Army Publishing: Action Officers Guide

DTIC Science & Technology

2002-04-30

types of lists: ordered (such as numerical, alphabetical, or sequential ), bulleted, or dashed. (4) Extracted material in an appendix must be identified...provide supporting, expanded, or sequential doctrinal manuals within a functional field (this number group must not exceed 3 digits). Table 13–2...rubup, opaquing, lineup , and register, and so forth 1,2 190 DA PAM 25–40 • 30 April 2002 Table J–5 Camera, platemaking, and related equipment—Continued

UArizona at the CLEF eRisk 2017 Pilot Task: Linear and Recurrent Models for Early Depression Detection

PubMed Central

Sadeque, Farig; Xu, Dongfang; Bethard, Steven

2017-01-01

The 2017 CLEF eRisk pilot task focuses on automatically detecting depression as early as possible from a users’ posts to Reddit. In this paper we present the techniques employed for the University of Arizona team’s participation in this early risk detection shared task. We leveraged external information beyond the small training set, including a preexisting depression lexicon and concepts from the Unified Medical Language System as features. For prediction, we used both sequential (recurrent neural network) and non-sequential (support vector machine) models. Our models perform decently on the test data, and the recurrent neural models perform better than the non-sequential support vector machines while using the same feature sets. PMID:29075167

Three-dimensional mapping of equiprobable hydrostratigraphic units at the Frenchman Flat Corrective Action Unit, Nevada Test Site

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

Shirley, C.; Pohlmann, K.; Andricevic, R.

1996-09-01

Geological and geophysical data are used with the sequential indicator simulation algorithm of Gomez-Hernandez and Srivastava to produce multiple, equiprobable, three-dimensional maps of informal hydrostratigraphic units at the Frenchman Flat Corrective Action Unit, Nevada Test Site. The upper 50 percent of the Tertiary volcanic lithostratigraphic column comprises the study volume. Semivariograms are modeled from indicator-transformed geophysical tool signals. Each equiprobable study volume is subdivided into discrete classes using the ISIM3D implementation of the sequential indicator simulation algorithm. Hydraulic conductivity is assigned within each class using the sequential Gaussian simulation method of Deutsch and Journel. The resulting maps show the contiguitymore » of high and low hydraulic conductivity regions.« less

Learning to Achieve Perfect Timesharing: Architectural Implications of Hazeltine, Teague, and Ivry (2002)

ERIC Educational Resources Information Center

Anderson, John R.; Taatgen, Niels A.; Byrne, Michael D.

2005-01-01

E. Hazeltine, D. Teague, and R. B. Ivry have presented data that have been interpreted as evidence against a central bottleneck. This article describes simulations of their Experiments 1 and 4 in the ACT-R cognitive architecture, which does possess a central bottleneck in production execution. The simulation model is capable of accounting for the…

Natural history of Ashkenazi intelligence.

PubMed

Cochran, Gregory; Hardy, Jason; Harpending, Henry

2006-09-01

This paper elaborates the hypothesis that the unique demography and sociology of Ashkenazim in medieval Europe selected for intelligence. Ashkenazi literacy, economic specialization, and closure to inward gene flow led to a social environment in which there was high fitness payoff to intelligence, specifically verbal and mathematical intelligence but not spatial ability. As with any regime of strong directional selection on a quantitative trait, genetic variants that were otherwise fitness reducing rose in frequency. In particular we propose that the well-known clusters of Ashkenazi genetic diseases, the sphingolipid cluster and the DNA repair cluster in particular, increase intelligence in heterozygotes. Other Ashkenazi disorders are known to increase intelligence. Although these disorders have been attributed to a bottleneck in Ashkenazi history and consequent genetic drift, there is no evidence of any bottleneck. Gene frequencies at a large number of autosomal loci show that if there was a bottleneck then subsequent gene flow from Europeans must have been very large, obliterating the effects of any bottleneck. The clustering of the disorders in only a few pathways and the presence at elevated frequency of more than one deleterious allele at many of them could not have been produced by drift. Instead these are signatures of strong and recent natural selection.

A boost and bounce theory of temporal attention.

PubMed

Olivers, Christian N L; Meeter, Martijn

2008-10-01

What is the time course of visual attention? Attentional blink studies have found that the 2nd of 2 targets is often missed when presented within about 500 ms from the 1st target, resulting in theories about relatively long-lasting capacity limitations or bottlenecks. Earlier studies, however, reported quite the opposite finding: Attention is transiently enhanced, rather than reduced, for several hundreds of milliseconds after a relevant event. The authors present a general theory, as well as a working computational model, that integrate these findings. There is no central role for capacity limitations or bottlenecks. Central is a rapidly responding gating system (or attentional filter) that seeks to enhance relevant and suppress irrelevant information. When items sufficiently match the target description, they elicit transient excitatory feedback activity (a "boost" function), meant to provide access to working memory. However, in the attentional blink task, the distractor after the target is accidentally boosted, resulting in subsequent strong inhibitory feedback response (a "bounce"), which, in effect, closes the gate to working memory. The theory explains many findings that are problematic for limited-capacity accounts, including a new experiment showing that the attentional blink can be postponed.

Species mtDNA genetic diversity explained by infrapopulation size in a host-symbiont system.

PubMed

Doña, Jorge; Moreno-García, Marina; Criscione, Charles D; Serrano, David; Jovani, Roger

2015-12-01

Understanding what shapes variation in genetic diversity among species remains a major challenge in evolutionary ecology, and it has been seldom studied in parasites and other host-symbiont systems. Here, we studied mtDNA variation in a host-symbiont non-model system: 418 individual feather mites from 17 feather mite species living on 17 different passerine bird species. We explored how a surrogate of census size, the median infrapopulation size (i.e., the median number of individual parasites per infected host individual), explains mtDNA genetic diversity. Feather mite species genetic diversity was positively correlated with mean infrapopulation size, explaining 34% of the variation. As expected from the biology of feather mites, we found bottleneck signatures for most of the species studied but, in particular, three species presented extremely low mtDNA diversity values given their infrapopulation size. Their star-like haplotype networks (in contrast with more reticulated networks for the other species) suggested that their low genetic diversity was the consequence of severe bottlenecks or selective sweeps. Our study shows for the first time that mtDNA diversity can be explained by infrapopulation sizes, and suggests that departures from this relationship could be informative of underlying ecological and evolutionary processes.

Probabilistic visual and electromagnetic data fusion for robust drift-free sequential mosaicking: application to fetoscopy

PubMed Central

Tella-Amo, Marcel; Peter, Loic; Shakir, Dzhoshkun I.; Deprest, Jan; Iglesias, Juan Eugenio; Ourselin, Sebastien

2018-01-01

Abstract. The most effective treatment for twin-to-twin transfusion syndrome is laser photocoagulation of the shared vascular anastomoses in the placenta. Vascular connections are extremely challenging to locate due to their caliber and the reduced field-of-view of the fetoscope. Therefore, mosaicking techniques are beneficial to expand the scene, facilitate navigation, and allow vessel photocoagulation decision-making. Local vision-based mosaicking algorithms inherently drift over time due to the use of pairwise transformations. We propose the use of an electromagnetic tracker (EMT) sensor mounted at the tip of the fetoscope to obtain camera pose measurements, which we incorporate into a probabilistic framework with frame-to-frame visual information to achieve globally consistent sequential mosaics. We parametrize the problem in terms of plane and camera poses constrained by EMT measurements to enforce global consistency while leveraging pairwise image relationships in a sequential fashion through the use of local bundle adjustment. We show that our approach is drift-free and performs similarly to state-of-the-art global alignment techniques like bundle adjustment albeit with much less computational burden. Additionally, we propose a version of bundle adjustment that uses EMT information. We demonstrate the robustness to EMT noise and loss of visual information and evaluate mosaics for synthetic, phantom-based and ex vivo datasets. PMID:29487889

On the specificity of sequential congruency effects in implicit learning of motor and perceptual sequences.

PubMed

D'Angelo, Maria C; Jiménez, Luis; Milliken, Bruce; Lupiáñez, Juan

2013-01-01

Individuals experience less interference from conflicting information following events that contain conflicting information. Recently, Jiménez, Lupiáñez, and Vaquero (2009) demonstrated that such adaptations to conflict occur even when the source of conflict arises from implicit knowledge of sequences. There is accumulating evidence that momentary changes in adaptations made in response to conflicting information are conflict-type specific (e.g., Funes, Lupiáñez, & Humphreys, 2010a), suggesting that there are multiple modes of control. The current study examined whether conflict-specific sequential congruency effects occur when the 2 sources of conflict are implicitly learned. Participants implicitly learned a motor sequence while simultaneously learning a perceptual sequence. In a first experiment, after learning the 2 orthogonal sequences, participants expressed knowledge of the 2 sequences independently of each other in a transfer phase. In Experiments 2 and 3, within each sequence, the presence of a single control trial disrupted the expression of this specific type of learning on the following trial. There was no evidence of cross-conflict modulations in the expression of sequence learning. The results suggest that the mechanisms involved in transient shifts in conflict-specific control, as reflected in sequential congruency effects, are also engaged when the source of conflict is implicit. (c) 2013 APA, all rights reserved.

Four disruptive strategies for removing drug discovery bottlenecks.

PubMed

Ekins, Sean; Waller, Chris L; Bradley, Mary P; Clark, Alex M; Williams, Antony J

2013-03-01

Drug discovery is shifting focus from industry to outside partners and, in the process, creating new bottlenecks. Technologies like high throughput screening (HTS) have moved to a larger number of academic and institutional laboratories in the USA, with little coordination or consideration of the outputs and creating a translational gap. Although there have been collaborative public-private partnerships in Europe to share pharmaceutical data, the USA has seemingly lagged behind and this may hold it back. Sharing precompetitive data and models may accelerate discovery across the board, while finding the best collaborators, mining social media and mobile approaches to open drug discovery should be evaluated in our efforts to remove drug discovery bottlenecks. We describe four strategies to rectify the current unsustainable situation. Copyright © 2012 Elsevier Ltd. All rights reserved.

Analysis of filter tuning techniques for sequential orbit determination

NASA Technical Reports Server (NTRS)

Lee, T.; Yee, C.; Oza, D.

1995-01-01

This paper examines filter tuning techniques for a sequential orbit determination (OD) covariance analysis. Recently, there has been a renewed interest in sequential OD, primarily due to the successful flight qualification of the Tracking and Data Relay Satellite System (TDRSS) Onboard Navigation System (TONS) using Doppler data extracted onboard the Extreme Ultraviolet Explorer (EUVE) spacecraft. TONS computes highly accurate orbit solutions onboard the spacecraft in realtime using a sequential filter. As the result of the successful TONS-EUVE flight qualification experiment, the Earth Observing System (EOS) AM-1 Project has selected TONS as the prime navigation system. In addition, sequential OD methods can be used successfully for ground OD. Whether data are processed onboard or on the ground, a sequential OD procedure is generally favored over a batch technique when a realtime automated OD system is desired. Recently, OD covariance analyses were performed for the TONS-EUVE and TONS-EOS missions using the sequential processing options of the Orbit Determination Error Analysis System (ODEAS). ODEAS is the primary covariance analysis system used by the Goddard Space Flight Center (GSFC) Flight Dynamics Division (FDD). The results of these analyses revealed a high sensitivity of the OD solutions to the state process noise filter tuning parameters. The covariance analysis results show that the state estimate error contributions from measurement-related error sources, especially those due to the random noise and satellite-to-satellite ionospheric refraction correction errors, increase rapidly as the state process noise increases. These results prompted an in-depth investigation of the role of the filter tuning parameters in sequential OD covariance analysis. This paper analyzes how the spacecraft state estimate errors due to dynamic and measurement-related error sources are affected by the process noise level used. This information is then used to establish guidelines for determining optimal filter tuning parameters in a given sequential OD scenario for both covariance analysis and actual OD. Comparisons are also made with corresponding definitive OD results available from the TONS-EUVE analysis.

Decision making and sequential sampling from memory

PubMed Central

Shadlen, Michael N.; Shohamy, Daphna

2016-01-01

Decisions take time, and as a rule more difficult decisions take more time. But this only raises the question of what consumes the time. For decisions informed by a sequence of samples of evidence, the answer is straightforward: more samples are available with more time. Indeed the speed and accuracy of such decisions are explained by the accumulation of evidence to a threshold or bound. However, the same framework seems to apply to decisions that are not obviously informed by sequences of evidence samples. Here we proffer the hypothesis that the sequential character of such tasks involves retrieval of evidence from memory. We explore this hypothesis by focusing on value-based decisions and argue that mnemonic processes can account for regularities in choice and decision time. We speculate on the neural mechanisms that link sampling of evidence from memory to circuits that represent the accumulated evidence bearing on a choice. We propose that memory processes may contribute to a wider class of decisions that conform to the regularities of choice-reaction time predicted by the sequential sampling framework. PMID:27253447

Meta-analyses and adaptive group sequential designs in the clinical development process.

PubMed

Jennison, Christopher; Turnbull, Bruce W

2005-01-01

The clinical development process can be viewed as a succession of trials, possibly overlapping in calendar time. The design of each trial may be influenced by results from previous studies and other currently proceeding trials, as well as by external information. Results from all of these trials must be considered together in order to assess the efficacy and safety of the proposed new treatment. Meta-analysis techniques provide a formal way of combining the information. We examine how such methods can be used in combining results from: (1) a collection of separate studies, (2) a sequence of studies in an organized development program, and (3) stages within a single study using a (possibly adaptive) group sequential design. We present two examples. The first example concerns the combining of results from a Phase IIb trial using several dose levels or treatment arms with those of the Phase III trial comparing the treatment selected in Phase IIb against a control This enables a "seamless transition" from Phase IIb to Phase III. The second example examines the use of combination tests to analyze data from an adaptive group sequential trial.

A Developmental Study of Shape Integration Over Space and Time.

ERIC Educational Resources Information Center

Enns, James T.; Girgus, Joan S.

1986-01-01

Three experiments with observers aged 6 to 21 years of age examined the integration of shape information over successive glances. Results indicated age-related improvements in the sequential integration of shape information, both when integration occurs through successive glimpses over space and when information is separated only in time. (HOD)

Words and Maps: Developmental Changes in Mental Models of Spatial Information Acquired from Descriptions and Depictions

ERIC Educational Resources Information Center

Uttal, David H.; Fisher, Joan A.; Taylor, Holly A.

2006-01-01

People acquire spatial information from many sources, including maps, verbal descriptions, and navigating in the environment. The different sources present spatial information in different ways. For example, maps can show many spatial relations simultaneously, but in a description, each spatial relation must be presented sequentially. The present…

Parallelization of sequential Gaussian, indicator and direct simulation algorithms

NASA Astrophysics Data System (ADS)

Nunes, Ruben; Almeida, José A.

2010-08-01

Improving the performance and robustness of algorithms on new high-performance parallel computing architectures is a key issue in efficiently performing 2D and 3D studies with large amount of data. In geostatistics, sequential simulation algorithms are good candidates for parallelization. When compared with other computational applications in geosciences (such as fluid flow simulators), sequential simulation software is not extremely computationally intensive, but parallelization can make it more efficient and creates alternatives for its integration in inverse modelling approaches. This paper describes the implementation and benchmarking of a parallel version of the three classic sequential simulation algorithms: direct sequential simulation (DSS), sequential indicator simulation (SIS) and sequential Gaussian simulation (SGS). For this purpose, the source used was GSLIB, but the entire code was extensively modified to take into account the parallelization approach and was also rewritten in the C programming language. The paper also explains in detail the parallelization strategy and the main modifications. Regarding the integration of secondary information, the DSS algorithm is able to perform simple kriging with local means, kriging with an external drift and collocated cokriging with both local and global correlations. SIS includes a local correction of probabilities. Finally, a brief comparison is presented of simulation results using one, two and four processors. All performance tests were carried out on 2D soil data samples. The source code is completely open source and easy to read. It should be noted that the code is only fully compatible with Microsoft Visual C and should be adapted for other systems/compilers.

Natural language processing and the Now-or-Never bottleneck.

PubMed

Gómez-Rodríguez, Carlos

2016-01-01

Researchers, motivated by the need to improve the efficiency of natural language processing tools to handle web-scale data, have recently arrived at models that remarkably match the expected features of human language processing under the Now-or-Never bottleneck framework. This provides additional support for said framework and highlights the research potential in the interaction between applied computational linguistics and cognitive science.

Implementation and performance of FDPS: a framework for developing parallel particle simulation codes

NASA Astrophysics Data System (ADS)

Iwasawa, Masaki; Tanikawa, Ataru; Hosono, Natsuki; Nitadori, Keigo; Muranushi, Takayuki; Makino, Junichiro

2016-08-01

We present the basic idea, implementation, measured performance, and performance model of FDPS (Framework for Developing Particle Simulators). FDPS is an application-development framework which helps researchers to develop simulation programs using particle methods for large-scale distributed-memory parallel supercomputers. A particle-based simulation program for distributed-memory parallel computers needs to perform domain decomposition, exchange of particles which are not in the domain of each computing node, and gathering of the particle information in other nodes which are necessary for interaction calculation. Also, even if distributed-memory parallel computers are not used, in order to reduce the amount of computation, algorithms such as the Barnes-Hut tree algorithm or the Fast Multipole Method should be used in the case of long-range interactions. For short-range interactions, some methods to limit the calculation to neighbor particles are required. FDPS provides all of these functions which are necessary for efficient parallel execution of particle-based simulations as "templates," which are independent of the actual data structure of particles and the functional form of the particle-particle interaction. By using FDPS, researchers can write their programs with the amount of work necessary to write a simple, sequential and unoptimized program of O(N2) calculation cost, and yet the program, once compiled with FDPS, will run efficiently on large-scale parallel supercomputers. A simple gravitational N-body program can be written in around 120 lines. We report the actual performance of these programs and the performance model. The weak scaling performance is very good, and almost linear speed-up was obtained for up to the full system of the K computer. The minimum calculation time per timestep is in the range of 30 ms (N = 107) to 300 ms (N = 109). These are currently limited by the time for the calculation of the domain decomposition and communication necessary for the interaction calculation. We discuss how we can overcome these bottlenecks.

Sequential estimation and satellite data assimilation in meteorology and oceanography

NASA Technical Reports Server (NTRS)

Ghil, M.

1986-01-01

The role of dynamics in estimating the state of the atmosphere and ocean from incomplete and noisy data is discussed and the classical applications of four-dimensional data assimilation to large-scale atmospheric dynamics are presented. It is concluded that sequential updating of a forecast model with continuously incoming conventional and remote-sensing data is the most natural way of extracting the maximum amount of information from the imperfectly known dynamics, on the one hand, and the inaccurate and incomplete observations, on the other.

Random Boolean networks for autoassociative memory: Optimization and sequential learning

NASA Astrophysics Data System (ADS)

Sherrington, D.; Wong, K. Y. M.

Conventional neural networks are based on synaptic storage of information, even when the neural states are discrete and bounded. In general, the set of potential local operations is much greater. Here we discuss some aspects of the properties of networks of binary neurons with more general Boolean functions controlling the local dynamics. Two specific aspects are emphasised; (i) optimization in the presence of noise and (ii) a simple model for short-term memory exhibiting primacy and recency in the recall of sequentially taught patterns.

Using a Mixed Methods Sequential Design to Identify Factors Associated with African American Mothers' Intention to Vaccinate Their Daughters Aged 9 to 12 for HPV with a Purpose of Informing a Culturally-Relevant, Theory-Based Intervention

ERIC Educational Resources Information Center

Cunningham, Jennifer L.

2013-01-01

The purpose of this sequential, explanatory mixed methods research study was to understand what factors influenced African American maternal intentions to get their daughters aged 9 years to 12 years vaccinated in Alabama. In the first, quantitative phase of the study, the research questions focused on identifying the predictive power of eleven…

High speed polling protocol for multiple node network with sequential flooding of a polling message and a poll-answering message

NASA Technical Reports Server (NTRS)

Marvit, Maclen (Inventor); Kirkham, Harold (Inventor)

1995-01-01

The invention is a multiple interconnected network of intelligent message-repeating remote nodes which employs a remote node polling process performed by a master node by transmitting a polling message generically addressed to all remote nodes associated with the master node. Each remote node responds upon receipt of the generically addressed polling message by sequentially flooding the network with a poll-answering informational message and with the polling message.

Program Completion of a Web-Based Tailored Lifestyle Intervention for Adults: Differences between a Sequential and a Simultaneous Approach

PubMed Central

Schneider, Francine; de Vries, Hein; van Osch, Liesbeth ADM; van Nierop, Peter WM; Kremers, Stef PJ

2012-01-01

Background Unhealthy lifestyle behaviors often co-occur and are related to chronic diseases. One effective method to change multiple lifestyle behaviors is web-based computer tailoring. Dropout from Internet interventions, however, is rather high, and it is challenging to retain participants in web-based tailored programs, especially programs targeting multiple behaviors. To date, it is unknown how much information people can handle in one session while taking part in a multiple behavior change intervention, which could be presented either sequentially (one behavior at a time) or simultaneously (all behaviors at once). Objectives The first objective was to compare dropout rates of 2 computer-tailored interventions: a sequential and a simultaneous strategy. The second objective was to assess which personal characteristics are associated with completion rates of the 2 interventions. Methods Using an RCT design, demographics, health status, physical activity, vegetable consumption, fruit consumption, alcohol intake, and smoking were self-assessed through web-based questionnaires among 3473 adults, recruited through Regional Health Authorities in the Netherlands in the autumn of 2009. First, a health risk appraisal was offered, indicating whether respondents were meeting the 5 national health guidelines. Second, psychosocial determinants of the lifestyle behaviors were assessed and personal advice was provided, about one or more lifestyle behaviors. Results Our findings indicate a high non-completion rate for both types of intervention (71.0%; n = 2167), with more incompletes in the simultaneous intervention (77.1%; n = 1169) than in the sequential intervention (65.0%; n = 998). In both conditions, discontinuation was predicted by a lower age (sequential condition: OR = 1.04; P < .001; CI = 1.02-1.05; simultaneous condition: OR = 1.04; P < .001; CI = 1.02-1.05) and an unhealthy lifestyle (sequential condition: OR = 0.86; P = .01; CI = 0.76-0.97; simultaneous condition: OR = 0.49; P < .001; CI = 0.42-0.58). In the sequential intervention, being male (OR = 1.27; P = .04; CI = 1.01-1.59) also predicted dropout. When respondents failed to adhere to at least 2 of the guidelines, those receiving the simultaneous intervention were more inclined to drop out than were those receiving the sequential intervention. Conclusion Possible reasons for the higher dropout rate in our simultaneous intervention may be the amount of time required and information overload. Strategies to optimize program completion as well as continued use of computer-tailored interventions should be studied. Trial Registration Dutch Trial Register NTR2168 PMID:22403770

Program completion of a web-based tailored lifestyle intervention for adults: differences between a sequential and a simultaneous approach.

PubMed

Schulz, Daniela N; Schneider, Francine; de Vries, Hein; van Osch, Liesbeth A D M; van Nierop, Peter W M; Kremers, Stef P J

2012-03-08

Unhealthy lifestyle behaviors often co-occur and are related to chronic diseases. One effective method to change multiple lifestyle behaviors is web-based computer tailoring. Dropout from Internet interventions, however, is rather high, and it is challenging to retain participants in web-based tailored programs, especially programs targeting multiple behaviors. To date, it is unknown how much information people can handle in one session while taking part in a multiple behavior change intervention, which could be presented either sequentially (one behavior at a time) or simultaneously (all behaviors at once). The first objective was to compare dropout rates of 2 computer-tailored interventions: a sequential and a simultaneous strategy. The second objective was to assess which personal characteristics are associated with completion rates of the 2 interventions. Using an RCT design, demographics, health status, physical activity, vegetable consumption, fruit consumption, alcohol intake, and smoking were self-assessed through web-based questionnaires among 3473 adults, recruited through Regional Health Authorities in the Netherlands in the autumn of 2009. First, a health risk appraisal was offered, indicating whether respondents were meeting the 5 national health guidelines. Second, psychosocial determinants of the lifestyle behaviors were assessed and personal advice was provided, about one or more lifestyle behaviors. Our findings indicate a high non-completion rate for both types of intervention (71.0%; n = 2167), with more incompletes in the simultaneous intervention (77.1%; n = 1169) than in the sequential intervention (65.0%; n = 998). In both conditions, discontinuation was predicted by a lower age (sequential condition: OR = 1.04; P < .001; CI = 1.02-1.05; simultaneous condition: OR = 1.04; P < .001; CI = 1.02-1.05) and an unhealthy lifestyle (sequential condition: OR = 0.86; P = .01; CI = 0.76-0.97; simultaneous condition: OR = 0.49; P < .001; CI = 0.42-0.58). In the sequential intervention, being male (OR = 1.27; P = .04; CI = 1.01-1.59) also predicted dropout. When respondents failed to adhere to at least 2 of the guidelines, those receiving the simultaneous intervention were more inclined to drop out than were those receiving the sequential intervention. Possible reasons for the higher dropout rate in our simultaneous intervention may be the amount of time required and information overload. Strategies to optimize program completion as well as continued use of computer-tailored interventions should be studied. Dutch Trial Register NTR2168.

An automatic eye detection and tracking technique for stereo video sequences

NASA Astrophysics Data System (ADS)

Paduru, Anirudh; Charalampidis, Dimitrios; Fouts, Brandon; Jovanovich, Kim

2009-05-01

Human-computer interfacing (HCI) describes a system or process with which two information processors, namely a human and a computer, attempt to exchange information. Computer-to-human (CtH) information transfer has been relatively effective through visual displays and sound devices. On the other hand, the human-tocomputer (HtC) interfacing avenue has yet to reach its full potential. For instance, the most common HtC communication means are the keyboard and mouse, which are already becoming a bottleneck in the effective transfer of information. The solution to the problem is the development of algorithms that allow the computer to understand human intentions based on their facial expressions, head motion patterns, and speech. In this work, we are investigating the feasibility of a stereo system to effectively determine the head position, including the head rotation angles, based on the detection of eye pupils.

Modular Engineering of l-Tyrosine Production in Escherichia coli

PubMed Central

Juminaga, Darmawi; Baidoo, Edward E. K.; Redding-Johanson, Alyssa M.; Batth, Tanveer S.; Burd, Helcio; Mukhopadhyay, Aindrila; Petzold, Christopher J.

2012-01-01

Efficient biosynthesis of l-tyrosine from glucose is necessary to make biological production economically viable. To this end, we designed and constructed a modular biosynthetic pathway for l-tyrosine production in E. coli MG1655 by encoding the enzymes for converting erythrose-4-phosphate (E4P) and phosphoenolpyruvate (PEP) to l-tyrosine on two plasmids. Rational engineering to improve l-tyrosine production and to identify pathway bottlenecks was directed by targeted proteomics and metabolite profiling. The bottlenecks in the pathway were relieved by modifications in plasmid copy numbers, promoter strength, gene codon usage, and the placement of genes in operons. One major bottleneck was due to the bifunctional activities of quinate/shikimate dehydrogenase (YdiB), which caused accumulation of the intermediates dehydroquinate (DHQ) and dehydroshikimate (DHS) and the side product quinate; this bottleneck was relieved by replacing YdiB with its paralog AroE, resulting in the production of over 700 mg/liter of shikimate. Another bottleneck in shikimate production, due to low expression of the dehydroquinate synthase (AroB), was alleviated by optimizing the first 15 codons of the gene. Shikimate conversion to l-tyrosine was improved by replacing the shikimate kinase AroK with its isozyme, AroL, which effectively consumed all intermediates formed in the first half of the pathway. Guided by the protein and metabolite measurements, the best producer, consisting of two medium-copy-number, dual-operon plasmids, was optimized to produce >2 g/liter l-tyrosine at 80% of the theoretical yield. This work demonstrates the utility of targeted proteomics and metabolite profiling in pathway construction and optimization, which should be applicable to other metabolic pathways. PMID:22020510

A Wide Range of 3243A>G/tRNALeu(UUR) (MELAS) Mutation Loads May Segregate in Offspring through the Female Germline Bottleneck

PubMed Central

Pallotti, Francesco; Binelli, Giorgio; Fabbri, Raffaella; Valentino, Maria L.; Vicenti, Rossella; Macciocca, Maria; Cevoli, Sabina; Baruzzi, Agostino; DiMauro, Salvatore; Carelli, Valerio

2014-01-01

Segregation of mutant mtDNA in human tissues and through the germline is debated, with no consensus about the nature and size of the bottleneck hypothesized to explain rapid generational shifts in mutant loads. We investigated two maternal lineages with an apparently different inheritance pattern of the same pathogenic mtDNA 3243A>G/tRNALeu(UUR) (MELAS) mutation. We collected blood cells, muscle biopsies, urinary epithelium and hair follicles from 20 individuals, as well as oocytes and an ovarian biopsy from one female mutation carrier, all belonging to the two maternal lineages to assess mutant mtDNA load, and calculated the theoretical germline bottleneck size (number of segregating units). We also evaluated “mother-to-offspring” segregations from the literature, for which heteroplasmy assessment was available in at least three siblings besides the proband. Our results showed that mutation load was prevalent in skeletal muscle and urinary epithelium, whereas in blood cells there was an inverse correlation with age, as previously reported. The histoenzymatic staining of the ovarian biopsy failed to show any cytochrome-c-oxidase defective oocyte. Analysis of four oocytes and one offspring from the same unaffected mother of the first family showed intermediate heteroplasmic mutant loads (10% to 75%), whereas very skewed loads of mutant mtDNA (0% or 81%) were detected in five offspring of another unaffected mother from the second family. Bottleneck size was 89 segregating units for the first mother and 84 for the second. This was remarkably close to 88, the number of “segregating units” in the “mother-to-offspring” segregations retrieved from literature. In conclusion, a wide range of mutant loads may be found in offspring tissues and oocytes, resulting from a similar theoretical bottleneck size. PMID:24805791

Consequences of a demographic bottleneck on genetic structure and variation in the Scandinavian brown bear.

PubMed

Xenikoudakis, G; Ersmark, E; Tison, J-L; Waits, L; Kindberg, J; Swenson, J E; Dalén, L

2015-07-01

The Scandinavian brown bear went through a major decline in population size approximately 100 years ago, due to intense hunting. After being protected, the population subsequently recovered and today numbers in the thousands. The genetic diversity in the contemporary population has been investigated in considerable detail, and it has been shown that the population consists of several subpopulations that display relatively high levels of genetic variation. However, previous studies have been unable to resolve the degree to which the demographic bottleneck impacted the contemporary genetic structure and diversity. In this study, we used mitochondrial and microsatellite DNA markers from pre- and postbottleneck Scandinavian brown bear samples to investigate the effect of the bottleneck. Simulation and multivariate analysis suggested the same genetic structure for the historical and modern samples, which are clustered into three subpopulations in southern, central and northern Scandinavia. However, the southern subpopulation appears to have gone through a marked change in allele frequencies. When comparing the mitochondrial DNA diversity in the whole population, we found a major decline in haplotype numbers across the bottleneck. However, the loss of autosomal genetic diversity was less pronounced, although a significant decline in allelic richness was observed in the southern subpopulation. Approximate Bayesian computations provided clear support for a decline in effective population size during the bottleneck, in both the southern and northern subpopulations. These results have implications for the future management of the Scandinavian brown bear because they indicate a recent loss in genetic diversity and also that the current genetic structure may have been caused by historical ecological processes rather than recent anthropogenic persecution. © 2015 John Wiley & Sons Ltd.

Spatial-sequential and spatial-simultaneous working memory in individuals with Williams syndrome.

PubMed

Lanfranchi, Silvia; De Mori, Letizia; Mammarella, Irene C; Carretti, Barbara; Vianello, Renzo

2015-05-01

The aim of the present study was to compare visuospatial working memory performance in 18 individuals with Williams syndrome (WS) and 18 typically developing (TD) children matched for nonverbal mental age. Two aspects were considered: task presentation format (i.e., spatial-sequential or spatial-simultaneous), and level of attentional control (i.e., passive or active tasks). Our results showed that individuals with WS performed less well than TD children in passive spatial-simultaneous tasks, but not in passive spatial-sequential tasks. The former's performance was also worse in both active tasks. These findings suggest an impairment in the spatial-simultaneous working memory of individuals with WS, together with a more generalized difficulty in tasks requiring information storage and concurrent processing, as seen in other etiologies of intellectual disability.

Emerging from the bottleneck: benefits of the comparative approach to modern neuroscience.

PubMed

Brenowitz, Eliot A; Zakon, Harold H

2015-05-01

Neuroscience has historically exploited a wide diversity of animal taxa. Recently, however, research has focused increasingly on a few model species. This trend has accelerated with the genetic revolution, as genomic sequences and genetic tools became available for a few species, which formed a bottleneck. This coalescence on a small set of model species comes with several costs that are often not considered, especially in the current drive to use mice explicitly as models for human diseases. Comparative studies of strategically chosen non-model species can complement model species research and yield more rigorous studies. As genetic sequences and tools become available for many more species, we are poised to emerge from the bottleneck and once again exploit the rich biological diversity offered by comparative studies. Copyright © 2015 Elsevier Ltd. All rights reserved.

[Application of ecosystem service value in land use change research: Bottlenecks and prospects].

PubMed

Zhang, Zhou; Wu, Ci-Fang; Tan, Rong

2013-02-01

In recent years, the application of ecosystem service value in land use change research is a hot topic in many famous international journals. However, policy makers are seldom taking into account the achievements of the related studies in practice. This paper summarized the three main bottlenecks in applying ecosystem service value in land management practices, i. e., the difficulty in measuring the service values, the complexity of driving factors, and the bias of evaluation criteria. Some solutions on the bottlenecks were provided, and the future research directions in China were prospected. It was suggested that in the studies of land use change based on ecosystem service value, it would be more appropriate to adopt comparative analysis method in small scale case studies, especially focusing on the natural ecological resources and the excessive loss of their values.

Airport security inspection process model and optimization based on GSPN

NASA Astrophysics Data System (ADS)

Mao, Shuainan

2018-04-01

Aiming at the efficiency of airport security inspection process, Generalized Stochastic Petri Net is used to establish the security inspection process model. The model is used to analyze the bottleneck problem of airport security inspection process. The solution to the bottleneck is given, which can significantly improve the efficiency and reduce the waiting time by adding the place for people to remove their clothes and the X-ray detector.

Non-Integrated Information and Communication Technologies in the Kidney Transplantation Process in Brazil.

PubMed

Peres Penteado, Alissa; Fábio Maciel, Rafael; Erbs, João; Feijó Ortolani, Cristina Lucia; Aguiar Roza, Bartira; Torres Pisa, Ivan

2015-01-01

The entire kidney transplantation process in Brazil is defined through laws, decrees, ordinances, and resolutions, but there is no defined theoretical map describing this process. From this representation it's possible to perform analysis, such as the identification of bottlenecks and information and communication technologies (ICTs) that support this process. The aim of this study was to analyze and represent the kidney transplantation workflow using business process modeling notation (BPMN) and then to identify the ICTs involved in the process. This study was conducted in eight steps, including document analysis and professional evaluation. The results include the BPMN model of the kidney transplantation process in Brazil and the identification of ICTs. We discovered that there are great delays in the process due to there being many different ICTs involved, which can cause information to be poorly integrated.

Investigation of the bottleneck leading to the domestication of maize

PubMed Central

Eyre-Walker, Adam; Gaut, Rebecca L.; Hilton, Holly; Feldman, Dawn L.; Gaut, Brandon S.

1998-01-01

Maize (Zea mays ssp. mays) is genetically diverse, yet it is also morphologically distinct from its wild relatives. These two observations are somewhat contradictory: the first observation is consistent with a large historical population size for maize, but the latter observation is consistent with strong, diversity-limiting selection during maize domestication. In this study, we sampled sequence diversity, coupled with simulations of the coalescent process, to study the dynamics of a population bottleneck during the domestication of maize. To do this, we determined the DNA sequence of a 1,400-bp region of the Adh1 locus from 19 individuals representing maize, its presumed progenitor (Z. mays ssp. parviglumis), and a more distant relative (Zea luxurians). The sequence data were used to guide coalescent simulations of population bottlenecks associated with domestication. Our study confirms high genetic diversity in maize—maize contains 75% of the variation found in its progenitor and is more diverse than its wild relative, Z. luxurians—but it also suggests that sequence diversity in maize can be explained by a bottleneck of short duration and very small size. For example, the breadth of genetic diversity in maize is consistent with a founding population of only 20 individuals when the domestication event is 10 generations in length. PMID:9539756

Genetics Show Current Decline and Pleistocene Expansion in Northern Spotted Owls

USGS Publications Warehouse

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

2008-01-01

The northern spotted owl (Strix occidentalis caurina) is one of the most controversial threatened subspecies ever listed under the U.S. Endangered Species Act. Because of concern for persistence of the subspecies, logging on Federal lands in the U.S. Pacific Northwest was dramatically reduced under the Northwest Forest Plan in 1994. Despite protection of its remaining forest habitat, recent field studies show continued demographic declines of northern spotted owls. One potential threat to northern spotted owls that has not yet been shown is loss of genetic variation from population bottlenecks that can increase inbreeding depression and decrease adaptive potential. Here, we show recent genetic bottlenecks in northern spotted owls using a large genetic dataset (352 individuals from across the subspecies' range and 11 microsatellite loci). The signature of bottlenecks was strongest in Washington State, in agreement with field data. Interestingly, we also found a genetic signature of Pleistocene expansion in the same study areas where recent bottlenecks were shown. Our results provide independent evidence that northern spotted owls have recently declined, and suggest that loss of genetic variation is an emerging threat to the subspecies' persistence. Reduced effective population size (Ne), shown here in addition to field evidence for demographic decline, highlights the increasing vulnerability of this bird to extinction.

Lagrangian-averaged model for magnetohydrodynamic turbulence and the absence of bottlenecks.

PubMed

Pietarila Graham, Jonathan; Mininni, Pablo D; Pouquet, Annick

2009-07-01

We demonstrate that, for the case of quasiequipartition between the velocity and the magnetic field, the Lagrangian-averaged magnetohydrodynamics (LAMHD) alpha model reproduces well both the large-scale and the small-scale properties of turbulent flows; in particular, it displays no increased (superfilter) bottleneck effect with its ensuing enhanced energy spectrum at the onset of the subfilter scales. This is in contrast to the case of the neutral fluid in which the Lagrangian-averaged Navier-Stokes alpha model is somewhat limited in its applications because of the formation of spatial regions with no internal degrees of freedom and subsequent contamination of superfilter-scale spectral properties. We argue that, as the Lorentz force breaks the conservation of circulation and enables spectrally nonlocal energy transfer (associated with Alfvén waves), it is responsible for the absence of a viscous bottleneck in magnetohydrodynamics (MHD), as compared to the fluid case. As LAMHD preserves Alfvén waves and the circulation properties of MHD, there is also no (superfilter) bottleneck found in LAMHD, making this method capable of large reductions in required numerical degrees of freedom; specifically, we find a reduction factor of approximately 200 when compared to a direct numerical simulation on a large grid of 1536;{3} points at the same Reynolds number.

Bottlenecks, concerns and needs in malaria operational research: the perspectives of key stakeholders in Nigeria.

PubMed

Onyiah, Pamela; Adamu, Al-Mukhtar Y; Afolabi, Rotimi F; Ajumobi, Olufemi; Ughasoro, Maduka D; Odeyinka, Oluwaseun; Nguku, Patrick; Ajayi, IkeOluwapo O

2018-05-04

We conducted a study to determine stakeholders' perspective of the bottlenecks, concerns and needs to malaria operational research (MOR) agenda setting in Nigeria. Eighty-five (37.9%) stakeholders identified lack of positive behavioural change as the major bottleneck to MOR across the malaria thematic areas comprising of malaria prevention 58.8% (50), case management 34.8% (39), advocacy communication and social mobilisation 4.7% (4) while procurement and supply chain management (PSM) and programme management experts had the least response of 1.2% (1) each. Other bottlenecks were inadequate capacity to implement (13.8%, n = 31), inadequate funds (11.6%, n = 26), poor supply management (9.4%, n = 21), administrative bureaucracy (5.8%, n = 13), inadequacy of experts (1.3%, n = 3) and poor policy implementation (4.9%, n = 11). Of the 31 stakeholders who opined lack of capacity to execute malaria operational research; 17 (54.8%), 10 (32.3%), 3 (9.7%) and 1 (3.2%) were experts in case management, malaria prevention, surveillance, monitoring and evaluation and PSM respectively. Improvement in community enlightenment and awareness strategies; and active involvement of health care workers public and private sectors were identified solutions to lack of positive behavioural change.

Target discovery focused approaches to overcome bottlenecks in the exploitation of antimycobacterial natural products.

PubMed

Baptista, Rafael; Bhowmick, Sumana; Nash, Robert J; Baillie, Les; Mur, Luis Aj

2018-04-01

Tuberculosis is a major global health hazard. The search for new antimycobacterials has focused on such as screening combinational chemistry libraries or designing chemicals to target predefined pockets of essential bacterial proteins. The relative ineffectiveness of these has led to a reappraisal of natural products for new antimycobacterial drug leads. However, progress has been limited, we suggest through a failure in many cases to define the drug target and optimize the hits using this information. We highlight methods of target discovery needed to develop a drug into a candidate for clinical trials. We incorporate these into suggested analysis pipelines which could inform the research strategies to accelerate the development of new drug leads from natural products.

Sequential quantum cloning under real-life conditions

NASA Astrophysics Data System (ADS)

Saberi, Hamed; Mardoukhi, Yousof

2012-05-01

We consider a sequential implementation of the optimal quantum cloning machine of Gisin and Massar and propose optimization protocols for experimental realization of such a quantum cloner subject to the real-life restrictions. We demonstrate how exploiting the matrix-product state (MPS) formalism and the ensuing variational optimization techniques reveals the intriguing algebraic structure of the Gisin-Massar output of the cloning procedure and brings about significant improvements to the optimality of the sequential cloning prescription of Delgado [Phys. Rev. Lett.PRLTAO0031-900710.1103/PhysRevLett.98.150502 98, 150502 (2007)]. Our numerical results show that the orthodox paradigm of optimal quantum cloning can in practice be realized in a much more economical manner by utilizing a considerably lesser amount of informational and numerical resources than hitherto estimated. Instead of the previously predicted linear scaling of the required ancilla dimension D with the number of qubits n, our recipe allows a realization of such a sequential cloning setup with an experimentally manageable ancilla of dimension at most D=3 up to n=15 qubits. We also address satisfactorily the possibility of providing an optimal range of sequential ancilla-qubit interactions for optimal cloning of arbitrary states under realistic experimental circumstances when only a restricted class of such bipartite interactions can be engineered in practice.

Genetic variation and population structure in Jamunapari goats using microsatellites, mitochondrial DNA, and milk protein genes.

PubMed

Rout, P K; Thangraj, K; Mandal, A; Roy, R

2012-01-01

Jamunapari, a dairy goat breed of India, has been gradually declining in numbers in its home tract over the years. We have analysed genetic variation and population history in Jamunapari goats based on 17 microsatellite loci, 2 milk protein loci, mitochondrial hypervariable region I (HVRI) sequencing, and three Y-chromosomal gene sequencing. We used the mitochondrial DNA (mtDNA) mismatch distribution, microsatellite data, and bottleneck tests to infer the population history and demography. The mean number of alleles per locus was 9.0 indicating that the allelic variation was high in all the loci and the mean heterozygosity was 0.769 at nuclear loci. Although the population size is smaller than 8,000 individuals, the amount of variability both in terms of allelic richness and gene diversity was high in all the microsatellite loci except ILST 005. The gene diversity and effective number of alleles at milk protein loci were higher than the 10 other Indian goat breeds that they were compared to. Mismatch analysis was carried out and the analysis revealed that the population curve was unimodal indicating the expansion of population. The genetic diversity of Y-chromosome genes was low in the present study. The observed mean M ratio in the population was above the critical significance value (Mc) and close to one indicating that it has maintained a slowly changing population size. The mode-shift test did not detect any distortion of allele frequency and the heterozygosity excess method showed that there was no significant departure from mutation-drift equilibrium detected in the population. However, the effects of genetic bottlenecks were observed in some loci due to decreased heterozygosity and lower level of M ratio. There were two observed genetic subdivisions in the population supporting the observations of farmers in different areas. This base line information on genetic diversity, bottleneck analysis, and mismatch analysis was obtained to assist the conservation decision and management of the breed.

Genetic Variation and Population Structure in Jamunapari Goats Using Microsatellites, Mitochondrial DNA, and Milk Protein Genes

PubMed Central

Rout, P. K.; Thangraj, K.; Mandal, A.; Roy, R.

2012-01-01

Jamunapari, a dairy goat breed of India, has been gradually declining in numbers in its home tract over the years. We have analysed genetic variation and population history in Jamunapari goats based on 17 microsatellite loci, 2 milk protein loci, mitochondrial hypervariable region I (HVRI) sequencing, and three Y-chromosomal gene sequencing. We used the mitochondrial DNA (mtDNA) mismatch distribution, microsatellite data, and bottleneck tests to infer the population history and demography. The mean number of alleles per locus was 9.0 indicating that the allelic variation was high in all the loci and the mean heterozygosity was 0.769 at nuclear loci. Although the population size is smaller than 8,000 individuals, the amount of variability both in terms of allelic richness and gene diversity was high in all the microsatellite loci except ILST 005. The gene diversity and effective number of alleles at milk protein loci were higher than the 10 other Indian goat breeds that they were compared to. Mismatch analysis was carried out and the analysis revealed that the population curve was unimodal indicating the expansion of population. The genetic diversity of Y-chromosome genes was low in the present study. The observed mean M ratio in the population was above the critical significance value (Mc) and close to one indicating that it has maintained a slowly changing population size. The mode-shift test did not detect any distortion of allele frequency and the heterozygosity excess method showed that there was no significant departure from mutation-drift equilibrium detected in the population. However, the effects of genetic bottlenecks were observed in some loci due to decreased heterozygosity and lower level of M ratio. There were two observed genetic subdivisions in the population supporting the observations of farmers in different areas. This base line information on genetic diversity, bottleneck analysis, and mismatch analysis was obtained to assist the conservation decision and management of the breed. PMID:22606053

Data simulation for the Lightning Imaging Sensor (LIS)

NASA Technical Reports Server (NTRS)

Boeck, William L.

1991-01-01

This project aims to build a data analysis system that will utilize existing video tape scenes of lightning as viewed from space. The resultant data will be used for the design and development of the Lightning Imaging Sensor (LIS) software and algorithm analysis. The desire for statistically significant metrics implies that a large data set needs to be analyzed. Before 1990 the quality and quantity of video was insufficient to build a usable data set. At this point in time, there is usable data from missions STS-34, STS-32, STS-31, STS-41, STS-37, and STS-39. During the summer of 1990, a manual analysis system was developed to demonstrate that the video analysis is feasible and to identify techniques to deduce information that was not directly available. Because the closed circuit television system used on the space shuttle was intended for documentary TV, the current value of the camera focal length and pointing orientation, which are needed for photoanalysis, are not included in the system data. A large effort was needed to discover ancillary data sources as well as develop indirect methods to estimate the necessary parameters. Any data system coping with full motion video faces an enormous bottleneck produced by the large data production rate and the need to move and store the digitized images. The manual system bypassed the video digitizing bottleneck by using a genlock to superimpose pixel coordinates on full motion video. Because the data set had to be obtained point by point by a human operating a computer mouse, the data output rate was small. The loan and subsequent acquisition of a Abekas digital frame store with a real time digitizer moved the bottleneck from data acquisition to a problem of data transfer and storage. The semi-automated analysis procedure was developed using existing equipment and is described. A fully automated system is described in the hope that the components may come on the market at reasonable prices in the next few years.

Research on laser marking speed optimization by using genetic algorithm.

PubMed

Wang, Dongyun; Yu, Qiwei; Zhang, Yu

2015-01-01

Laser Marking Machine is the most common coding equipment on product packaging lines. However, the speed of laser marking has become a bottleneck of production. In order to remove this bottleneck, a new method based on a genetic algorithm is designed. On the basis of this algorithm, a controller was designed and simulations and experiments were performed. The results show that using this algorithm could effectively improve laser marking efficiency by 25%.

Dual-Task Interference When A Response is Not Required

NASA Technical Reports Server (NTRS)

VanSelst, Mark; Johnston, James C.; Shafto, Michael (Technical Monitor)

2002-01-01

When subjects are required to respond to two stimuli presented in rapid succession, responses to the second stimulus are delayed. Such dual-task interference has been attributed to a fundamental processing bottleneck preventing simultaneous processing on both tasks. Two experiments show dual-task interference even when the first task does not require a response. The observed interference is caused by a bottleneck in central cognitive processing, rather than in response initiation or execution.

Squeezing through the Now-or-Never bottleneck: Reconnecting language processing, acquisition, change, and structure.

PubMed

Chater, Nick; Christiansen, Morten H

2016-01-01

If human language must be squeezed through a narrow cognitive bottleneck, what are the implications for language processing, acquisition, change, and structure? In our target article, we suggested that the implications are far-reaching and form the basis of an integrated account of many apparently unconnected aspects of language and language processing, as well as suggesting revision of many existing theoretical accounts. With some exceptions, commentators were generally supportive both of the existence of the bottleneck and its potential implications. Many commentators suggested additional theoretical and linguistic nuances and extensions, links with prior work, and relevant computational and neuroscientific considerations; some argued for related but distinct viewpoints; a few, though, felt traditional perspectives were being abandoned too readily. Our response attempts to build on the many suggestions raised by the commentators and to engage constructively with challenges to our approach.

Topographic Steering of Enhanced Ice Flow at the Bottleneck Between East and West Antarctica

NASA Astrophysics Data System (ADS)

Winter, Kate; Ross, Neil; Ferraccioli, Fausto; Jordan, Tom A.; Corr, Hugh F. J.; Forsberg, René; Matsuoka, Kenichi; Olesen, Arne V.; Casal, Tania G.

2018-05-01

Hypothesized drawdown of the East Antarctic Ice Sheet through the "bottleneck" zone between East and West Antarctica would have significant impacts for a large proportion of the Antarctic Ice Sheet. Earth observation satellite orbits and a sparseness of radio echo sounding data have restricted investigations of basal boundary controls on ice flow in this region until now. New airborne radio echo sounding surveys reveal complex topography of high relief beneath the southernmost Weddell/Ross ice divide, with three subglacial troughs connecting interior Antarctica to the Foundation and Patuxent Ice Streams and Siple Coast ice streams. These troughs route enhanced ice flow through the interior of Antarctica but limit potential drawdown of the East Antarctic Ice Sheet through the bottleneck zone. In a thinning or retreating scenario, these topographically controlled corridors of enhanced flow could however drive ice divide migration and increase mass discharge from interior West Antarctica to the Southern Ocean.

Zero-temperature quantum annealing bottlenecks in the spin-glass phase.

PubMed

Knysh, Sergey

2016-08-05

A promising approach to solving hard binary optimization problems is quantum adiabatic annealing in a transverse magnetic field. An instantaneous ground state-initially a symmetric superposition of all possible assignments of N qubits-is closely tracked as it becomes more and more localized near the global minimum of the classical energy. Regions where the energy gap to excited states is small (for instance at the phase transition) are the algorithm's bottlenecks. Here I show how for large problems the complexity becomes dominated by O(log N) bottlenecks inside the spin-glass phase, where the gap scales as a stretched exponential. For smaller N, only the gap at the critical point is relevant, where it scales polynomially, as long as the phase transition is second order. This phenomenon is demonstrated rigorously for the two-pattern Gaussian Hopfield model. Qualitative comparison with the Sherrington-Kirkpatrick model leads to similar conclusions.

Dual-task interference with equal task emphasis: graded capacity sharing or central postponement?

NASA Technical Reports Server (NTRS)

Ruthruff, Eric; Pashler, Harold E.; Hazeltine, Eliot

2003-01-01

Most studies using the psychological refractory period (PRP) design suggest that dual-task performance is limited by a central bottleneck. Because subjects are usually told to emphasize Task 1, however, the bottleneck might reflect a strategic choice rather than a structural limitation. To evaluate the possibility that central operations can proceed in parallel, albeit with capacity limitations, we conducted two dual-task experiments with equal task emphasis. In both experiments, subjects tended to either group responses together or respond to one task well before the other. In addition, stimulus-response compatibility effects were roughly constant across stimulus onset asynchronies (SOAs). At the short SOA, compatibility effects also carried over onto response times for the other task. This pattern of results is difficult to reconcile with the possibility that subjects share capacity roughly equally between simultaneous central operations. However, this pattern is consistent with the existence of a structural central bottleneck.

Sequential Ideal-Observer Analysis of Visual Discriminations.

ERIC Educational Resources Information Center

Geisler, Wilson S.

1989-01-01

A new analysis, based on the concept of the ideal observer in signal detection theory, is described. It allows: tracing of the flow of discrimination information through the initial physiological stages of visual processing for arbitrary spatio-chromatic stimuli, and measurement of the information content of said visual stimuli. (TJH)

Item Selection in Multidimensional Computerized Adaptive Testing--Gaining Information from Different Angles

ERIC Educational Resources Information Center

Wang, Chun; Chang, Hua-Hua

2011-01-01

Over the past thirty years, obtaining diagnostic information from examinees' item responses has become an increasingly important feature of educational and psychological testing. The objective can be achieved by sequentially selecting multidimensional items to fit the class of latent traits being assessed, and therefore Multidimensional…

Say again? How complexity and format of air traffic control instructions affect pilot recall

DOT National Transportation Integrated Search

1999-01-01

This study compared the recall of ATC information presented in cither grouped or sequential format : in a part-task simulation. It also tested the effect of complexity of ATC clearances on recall, that is, : how many pieces of information a single tr...

Implications of Neuropsychological Research for School Psychology.

ERIC Educational Resources Information Center

Dean, Raymond S.; Gray, Jeffrey W.

Research has suggested that the two hemispheres of the brain serve specialized functions, with the most recent studies portraying the left hemisphere as processing information in a linear, serial, or sequential manner and the right hemisphere as processing information in a holistic, concrete, or visual mode. Although few systematic studies have…

Mutual Information Item Selection in Adaptive Classification Testing

ERIC Educational Resources Information Center

Weissman, Alexander

2007-01-01

A general approach for item selection in adaptive multiple-category classification tests is provided. The approach uses mutual information (MI), a special case of the Kullback-Leibler distance, or relative entropy. MI works efficiently with the sequential probability ratio test and alleviates the difficulties encountered with using other local-…

On the Specificity of Sequential Congruency Effects in Implicit Learning of Motor and Perceptual Sequences

ERIC Educational Resources Information Center

D'Angelo, Maria C.; Jimenez, Luis; Milliken, Bruce; Lupianez, Juan

2013-01-01

Individuals experience less interference from conflicting information following events that contain conflicting information. Recently, Jimenez, Lupianez, and Vaquero (2009) demonstrated that such adaptations to conflict occur even when the source of conflict arises from implicit knowledge of sequences. There is accumulating evidence that momentary…

Sequentially Observed Periodic Surveys of Management Compartments to Monitor Red-cockaded Woodpecker Populations

Treesearch

Robert G. Hooper; H. David Muse

1989-01-01

Management of the red-cockaded woodpeckcer (Picoides borealis) requires knowledge of size and trend of individual poulations. Periodic entry into management compartments for thinning and regeneration of stands provides considerable information on individual cavity trees and colonies. The statistical rationale and formulas for using this information...

A Game-Theoretic Approach to Information-Flow Control via Protocol Composition

NASA Astrophysics Data System (ADS)

Alvim, Mário; Chatzikokolakis, Konstantinos; Kawamoto, Yusuke; Palamidessi, Catuscia

2018-05-01

In the inference attacks studied in Quantitative Information Flow (QIF), the attacker typically tries to interfere with the system in the attempt to increase its leakage of secret information. The defender, on the other hand, typically tries to decrease leakage by introducing some controlled noise. This noise introduction can be modeled as a type of protocol composition, i.e., a probabilistic choice among different protocols, and its effect on the amount of leakage depends heavily on whether or not this choice is visible to the attacker. In this work, we consider operators for modeling visible and hidden choice in protocol composition, and we study their algebraic properties. We then formalize the interplay between defender and attacker in a game-theoretic framework adapted to the specific issues of QIF, where the payoff is information leakage. We consider various kinds of leakage games, depending on whether players act simultaneously or sequentially, and on whether or not the choices of the defender are visible to the attacker. In the case of sequential games, the choice of the second player is generally a function of the choice of the first player, and his/her probabilistic choice can be either over the possible functions (mixed strategy) or it can be on the result of the function (behavioral strategy). We show that when the attacker moves first in a sequential game with a hidden choice, then behavioral strategies are more advantageous for the defender than mixed strategies. This contrasts with the standard game theory, where the two types of strategies are equivalent. Finally, we establish a hierarchy of these games in terms of their information leakage and provide methods for finding optimal strategies (at the points of equilibrium) for both attacker and defender in the various cases.

How to improve an un-alterable model forecast? A sequential data assimilation based error updating approach

NASA Astrophysics Data System (ADS)

Gragne, A. S.; Sharma, A.; Mehrotra, R.; Alfredsen, K. T.

2012-12-01

Accuracy of reservoir inflow forecasts is instrumental for maximizing value of water resources and influences operation of hydropower reservoirs significantly. Improving hourly reservoir inflow forecasts over a 24 hours lead-time is considered with the day-ahead (Elspot) market of the Nordic exchange market in perspectives. The procedure presented comprises of an error model added on top of an un-alterable constant parameter conceptual model, and a sequential data assimilation routine. The structure of the error model was investigated using freely available software for detecting mathematical relationships in a given dataset (EUREQA) and adopted to contain minimum complexity for computational reasons. As new streamflow data become available the extra information manifested in the discrepancies between measurements and conceptual model outputs are extracted and assimilated into the forecasting system recursively using Sequential Monte Carlo technique. Besides improving forecast skills significantly, the probabilistic inflow forecasts provided by the present approach entrains suitable information for reducing uncertainty in decision making processes related to hydropower systems operation. The potential of the current procedure for improving accuracy of inflow forecasts at lead-times unto 24 hours and its reliability in different seasons of the year will be illustrated and discussed thoroughly.

Sequential Auctions with Partially Substitutable Goods

NASA Astrophysics Data System (ADS)

Vetsikas, Ioannis A.; Jennings, Nicholas R.

In this paper, we examine a setting in which a number of partially substitutable goods are sold in sequential single unit auctions. Each bidder needs to buy exactly one of these goods. In previous work, this setting has been simplified by assuming that bidders do not know their valuations for all items a priori, but rather are informed of their true valuation for each item right before the corresponding auction takes place. This assumption simplifies the strategies of bidders, as the expected revenue from future auctions is the same for all bidders due to the complete lack of private information. In our analysis we don't make this assumption. This complicates the computation of the equilibrium strategies significantly. We examine this setting both for first and second-price auction variants, initially when the closing prices are not announced, for which we prove that sequential first and second-price auctions are revenue equivalent. Then we assume that the prices are announced; because of the asymmetry in the announced prices between the two auction variants, revenue equivalence does not hold in this case. We finish the paper, by giving some initial results about the case when free disposal is allowed, and therefore a bidder can purchase more than one item.

Identity-level representations affect unfamiliar face matching performance in sequential but not simultaneous tasks.

PubMed

Menon, Nadia; White, David; Kemp, Richard I

2015-01-01

According to cognitive and neurological models of the face-processing system, faces are represented at two levels of abstraction. First, image-based pictorial representations code a particular instance of a face and include information that is unrelated to identity-such as lighting, pose, and expression. Second, at a more abstract level, identity-specific representations combine information from various encounters with a single face. Here we tested whether identity-level representations mediate unfamiliar face matching performance. Across three experiments we manipulated identity attributions to pairs of target images and measured the effect on subsequent identification decisions. Participants were instructed that target images were either two photos of the same person (1ID condition) or photos of two different people (2ID condition). This manipulation consistently affected performance in sequential matching: 1ID instructions improved accuracy on "match" trials and caused participants to adopt a more liberal response bias than the 2ID condition. However, this manipulation did not affect performance in simultaneous matching. We conclude that identity-level representations, generated in working memory, influence the amount of variation tolerated between images, when making identity judgements in sequential face matching.

Basis Expansion Approaches for Regularized Sequential Dictionary Learning Algorithms With Enforced Sparsity for fMRI Data Analysis.

PubMed

Seghouane, Abd-Krim; Iqbal, Asif

2017-09-01

Sequential dictionary learning algorithms have been successfully applied to functional magnetic resonance imaging (fMRI) data analysis. fMRI data sets are, however, structured data matrices with the notions of temporal smoothness in the column direction. This prior information, which can be converted into a constraint of smoothness on the learned dictionary atoms, has seldomly been included in classical dictionary learning algorithms when applied to fMRI data analysis. In this paper, we tackle this problem by proposing two new sequential dictionary learning algorithms dedicated to fMRI data analysis by accounting for this prior information. These algorithms differ from the existing ones in their dictionary update stage. The steps of this stage are derived as a variant of the power method for computing the SVD. The proposed algorithms generate regularized dictionary atoms via the solution of a left regularized rank-one matrix approximation problem where temporal smoothness is enforced via regularization through basis expansion and sparse basis expansion in the dictionary update stage. Applications on synthetic data experiments and real fMRI data sets illustrating the performance of the proposed algorithms are provided.

ASPECTS OF ARCTIC SEA ICE OBSERVABLE BY SEQUENTIAL PASSIVE MICROWAVE OBSERVATIONS FROM THE NIMBUS-5 SATELLITE.

USGS Publications Warehouse

Campbell, William J.; Gloersen, Per; Zwally, H. Jay; ,

1984-01-01

Observations made from 1972 to 1976 with the Electrically Scanning Microwave Radiometer on board the Nimbus-5 satellite provide sequential synoptic information of the Arctic sea ice cover. This four-year data set was used to construct a fairly continuous series of three-day average 19-GHz passive microwave images which has become a valuable source of polar information, yielding many anticipated and unanticipated discoveries of the sea ice canopy observed in its entirety through the clouds and during the polar night. Short-term, seasonal, and annual variations of key sea ice parameters, such as ice edge position, ice types, mixtures of ice types, ice concentrations, and snow melt on the ice, are presented for various parts of the Arctic.

Error Control Coding Techniques for Space and Satellite Communications

NASA Technical Reports Server (NTRS)

Costello, Daniel J., Jr.; Cabral, Hermano A.; He, Jiali

1997-01-01

Bootstrap Hybrid Decoding (BHD) (Jelinek and Cocke, 1971) is a coding/decoding scheme that adds extra redundancy to a set of convolutionally encoded codewords and uses this redundancy to provide reliability information to a sequential decoder. Theoretical results indicate that bit error probability performance (BER) of BHD is close to that of Turbo-codes, without some of their drawbacks. In this report we study the use of the Multiple Stack Algorithm (MSA) (Chevillat and Costello, Jr., 1977) as the underlying sequential decoding algorithm in BHD, which makes possible an iterative version of BHD.

On the error probability of general tree and trellis codes with applications to sequential decoding

NASA Technical Reports Server (NTRS)

Johannesson, R.

1973-01-01

An upper bound on the average error probability for maximum-likelihood decoding of the ensemble of random binary tree codes is derived and shown to be independent of the length of the tree. An upper bound on the average error probability for maximum-likelihood decoding of the ensemble of random L-branch binary trellis codes of rate R = 1/n is derived which separates the effects of the tail length T and the memory length M of the code. It is shown that the bound is independent of the length L of the information sequence. This implication is investigated by computer simulations of sequential decoding utilizing the stack algorithm. These simulations confirm the implication and further suggest an empirical formula for the true undetected decoding error probability with sequential decoding.

Versatile telluracycle synthesis via the sequential electrophilic telluration of C(sp2)–Zn and C(sp2)–H bonds† †Electronic supplementary information (ESI) available. CCDC 1523262–1523264. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c7sc01162h Click here for additional data file. Click here for additional data file.

PubMed Central

Wu, Bin; Melvina; Wu, Xiangyang; Lee Yeow, Edwin Kok

2017-01-01

We report herein a new approach for the synthesis of tellurium-bridged aromatic compounds based on the sequential electrophilic telluration of C(sp2)–Zn and C(sp2)–H bonds with tellurium(iv) chlorides. A combination of transition metal-catalyzed (migratory) arylmetalation of alkynes and sequential telluration allows for the expedient construction of a library of functionalized benzo[b]tellurophenes. Furthermore, a variety of heteroarene-fused benzotellurophenes and other novel tellurium-embedded polycyclic aromatics can be readily synthesized from the corresponding 2-iodoheterobiaryls. PMID:28970880

To have and to hold: personnel shortage in a Finnish healthcare organisation.

PubMed

Heilmann, Pia

2010-07-01

Retirements of baby boomers will create a talent shortage in Finnish health care. Concurrently, difficulties exist in recruiting new personnel. This paper provides an overview concerning the bottlenecks in talent management in a Finnish hospital, and finds solutions for recruitment and retention problems of healthcare professionals (nurses and physicians). Because the healthcare staffing shortage is worldwide, the results of this paper are also useful internationally. The research was a qualitative case study and the research method used was group interview. Background data was gathered from the public media and healthcare trade organisations. The bottlenecks of talent management in hospital organisation seem to relate to retaining actions of senior personnel. Concurrently, the organisation should develop new practices for attracting new personnel. Very few efforts on image marketing and recruitment have been done. The Internet has not been fully exploited and recruitment information has not been sent even to the neighbouring nursing college. Job rotation has not been used as a help in recruitment and competence development. Difficulties exist in transmitting tacit knowledge from a retiring nurse to a junior nurse. Leadership skills of the superior seem to be important when retaining and committing senior personnel. Recruitment and retention problems encourage organisations to develop new recruitment and commitment practices as well as management and leadership skills.

Bridging the gap between fluxomics and industrial biotechnology.

PubMed

Feng, Xueyang; Page, Lawrence; Rubens, Jacob; Chircus, Lauren; Colletti, Peter; Pakrasi, Himadri B; Tang, Yinjie J

2010-01-01

Metabolic flux analysis is a vital tool used to determine the ultimate output of cellular metabolism and thus detect biotechnologically relevant bottlenecks in productivity. ¹³C-based metabolic flux analysis (¹³C-MFA) and flux balance analysis (FBA) have many potential applications in biotechnology. However, noteworthy hurdles in fluxomics study are still present. First, several technical difficulties in both ¹³C-MFA and FBA severely limit the scope of fluxomics findings and the applicability of obtained metabolic information. Second, the complexity of metabolic regulation poses a great challenge for precise prediction and analysis of metabolic networks, as there are gaps between fluxomics results and other omics studies. Third, despite identified metabolic bottlenecks or sources of host stress from product synthesis, it remains difficult to overcome inherent metabolic robustness or to efficiently import and express nonnative pathways. Fourth, product yields often decrease as the number of enzymatic steps increases. Such decrease in yield may not be caused by rate-limiting enzymes, but rather is accumulated through each enzymatic reaction. Fifth, a high-throughput fluxomics tool hasnot been developed for characterizing nonmodel microorganisms and maximizing their application in industrial biotechnology. Refining fluxomics tools and understanding these obstacles will improve our ability to engineer highly efficient metabolic pathways in microbial hosts.

Bottlenecks and multiple introductions: Population genetics of the vector of avian malaria in Hawaii

USGS Publications Warehouse

Fonseca, Dina M.; LaPointe, Dennis A.; Fleischer, Robert C.

2000-01-01

Avian malaria has had a profound impact on the demographics and behaviour of Hawaiian forest birds since its vector, Culex quinquefasciatusthe southern house mosquito, was first introduced to Hawaii around 1830. In order to understand the dynamics of the disease in Hawaii and gain insights into the evolution of vector-mediated parasite–host interactions in general we studied the population genetics of Cx. quinquefasciatus in the Hawaiian Islands. We used both microsatellite and mitochondrial loci. Not surprisingly we found that mosquitoes in Midway, a small island in the Western group, are quite distinct from the populations in the main Hawaiian Islands. However, we also found that in general mosquito populations are relatively isolated even among the main islands, in particular between Hawaii (the Big Island) and the remaining Hawaiian Islands. We found evidence of bottlenecks among populations within the Big Island and an excess of alleles in Maui, the site of the original introduction. The mitochondrial diversity was typically low but higher than expected. The current distribution of mitochondrial haplotypes combined with the microsatellite information lead us to conclude that there have been several introductions and to speculate on some processes that may be responsible for the current population genetics of vectors of avian malaria in Hawaii.

Birds in space and time: genetic changes accompanying anthropogenic habitat fragmentation in the endangered black-capped vireo (Vireo atricapilla)

PubMed Central

Athrey, Giridhar; Barr, Kelly R; Lance, Richard F; Leberg, Paul L

2012-01-01

Anthropogenic alterations in the natural environment can be a potent evolutionary force. For species that have specific habitat requirements, habitat loss can result in substantial genetic effects, potentially impeding future adaptability and evolution. The endangered black-capped vireo (Vireo atricapilla) suffered a substantial contraction of breeding habitat and population size during much of the 20th century. In a previous study, we reported significant differentiation between remnant populations, but failed to recover a strong genetic signal of bottlenecks. In this study, we used a combination of historical and contemporary sampling from Oklahoma and Texas to (i) determine whether population structure and genetic diversity have changed over time and (ii) evaluate alternate demographic hypotheses using approximate Bayesian computation (ABC). We found lower genetic diversity and increased differentiation in contemporary samples compared to historical samples, indicating nontrivial impacts of fragmentation. ABC analysis suggests a bottleneck having occurred in the early part of the 20th century, resulting in a magnitude decline in effective population size. Genetic monitoring with temporally spaced samples, such as used in this study, can be highly informative for assessing the genetic impacts of anthropogenic fragmentation on threatened or endangered species, as well as revealing the dynamics of small populations over time. PMID:23028396

Sequential assessment of prey through the use of multiple sensory cues by an eavesdropping bat

NASA Astrophysics Data System (ADS)

Page, Rachel A.; Schnelle, Tanja; Kalko, Elisabeth K. V.; Bunge, Thomas; Bernal, Ximena E.

2012-06-01

Predators are often confronted with a broad diversity of potential prey. They rely on cues associated with prey quality and palatability to optimize their hunting success and to avoid consuming toxic prey. Here, we investigate a predator's ability to assess prey cues during capture, handling, and consumption when confronted with conflicting information about prey quality. We used advertisement calls of a preferred prey item (the túngara frog) to attract fringe-lipped bats, Trachops cirrhosus, then offered palatable, poisonous, and chemically manipulated anurans as prey. Advertisement calls elicited an attack response, but as bats approached, they used additional sensory cues in a sequential manner to update their information about prey size and palatability. While both palatable and poisonous small anurans were readily captured, large poisonous toads were approached but not contacted suggesting the use of echolocation for assessment of prey size at close range. Once prey was captured, bats used chemical cues to make final, post-capture decisions about whether to consume the prey. Bats dropped small, poisonous toads as well as palatable frogs coated in toad toxins either immediately or shortly after capture. Our study suggests that echolocation and chemical cues obtained at close range supplement information obtained from acoustic cues at long range. Updating information about prey quality minimizes the occurrence of costly errors and may be advantageous in tracking temporal and spatial fluctuations of prey and exploiting novel food sources. These findings emphasize the sequential, complex nature of prey assessment that may allow exploratory and flexible hunting behaviors.

Research on Laser Marking Speed Optimization by Using Genetic Algorithm

PubMed Central

Wang, Dongyun; Yu, Qiwei; Zhang, Yu

2015-01-01

Laser Marking Machine is the most common coding equipment on product packaging lines. However, the speed of laser marking has become a bottleneck of production. In order to remove this bottleneck, a new method based on a genetic algorithm is designed. On the basis of this algorithm, a controller was designed and simulations and experiments were performed. The results show that using this algorithm could effectively improve laser marking efficiency by 25%. PMID:25955831

Impact of population structure, effective bottleneck time, and allele frequency on linkage disequilibrium maps

PubMed Central

Zhang, Weihua; Collins, Andrew; Gibson, Jane; Tapper, William J.; Hunt, Sarah; Deloukas, Panos; Bentley, David R.; Morton, Newton E.

2004-01-01

Genetic maps in linkage disequilibrium (LD) units play the same role for association mapping as maps in centimorgans provide at much lower resolution for linkage mapping. Association mapping of genes determining disease susceptibility and other phenotypes is based on the theory of LD, here applied to relations with three phenomena. To test the theory, markers at high density along a 10-Mb continuous segment of chromosome 20q were studied in African-American, Asian, and Caucasian samples. Population structure, whether created by pooling samples from divergent populations or by the mating pattern in a mixed population, is accurately bioassayed from genotype frequencies. The effective bottleneck time for Eurasians is substantially less than for migration out of Africa, reflecting later bottlenecks. The classical dependence of allele frequency on mutation age does not hold for the generally shorter time span of inbreeding and LD. Limitation of the classical theory to mutation age justifies the assumption of constant time in a LD map, except for alleles that were rare at the effective bottleneck time or have arisen since. This assumption is derived from the Malecot model and verified in all samples. Tested measures of relative efficiency, support intervals, and localization error determine the operating characteristics of LD maps that are applicable to every sexually reproducing species, with implications for association mapping, high-resolution linkage maps, evolutionary inference, and identification of recombinogenic sequences. PMID:15604137

Impact of population structure, effective bottleneck time, and allele frequency on linkage disequilibrium maps.

PubMed

Zhang, Weihua; Collins, Andrew; Gibson, Jane; Tapper, William J; Hunt, Sarah; Deloukas, Panos; Bentley, David R; Morton, Newton E

2004-12-28

Genetic maps in linkage disequilibrium (LD) units play the same role for association mapping as maps in centimorgans provide at much lower resolution for linkage mapping. Association mapping of genes determining disease susceptibility and other phenotypes is based on the theory of LD, here applied to relations with three phenomena. To test the theory, markers at high density along a 10-Mb continuous segment of chromosome 20q were studied in African-American, Asian, and Caucasian samples. Population structure, whether created by pooling samples from divergent populations or by the mating pattern in a mixed population, is accurately bioassayed from genotype frequencies. The effective bottleneck time for Eurasians is substantially less than for migration out of Africa, reflecting later bottlenecks. The classical dependence of allele frequency on mutation age does not hold for the generally shorter time span of inbreeding and LD. Limitation of the classical theory to mutation age justifies the assumption of constant time in a LD map, except for alleles that were rare at the effective bottleneck time or have arisen since. This assumption is derived from the Malecot model and verified in all samples. Tested measures of relative efficiency, support intervals, and localization error determine the operating characteristics of LD maps that are applicable to every sexually reproducing species, with implications for association mapping, high-resolution linkage maps, evolutionary inference, and identification of recombinogenic sequences.

Bottleneck effects on the bidirectional crowd dynamics

NASA Astrophysics Data System (ADS)

Yang, Xiao-Xia; Dong, Hai-Rong; Yao, Xiu-Ming; Sun, Xu-Bin

2016-12-01

The bottleneck effect on bidirectional crowd dynamics is of great theoretical and practical significance, especially for the designing of corridors in public places, such as subway stations or airports. Based on the famous social force model, this paper investigates the bottleneck effects on the free flow dynamics and breakdown phenomenon under different scenarios, in which different corridor shapes and inflow ratios are considered simultaneously. Numerical simulation finds an interesting self-organization phenomenon in the bidirectional flow, a typical characteristic of such a phenomenon is called lane formation, and the existence of which is independent of the corridor’s shape and inflow rate. However, the pattern of the lane formed by pedestrian flow is related to the corridor’s shape, and the free flow efficiency has close relationship with the inflow rate. Specifically, breakdown phenomenon occurs when inflows from both sides of the corridor are large enough, which mostly originates from the bottleneck and then gradually spreads to the other regions. Simulation results further indicate that the leaving efficiency becomes low as breakdown occurs, and the degree of congestion is proportional to the magnitude of inflow. The findings presented in this paper match well with some of our daily observations, hence it is possible to use them to provide us with theoretical suggestions in design of infrastructures. Project supported jointly by the National Natural Science Foundation of China (Grant Nos. 61322307 and 2016YJS023).

Process-based Assignment-Setting Change for Support of Overcoming Bottlenecks in Learning by Problem-Posing in Arithmetic Word Problems

NASA Astrophysics Data System (ADS)

Supianto, A. A.; Hayashi, Y.; Hirashima, T.

2017-02-01

Problem-posing is well known as an effective activity to learn problem-solving methods. Monsakun is an interactive problem-posing learning environment to facilitate arithmetic word problems learning for one operation of addition and subtraction. The characteristic of Monsakun is problem-posing as sentence-integration that lets learners make a problem of three sentences. Monsakun provides learners with five or six sentences including dummies, which are designed through careful considerations by an expert teacher as a meaningful distraction to the learners in order to learn the structure of arithmetic word problems. The results of the practical use of Monsakun in elementary schools show that many learners have difficulties in arranging the proper answer at the high level of assignments. The analysis of the problem-posing process of such learners found that their misconception of arithmetic word problems causes impasses in their thinking and mislead them to use dummies. This study proposes a method of changing assignments as a support for overcoming bottlenecks of thinking. In Monsakun, the bottlenecks are often detected as a frequently repeated use of a specific dummy. If such dummy can be detected, it is the key factor to support learners to overcome their difficulty. This paper discusses how to detect the bottlenecks and to realize such support in learning by problem-posing.

Cheaper Adjoints by Reversing Address Computations

DOE PAGES

Hascoët, L.; Utke, J.; Naumann, U.

2008-01-01

The reverse mode of automatic differentiation is widely used in science and engineering. A severe bottleneck for the performance of the reverse mode, however, is the necessity to recover certain intermediate values of the program in reverse order. Among these values are computed addresses, which traditionally are recovered through forward recomputation and storage in memory. We propose an alternative approach for recovery that uses inverse computation based on dependency information. Address storage constitutes a significant portion of the overall storage requirements. An example illustrates substantial gains that the proposed approach yields, and we show use cases in practical applications.

Use of combinatorial chemistry to speed drug discovery.

PubMed

Rádl, S

1998-10-01

IBC's International Conference on Integrating Combinatorial Chemistry into the Discovery Pipeline was held September 14-15, 1998. The program started with a pre-conference workshop on High-Throughput Compound Characterization and Purification. The agenda of the main conference was divided into sessions of Synthesis, Automation and Unique Chemistries; Integrating Combinatorial Chemistry, Medicinal Chemistry and Screening; Combinatorial Chemistry Applications for Drug Discovery; and Information and Data Management. This meeting was an excellent opportunity to see how big pharma, biotech and service companies are addressing the current bottlenecks in combinatorial chemistry to speed drug discovery. (c) 1998 Prous Science. All rights reserved.

Research on parallel algorithm for sequential pattern mining

NASA Astrophysics Data System (ADS)

Zhou, Lijuan; Qin, Bai; Wang, Yu; Hao, Zhongxiao

2008-03-01

Sequential pattern mining is the mining of frequent sequences related to time or other orders from the sequence database. Its initial motivation is to discover the laws of customer purchasing in a time section by finding the frequent sequences. In recent years, sequential pattern mining has become an important direction of data mining, and its application field has not been confined to the business database and has extended to new data sources such as Web and advanced science fields such as DNA analysis. The data of sequential pattern mining has characteristics as follows: mass data amount and distributed storage. Most existing sequential pattern mining algorithms haven't considered the above-mentioned characteristics synthetically. According to the traits mentioned above and combining the parallel theory, this paper puts forward a new distributed parallel algorithm SPP(Sequential Pattern Parallel). The algorithm abides by the principal of pattern reduction and utilizes the divide-and-conquer strategy for parallelization. The first parallel task is to construct frequent item sets applying frequent concept and search space partition theory and the second task is to structure frequent sequences using the depth-first search method at each processor. The algorithm only needs to access the database twice and doesn't generate the candidated sequences, which abates the access time and improves the mining efficiency. Based on the random data generation procedure and different information structure designed, this paper simulated the SPP algorithm in a concrete parallel environment and implemented the AprioriAll algorithm. The experiments demonstrate that compared with AprioriAll, the SPP algorithm had excellent speedup factor and efficiency.

ARINC 818 adds capabilities for high-speed sensors and systems

NASA Astrophysics Data System (ADS)

Keller, Tim; Grunwald, Paul

2014-06-01

ARINC 818, titled Avionics Digital Video Bus (ADVB), is the standard for cockpit video that has gained wide acceptance in both the commercial and military cockpits including the Boeing 787, the A350XWB, the A400M, the KC- 46A and many others. Initially conceived of for cockpit displays, ARINC 818 is now propagating into high-speed sensors, such as infrared and optical cameras due to its high-bandwidth and high reliability. The ARINC 818 specification that was initially release in the 2006 and has recently undergone a major update that will enhance its applicability as a high speed sensor interface. The ARINC 818-2 specification was published in December 2013. The revisions to the specification include: video switching, stereo and 3-D provisions, color sequential implementations, regions of interest, data-only transmissions, multi-channel implementations, bi-directional communication, higher link rates to 32Gbps, synchronization signals, options for high-speed coax interfaces and optical interface details. The additions to the specification are especially appealing for high-bandwidth, multi sensor systems that have issues with throughput bottlenecks and SWaP concerns. ARINC 818 is implemented on either copper or fiber optic high speed physical layers, and allows for time multiplexing multiple sensors onto a single link. This paper discusses each of the new capabilities in the ARINC 818-2 specification and the benefits for ISR and countermeasures implementations, several examples are provided.

Adaptive potential of northernmost tree populations to climate change, with emphasis on Scots pine (Pinus sylvestris L.).

PubMed

Savolainen, Outi; Kujala, Sonja T; Sokol, Catherina; Pyhäjärvi, Tanja; Avia, Komlan; Knürr, Timo; Kärkkäinen, Katri; Hicks, Sheila

2011-01-01

The adaptive potential of the northernmost Pinus sylvestris L. (and other northern tree) populations is considered by examining first the current patterns of quantitative genetic adaptive traits, which show high population differentiation and clines. We then consider the postglacial history of the populations using both paleobiological and genetic data. The current patterns of diversity at nuclear genes suggest that the traces of admixture are mostly visible in mitochondrial DNA variation patterns. There is little evidence of increased diversity due to admixture between an eastern and western colonization lineage, but no signal of reduced diversity (due to sequential bottlenecks) either. Quantitative trait variation in the north is not associated with the colonizing lineages. The current clines arose rapidly and may be based on standing genetic variation. The initial phenotypic response of Scots pine in the north is predicted to be increased survival and growth. The genetic responses are examined based on quantitative genetic predictions of sustained selection response and compared with earlier simulation results that have aimed at more ecological realism. The phenotypic responses of increased growth and survival reduce the opportunity for selection and delay the evolutionary responses. The lengthening of the thermal growing period also causes selection on the critical photoperiod in the different populations. Future studies should aim at including multiple ecological and genetic factors in evaluating potential responses.

Reducing Patient Waiting Times for Radiation Therapy and Improving the Treatment Planning Process: a Discrete-event Simulation Model (Radiation Treatment Planning).

PubMed

Babashov, V; Aivas, I; Begen, M A; Cao, J Q; Rodrigues, G; D'Souza, D; Lock, M; Zaric, G S

2017-06-01

We analysed the radiotherapy planning process at the London Regional Cancer Program to determine the bottlenecks and to quantify the effect of specific resource levels with the goal of reducing waiting times. We developed a discrete-event simulation model of a patient's journey from the point of referral to a radiation oncologist to the start of radiotherapy, considering the sequential steps and resources of the treatment planning process. We measured the effect of several resource changes on the ready-to-treat to treatment (RTTT) waiting time and on the percentage treated within a 14 calendar day target. Increasing the number of dosimetrists by one reduced the mean RTTT by 6.55%, leading to 84.92% of patients being treated within the 14 calendar day target. Adding one more oncologist decreased the mean RTTT from 10.83 to 10.55 days, whereas a 15% increase in arriving patients increased the waiting time by 22.53%. The model was relatively robust to the changes in quantity of other resources. Our model identified sensitive and non-sensitive system parameters. A similar approach could be applied by other cancer programmes, using their respective data and individualised adjustments, which may be beneficial in making the most effective use of limited resources. Copyright © 2017 The Royal College of Radiologists. Published by Elsevier Ltd. All rights reserved.

How is visual salience computed in the brain? Insights from behaviour, neurobiology and modelling

PubMed Central

Veale, Richard; Hafed, Ziad M.

2017-01-01

Inherent in visual scene analysis is a bottleneck associated with the need to sequentially sample locations with foveating eye movements. The concept of a ‘saliency map’ topographically encoding stimulus conspicuity over the visual scene has proven to be an efficient predictor of eye movements. Our work reviews insights into the neurobiological implementation of visual salience computation. We start by summarizing the role that different visual brain areas play in salience computation, whether at the level of feature analysis for bottom-up salience or at the level of goal-directed priority maps for output behaviour. We then delve into how a subcortical structure, the superior colliculus (SC), participates in salience computation. The SC represents a visual saliency map via a centre-surround inhibition mechanism in the superficial layers, which feeds into priority selection mechanisms in the deeper layers, thereby affecting saccadic and microsaccadic eye movements. Lateral interactions in the local SC circuit are particularly important for controlling active populations of neurons. This, in turn, might help explain long-range effects, such as those of peripheral cues on tiny microsaccades. Finally, we show how a combination of in vitro neurophysiology and large-scale computational modelling is able to clarify how salience computation is implemented in the local circuit of the SC. This article is part of the themed issue ‘Auditory and visual scene analysis’. PMID:28044023

Dynamics assembly of magnetic microparticles suspended in moving droplets under the influence of magnetic fields

NASA Astrophysics Data System (ADS)

Strey, Helmut; Brouzes, Eric; Kruse, Travis

2013-03-01

Droplet microfluidics has experienced tremendous growth, particularly since it is well suited for single-cell manipulation and analysis. As mature methods for high throughput droplet manipulation have been developed a technological bottleneck of current droplet microfluidics is that because droplets are separated, sequential chemical reactions are more difficult to achieve. For example, it is very difficult to concentrate target molecules, especially since every reaction step adds volume to the droplets. Our solution to this problem is to employ functionalized magnetic beads inside droplets. The basic idea is that an external magnetic field could be used to concentrate the magnetic beads in one part of the droplet and those could then be extracted by splitting the droplet. Here we present an experimental study of the self-assembly of superparamagnetic microparticles that are suspended in moving droplets and experience a combination of forces due to the internal fluid flow fields and external magnetic fields. We observed that this interplay of flow fields coupled to the formation of particle assemblies leads to the formations of stable patterns depending on the flow speed and magnetic field strength. An understanding of this dynamic assembly is critical in employing external forces for applications in separation and sorting. Funding through NYSTAR, Center for Advanced Technology and a grant from NIH-NHGRI (1 R21 HG006206-01).

Computational time reduction for sequential batch solutions in GNSS precise point positioning technique

NASA Astrophysics Data System (ADS)

Martín Furones, Angel; Anquela Julián, Ana Belén; Dimas-Pages, Alejandro; Cos-Gayón, Fernando

2017-08-01

Precise point positioning (PPP) is a well established Global Navigation Satellite System (GNSS) technique that only requires information from the receiver (or rover) to obtain high-precision position coordinates. This is a very interesting and promising technique because eliminates the need for a reference station near the rover receiver or a network of reference stations, thus reducing the cost of a GNSS survey. From a computational perspective, there are two ways to solve the system of observation equations produced by static PPP either in a single step (so-called batch adjustment) or with a sequential adjustment/filter. The results of each should be the same if they are both well implemented. However, if a sequential solution (that is, not only the final coordinates, but also those observed in previous GNSS epochs), is needed, as for convergence studies, finding a batch solution becomes a very time consuming task owing to the need for matrix inversion that accumulates with each consecutive epoch. This is not a problem for the filter solution, which uses information computed in the previous epoch for the solution of the current epoch. Thus filter implementations need extra considerations of user dynamics and parameter state variations between observation epochs with appropriate stochastic update parameter variances from epoch to epoch. These filtering considerations are not needed in batch adjustment, which makes it attractive. The main objective of this research is to significantly reduce the computation time required to obtain sequential results using batch adjustment. The new method we implemented in the adjustment process led to a mean reduction in computational time by 45%.

Shape Recognition in Infancy: Visual Integration of Sequential Information.

ERIC Educational Resources Information Center

Rose, Susan A

1988-01-01

Investigated infants' integration of visual information across space and time. In four experiments, infants aged 12 months and 6 months viewed objects after watching light trace similar and dissimilar shapes. Infants looked longer at novel shapes, although six-month-olds did not recognize figures taking more than 10 seconds to trace. One-year-old…

Financial Statistics. Higher Education General Information Survey (HEGIS) [machine-readable data file].

ERIC Educational Resources Information Center

Center for Education Statistics (ED/OERI), Washington, DC.

The Financial Statistics machine-readable data file (MRDF) is a subfile of the larger Higher Education General Information Survey (HEGIS). It contains basic financial statistics for over 3,000 institutions of higher education in the United States and its territories. The data are arranged sequentially by institution, with institutional…

Understanding the Periodic Table of Elements via Iconic Mapping and Sequential Diagramming: The Roundhouse Strategy

ERIC Educational Resources Information Center

Ward, Robin E.; Lee, William D.

2006-01-01

Roundhouse is a visually creative information-processing tool (J. E. Trowbridge and J. H. Wandersee 1998). The procedure requires learners to construct knowledge using "mindful" connections to replace less effective practices of memorizing fragmented information. Students create observable organization schemes of related ideas and icons in a…

Sensory Mode and "Information Load": Examining the Effects of Timing on Multisensory Processing.

ERIC Educational Resources Information Center

Tiene, Drew

2000-01-01

Discussion of the development of instructional multimedia materials focuses on a study of undergraduates that examined how the use of visual icons affected learning, differences in the instructional effectiveness of visual versus auditory processing of the same information, and timing (whether simultaneous or sequential presentation is more…

Social Media Adoption and Use among Information Technology Professionals and Implications for Leadership

ERIC Educational Resources Information Center

Lundahl Philpot, Eva

2013-01-01

This sequential, mixed methods research addressed emerging social media use practices among IT professionals and explored lived experiences of senior IT leaders relative to successful organizational social media adoption and use. The study was informed by structuration theory and elements from the universal technology adoption and use (UTAUT)…

Differences in the Selection Bottleneck between Modes of Sexual Transmission Influence the Genetic Composition of the HIV-1 Founder Virus

PubMed Central

Tully, Damien C.; Ogilvie, Colin B.; Batorsky, Rebecca E.; Bean, David J.; Power, Karen A.; Ghebremichael, Musie; Bedard, Hunter E.; Gladden, Adrianne D.; Seese, Aaron M.; Amero, Molly A.; Lane, Kimberly; McGrath, Graham; Bazner, Suzane B.; Tinsley, Jake; Lennon, Niall J.; Henn, Matthew R.; Brumme, Zabrina L.; Norris, Philip J.; Rosenberg, Eric S.; Mayer, Kenneth H.; Jessen, Heiko; Kosakovsky Pond, Sergei L.; Walker, Bruce D.; Altfeld, Marcus; Carlson, Jonathan M.; Allen, Todd M.

2016-01-01

Due to the stringent population bottleneck that occurs during sexual HIV-1 transmission, systemic infection is typically established by a limited number of founder viruses. Elucidation of the precise forces influencing the selection of founder viruses may reveal key vulnerabilities that could aid in the development of a vaccine or other clinical interventions. Here, we utilize deep sequencing data and apply a genetic distance-based method to investigate whether the mode of sexual transmission shapes the nascent founder viral genome. Analysis of 74 acute and early HIV-1 infected subjects revealed that 83% of men who have sex with men (MSM) exhibit a single founder virus, levels similar to those previously observed in heterosexual (HSX) transmission. In a metadata analysis of a total of 354 subjects, including HSX, MSM and injecting drug users (IDU), we also observed no significant differences in the frequency of single founder virus infections between HSX and MSM transmissions. However, comparison of HIV-1 envelope sequences revealed that HSX founder viruses exhibited a greater number of codon sites under positive selection, as well as stronger transmission indices possibly reflective of higher fitness variants. Moreover, specific genetic “signatures” within MSM and HSX founder viruses were identified, with single polymorphisms within gp41 enriched among HSX viruses while more complex patterns, including clustered polymorphisms surrounding the CD4 binding site, were enriched in MSM viruses. While our findings do not support an influence of the mode of sexual transmission on the number of founder viruses, they do demonstrate that there are marked differences in the selection bottleneck that can significantly shape their genetic composition. This study illustrates the complex dynamics of the transmission bottleneck and reveals that distinct genetic bottleneck processes exist dependent upon the mode of HIV-1 transmission. PMID:27163788

Reducing bottlenecks: professionals’ and adolescents’ experiences with transitional care delivery

PubMed Central

2014-01-01

Background The purpose of this study was to describe the interventions implemented in a quality improvement programme to improve transitional care and evaluate its effectiveness in reducing bottlenecks as perceived by professionals and improving chronically ill adolescents’ experiences with care delivery. Methods This longitudinal study was undertaken with adolescents and professionals who participated in the Dutch ‘On Your Own Feet Ahead!’ quality improvement programme. This programme followed the Breakthrough Series improvement and implementation strategy. A total of 102/128 (79.7%) professionals from 21 hospital teams filled out a questionnaire at the start of the programme (T0), and 79/123 (64.2%; five respondents had changed jobs) professionals completed the same questionnaire 1 year later (T1). Seventy-two (58.5%) professionals from 21 teams returned questionnaires at both time points. Of 389 and 430 participating adolescents, 36% and 41% returned questionnaires at T0 and T1, respectively. We used descriptive statistics and two-tailed, paired t-tests to investigate improvements in bottlenecks in transitional care (perceived by professionals) and care delivery (perceived by adolescents). Results Professionals observed improvement in all bottlenecks at T1 (vs. T0; p < 0.05), especially in the organisation of care, such as the presence of a joint mission between paediatric and adult care, coordination of care, and availability of more resources for joint care services. Within a 1-year period, the transition programme improved some aspects of patients’ experiences with care delivery, such as the provision of opportunities for adolescents to visit the clinic alone (p < 0.001) and to decide who should be present during consultations (p < 0.05). Conclusions This study demonstrated that transitional care interventions may improve the organisation and coordination of transitional care and better prepare adolescents for the transition to adult care within a 1-year period. By setting specific goals based on experiences with bottlenecks, the breakthrough approach helped to improve transitional care delivery for adolescents with chronic conditions. PMID:24485282

Differences in the Selection Bottleneck between Modes of Sexual Transmission Influence the Genetic Composition of the HIV-1 Founder Virus.

PubMed

Tully, Damien C; Ogilvie, Colin B; Batorsky, Rebecca E; Bean, David J; Power, Karen A; Ghebremichael, Musie; Bedard, Hunter E; Gladden, Adrianne D; Seese, Aaron M; Amero, Molly A; Lane, Kimberly; McGrath, Graham; Bazner, Suzane B; Tinsley, Jake; Lennon, Niall J; Henn, Matthew R; Brumme, Zabrina L; Norris, Philip J; Rosenberg, Eric S; Mayer, Kenneth H; Jessen, Heiko; Kosakovsky Pond, Sergei L; Walker, Bruce D; Altfeld, Marcus; Carlson, Jonathan M; Allen, Todd M

2016-05-01

Due to the stringent population bottleneck that occurs during sexual HIV-1 transmission, systemic infection is typically established by a limited number of founder viruses. Elucidation of the precise forces influencing the selection of founder viruses may reveal key vulnerabilities that could aid in the development of a vaccine or other clinical interventions. Here, we utilize deep sequencing data and apply a genetic distance-based method to investigate whether the mode of sexual transmission shapes the nascent founder viral genome. Analysis of 74 acute and early HIV-1 infected subjects revealed that 83% of men who have sex with men (MSM) exhibit a single founder virus, levels similar to those previously observed in heterosexual (HSX) transmission. In a metadata analysis of a total of 354 subjects, including HSX, MSM and injecting drug users (IDU), we also observed no significant differences in the frequency of single founder virus infections between HSX and MSM transmissions. However, comparison of HIV-1 envelope sequences revealed that HSX founder viruses exhibited a greater number of codon sites under positive selection, as well as stronger transmission indices possibly reflective of higher fitness variants. Moreover, specific genetic "signatures" within MSM and HSX founder viruses were identified, with single polymorphisms within gp41 enriched among HSX viruses while more complex patterns, including clustered polymorphisms surrounding the CD4 binding site, were enriched in MSM viruses. While our findings do not support an influence of the mode of sexual transmission on the number of founder viruses, they do demonstrate that there are marked differences in the selection bottleneck that can significantly shape their genetic composition. This study illustrates the complex dynamics of the transmission bottleneck and reveals that distinct genetic bottleneck processes exist dependent upon the mode of HIV-1 transmission.

Spatial-simultaneous and spatial-sequential working memory in individuals with Down syndrome: the effect of configuration.

PubMed

Carretti, Barbara; Lanfranchi, Silvia; Mammarella, Irene C

2013-01-01

Earlier research showed that visuospatial working memory (VSWM) is better preserved in Down syndrome (DS) than verbal WM. Some differences emerged, however, when VSWM performance was broken down into its various components, and more recent studies revealed that the spatial-simultaneous component of VSWM is more impaired than the spatial-sequential one. The difficulty of managing more than one item at a time is also evident when the information to be recalled is structured. To further analyze this issue, we investigated the advantage of material being structured in spatial-simultaneous and spatial-sequential tasks by comparing the performance of a group of individuals with DS and a group of typically-developing children matched for mental age. Both groups were presented with VSWM tasks in which both the presentation format (simultaneous vs. sequential) and the type of configuration (pattern vs. random) were manipulated. Findings indicated that individuals with DS took less advantage of the pattern configuration in the spatial-simultaneous task than TD children; in contrast, the two groups' performance did not differ in the pattern configuration of the spatial-sequential task. Taken together, these results confirmed difficulties relating to the spatial-simultaneous component of VSWM in individuals with DS, supporting the importance of distinguishing between different components within this system. The findings are discussed in terms of factors influencing this specific deficit. Copyright © 2012 Elsevier Ltd. All rights reserved.

Uncovering the transmission dynamics of Plasmodium vivax using population genetics

PubMed Central

Barry, Alyssa E.; Waltmann, Andreea; Koepfli, Cristian; Barnadas, Celine; Mueller, Ivo

2015-01-01

Population genetic analysis of malaria parasites has the power to reveal key insights into malaria epidemiology and transmission dynamics with the potential to deliver tools to support control and elimination efforts. Analyses of parasite genetic diversity have suggested that Plasmodium vivax populations are more genetically diverse and less structured than those of Plasmodium falciparum indicating that P. vivax may be a more ancient parasite of humans and/or less susceptible to population bottlenecks, as well as more efficient at disseminating its genes. These population genetic insights into P. vivax transmission dynamics provide an explanation for its relative resilience to control efforts. Here, we describe current knowledge on P. vivax population genetic structure, its relevance to understanding transmission patterns and relapse and how this information can inform malaria control and elimination programmes. PMID:25891915

B-HIT - A Tool for Harvesting and Indexing Biodiversity Data

PubMed Central

Barker, Katharine; Braak, Kyle; Cawsey, E. Margaret; Coddington, Jonathan; Robertson, Tim; Whitacre, Jamie

2015-01-01

With the rapidly growing number of data publishers, the process of harvesting and indexing information to offer advanced search and discovery becomes a critical bottleneck in globally distributed primary biodiversity data infrastructures. The Global Biodiversity Information Facility (GBIF) implemented a Harvesting and Indexing Toolkit (HIT), which largely automates data harvesting activities for hundreds of collection and observational data providers. The team of the Botanic Garden and Botanical Museum Berlin-Dahlem has extended this well-established system with a range of additional functions, including improved processing of multiple taxon identifications, the ability to represent associations between specimen and observation units, new data quality control and new reporting capabilities. The open source software B-HIT can be freely installed and used for setting up thematic networks serving the demands of particular user groups. PMID:26544980

B-HIT - A Tool for Harvesting and Indexing Biodiversity Data.

PubMed

Kelbert, Patricia; Droege, Gabriele; Barker, Katharine; Braak, Kyle; Cawsey, E Margaret; Coddington, Jonathan; Robertson, Tim; Whitacre, Jamie; Güntsch, Anton

2015-01-01

With the rapidly growing number of data publishers, the process of harvesting and indexing information to offer advanced search and discovery becomes a critical bottleneck in globally distributed primary biodiversity data infrastructures. The Global Biodiversity Information Facility (GBIF) implemented a Harvesting and Indexing Toolkit (HIT), which largely automates data harvesting activities for hundreds of collection and observational data providers. The team of the Botanic Garden and Botanical Museum Berlin-Dahlem has extended this well-established system with a range of additional functions, including improved processing of multiple taxon identifications, the ability to represent associations between specimen and observation units, new data quality control and new reporting capabilities. The open source software B-HIT can be freely installed and used for setting up thematic networks serving the demands of particular user groups.

A Femtosecond Visible/Visible and Visible/Mid-Infrared Transient Absorption Study of the Light Harvesting Complex II

PubMed Central

Stahl, Andreas D.; Di Donato, Mariangela; van Stokkum, Ivo; van Grondelle, Rienk; Groot, Marie Louise

2009-01-01

Abstract Light harvesting complex II (LHCII) is the most abundant protein in the thylakoid membrane of higher plants and green algae. LHCII acts to collect solar radiation, transferring this energy mainly toward photosystem II, with a smaller amount going to photosystem I; it is then converted into a chemical, storable form. We performed time-resolved femtosecond visible pump/mid-infrared probe and visible pump/visible probe absorption difference spectroscopy on purified LHCII to gain insight into the energy transfer in this complex occurring in the femto-picosecond time regime. We find that information derived from mid-infrared spectra, together with structural and modeling information, provides a unique visualization of the flow of energy via the bottleneck pigment chlorophyll a604. PMID:20006959

Context Effects in Forensic Entomology and Use of Sequential Unmasking in Casework.

PubMed

Archer, Melanie S; Wallman, James F

2016-09-01

Context effects are pervasive in forensic science, and are being recognized by a growing number of disciplines as a threat to objectivity. Cognitive processes can be affected by extraneous context information, and many proactive scientists are therefore introducing context-minimizing systems into their laboratories. Forensic entomologists are also subject to context effects, both in the processes they undertake (e.g., evidence collection) and decisions they make (e.g., whether an invertebrate taxon is found in a certain geographic area). We stratify the risk of bias into low, medium, and high for the decisions and processes undertaken by forensic entomologists, and propose that knowledge of the time the deceased was last seen alive is the most potentially biasing piece of information for forensic entomologists. Sequential unmasking is identified as the best system for minimizing context information, illustrated with the results of a casework trial (n = 19) using this approach in Victoria, Australia. © 2016 American Academy of Forensic Sciences.

SIMPLE: a sequential immunoperoxidase labeling and erasing method.

PubMed

Glass, George; Papin, Jason A; Mandell, James W

2009-10-01

The ability to simultaneously visualize expression of multiple antigens in cells and tissues can provide powerful insights into cellular and organismal biology. However, standard methods are limited to the use of just two or three simultaneous probes and have not been widely adopted for routine use in paraffin-embedded tissue. We have developed a novel approach called sequential immunoperoxidase labeling and erasing (SIMPLE) that enables the simultaneous visualization of at least five markers within a single tissue section. Utilizing the alcohol-soluble peroxidase substrate 3-amino-9-ethylcarbazole, combined with a rapid non-destructive method for antibody-antigen dissociation, we demonstrate the ability to erase the results of a single immunohistochemical stain while preserving tissue antigenicity for repeated rounds of labeling. SIMPLE is greatly facilitated by the use of a whole-slide scanner, which can capture the results of each sequential stain without any information loss.

PARTICLE FILTERING WITH SEQUENTIAL PARAMETER LEARNING FOR NONLINEAR BOLD fMRI SIGNALS.

PubMed

Xia, Jing; Wang, Michelle Yongmei

Analyzing the blood oxygenation level dependent (BOLD) effect in the functional magnetic resonance imaging (fMRI) is typically based on recent ground-breaking time series analysis techniques. This work represents a significant improvement over existing approaches to system identification using nonlinear hemodynamic models. It is important for three reasons. First, instead of using linearized approximations of the dynamics, we present a nonlinear filtering based on the sequential Monte Carlo method to capture the inherent nonlinearities in the physiological system. Second, we simultaneously estimate the hidden physiological states and the system parameters through particle filtering with sequential parameter learning to fully take advantage of the dynamic information of the BOLD signals. Third, during the unknown static parameter learning, we employ the low-dimensional sufficient statistics for efficiency and avoiding potential degeneration of the parameters. The performance of the proposed method is validated using both the simulated data and real BOLD fMRI data.

Facilitated assignment of large protein NMR signals with covariance sequential spectra using spectral derivatives.

PubMed

Harden, Bradley J; Nichols, Scott R; Frueh, Dominique P

2014-09-24

Nuclear magnetic resonance (NMR) studies of larger proteins are hampered by difficulties in assigning NMR resonances. Human intervention is typically required to identify NMR signals in 3D spectra, and subsequent procedures depend on the accuracy of this so-called peak picking. We present a method that provides sequential connectivities through correlation maps constructed with covariance NMR, bypassing the need for preliminary peak picking. We introduce two novel techniques to minimize false correlations and merge the information from all original 3D spectra. First, we take spectral derivatives prior to performing covariance to emphasize coincident peak maxima. Second, we multiply covariance maps calculated with different 3D spectra to destroy erroneous sequential correlations. The maps are easy to use and can readily be generated from conventional triple-resonance experiments. Advantages of the method are demonstrated on a 37 kDa nonribosomal peptide synthetase domain subject to spectral overlap.

Hydroetching of high surface area ceramics using moist supercritical fluids

DOEpatents

Fryxell, Glen; Zemanian, Thomas S.

2004-11-02

Aerogels having a high density of hydroxyl groups and a more uniform pore size with fewer bottlenecks are described. The aerogel is exposed to a mixture of a supercritical fluid and water, whereupon the aerogel forms a high density of hydroxyl groups. The process also relaxes the aerogel into a more open uniform internal structure, in a process referred to as hydroetching. The hydroetching process removes bottlenecks from the aerogels, and forms the hydrogels into more standard pore sizes while preserving their high surface area.

Cultural Evolutionary Tipping Points in the Storage and Transmission of Information

PubMed Central

Bentley, R. Alexander; O’Brien, Michael J.

2012-01-01

Human culture has evolved through a series of major tipping points in information storage and communication. The first was the appearance of language, which enabled communication between brains and allowed humans to specialize in what they do and to participate in complex mating games. The second was information storage outside the brain, most obviously expressed in the “Upper Paleolithic Revolution” – the sudden proliferation of cave art, personal adornment, and ritual in Europe some 35,000–45,000 years ago. More recently, this storage has taken the form of writing, mass media, and now the Internet, which is arguably overwhelming humans’ ability to discern relevant information. The third tipping point was the appearance of technology capable of accumulating and manipulating vast amounts of information outside humans, thus removing them as bottlenecks to a seemingly self-perpetuating process of knowledge explosion. Important components of any discussion of cultural evolutionary tipping points are tempo and mode, given that the rate of change, as well as the kind of change, in information storage and transmission has not been constant over the previous million years. PMID:23267338

Cultural evolutionary tipping points in the storage and transmission of information.

PubMed

Bentley, R Alexander; O'Brien, Michael J

2012-01-01

Human culture has evolved through a series of major tipping points in information storage and communication. The first was the appearance of language, which enabled communication between brains and allowed humans to specialize in what they do and to participate in complex mating games. The second was information storage outside the brain, most obviously expressed in the "Upper Paleolithic Revolution" - the sudden proliferation of cave art, personal adornment, and ritual in Europe some 35,000-45,000 years ago. More recently, this storage has taken the form of writing, mass media, and now the Internet, which is arguably overwhelming humans' ability to discern relevant information. The third tipping point was the appearance of technology capable of accumulating and manipulating vast amounts of information outside humans, thus removing them as bottlenecks to a seemingly self-perpetuating process of knowledge explosion. Important components of any discussion of cultural evolutionary tipping points are tempo and mode, given that the rate of change, as well as the kind of change, in information storage and transmission has not been constant over the previous million years.

Naturally rare versus newly rare: demographic inferences on two timescales inform conservation of Galápagos giant tortoises

PubMed Central

Garrick, Ryan C; Kajdacsi, Brittney; Russello, Michael A; Benavides, Edgar; Hyseni, Chaz; Gibbs, James P; Tapia, Washington; Caccone, Adalgisa

2015-01-01

Long-term population history can influence the genetic effects of recent bottlenecks. Therefore, for threatened or endangered species, an understanding of the past is relevant when formulating conservation strategies. Levels of variation at neutral markers have been useful for estimating local effective population sizes (Ne) and inferring whether population sizes increased or decreased over time. Furthermore, analyses of genotypic, allelic frequency, and phylogenetic information can potentially be used to separate historical from recent demographic changes. For 15 populations of Galápagos giant tortoises (Chelonoidis sp.), we used 12 microsatellite loci and DNA sequences from the mitochondrial control region and a nuclear intron, to reconstruct demographic history on shallow (past ∽100 generations, ∽2500 years) and deep (pre-Holocene, >10 thousand years ago) timescales. At the deep timescale, three populations showed strong signals of growth, but with different magnitudes and timing, indicating different underlying causes. Furthermore, estimated historical Ne of populations across the archipelago showed no correlation with island age or size, underscoring the complexity of predicting demographic history a priori. At the shallow timescale, all populations carried some signature of a genetic bottleneck, and for 12 populations, point estimates of contemporary Ne were very small (i.e., < 50). On the basis of the comparison of these genetic estimates with published census size data, Ne generally represented ∽0.16 of the census size. However, the variance in this ratio across populations was considerable. Overall, our data suggest that idiosyncratic and geographically localized forces shaped the demographic history of tortoise populations. Furthermore, from a conservation perspective, the separation of demographic events occurring on shallow versus deep timescales permits the identification of naturally rare versus newly rare populations; this distinction should facilitate prioritization of management action. PMID:25691990

Differential clonal evolution in oesophageal cancers in response to neo-adjuvant chemotherapy.

PubMed

Findlay, John M; Castro-Giner, Francesc; Makino, Seiko; Rayner, Emily; Kartsonaki, Christiana; Cross, William; Kovac, Michal; Ulahannan, Danny; Palles, Claire; Gillies, Richard S; MacGregor, Thomas P; Church, David; Maynard, Nicholas D; Buffa, Francesca; Cazier, Jean-Baptiste; Graham, Trevor A; Wang, Lai-Mun; Sharma, Ricky A; Middleton, Mark; Tomlinson, Ian

2016-04-05

How chemotherapy affects carcinoma genomes is largely unknown. Here we report whole-exome and deep sequencing of 30 paired oesophageal adenocarcinomas sampled before and after neo-adjuvant chemotherapy. Most, but not all, good responders pass through genetic bottlenecks, a feature associated with higher mutation burden pre-treatment. Some poor responders pass through bottlenecks, but re-grow by the time of surgical resection, suggesting a missed therapeutic opportunity. Cancers often show major changes in driver mutation presence or frequency after treatment, owing to outgrowth persistence or loss of sub-clones, copy number changes, polyclonality and/or spatial genetic heterogeneity. Post-therapy mutation spectrum shifts are also common, particularly C>A and TT>CT changes in good responders or bottleneckers. Post-treatment samples may also acquire mutations in known cancer driver genes (for example, SF3B1, TAF1 and CCND2) that are absent from the paired pre-treatment sample. Neo-adjuvant chemotherapy can rapidly and profoundly affect the oesophageal adenocarcinoma genome. Monitoring molecular changes during treatment may be clinically useful.

Improving the delivery of global tobacco control.

PubMed

Bitton, Asaf; Green, Carol; Colbert, James

2011-01-01

Tobacco control must remain a critical global health priority given the growing burden of tobacco-induced disease in the developing world. Insights from the emerging field of global health delivery suggest that tobacco control could be improved through a systematic, granular analysis of the processes through which it is promoted, implemented, and combated. Using this framework, a critical bottleneck to the delivery of proven health promotion emerges in the role that the tobacco industry plays in promoting tobacco use and blocking effective tobacco-control policies. This "corporate bottleneck" can also be understood as a root cause of massive disease and suffering upon vulnerable populations worldwide, for the goal of maximizing corporate profit. Naming, understanding, and responding to this corporate bottleneck is crucial to the success of tobacco-control policies. Three case studies of tobacco-control policy--South Africa, the Framework Convention on Tobacco Control, and Uruguay--are presented to explore and understand the implications of this analysis. © 2011 Mount Sinai School of Medicine.

Understanding of empty container movement: A study on a bottleneck at an off-dock depot

NASA Astrophysics Data System (ADS)

Zain, Rosmaizura Mohd; Rahman, Mohd Nizam Ab; Nopiah, Zulkifli Mohd; Saibani, Nizaroyani

2014-09-01

Port not only function as connections between marine and land transportation but also as core business areas. In a port terminal, available space is limited, but the influx of container is growing. The off-dock depot is one of the key supply chain players that hold empty containers in the inventory. Therefore, this paper aims to identify the main factors of bottlenecks or congestion that hinder the rapid movement of empty containers from the off-dock depot to the customers. Thirty interviews were conducted with individuals who are key players in the container supply chain. The data were analyzed using Atlas.ti software and the analytic hierarchy process to rank the priority factors of bottlenecks. Findings show that several pertinent factors act as barriers to the key players in the container movement in the day-to-day operations. In future studies, strategies to overcome fragmentation in the container supply chain and logistics must be determined.

STEPS: lean thinking, theory of constraints and identifying bottlenecks in an emergency department.

PubMed

Ryan, A; Hunter, K; Cunningham, K; Williams, J; O'Shea, H; Rooney, P; Hickey, F

2013-04-01

This study aimed to identify the bottlenecks in patients' journeys through an emergency department (ED). For each stage of the patient journey, the average times were compared between two groups divided according to the four hour time frame and disproportionate delays were identified using a significance test These bottlenecks were evaluated with reference to a lean thinking value-stream map and the five focusing steps of the theory of constraints. A total of 434 (72.5%) ED patients were tracked over one week. Logistic regression showed that patients who had radiological tests, blood tests or who were admitted were 4.4, 4.1 and 7.7 times more likely, respectively, to stay over four hours in the ED than those who didn't The stages that were significantly delayed were the time spent waiting for radiology (p = 0.001), waiting for the in-patient team (p = 0.004), waiting for a bed (p < 0.001) and ED doctor turnaround time (p < 0.001).

Are all intertidal wetlands naturally created equal? Bottlenecks, thresholds and knowledge gaps to mangrove and saltmarsh ecosystems

USGS Publications Warehouse

Friess, Daniel A.; Krauss, Ken W.; Horstman, Erik M.; Balke, Thorsten; Bouma, Tjeerd J.; Galli, Demis; Webb, Edward L.

2011-01-01

Intertidal wetlands such as saltmarshes and mangroves provide numerous important ecological functions, though they are in rapid and global decline. To better conserve and restore these wetland ecosystems, we need an understanding of the fundamental natural bottlenecks and thresholds to their establishment and long-term ecological maintenance. Despite inhabiting similar intertidal positions, the biological traits of these systems differ markedly in structure, phenology, life history, phylogeny and dispersal, suggesting large differences in biophysical interactions. By providing the first systematic comparison between saltmarshes and mangroves, we unravel how the interplay between species-specific life-history traits, biophysical interactions and biogeomorphological feedback processes determine where, when and what wetland can establish, the thresholds to long-term ecosystem stability, and constraints to genetic connectivity between intertidal wetland populations at the landscape level. To understand these process interactions, research into the constraints to wetland development, and biological adaptations to overcome these critical bottlenecks and thresholds requires a truly interdisciplinary approach.

Impact of memory bottleneck on the performance of graphics processing units

NASA Astrophysics Data System (ADS)

Son, Dong Oh; Choi, Hong Jun; Kim, Jong Myon; Kim, Cheol Hong

2015-12-01

Recent graphics processing units (GPUs) can process general-purpose applications as well as graphics applications with the help of various user-friendly application programming interfaces (APIs) supported by GPU vendors. Unfortunately, utilizing the hardware resource in the GPU efficiently is a challenging problem, since the GPU architecture is totally different to the traditional CPU architecture. To solve this problem, many studies have focused on the techniques for improving the system performance using GPUs. In this work, we analyze the GPU performance varying GPU parameters such as the number of cores and clock frequency. According to our simulations, the GPU performance can be improved by 125.8% and 16.2% on average as the number of cores and clock frequency increase, respectively. However, the performance is saturated when memory bottleneck problems incur due to huge data requests to the memory. The performance of GPUs can be improved as the memory bottleneck is reduced by changing GPU parameters dynamically.

Helical bottleneck effect in 3D homogeneous isotropic turbulence

NASA Astrophysics Data System (ADS)

Stepanov, Rodion; Golbraikh, Ephim; Frick, Peter; Shestakov, Alexander

2018-02-01

We present the results of modelling the development of homogeneous and isotropic turbulence with a large-scale source of energy and a source of helicity distributed over scales. We use the shell model for numerical simulation of the turbulence at high Reynolds number. The results show that the helicity injection leads to a significant change in the behavior of the energy and helicity spectra in scales larger and smaller than the energy injection scale. We suggest the phenomenology for direct turbulent cascades with the helicity effect, which reduces the efficiency of the spectral energy transfer. Therefore the energy is accumulated and redistributed so that non-linear interactions will be sufficient to provide a constant energy flux. It can be interpreted as the ‘helical bottleneck effect’ which, depending on the parameters of the injection helicity, reminds one of the well-known bottleneck effect at the end of inertial range. Simulations which included the infrared part of the spectrum show that the inverse cascade hardly develops under distributed helicity forcing.

Selective Bottlenecks Shape Evolutionary Pathways Taken during Mammalian Adaptation of a 1918-like Avian Influenza Virus.

PubMed

Moncla, Louise H; Zhong, Gongxun; Nelson, Chase W; Dinis, Jorge M; Mutschler, James; Hughes, Austin L; Watanabe, Tokiko; Kawaoka, Yoshihiro; Friedrich, Thomas C

2016-02-10

Avian influenza virus reassortants resembling the 1918 human pandemic virus can become transmissible among mammals by acquiring mutations in hemagglutinin (HA) and polymerase. Using the ferret model, we trace the evolutionary pathway by which an avian-like virus evolves the capacity for mammalian replication and airborne transmission. During initial infection, within-host HA diversity increased drastically. Then, airborne transmission fixed two polymerase mutations that do not confer a detectable replication advantage. In later transmissions, selection fixed advantageous HA1 variants. Transmission initially involved a "loose" bottleneck, which became strongly selective after additional HA mutations emerged. The stringency and evolutionary forces governing between-host bottlenecks may therefore change throughout host adaptation. Mutations occurred in multiple combinations in transmitted viruses, suggesting that mammalian transmissibility can evolve through multiple genetic pathways despite phenotypic constraints. Our data provide a glimpse into avian influenza virus adaptation in mammals, with broad implications for surveillance on potentially zoonotic viruses. Copyright © 2016 Elsevier Inc. All rights reserved.

A novel cell autolysis system for cost-competitive downstream processing.

PubMed

Hajnal, Ivan; Chen, Xiangbin; Chen, Guo-Qiang

2016-11-01

The industrial production of low value-added biological products poses significant challenges due to cost pressures. In recent years, it has been argued that synthetic biology approaches will lead to breakthroughs that eliminate price bottlenecks for the production of a wide range of biological products including bioplastics and biofuels. One significant bottleneck lies in the necessity to break the tough cell walls of microbes in order to release intracellular products. We here report the implementation of the first synthetic biology standard part based on the lambda phage SRRz genes and a synthetic ribosome binding site (RBS) that works in Escherichia coli and Halomonas campaniensis, which enables the producer strains to induce lysis after the addition of small amounts (1-5 %) of solvents or to spontaneously lyse during the stresses of downstream processing, and thus has the potential to eliminate the mechanical cell disruption step as both an efficiency bottleneck and a significant capex barrier when implementing downstream bioprocesses.

Room-Temperature Coherent Optical Phonon in 2D Electronic Spectra of CH 3NH 3PbI 3 Perovskite as a Possible Cooling Bottleneck

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

Monahan, Daniele M.; Guo, Liang; Lin, Jia

2017-06-29

A hot phonon bottleneck may be responsible for slow hot carrier cooling in methylammonium lead iodide hybrid perovskite, creating the potential for more efficient hot carrier photovoltaics. In room-temperature 2D electronic spectra near the band edge, we observe in this paper amplitude oscillations due to a remarkably long lived 0.9 THz coherent phonon population at room temperature. This phonon (or set of phonons) is assigned to angular distortions of the Pb–I lattice, not coupled to cation rotations. The strong coupling between the electronic transition and the 0.9 THz mode(s), together with relative isolation from other phonon modes, makes it likelymore » to cause a phonon bottleneck. Finally, the pump frequency resolution of the 2D spectra also enables independent observation of photoinduced absorptions and bleaches independently and confirms that features due to band gap renormalization are longer-lived than in transient absorption spectra.« less

The Suite for Embedded Applications and Kernels

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

2016-05-10

Many applications of high performance embedded computing are limited by performance or power bottlenecks. We havedesigned SEAK, a new benchmark suite, (a) to capture these bottlenecks in a way that encourages creative solutions to these bottlenecks? and (b) to facilitate rigorous, objective, end-user evaluation for their solutions. To avoid biasing solutions toward existing algorithms, SEAK benchmarks use a mission-centric (abstracted from a particular algorithm) andgoal-oriented (functional) specification. To encourage solutions that are any combination of software or hardware, we use an end-user blackbox evaluation that can capture tradeoffs between performance, power, accuracy, size, and weight. The tradeoffs are especially informativemore » for procurement decisions. We call our benchmarks future proof because each mission-centric interface and evaluation remains useful despite shifting algorithmic preferences. It is challenging to create both concise and precise goal-oriented specifications for mission-centric problems. This paper describes the SEAK benchmark suite and presents an evaluation of sample solutions that highlights power and performance tradeoffs.« less

Physics of automated driving in framework of three-phase traffic theory.

PubMed

Kerner, Boris S

2018-04-01

We have revealed physical features of automated driving in the framework of the three-phase traffic theory for which there is no fixed time headway to the preceding vehicle. A comparison with the classical model approach to automated driving for which an automated driving vehicle tries to reach a fixed (desired or "optimal") time headway to the preceding vehicle has been made. It turns out that automated driving in the framework of the three-phase traffic theory can exhibit the following advantages in comparison with the classical model of automated driving: (i) The absence of string instability. (ii) Considerably smaller speed disturbances at road bottlenecks. (iii) Automated driving vehicles based on the three-phase theory can decrease the probability of traffic breakdown at the bottleneck in mixed traffic flow consisting of human driving and automated driving vehicles; on the contrary, even a single automated driving vehicle based on the classical approach can provoke traffic breakdown at the bottleneck in mixed traffic flow.

Physics of automated driving in framework of three-phase traffic theory

NASA Astrophysics Data System (ADS)

Kerner, Boris S.

2018-04-01

We have revealed physical features of automated driving in the framework of the three-phase traffic theory for which there is no fixed time headway to the preceding vehicle. A comparison with the classical model approach to automated driving for which an automated driving vehicle tries to reach a fixed (desired or "optimal") time headway to the preceding vehicle has been made. It turns out that automated driving in the framework of the three-phase traffic theory can exhibit the following advantages in comparison with the classical model of automated driving: (i) The absence of string instability. (ii) Considerably smaller speed disturbances at road bottlenecks. (iii) Automated driving vehicles based on the three-phase theory can decrease the probability of traffic breakdown at the bottleneck in mixed traffic flow consisting of human driving and automated driving vehicles; on the contrary, even a single automated driving vehicle based on the classical approach can provoke traffic breakdown at the bottleneck in mixed traffic flow.

Bayesian inference of a historical bottleneck in a heavily exploited marine mammal.

PubMed

Hoffman, J I; Grant, S M; Forcada, J; Phillips, C D

2011-10-01

Emerging Bayesian analytical approaches offer increasingly sophisticated means of reconstructing historical population dynamics from genetic data, but have been little applied to scenarios involving demographic bottlenecks. Consequently, we analysed a large mitochondrial and microsatellite dataset from the Antarctic fur seal Arctocephalus gazella, a species subjected to one of the most extreme examples of uncontrolled exploitation in history when it was reduced to the brink of extinction by the sealing industry during the late eighteenth and nineteenth centuries. Classical bottleneck tests, which exploit the fact that rare alleles are rapidly lost during demographic reduction, yielded ambiguous results. In contrast, a strong signal of recent demographic decline was detected using both Bayesian skyline plots and Approximate Bayesian Computation, the latter also allowing derivation of posterior parameter estimates that were remarkably consistent with historical observations. This was achieved using only contemporary samples, further emphasizing the potential of Bayesian approaches to address important problems in conservation and evolutionary biology. © 2011 Blackwell Publishing Ltd.

Value for money in changing clinical practice: should decisions about guidelines and implementation strategies be made sequentially or simultaneously?

PubMed

Hoomans, Ties; Severens, Johan L; Evers, Silvia M A A; Ament, Andre J H A

2009-01-01

Decisions about clinical practice change, that is, which guidelines to adopt and how to implement them, can be made sequentially or simultaneously. Decision makers adopting a sequential approach first compare the costs and effects of alternative guidelines to select the best set of guideline recommendations for patient management and subsequently examine the implementation costs and effects to choose the best strategy to implement the selected guideline. In an integral approach, decision makers simultaneously decide about the guideline and the implementation strategy on the basis of the overall value for money in changing clinical practice. This article demonstrates that the decision to use a sequential v. an integral approach affects the need for detailed information and the complexity of the decision analytic process. More importantly, it may lead to different choices of guidelines and implementation strategies for clinical practice change. The differences in decision making and decision analysis between the alternative approaches are comprehensively illustrated using 2 hypothetical examples. We argue that, in most cases, an integral approach to deciding about change in clinical practice is preferred, as this provides more efficient use of scarce health-care resources.

Sequential defense against random and intentional attacks in complex networks.

PubMed

Chen, Pin-Yu; Cheng, Shin-Ming

2015-02-01

Network robustness against attacks is one of the most fundamental researches in network science as it is closely associated with the reliability and functionality of various networking paradigms. However, despite the study on intrinsic topological vulnerabilities to node removals, little is known on the network robustness when network defense mechanisms are implemented, especially for networked engineering systems equipped with detection capabilities. In this paper, a sequential defense mechanism is first proposed in complex networks for attack inference and vulnerability assessment, where the data fusion center sequentially infers the presence of an attack based on the binary attack status reported from the nodes in the network. The network robustness is evaluated in terms of the ability to identify the attack prior to network disruption under two major attack schemes, i.e., random and intentional attacks. We provide a parametric plug-in model for performance evaluation on the proposed mechanism and validate its effectiveness and reliability via canonical complex network models and real-world large-scale network topology. The results show that the sequential defense mechanism greatly improves the network robustness and mitigates the possibility of network disruption by acquiring limited attack status information from a small subset of nodes in the network.

Behavioral preference in sequential decision-making and its association with anxiety.

PubMed

Zhang, Dandan; Gu, Ruolei

2018-06-01

In daily life, people often make consecutive decisions before the ultimate goal is reached (i.e., sequential decision-making). However, this kind of decision-making has been largely overlooked in the literature. The current study investigated whether behavioral preference would change during sequential decisions, and the neural processes underlying the potential changes. For this purpose, we revised the classic balloon analogue risk task and recorded the electroencephalograph (EEG) signals associated with each step of decision-making. Independent component analysis performed on EEG data revealed that four EEG components elicited by periodic feedback in the current step predicted participants' decisions (gamble vs. no gamble) in the next step. In order of time sequence, these components were: bilateral occipital alpha rhythm, bilateral frontal theta rhythm, middle frontal theta rhythm, and bilateral sensorimotor mu rhythm. According to the information flows between these EEG oscillations, we proposed a brain model that describes the temporal dynamics of sequential decision-making. Finally, we found that the tendency to gamble (as well as the power intensity of bilateral frontal theta rhythms) was sensitive to the individual level of trait anxiety in certain steps, which may help understand the role of emotion in decision-making. © 2018 Wiley Periodicals, Inc.

Analyzing multicomponent receptive fields from neural responses to natural stimuli

PubMed Central

Rowekamp, Ryan; Sharpee, Tatyana O

2011-01-01

The challenge of building increasingly better models of neural responses to natural stimuli is to accurately estimate the multiple stimulus features that may jointly affect the neural spike probability. The selectivity for combinations of features is thought to be crucial for achieving classical properties of neural responses such as contrast invariance. The joint search for these multiple stimulus features is difficult because estimating spike probability as a multidimensional function of stimulus projections onto candidate relevant dimensions is subject to the curse of dimensionality. An attractive alternative is to search for relevant dimensions sequentially, as in projection pursuit regression. Here we demonstrate using analytic arguments and simulations of model cells that different types of sequential search strategies exhibit systematic biases when used with natural stimuli. Simulations show that joint optimization is feasible for up to three dimensions with current algorithms. When applied to the responses of V1 neurons to natural scenes, models based on three jointly optimized dimensions had better predictive power in a majority of cases compared to dimensions optimized sequentially, with different sequential methods yielding comparable results. Thus, although the curse of dimensionality remains, at least several relevant dimensions can be estimated by joint information maximization. PMID:21780916

Modality-specific spectral dynamics in response to visual and tactile sequential shape information processing tasks: An MEG study using multivariate pattern classification analysis.

PubMed

Gohel, Bakul; Lee, Peter; Jeong, Yong

2016-08-01

Brain regions that respond to more than one sensory modality are characterized as multisensory regions. Studies on the processing of shape or object information have revealed recruitment of the lateral occipital cortex, posterior parietal cortex, and other regions regardless of input sensory modalities. However, it remains unknown whether such regions show similar (modality-invariant) or different (modality-specific) neural oscillatory dynamics, as recorded using magnetoencephalography (MEG), in response to identical shape information processing tasks delivered to different sensory modalities. Modality-invariant or modality-specific neural oscillatory dynamics indirectly suggest modality-independent or modality-dependent participation of particular brain regions, respectively. Therefore, this study investigated the modality-specificity of neural oscillatory dynamics in the form of spectral power modulation patterns in response to visual and tactile sequential shape-processing tasks that are well-matched in terms of speed and content between the sensory modalities. Task-related changes in spectral power modulation and differences in spectral power modulation between sensory modalities were investigated at source-space (voxel) level, using a multivariate pattern classification (MVPC) approach. Additionally, whole analyses were extended from the voxel level to the independent-component level to take account of signal leakage effects caused by inverse solution. The modality-specific spectral dynamics in multisensory and higher-order brain regions, such as the lateral occipital cortex, posterior parietal cortex, inferior temporal cortex, and other brain regions, showed task-related modulation in response to both sensory modalities. This suggests modality-dependency of such brain regions on the input sensory modality for sequential shape-information processing. Copyright © 2016 Elsevier B.V. All rights reserved.

A three-dimensional quality-guided phase unwrapping method for MR elastography

NASA Astrophysics Data System (ADS)

Wang, Huifang; Weaver, John B.; Perreard, Irina I.; Doyley, Marvin M.; Paulsen, Keith D.

2011-07-01

Magnetic resonance elastography (MRE) uses accumulated phases that are acquired at multiple, uniformly spaced relative phase offsets, to estimate harmonic motion information. Heavily wrapped phase occurs when the motion is large and unwrapping procedures are necessary to estimate the displacements required by MRE. Two unwrapping methods were developed and compared in this paper. The first method is a sequentially applied approach. The three-dimensional MRE phase image block for each slice was processed by two-dimensional unwrapping followed by a one-dimensional phase unwrapping approach along the phase-offset direction. This unwrapping approach generally works well for low noise data. However, there are still cases where the two-dimensional unwrapping method fails when noise is high. In this case, the baseline of the corrupted regions within an unwrapped image will not be consistent. Instead of separating the two-dimensional and one-dimensional unwrapping in a sequential approach, an interleaved three-dimensional quality-guided unwrapping method was developed to combine both the two-dimensional phase image continuity and one-dimensional harmonic motion information. The quality of one-dimensional harmonic motion unwrapping was used to guide the three-dimensional unwrapping procedures and it resulted in stronger guidance than in the sequential method. In this work, in vivo results generated by the two methods were compared.

How Do Parents Acquire Information to Support Their Child with a Disability and Navigate Individualised Funding Schemes?

ERIC Educational Resources Information Center

Tracey, Danielle; Johnston, Christine; Papps, Fiona Ann; Mahmic, Sylvana

2018-01-01

With the international trend towards individualised funding packages that allocate funds to individuals to spend on disability support needs, the challenge of ensuring parents can readily access useful information to make decisions becomes paramount. The present research used a two stage, mixed method sequential approach (with 291 parents surveyed…

A review and evaluation of the Langley Research Center's Scientific and Technical Information Program: Results of phase 6: The technical report. A survey and analysis

NASA Technical Reports Server (NTRS)

Mccullough, R. A.; Pinelli, T. E.; Pilley, D. D.; Stohrer, F. F.

1982-01-01

Current practice and usage using selected technical reports; literature relative to the sequential, language, and presentation components of technical reports; and NASA technical report publications standards are discussed. The effctiveness of the technical report as a product for information dissemination is considered.

Electron-Phonon Coupling and Resonant Relaxation from 1D and 1P States in PbS Quantum Dots.

PubMed

Kennehan, Eric R; Doucette, Grayson S; Marshall, Ashley R; Grieco, Christopher; Munson, Kyle T; Beard, Matthew C; Asbury, John B

2018-05-31

Observations of the hot-phonon bottleneck, which is predicted to slow the rate of hot carrier cooling in quantum confined nanocrystals, have been limited to date for reasons that are not fully understood. We used time-resolved infrared spectroscopy to directly measure higher energy intraband transitions in PbS colloidal quantum dots. Direct measurements of these intraband transitions permitted detailed analysis of the electronic overlap of the quantum confined states that may influence their relaxation processes. In smaller PbS nanocrystals, where the hot-phonon bottleneck is expected to be most pronounced, we found that relaxation of parity selection rules combined with stronger electron-phonon coupling led to greater spectral overlap of transitions among the quantum confined states. This created pathways for fast energy transfer and relaxation that may bypass the predicted hot-phonon bottleneck. In contrast, larger, but still quantum confined nanocrystals did not exhibit such relaxation of the parity selection rules and possessed narrower intraband states. These observations were consistent with slower relaxation dynamics that have been measured in larger quantum confined systems. These findings indicated that, at small radii, electron-phonon interactions overcome the advantageous increase in energetic separation of the electronic states for PbS quantum dots. Selection of appropriately sized quantum dots, which minimize spectral broadening due to electron-phonon interactions while maximizing electronic state separation, is necessary to observe the hot-phonon bottleneck. Such optimization may provide a framework for achieving efficient hot carrier collection and multiple exciton generation.

Nucleotide Diversity and Selection Signature in the Domesticated Silkworm, Bombyx mori, and Wild Silkworm, Bombyx mandarina

PubMed Central

Guo, Yi; Shen, Yi-Hong; Sun, Wei; Kishino, Hirohisa; Xiang, Zhong-Huai; Zhang, Ze

2011-01-01

To investigate the patterns of nucleotide diversity in domesticated silkworm, Bombyx mori L. (Lepidoptera: Bombycidae) and its wild relative, Chinese wild silkworm, Bombyx mandarina Moore, we sequenced nine nuclear genes. Neutrality test and coalescent simulation for these genes were performed to look at bottleneck intensity and selection signature; linkage disequilibrium (LD) within and between loci was employed to investigate allele association. As a result, B. mori lost 33–49% of nucleotide diversity relative to wild silkworm, which is similar to the loss levels found in major cultivated crops. Diversity of B. mori is significantly lower than that of B. mandarina measured as πtotal (0.01166 vs. 0.1741) or θW(0.01124 vs. 0.02206). Bottleneck intensity of domesticated silkworm is 1.5 (in terms of k = Nb/d, Nb-bottleneck population size; d-bottleneck duration) with different durations. Gene DefA showed signature of artificial selection by all analysis methods and might experience strong artificial selection in B. mori during domestication. For nine loci, both curves of LD decay rapidly within 200 bp and drop slowly when distance is > 200 bp, although that of B. mori decays slower than B. mandarina at loci investigated. However, LD could not be estimated at DefA in B. mori and at ER in both silkworms. Elevated LD observed in B. mori may be indicator of selection and demographic events. PMID:22239062

The Effects of Intravenous Immunoglobulins in Women with Recurrent Miscarriages: A Systematic Review of Randomised Trials with Meta-Analyses and Trial Sequential Analyses Including Individual Patient Data

PubMed Central

Egerup, Pia; Lindschou, Jane; Gluud, Christian; Christiansen, Ole Bjarne

2015-01-01

Background Immunological disturbances are hypothesised to play a role in recurrent miscarriage (RM) and therefore intravenous immunoglubulins (IVIg) have been tested in RM patients. Objectives The objectives were to investigate the benefits and harms of IVIg versus placebo, no intervention, or treatment as usual in women with RM. Search Strategy We searched the published literature in all relevant databases. Selection Criteria Randomised trials investigating IVIg versus placebo, no intervention, or treatment as usual in women with RM. Data Collection and Analysis We undertook meta-analyses of aggregated data and individual patient data using a two-step approach, and we conducted bias domain assessments and trial sequential analyses to assess the risks of systematic and random errors. Main Results We identified 11 randomised clinical trials. No significant difference in the frequency of no live birth was found when IVIg was compared with placebo or treatment as usual (RR 0.92, 95% CI 0.75–1.12, p = 0.42). Trial sequential analysis showed that the required information size of 1,008 participants was not obtained. IVIg compared with placebo seems to increase the risk of adverse events. Subgroup analysis suggests that women with RM after a birth (secondary RM) seemed most likely to obtain a potential beneficial effect of IVIg (RR for no live birth 0.77, 95%CI 0.58–1.02, p = 0.06), however, trial sequential analysis showed that insufficient information is presently accrued. Conclusion We cannot recommend or refute IVIg in women with RM. IVIg should therefore be assessed in further randomised clinical trials with positive outcomes before any clinical use is considered. PMID:26517123

The Effects of Intravenous Immunoglobulins in Women with Recurrent Miscarriages: A Systematic Review of Randomised Trials with Meta-Analyses and Trial Sequential Analyses Including Individual Patient Data.

PubMed

Egerup, Pia; Lindschou, Jane; Gluud, Christian; Christiansen, Ole Bjarne

2015-01-01

Immunological disturbances are hypothesised to play a role in recurrent miscarriage (RM) and therefore intravenous immunoglubulins (IVIg) have been tested in RM patients. The objectives were to investigate the benefits and harms of IVIg versus placebo, no intervention, or treatment as usual in women with RM. We searched the published literature in all relevant databases. Randomised trials investigating IVIg versus placebo, no intervention, or treatment as usual in women with RM. We undertook meta-analyses of aggregated data and individual patient data using a two-step approach, and we conducted bias domain assessments and trial sequential analyses to assess the risks of systematic and random errors. We identified 11 randomised clinical trials. No significant difference in the frequency of no live birth was found when IVIg was compared with placebo or treatment as usual (RR 0.92, 95% CI 0.75-1.12, p = 0.42). Trial sequential analysis showed that the required information size of 1,008 participants was not obtained. IVIg compared with placebo seems to increase the risk of adverse events. Subgroup analysis suggests that women with RM after a birth (secondary RM) seemed most likely to obtain a potential beneficial effect of IVIg (RR for no live birth 0.77, 95%CI 0.58-1.02, p = 0.06), however, trial sequential analysis showed that insufficient information is presently accrued. We cannot recommend or refute IVIg in women with RM. IVIg should therefore be assessed in further randomised clinical trials with positive outcomes before any clinical use is considered.

Low-dose cerebral perfusion computed tomography image restoration via low-rank and total variation regularizations

PubMed Central

Niu, Shanzhou; Zhang, Shanli; Huang, Jing; Bian, Zhaoying; Chen, Wufan; Yu, Gaohang; Liang, Zhengrong; Ma, Jianhua

2016-01-01

Cerebral perfusion x-ray computed tomography (PCT) is an important functional imaging modality for evaluating cerebrovascular diseases and has been widely used in clinics over the past decades. However, due to the protocol of PCT imaging with repeated dynamic sequential scans, the associative radiation dose unavoidably increases as compared with that used in conventional CT examinations. Minimizing the radiation exposure in PCT examination is a major task in the CT field. In this paper, considering the rich similarity redundancy information among enhanced sequential PCT images, we propose a low-dose PCT image restoration model by incorporating the low-rank and sparse matrix characteristic of sequential PCT images. Specifically, the sequential PCT images were first stacked into a matrix (i.e., low-rank matrix), and then a non-convex spectral norm/regularization and a spatio-temporal total variation norm/regularization were then built on the low-rank matrix to describe the low rank and sparsity of the sequential PCT images, respectively. Subsequently, an improved split Bregman method was adopted to minimize the associative objective function with a reasonable convergence rate. Both qualitative and quantitative studies were conducted using a digital phantom and clinical cerebral PCT datasets to evaluate the present method. Experimental results show that the presented method can achieve images with several noticeable advantages over the existing methods in terms of noise reduction and universal quality index. More importantly, the present method can produce more accurate kinetic enhanced details and diagnostic hemodynamic parameter maps. PMID:27440948

COMPARISON OF HYDROGEN CONCENTRATIONS IN PCE-DEHALOGENATING AND SULFATE-REDUCING ESTUARINE SEDIMENTS

EPA Science Inventory

The primary transformation pathway for PCE in anoxic environments is through sequential reductive dehalogenation, and information concerning dehalogenation processes that occur in environments containing alternative electron acceptors (sulfate) is limited. Hydrogen is postulated ...

Sequential visibility-graph motifs

NASA Astrophysics Data System (ADS)

Iacovacci, Jacopo; Lacasa, Lucas

2016-04-01

Visibility algorithms transform time series into graphs and encode dynamical information in their topology, paving the way for graph-theoretical time series analysis as well as building a bridge between nonlinear dynamics and network science. In this work we introduce and study the concept of sequential visibility-graph motifs, smaller substructures of n consecutive nodes that appear with characteristic frequencies. We develop a theory to compute in an exact way the motif profiles associated with general classes of deterministic and stochastic dynamics. We find that this simple property is indeed a highly informative and computationally efficient feature capable of distinguishing among different dynamics and robust against noise contamination. We finally confirm that it can be used in practice to perform unsupervised learning, by extracting motif profiles from experimental heart-rate series and being able, accordingly, to disentangle meditative from other relaxation states. Applications of this general theory include the automatic classification and description of physical, biological, and financial time series.

Segmentation of remotely sensed data using parallel region growing

NASA Technical Reports Server (NTRS)

Tilton, J. C.; Cox, S. C.

1983-01-01

The improved spatial resolution of the new earth resources satellites will increase the need for effective utilization of spatial information in machine processing of remotely sensed data. One promising technique is scene segmentation by region growing. Region growing can use spatial information in two ways: only spatially adjacent regions merge together, and merging criteria can be based on region-wide spatial features. A simple region growing approach is described in which the similarity criterion is based on region mean and variance (a simple spatial feature). An effective way to implement region growing for remote sensing is as an iterative parallel process on a large parallel processor. A straightforward parallel pixel-based implementation of the algorithm is explored and its efficiency is compared with sequential pixel-based, sequential region-based, and parallel region-based implementations. Experimental results from on aircraft scanner data set are presented, as is a discussioon of proposed improvements to the segmentation algorithm.

Spatial-dependence recurrence sample entropy

NASA Astrophysics Data System (ADS)

Pham, Tuan D.; Yan, Hong

2018-03-01

Measuring complexity in terms of the predictability of time series is a major area of research in science and engineering, and its applications are spreading throughout many scientific disciplines, where the analysis of physiological signals is perhaps the most widely reported in literature. Sample entropy is a popular measure for quantifying signal irregularity. However, the sample entropy does not take sequential information, which is inherently useful, into its calculation of sample similarity. Here, we develop a method that is based on the mathematical principle of the sample entropy and enables the capture of sequential information of a time series in the context of spatial dependence provided by the binary-level co-occurrence matrix of a recurrence plot. Experimental results on time-series data of the Lorenz system, physiological signals of gait maturation in healthy children, and gait dynamics in Huntington's disease show the potential of the proposed method.

Validity of the mockwitness paradigm: testing the assumptions.

PubMed

McQuiston, Dawn E; Malpass, Roy S

2002-08-01

Mockwitness identifications are used to provide a quantitative measure of lineup fairness. Some theoretical and practical assumptions of this paradigm have not been studied in terms of mockwitnesses' decision processes and procedural variation (e.g., instructions, lineup presentation method), and the current experiment was conducted to empirically evaluate these assumptions. Four hundred and eighty mockwitnesses were given physical information about a culprit, received 1 of 4 variations of lineup instructions, and were asked to identify the culprit from either a fair or unfair sequential lineup containing 1 of 2 targets. Lineup bias estimates varied as a result of lineup fairness and the target presented. Mockwitnesses generally reported that the target's physical description was their main source of identifying information. Our findings support the use of mockwitness identifications as a useful technique for sequential lineup evaluation, but only for mockwitnesses who selected only 1 lineup member. Recommendations for the use of this evaluation procedure are discussed.

An efficiency improvement in warehouse operation using simulation analysis

NASA Astrophysics Data System (ADS)

Samattapapong, N.

2017-11-01

In general, industry requires an efficient system for warehouse operation. There are many important factors that must be considered when designing an efficient warehouse system. The most important is an effective warehouse operation system that can help transfer raw material, reduce costs and support transportation. By all these factors, researchers are interested in studying about work systems and warehouse distribution. We start by collecting the important data for storage, such as the information on products, information on size and location, information on data collection and information on production, and all this information to build simulation model in Flexsim® simulation software. The result for simulation analysis found that the conveyor belt was a bottleneck in the warehouse operation. Therefore, many scenarios to improve that problem were generated and testing through simulation analysis process. The result showed that an average queuing time was reduced from 89.8% to 48.7% and the ability in transporting the product increased from 10.2% to 50.9%. Thus, it can be stated that this is the best method for increasing efficiency in the warehouse operation.

Curvature and bottlenecks control molecular transport in inverse bicontinuous cubic phases

NASA Astrophysics Data System (ADS)

Assenza, Salvatore; Mezzenga, Raffaele

2018-02-01

We perform a simulation study of the diffusion of small solutes in the confined domains imposed by inverse bicontinuous cubic phases for the primitive, diamond, and gyroid symmetries common to many lipid/water mesophase systems employed in experiments. For large diffusing domains, the long-time diffusion coefficient shows universal features when the size of the confining domain is renormalized by the Gaussian curvature of the triply periodic minimal surface. When bottlenecks are widely present, they become the most relevant factor for transport, regardless of the connectivity of the cubic phase.

RAMA: A file system for massively parallel computers

NASA Technical Reports Server (NTRS)

Miller, Ethan L.; Katz, Randy H.

1993-01-01

This paper describes a file system design for massively parallel computers which makes very efficient use of a few disks per processor. This overcomes the traditional I/O bottleneck of massively parallel machines by storing the data on disks within the high-speed interconnection network. In addition, the file system, called RAMA, requires little inter-node synchronization, removing another common bottleneck in parallel processor file systems. Support for a large tertiary storage system can easily be integrated in lo the file system; in fact, RAMA runs most efficiently when tertiary storage is used.

Breaking CFD Bottlenecks in Gas-Turbine Flow-Path Design

NASA Technical Reports Server (NTRS)

Davis, Roger L.; Dannenhoffer, John F., III; Clark, John P.

2010-01-01

New ideas are forthcoming to break existing bottlenecks in using CFD during design. CAD-based automated grid generation. Multi-disciplinary use of embedded, overset grids to eliminate complex gridding problems. Use of time-averaged detached-eddy simulations as norm instead of "steady" RANS to include effects of self-excited unsteadiness. Combined GPU/Core parallel computing to provide over an order of magnitude increase in performance/price ratio. Gas-turbine applications are shown here but these ideas can be used for other Air Force, Navy, and NASA applications.

The Plasmodium bottleneck: malaria parasite losses in the mosquito vector

PubMed Central

Smith, Ryan C; Vega-Rodríguez, Joel; Jacobs-Lorena, Marcelo

2014-01-01

Nearly one million people are killed every year by the malaria parasite Plasmodium. Although the disease-causing forms of the parasite exist only in the human blood, mosquitoes of the genus Anopheles are the obligate vector for transmission. Here, we review the parasite life cycle in the vector and highlight the human and mosquito contributions that limit malaria parasite development in the mosquito host. We address parasite killing in its mosquito host and bottlenecks in parasite numbers that might guide intervention strategies to prevent transmission. PMID:25185005

Spin bottleneck in resonant tunneling through double quantum dots with different Zeeman splittings.

PubMed

Huang, S M; Tokura, Y; Akimoto, H; Kono, K; Lin, J J; Tarucha, S; Ono, K

2010-04-02

We investigated the electron transport property of the InGaAs/GaAs double quantum dots, the electron g factors of which are different from each other. We found that in a magnetic field, the resonant tunneling is suppressed even if one of the Zeeman sublevels is aligned. This is because the other misaligned Zeeman sublevels limit the total current. A finite broadening of the misaligned sublevel partially relieves this bottleneck effect, and the maximum current is reached when interdot detuning is half the Zeeman energy difference.

Sequential Revision of Belief, Trust Type, and the Order Effect.

PubMed

Entin, Elliot E; Serfaty, Daniel

2017-05-01

Objective To investigate how people's sequential adjustments to their position are impacted by the source of the information. Background There is an extensive body of research on how the order in which new information is received affects people's final views and decisions as well as research on how they adjust their views in light of new information. Method Seventy college-aged students, 60% of whom were women, completed one of eight different randomly distributed booklets prepared to create the eight different between-subjects treatment conditions created by crossing the two levels of information source with the four level of order conditions. Based on the information provided, participants estimated the probability of an attack, the dependent measure. Results Confirming information from an expert intelligence officer significantly increased the attack probability from the initial position more than confirming information from a longtime friend. Conversely, disconfirming information from a longtime friend decreased the attack probability significantly more than the same information from an intelligence officer. Conclusion It was confirmed that confirming and disconfirming evidence were differentially affected depending on information source, either an expert or a close friend. The difference appears to be due to the existence of two kinds of trust: cognitive-based imbued to an expert and affective-based imbued to a close friend. Application Purveyors of information need to understand that it is not only the content of a message that counts but that other forces are at work such as the order in which information is received and characteristics of the information source.

Conservation genetics of extremely isolated urban populations of the northern dusky salamander (Desmognathus fuscus) in New York City

PubMed Central

Zak, Yana; Pehek, Ellen

2013-01-01

Urbanization is a major cause of amphibian decline. Stream-dwelling plethodontid salamanders are particularly susceptible to urbanization due to declining water quality and hydrological changes, but few studies have examined these taxa in cities. The northern dusky salamander (Desmognathus fuscus) was once common in the New York City metropolitan area, but has substantially declined throughout the region in recent decades. We used five tetranucleotide microsatellite loci to examine population differentiation, genetic variation, and bottlenecks among five remnant urban populations of dusky salamanders in NYC. These genetic measures provide information on isolation, prevalence of inbreeding, long-term prospects for population persistence, and potential for evolutionary responses to future environmental change. All populations were genetically differentiated from each other, and the most isolated populations in Manhattan have maintained very little genetic variation (i.e. <20% heterozygosity). A majority of the populations also exhibited evidence of genetic bottlenecks. These findings contrast with published estimates of high genetic variation within and lack of structure between populations of other desmognathine salamanders sampled over similar or larger spatial scales. Declines in genetic variation likely resulted from population extirpations and the degradation of stream and terrestrial paths for dispersal in NYC. Loss of genetic variability in populations isolated by human development may be an underappreciated cause and/or consequence of the decline of this species in urbanized areas of the northeast USA. PMID:23646283

Population bottleneck triggering millennial-scale morphospace shifts in endemic thermal-spring melanopsids.

PubMed

Neubauer, Thomas A; Harzhauser, Mathias; Georgopoulou, Elisavet; Wrozyna, Claudia

2014-11-15

For more than hundred years the thermal spring-fed Lake Pețea near Oradea, Romania, was studied for its highly endemic subfossil and recent fauna and flora. One point of focus was the species lineage of the melanopsid gastropod Microcolpia parreyssii , which exhibited a tremendous diversity of shapes during the earlier Holocene. As a consequence many new species, subspecies, and variety-names have been introduced over time, trying to categorize this overwhelming variability. In contrast to the varied subfossil assemblage, only a single phenotype is present today. We critically review the apparent "speciation event" implied by the taxonomy, based on the presently available information and new data from morphometric analyses of shell outlines and oxygen and carbon isotope data. This synthesis shows that one turning point in morphological evolution coincides with high accumulation of peaty deposits during a short time interval of maximally a few thousand years. The formation of a small, highly eutrophic swamp with increased input of organic matter marginalized the melanopsids and reduced population size. The presented data make natural selection as the dominating force unlikely but rather indicates genetic drift following a bottleneck effect induced by the environmental changes. This claim contrasts the "obvious trend" and shows that great morphological variability has to be carefully and objectively evaluated in order to allow sound interpretations of the underlying mechanisms.

Resource Management for Distributed Parallel Systems

NASA Technical Reports Server (NTRS)

Neuman, B. Clifford; Rao, Santosh

1993-01-01

Multiprocessor systems should exist in the the larger context of distributed systems, allowing multiprocessor resources to be shared by those that need them. Unfortunately, typical multiprocessor resource management techniques do not scale to large networks. The Prospero Resource Manager (PRM) is a scalable resource allocation system that supports the allocation of processing resources in large networks and multiprocessor systems. To manage resources in such distributed parallel systems, PRM employs three types of managers: system managers, job managers, and node managers. There exist multiple independent instances of each type of manager, reducing bottlenecks. The complexity of each manager is further reduced because each is designed to utilize information at an appropriate level of abstraction.

Plasmodium Sporozoite Biology.

PubMed

Frischknecht, Friedrich; Matuschewski, Kai

2017-05-01

Plasmodium sporozoite transmission is a critical population bottleneck in parasite life-cycle progression and, hence, a target for prophylactic drugs and vaccines. The recent progress of a candidate antisporozoite subunit vaccine formulation to licensure highlights the importance of sporozoite transmission intervention in the malaria control portfolio. Sporozoites colonize mosquito salivary glands, migrate through the skin, penetrate blood vessels, breach the liver sinusoid, and invade hepatocytes. Understanding the molecular and cellular mechanisms that mediate the remarkable sporozoite journey in the invertebrate vector and the vertebrate host can inform evidence-based next-generation drug development programs and immune intervention strategies. Copyright © 2017 Cold Spring Harbor Laboratory Press; all rights reserved.

The Impact of an Informal Science Program on Students' Science Knowledge and Interest

ERIC Educational Resources Information Center

Zandstra, Anne Maria

2012-01-01

In this sequential explanatory mixed methods study, quantitative and qualitative data were used to measure the impact of an informal science program on eleventh grade students' science knowledge and interest. The local GEAR UP project has been working for six years with a cohort of students who were in eleventh and twelfth grade during the time of…

Evaluation of non-animal methods for assessing skin sensitisation hazard: A Bayesian Value-of-Information analysis.

PubMed

Leontaridou, Maria; Gabbert, Silke; Van Ierland, Ekko C; Worth, Andrew P; Landsiedel, Robert

2016-07-01

This paper offers a Bayesian Value-of-Information (VOI) analysis for guiding the development of non-animal testing strategies, balancing information gains from testing with the expected social gains and costs from the adoption of regulatory decisions. Testing is assumed to have value, if, and only if, the information revealed from testing triggers a welfare-improving decision on the use (or non-use) of a substance. As an illustration, our VOI model is applied to a set of five individual non-animal prediction methods used for skin sensitisation hazard assessment, seven battery combinations of these methods, and 236 sequential 2-test and 3-test strategies. Their expected values are quantified and compared to the expected value of the local lymph node assay (LLNA) as the animal method. We find that battery and sequential combinations of non-animal prediction methods reveal a significantly higher expected value than the LLNA. This holds for the entire range of prior beliefs. Furthermore, our results illustrate that the testing strategy with the highest expected value does not necessarily have to follow the order of key events in the sensitisation adverse outcome pathway (AOP). 2016 FRAME.

"Looking-at-nothing" during sequential sensorimotor actions: Long-term memory-based eye scanning of remembered target locations.

PubMed

Foerster, Rebecca M

2018-03-01

Before acting humans saccade to a target object to extract relevant visual information. Even when acting on remembered objects, locations previously occupied by relevant objects are fixated during imagery and memory tasks - a phenomenon called "looking-at-nothing". While looking-at-nothing was robustly found in tasks encouraging declarative memory built-up, results are mixed in the case of procedural sensorimotor tasks. Eye-guidance to manual targets in complete darkness was observed in a task practiced for days beforehand, while investigations using only a single session did not find fixations to remembered action targets. Here, it is asked whether looking-at-nothing can be found in a single sensorimotor session and thus independent from sleep consolidation, and how it progresses when visual information is repeatedly unavailable. Eye movements were investigated in a computerized version of the trail making test. Participants clicked on numbered circles in ascending sequence. Fifty trials were performed with the same spatial arrangement of 9 visual targets to enable long-term memory consolidation. During 50 consecutive trials, participants had to click the remembered target sequence on an empty screen. Participants scanned the visual targets and also the empty target locations sequentially with their eyes, however, the latter less precise than the former. Over the course of the memory trials, manual and oculomotor sequential target scanning became more similar to the visual trials. Results argue for robust looking-at-nothing during procedural sensorimotor tasks provided that long-term memory information is sufficient. Copyright © 2018 Elsevier Ltd. All rights reserved.

A sequential method for spline approximation with variable knots. [recursive piecewise polynomial signal processing

NASA Technical Reports Server (NTRS)

Mier Muth, A. M.; Willsky, A. S.

1978-01-01

In this paper we describe a method for approximating a waveform by a spline. The method is quite efficient, as the data are processed sequentially. The basis of the approach is to view the approximation problem as a question of estimation of a polynomial in noise, with the possibility of abrupt changes in the highest derivative. This allows us to bring several powerful statistical signal processing tools into play. We also present some initial results on the application of our technique to the processing of electrocardiograms, where the knot locations themselves may be some of the most important pieces of diagnostic information.

Dyslexia, an Imbalance in Cerebral Information-Processing Strategies.

ERIC Educational Resources Information Center

Aaron, P. G.

1978-01-01

Twenty-eight reading disabled children (in grades 2-4) were divided (on the basis of the nature of errors made in a writing from dictation task), into two groups--analytic-sequential deficient and holistic-simultaneous deficient. (Author/PHR)

How physician electronic health record screen sharing affects patient and doctor non-verbal communication in primary care.

PubMed

Asan, Onur; Young, Henry N; Chewning, Betty; Montague, Enid

2015-03-01

Use of electronic health records (EHRs) in primary-care exam rooms changes the dynamics of patient-physician interaction. This study examines and compares doctor-patient non-verbal communication (eye-gaze patterns) during primary care encounters for three different screen/information sharing groups: (1) active information sharing, (2) passive information sharing, and (3) technology withdrawal. Researchers video recorded 100 primary-care visits and coded the direction and duration of doctor and patient gaze. Descriptive statistics compared the length of gaze patterns as a percentage of visit length. Lag sequential analysis determined whether physician eye-gaze influenced patient eye gaze, and vice versa, and examined variations across groups. Significant differences were found in duration of gaze across groups. Lag sequential analysis found significant associations between several gaze patterns. Some, such as DGP-PGD ("doctor gaze patient" followed by "patient gaze doctor") were significant for all groups. Others, such DGT-PGU ("doctor gaze technology" followed by "patient gaze unknown") were unique to one group. Some technology use styles (active information sharing) seem to create more patient engagement, while others (passive information sharing) lead to patient disengagement. Doctors can engage patients in communication by using EHRs in the visits. EHR training and design should facilitate this. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Traditional healers, faith healers and medical practitioners: the contribution of medical pluralism to bottlenecks along the cascade of care for HIV/AIDS in Eastern and Southern Africa

PubMed Central

Bukenya, Dominic; Darong, Gabriel; Wamoyi, Joyce; McLean, Estelle; Skovdal, Morten; Ddaaki, William; Ondeng’e, Kenneth; Bonnington, Oliver; Seeley, Janet; Hosegood, Victoria; Wringe, Alison

2017-01-01

Objectives There are concerns that medical pluralism may delay patients’ progression through the HIV cascade-of-care. However, the pathways of impact through which medical pluralism influence the care of people living with HIV (PLHIV) in African settings remain unclear. We sought to establish the manifestation of medical pluralism among PLHIV, and explore mechanisms through which medical pluralism contributes bottlenecks along the HIV care cascade. Methods We conducted a multicountry exploratory qualitative study in seven health and demographic surveillance sites in six eastern and southern African countries: Uganda, Kenya, Tanzania, Malawi, Zimbabwe and South Africa. We interviewed 258 PLHIV at different stages of the HIV cascade-of-care, 48 family members of deceased PLHIV and 53 HIV healthcare workers. Interviews were conducted using shared standardised topic guides, and data managed through NVIVO 8/10/11. We conducted a thematic analysis of healthcare pathways and bottlenecks related to medical pluralism. Results Medical pluralism, manifesting across traditional, faith-based and biomedical health-worlds, contributed to the care cascade bottlenecks for PLHIV through three pathways of impact. First, access to HIV treatment was delayed through the nature of health-related beliefs, knowledge and patient journeys. Second, HIV treatment was interrupted by availability of alternative options, perceived failed treatment and exploitation of PLHIV by opportunistic traders and healers. Lastly, the mixing of biomedical healthcare providers and treatment with traditional and faith-based options fuelled tensions driven by fear of drug-to-drug interactions and mistrust between providers operating in different health-worlds. Conclusion Medical pluralism contributes to delays and interruptions of care along the HIV cascade, and mistrust between health providers. Region-wide interventions and policies are urgently needed in sub-Saharan Africa to minimise potential harm and consequences of medical pluralism for PLHIV. The role of sociocultural beliefs in mediating bottlenecks necessitate adoption of culture-sensitive approaches intervention designs and policy reforms appropriate to the context of sub-Saharan Africa. PMID:28736393

Traditional healers, faith healers and medical practitioners: the contribution of medical pluralism to bottlenecks along the cascade of care for HIV/AIDS in Eastern and Southern Africa.

PubMed

Moshabela, Mosa; Bukenya, Dominic; Darong, Gabriel; Wamoyi, Joyce; McLean, Estelle; Skovdal, Morten; Ddaaki, William; Ondeng'e, Kenneth; Bonnington, Oliver; Seeley, Janet; Hosegood, Victoria; Wringe, Alison

2017-07-01

There are concerns that medical pluralism may delay patients' progression through the HIV cascade-of-care. However, the pathways of impact through which medical pluralism influence the care of people living with HIV (PLHIV) in African settings remain unclear. We sought to establish the manifestation of medical pluralism among PLHIV, and explore mechanisms through which medical pluralism contributes bottlenecks along the HIV care cascade. We conducted a multicountry exploratory qualitative study in seven health and demographic surveillance sites in six eastern and southern African countries: Uganda, Kenya, Tanzania, Malawi, Zimbabwe and South Africa. We interviewed 258 PLHIV at different stages of the HIV cascade-of-care, 48 family members of deceased PLHIV and 53 HIV healthcare workers. Interviews were conducted using shared standardised topic guides, and data managed through NVIVO 8/10/11. We conducted a thematic analysis of healthcare pathways and bottlenecks related to medical pluralism. Medical pluralism, manifesting across traditional, faith-based and biomedical health-worlds, contributed to the care cascade bottlenecks for PLHIV through three pathways of impact. First, access to HIV treatment was delayed through the nature of health-related beliefs, knowledge and patient journeys. Second, HIV treatment was interrupted by availability of alternative options, perceived failed treatment and exploitation of PLHIV by opportunistic traders and healers. Lastly, the mixing of biomedical healthcare providers and treatment with traditional and faith-based options fuelled tensions driven by fear of drug-to-drug interactions and mistrust between providers operating in different health-worlds. Medical pluralism contributes to delays and interruptions of care along the HIV cascade, and mistrust between health providers. Region-wide interventions and policies are urgently needed in sub-Saharan Africa to minimise potential harm and consequences of medical pluralism for PLHIV. The role of sociocultural beliefs in mediating bottlenecks necessitate adoption of culture-sensitive approaches intervention designs and policy reforms appropriate to the context of sub-Saharan Africa. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Testing founder effect speciation: Divergence population genetics of the Spoonbills Platalea regia and Pl. minor (Threskiornithidae, Aves)

USGS Publications Warehouse

Yeung, Carol K.L.; Tsai, Pi-Wen; Chesser, R. Terry; Lin, Rong-Chien; Yao, Cheng-Te; Tian, Xiu-Hua; Li, Shou-Hsien

2011-01-01

Although founder effect speciation has been a popular theoretical model for the speciation of geographically isolated taxa, its empirical importance has remained difficult to evaluate due to the intractability of past demography, which in a founder effect speciation scenario would involve a speciational bottleneck in the emergent species and the complete cessation of gene flow following divergence. Using regression-weighted approximate Bayesian computation, we tested the validity of these two fundamental conditions of founder effect speciation in a pair of sister species with disjunct distributions: the royal spoonbill Platalea regia in Australasia and the black-faced spoonbill Pl. minor in eastern Asia. When compared with genetic polymorphism observed at 20 nuclear loci in the two species, simulations showed that the founder effect speciation model had an extremely low posterior probability (1.55 × 10-8) of producing the extant genetic pattern. In contrast, speciation models that allowed for postdivergence gene flow were much more probable (posterior probabilities were 0.37 and 0.50 for the bottleneck with gene flow and the gene flow models, respectively) and postdivergence gene flow persisted for a considerable period of time (more than 80% of the divergence history in both models) following initial divergence (median = 197,000 generations, 95% credible interval [CI]: 50,000-478,000, for the bottleneck with gene flow model; and 186,000 generations, 95% CI: 45,000-477,000, for the gene flow model). Furthermore, the estimated population size reduction in Pl. regia to 7,000 individuals (median, 95% CI: 487-12,000, according to the bottleneck with gene flow model) was unlikely to have been severe enough to be considered a bottleneck. Therefore, these results do not support founder effect speciation in Pl. regia but indicate instead that the divergence between Pl. regia and Pl. minor was probably driven by selection despite continuous gene flow. In this light, we discuss the potential importance of evolutionarily labile traits with significant fitness consequences, such as migratory behavior and habitat preference, in facilitating divergence of the spoonbills.

Process modeling and bottleneck mining in online peer-review systems.

PubMed

Premchaiswadi, Wichian; Porouhan, Parham

2015-01-01

This paper is divided into three main parts. In the first part of the study, we captured, collected and formatted an event log describing the handling of reviews for proceedings of an international conference in Thailand. In the second part, we used several process mining techniques in order to discover process models, social, organizational, and hierarchical structures from the proceeding's event log. In the third part, we detected the deviations and bottlenecks of the peer review process by comparing the observed events (i.e., authentic dataset) with a pre-defined model (i.e., master map). Finally, we investigated the performance information as well as the total waiting time in order to improve the effectiveness and efficiency of the online submission and peer review system for the prospective conferences and seminars. Consequently, the main goals of the study were as follows: (1) to convert the collected event log into the appropriate format supported by process mining analysis tools, (2) to discover process models and to construct social networks based on the collected event log, and (3) to find deviations, discrepancies and bottlenecks between the collected event log and the master pre-defined model. The results showed that although each paper was initially sent to three different reviewers; it was not always possible to make a decision after the first round of reviewing; therefore, additional reviewers were invited. In total, all the accepted and rejected manuscripts were reviewed by an average of 3.9 and 3.2 expert reviewers, respectively. Moreover, obvious violations of the rules and regulations relating to careless or inappropriate peer review of a manuscript-committed by the editorial board and other staff-were identified. Nine blocks of activity in the authentic dataset were not completely compatible with the activities defined in the master model. Also, five of the activity traces were not correctly enabled, and seven activities were missed within the online submission system. On the other hand, dealing with the feedback (comments) received from the first and the third reviewers; the conference committee members and the organizers did not attend to those feedback/comments in a timely manner.

Bottom-up implementation of disease-management programmes: results of a multisite comparison.

PubMed

Lemmens, K M M; Nieboer, A P; Rutten-Van Mölken, M P M H; van Schayck, C P; Spreeuwenberg, C; Asin, J D; Huijsman, R

2011-01-01

To evaluate the implementation of three regional disease-management programmes on chronic obstructive pulmonary disease (COPD) based on bottlenecks experienced in professional practice. The authors performed a multisite comparison of three Dutch regional disease-management programmes combining patient-related, professional-directed and organisational interventions. Process (Assessing Chronic Illness Care survey) and outcome (disease specific quality of life (clinical COPD questionnaire (CCQ); chronic respiratory questionnaire (CRQ)), Medical Research Council dyspnoea and patients' experiences) data were collected for 370 COPD patients and their care providers. Bottlenecks in region A were mostly related to patient involvement, in region B to organisational issues and in region C to both. Selected interventions related to identified bottlenecks were implemented in all programmes, except for patient-related interventions in programme A. Within programmes, significant improvements were found on dyspnoea and patients' experiences with practice nurses. Outcomes on quality of life differed between programmes: programme A did not show any significant improvements; programme B did show any significant improvements on CCQ total (p<0.001), functional (p=0.011) and symptom (p<0.001), CRQ fatigue (p<0.001) and emotional scales (p<0.001); in programme C, CCQ symptom (p<0.001) improved significantly, whereas CCQ mental score (p<0.001) deteriorated significantly. Regression analyses showed that programmes with better implementation of selected interventions resulted in relatively larger improvements in quality of life (CCQ). Bottom-up implementation of COPD disease-management programmes is a feasible approach, which in multiple settings leads to significant improvements in outcomes of care. Programmes with a better fit between implemented interventions and bottlenecks showed more positive changes in outcomes.

A Qualitative Study of Bottlenecks and Causes of Fractions for Dedicated Incomes of Health Centers and Solutions for their Reduction.

PubMed

Tabrizi, Jafar Sadegh; Alidoost, Saeide; Mashhadi Abdolahi, Hossein

2016-09-01

Primary health care is one of effective approaches for improving public health. Providing optimal cares requires supplication of various resources such as financial resources. "Fractions of incomes" in health centers is one of the remarkable problems for the domain of financial resources management in Iran. This study was aimed to identify bottlenecks and causes of fractions for incomes in health centers and solutions for their reduction. The current study was conducted in a qualitative phenomenology method in East Azerbaijan province of Iran in 2014. Data collection method was focus group discussion and semi-structured interview. Purposive sampling was used for selecting participants. Focus group discussions and interviews were conducted based on pre-prepared guidance and continued till data saturation. Validity of guidance was approved by qualitative studies experts. Data were analyzed using content analysis method. Based on the opinions of participants, two and six themes were respectively extracted for bottlenecks of fractions and causes and solutions for their reduction. Themes for bottlenecks of fractions included cash (monetary) and non-cash (non-monetary) fractions and themes for causes and solutions included causes and solutions for fractions per capita, insurance deductions, fractions related to sending documents, registration fractions, discounts fractions, and incomplete deposit of cash incomes. All cash and non-cash incomes of health centers are subject to fractions. The causes of fractions are related to the whole process of converting services to incomes and insurance requirements. Identified solutions and interventions also focus on these areas.

Mitochondrial DNA sequence characteristics modulate the size of the genetic bottleneck.

PubMed

Wilson, Ian J; Carling, Phillipa J; Alston, Charlotte L; Floros, Vasileios I; Pyle, Angela; Hudson, Gavin; Sallevelt, Suzanne C E H; Lamperti, Costanza; Carelli, Valerio; Bindoff, Laurence A; Samuels, David C; Wonnapinij, Passorn; Zeviani, Massimo; Taylor, Robert W; Smeets, Hubert J M; Horvath, Rita; Chinnery, Patrick F

2016-03-01

With a combined carrier frequency of 1:200, heteroplasmic mitochondrial DNA (mtDNA) mutations cause human disease in ∼1:5000 of the population. Rapid shifts in the level of heteroplasmy seen within a single generation contribute to the wide range in the severity of clinical phenotypes seen in families transmitting mtDNA disease, consistent with a genetic bottleneck during transmission. Although preliminary evidence from human pedigrees points towards a random drift process underlying the shifting heteroplasmy, some reports describe differences in segregation pattern between different mtDNA mutations. However, based on limited observations and with no direct comparisons, it is not clear whether these observations simply reflect pedigree ascertainment and publication bias. To address this issue, we studied 577 mother-child pairs transmitting the m.11778G>A, m.3460G>A, m.8344A>G, m.8993T>G/C and m.3243A>G mtDNA mutations. Our analysis controlled for inter-assay differences, inter-laboratory variation and ascertainment bias. We found no evidence of selection during transmission but show that different mtDNA mutations segregate at different rates in human pedigrees. m.8993T>G/C segregated significantly faster than m.11778G>A, m.8344A>G and m.3243A>G, consistent with a tighter mtDNA genetic bottleneck in m.8993T>G/C pedigrees. Our observations support the existence of different genetic bottlenecks primarily determined by the underlying mtDNA mutation, explaining the different inheritance patterns observed in human pedigrees transmitting pathogenic mtDNA mutations. © The Author 2016. Published by Oxford University Press.

Historical and Contemporary DNA Indicate Fisher Decline and Isolation Occurred Prior to the European Settlement of California

PubMed Central

Tucker, Jody M.; Schwartz, Michael K.; Truex, Richard L.; Pilgrim, Kristine L.; Allendorf, Fred W.

2012-01-01

Establishing if species contractions were the result of natural phenomena or human induced landscape changes is essential for managing natural populations. Fishers (Martes pennanti) in California occur in two geographically and genetically isolated populations in the northwestern mountains and southern Sierra Nevada. Their isolation is hypothesized to have resulted from a decline in abundance and distribution associated with European settlement in the 1800s. However, there is little evidence to establish that fisher occupied the area between the two extant populations at that time. We analyzed 10 microsatellite loci from 275 contemporary and 21 historical fisher samples (1880–1920) to evaluate the demographic history of fisher in California. We did not find any evidence of a recent (post-European) bottleneck in the northwestern population. In the southern Sierra Nevada, genetic subdivision within the population strongly influenced bottleneck tests. After accounting for genetic subdivision, we found a bottleneck signal only in the northern and central portions of the southern Sierra Nevada, indicating that the southernmost tip of these mountains may have acted as a refugium for fisher during the anthropogenic changes of the late 19th and early 20th centuries. Using a coalescent-based Bayesian analysis, we detected a 90% decline in effective population size and dated the time of decline to over a thousand years ago. We hypothesize that fisher distribution in California contracted to the two current population areas pre-European settlement, and that portions of the southern Sierra Nevada subsequently experienced another more recent bottleneck post-European settlement. PMID:23300783

Bottlenecks and selective sweeps during domestication have increased deleterious genetic variation in dogs.

PubMed

Marsden, Clare D; Ortega-Del Vecchyo, Diego; O'Brien, Dennis P; Taylor, Jeremy F; Ramirez, Oscar; Vilà, Carles; Marques-Bonet, Tomas; Schnabel, Robert D; Wayne, Robert K; Lohmueller, Kirk E

2016-01-05

Population bottlenecks, inbreeding, and artificial selection can all, in principle, influence levels of deleterious genetic variation. However, the relative importance of each of these effects on genome-wide patterns of deleterious variation remains controversial. Domestic and wild canids offer a powerful system to address the role of these factors in influencing deleterious variation because their history is dominated by known bottlenecks and intense artificial selection. Here, we assess genome-wide patterns of deleterious variation in 90 whole-genome sequences from breed dogs, village dogs, and gray wolves. We find that the ratio of amino acid changing heterozygosity to silent heterozygosity is higher in dogs than in wolves and, on average, dogs have 2-3% higher genetic load than gray wolves. Multiple lines of evidence indicate this pattern is driven by less efficient natural selection due to bottlenecks associated with domestication and breed formation, rather than recent inbreeding. Further, we find regions of the genome implicated in selective sweeps are enriched for amino acid changing variants and Mendelian disease genes. To our knowledge, these results provide the first quantitative estimates of the increased burden of deleterious variants directly associated with domestication and have important implications for selective breeding programs and the conservation of rare and endangered species. Specifically, they highlight the costs associated with selective breeding and question the practice favoring the breeding of individuals that best fit breed standards. Our results also suggest that maintaining a large population size, rather than just avoiding inbreeding, is a critical factor for preventing the accumulation of deleterious variants.

Bottlenecks and selective sweeps during domestication have increased deleterious genetic variation in dogs

PubMed Central

Marsden, Clare D.; Ortega-Del Vecchyo, Diego; O’Brien, Dennis P.; Taylor, Jeremy F.; Ramirez, Oscar; Vilà, Carles; Marques-Bonet, Tomas; Schnabel, Robert D.; Wayne, Robert K.; Lohmueller, Kirk E.

2016-01-01

Population bottlenecks, inbreeding, and artificial selection can all, in principle, influence levels of deleterious genetic variation. However, the relative importance of each of these effects on genome-wide patterns of deleterious variation remains controversial. Domestic and wild canids offer a powerful system to address the role of these factors in influencing deleterious variation because their history is dominated by known bottlenecks and intense artificial selection. Here, we assess genome-wide patterns of deleterious variation in 90 whole-genome sequences from breed dogs, village dogs, and gray wolves. We find that the ratio of amino acid changing heterozygosity to silent heterozygosity is higher in dogs than in wolves and, on average, dogs have 2–3% higher genetic load than gray wolves. Multiple lines of evidence indicate this pattern is driven by less efficient natural selection due to bottlenecks associated with domestication and breed formation, rather than recent inbreeding. Further, we find regions of the genome implicated in selective sweeps are enriched for amino acid changing variants and Mendelian disease genes. To our knowledge, these results provide the first quantitative estimates of the increased burden of deleterious variants directly associated with domestication and have important implications for selective breeding programs and the conservation of rare and endangered species. Specifically, they highlight the costs associated with selective breeding and question the practice favoring the breeding of individuals that best fit breed standards. Our results also suggest that maintaining a large population size, rather than just avoiding inbreeding, is a critical factor for preventing the accumulation of deleterious variants. PMID:26699508

A Qualitative Study of Bottlenecks and Causes of Fractions for Dedicated Incomes of Health Centers and Solutions for their Reduction

PubMed Central

Tabrizi, Jafar Sadegh; Alidoost, Saeide; Abdolahi, Hossein Mashhadi

2016-01-01

Background: Primary health care is one of effective approaches for improving public health. Providing optimal cares requires supplication of various resources such as financial resources. “Fractions of incomes” in health centers is one of the remarkable problems for the domain of financial resources management in Iran. This study was aimed to identify bottlenecks and causes of fractions for incomes in health centers and solutions for their reduction. Methods: The current study was conducted in a qualitative phenomenology method in East Azerbaijan province of Iran in 2014. Data collection method was focus group discussion and semi-structured interview. Purposive sampling was used for selecting participants. Focus group discussions and interviews were conducted based on pre-prepared guidance and continued till data saturation. Validity of guidance was approved by qualitative studies experts. Data were analyzed using content analysis method. Results: Based on the opinions of participants, two and six themes were respectively extracted for bottlenecks of fractions and causes and solutions for their reduction. Themes for bottlenecks of fractions included cash (monetary) and non-cash (non-monetary) fractions and themes for causes and solutions included causes and solutions for fractions per capita, insurance deductions, fractions related to sending documents, registration fractions, discounts fractions, and incomplete deposit of cash incomes. Conclusion: All cash and non-cash incomes of health centers are subject to fractions. The causes of fractions are related to the whole process of converting services to incomes and insurance requirements. Identified solutions and interventions also focus on these areas. PMID:27157155

Stochastic Modeling of Sediment Connectivity for Reconstructing Sand Fluxes and Origins in the Unmonitored Se Kong, Se San, and Sre Pok Tributaries of the Mekong River

NASA Astrophysics Data System (ADS)

Schmitt, R. J. P.; Bizzi, S.; Castelletti, A. F.; Kondolf, G. M.

2018-01-01

Sediment supply to rivers, subsequent fluvial transport, and the resulting sediment connectivity on network scales are often sparsely monitored and subject to major uncertainty. We propose to approach that uncertainty by adopting a stochastic method for modeling network sediment connectivity, which we present for the Se Kong, Se San, and Sre Pok (3S) tributaries of the Mekong. We quantify how unknown properties of sand sources translate into uncertainty regarding network connectivity by running the CASCADE (CAtchment Sediment Connectivity And DElivery) modeling framework in a Monte Carlo approach for 7,500 random realizations. Only a small ensemble of realizations reproduces downstream observations of sand transport. This ensemble presents an inverse stochastic approximation of the magnitude and variability of transport capacity, sediment flux, and grain size distribution of the sediment transported in the network (i.e., upscaling point observations to the entire network). The approximated magnitude of sand delivered from each tributary to the Mekong is controlled by reaches of low transport capacity ("bottlenecks"). These bottlenecks limit the ability to predict transport in the upper parts of the catchment through inverse stochastic approximation, a limitation that could be addressed by targeted monitoring upstream of identified bottlenecks. Nonetheless, bottlenecks also allow a clear partitioning of natural sand deliveries from the 3S to the Mekong, with the Se Kong delivering less (1.9 Mt/yr) and coarser (median grain size: 0.4 mm) sand than the Se San (5.3 Mt/yr, 0.22 mm) and Sre Pok (11 Mt/yr, 0.19 mm).

Repeated cis-regulatory tuning of a metabolic bottleneck gene during evolution.

PubMed

Kuang, Meihua Christina; Kominek, Jacek; Alexander, William G; Cheng, Jan-Fang; Wrobel, Russell L; Hittinger, Chris Todd

2018-05-21

Repeated evolutionary events imply underlying genetic constraints that can make evolutionary mechanisms predictable. Morphological traits are thought to evolve frequently through cis-regulatory changes because these mechanisms bypass constraints in pleiotropic genes that are reused during development. In contrast, the constraints acting on metabolic traits during evolution are less well studied. Here we show how a metabolic bottleneck gene has repeatedly adopted similar cis-regulatory solutions during evolution, likely due to its pleiotropic role integrating flux from multiple metabolic pathways. Specifically, the genes encoding phosphoglucomutase activity (PGM1/PGM2), which connect GALactose catabolism to glycolysis, have gained and lost direct regulation by the transcription factor Gal4 several times during yeast evolution. Through targeted mutations of predicted Gal4-binding sites in yeast genomes, we show this galactose-mediated regulation of PGM1/2 supports vigorous growth on galactose in multiple yeast species, including Saccharomyces uvarum and Lachancea kluyveri. Furthermore, the addition of galactose-inducible PGM1 alone is sufficient to improve the growth on galactose of multiple species that lack this regulation, including Saccharomyces cerevisiae. The strong association between regulation of PGM1/2 by Gal4 even enables remarkably accurate predictions of galactose growth phenotypes between closely related species. This repeated mode of evolution suggests that this specific cis-regulatory connection is a common way that diverse yeasts can govern flux through the pathway, likely due to the constraints imposed by this pleiotropic bottleneck gene. Since metabolic pathways are highly interconnected, we argue that cis-regulatory evolution might be widespread at pleiotropic genes that control metabolic bottlenecks and intersections.

Computer vision for driver assistance systems

NASA Astrophysics Data System (ADS)

Handmann, Uwe; Kalinke, Thomas; Tzomakas, Christos; Werner, Martin; von Seelen, Werner

1998-07-01

Systems for automated image analysis are useful for a variety of tasks and their importance is still increasing due to technological advances and an increase of social acceptance. Especially in the field of driver assistance systems the progress in science has reached a level of high performance. Fully or partly autonomously guided vehicles, particularly for road-based traffic, pose high demands on the development of reliable algorithms due to the conditions imposed by natural environments. At the Institut fur Neuroinformatik, methods for analyzing driving relevant scenes by computer vision are developed in cooperation with several partners from the automobile industry. We introduce a system which extracts the important information from an image taken by a CCD camera installed at the rear view mirror in a car. The approach consists of a sequential and a parallel sensor and information processing. Three main tasks namely the initial segmentation (object detection), the object tracking and the object classification are realized by integration in the sequential branch and by fusion in the parallel branch. The main gain of this approach is given by the integrative coupling of different algorithms providing partly redundant information.

Synthesizing a novel genetic sequential logic circuit: a push-on push-off switch

PubMed Central

Lou, Chunbo; Liu, Xili; Ni, Ming; Huang, Yiqi; Huang, Qiushi; Huang, Longwen; Jiang, Lingli; Lu, Dan; Wang, Mingcong; Liu, Chang; Chen, Daizhuo; Chen, Chongyi; Chen, Xiaoyue; Yang, Le; Ma, Haisu; Chen, Jianguo; Ouyang, Qi

2010-01-01

Design and synthesis of basic functional circuits are the fundamental tasks of synthetic biologists. Before it is possible to engineer higher-order genetic networks that can perform complex functions, a toolkit of basic devices must be developed. Among those devices, sequential logic circuits are expected to be the foundation of the genetic information-processing systems. In this study, we report the design and construction of a genetic sequential logic circuit in Escherichia coli. It can generate different outputs in response to the same input signal on the basis of its internal state, and ‘memorize' the output. The circuit is composed of two parts: (1) a bistable switch memory module and (2) a double-repressed promoter NOR gate module. The two modules were individually rationally designed, and they were coupled together by fine-tuning the interconnecting parts through directed evolution. After fine-tuning, the circuit could be repeatedly, alternatively triggered by the same input signal; it functions as a push-on push-off switch. PMID:20212522

Synthesizing a novel genetic sequential logic circuit: a push-on push-off switch.

PubMed

Lou, Chunbo; Liu, Xili; Ni, Ming; Huang, Yiqi; Huang, Qiushi; Huang, Longwen; Jiang, Lingli; Lu, Dan; Wang, Mingcong; Liu, Chang; Chen, Daizhuo; Chen, Chongyi; Chen, Xiaoyue; Yang, Le; Ma, Haisu; Chen, Jianguo; Ouyang, Qi

2010-01-01

Design and synthesis of basic functional circuits are the fundamental tasks of synthetic biologists. Before it is possible to engineer higher-order genetic networks that can perform complex functions, a toolkit of basic devices must be developed. Among those devices, sequential logic circuits are expected to be the foundation of the genetic information-processing systems. In this study, we report the design and construction of a genetic sequential logic circuit in Escherichia coli. It can generate different outputs in response to the same input signal on the basis of its internal state, and 'memorize' the output. The circuit is composed of two parts: (1) a bistable switch memory module and (2) a double-repressed promoter NOR gate module. The two modules were individually rationally designed, and they were coupled together by fine-tuning the interconnecting parts through directed evolution. After fine-tuning, the circuit could be repeatedly, alternatively triggered by the same input signal; it functions as a push-on push-off switch.

Speckle pattern sequential extraction metric for estimating the focus spot size on a remote diffuse target.

PubMed

Yu, Zhan; Li, Yuanyang; Liu, Lisheng; Guo, Jin; Wang, Tingfeng; Yang, Guoqing

2017-11-10

The speckle pattern (line by line) sequential extraction (SPSE) metric is proposed by the one-dimensional speckle intensity level crossing theory. Through the sequential extraction of received speckle information, the speckle metrics for estimating the variation of focusing spot size on a remote diffuse target are obtained. Based on the simulation, we will give some discussions about the SPSE metric range of application under the theoretical conditions, and the aperture size will affect the metric performance of the observation system. The results of the analyses are verified by the experiment. This method is applied to the detection of relative static target (speckled jitter frequency is less than the CCD sampling frequency). The SPSE metric can determine the variation of the focusing spot size over a long distance, moreover, the metric will estimate the spot size under some conditions. Therefore, the monitoring and the feedback of far-field spot will be implemented laser focusing system applications and help the system to optimize the focusing performance.

Sequential ChIP Protocol for Profiling Bivalent Epigenetic Modifications (ReChIP).

PubMed

Desvoyes, Bénédicte; Sequeira-Mendes, Joana; Vergara, Zaida; Madeira, Sofia; Gutierrez, Crisanto

2018-01-01

Identification of chromatin modifications, e.g., histone acetylation and methylation, among others, is widely carried out by using a chromatin immunoprecipitation (ChIP) strategy. The information obtained with these procedures is useful to gain an overall picture of modifications present in all cells of the population under study. It also serves as a basis to figure out the mechanisms of chromatin organization and gene regulation at the population level. However, the ultimate goal is to understand gene regulation at the level of single chromatin fibers. This requires the identification of chromatin modifications that occur at a given genomic location and within the same chromatin fiber. This is achieved by following a sequential ChIP strategy using two antibodies to distinguish different chromatin modifications. Here, we describe a sequential ChIP protocol (Re-ChIP), paying special attention to the controls needed and the required steps to obtain meaningful and reproducible results. The protocol is developed for young Arabidopsis seedlings but could be adapted to other plant materials.

Detection, mapping and estimation of rate of spread of grass fires from southern African ERTS-1 imagery

NASA Technical Reports Server (NTRS)

Wightman, J. M.

1973-01-01

Sequential band-6 imagery of the Zambesi Basin of southern Africa recorded substantial changes in burn patterns resulting from late dry season grass fires. One example from northern Botswana, indicates that a fire consumed approximately 70 square miles of grassland over a 24-hour period. Another example from western Zambia indicates increased fire activity over a 19-day period. Other examples clearly define the area of widespread grass fires in Angola, Botswana, Rhodesia and Zambia. From the fire patterns visible on the sequential portions of the imagery, and the time intervals involved, the rates of spread of the fires are estimated and compared with estimates derived from experimental burning plots in Zambia and Canada. It is concluded that sequential ERTS-1 imagery, of the quality studied, clearly provides the information needed to detect and map grass fires and to monitor their rates of spread in this region during the late dry season.

Novel 2D Triple-Resonance NMR Experiments for Sequential Resonance Assignments of Proteins

NASA Astrophysics Data System (ADS)

Ding, Keyang; Gronenborn, Angela M.

2002-06-01

We present 2D versions of the popular triple resonance HN(CO) CACB, HN(COCA)CACB, HN(CO)CAHA, and HN(COCA) CAHA experiments, commonly used for sequential resonance assignments of proteins. These experiments provide information about correlations between amino proton and nitrogen chemical shifts and the α- and β-carbon and α-proton chemical shifts within and between amino acid residues. Using these 2D spectra, sequential resonance assignments of H N, N, C α, C β, and H α nuclei are easily achieved. The resolution of these spectra is identical to the well-resolved 2D 15N- 1H HSQC and H(NCO)CA spectra, with slightly reduced sensitivity compared to their 3D and 4D versions. These types of spectra are ideally suited for exploitation in automated assignment procedures and thereby constitute a fast and efficient means for NMR structural determination of small and medium-sized proteins in solution in structural genomics programs.

Mitogenomics data reveal effective population size, historical bottlenecks, and the effects of hunting on New Zealand fur seals (Arctocephalus forsteri).

PubMed

Emami-Khoyi, Arsalan; Paterson, Adrian M; Hartley, David A; Boren, Laura J; Cruickshank, Robert H; Ross, James G; Murphy, Elaine C; Else, Terry-Ann

2018-05-01

The New Zealand fur seal (Arctocephalus forsteri) passed through a population bottleneck due to commercial sealing during the eighteenth to nineteenth centuries. To facilitate future management options, we reconstructed the demographic history of New Zealand fur seals in a Bayesian framework using maternally inherited, mitochondrial DNA sequences. Mitogenomic data suggested two separate clades (most recent common ancestor 5000 years ago) of New Zealand fur seals that survived large-scale human harvest. Mitochondrial haplotype diversity was high, with 45 singletons identified from 46 individuals although mean nucleotide diversity was low (0.012 ± 0.0061). Variation was not constrained geographically. Analyses of mitogenomes support the hypothesis for a population bottleneck approximately 35 generations ago, which coincides with the peak of commercial sealing. Mitogenomic data are consistent with a pre-human effective population size of approximately 30,000 that first declined to around 10,000 (due to the impact of Polynesian colonization, particularly in the first 100 years of their arrival into New Zealand), and then to 100-200 breeding individuals during peak of commercial sealing.

Flagella-Driven Flows Circumvent Diffusive Bottlenecks that Inhibit Metabolite Exchange

NASA Astrophysics Data System (ADS)

Short, Martin; Solari, Cristian; Ganguly, Sujoy; Kessler, John; Goldstein, Raymond; Powers, Thomas

2006-03-01

The evolution of single cells to large and multicellular organisms requires matching the organisms' needs to the rate of exchange of metabolites with the environment. This logistic problem can be a severe constraint on development. For organisms with a body plan that approximates a spherical shell, such as colonies of the volvocine green algae, the required current of metabolites grows quadratically with colony radius whereas the rate at which diffusion can exchange metabolites grows only linearly with radius. Hence, there is a bottleneck radius beyond which the diffusive current cannot keep up with metabolic demands. Using Volvox carteri as a model organism, we examine experimentally and theoretically the role that advection of fluid by surface-mounted flagella plays in enhancing nutrient uptake. We show that fluid flow driven by the coordinated beating of flagella produces a convective boundary layer in the concentration of a diffusing solute which in turn renders the metabolite exchange rate quadratic in the colony radius. This enhanced transport circumvents the diffusive bottleneck, allowing increase in size and thus evolutionary transitions to multicellularity in the Volvocales.

Traffic dynamics around weaving section influenced by accident: Cellular automata approach

NASA Astrophysics Data System (ADS)

Kong, Lin-Peng; Li, Xin-Gang; Lam, William H. K.

2015-07-01

The weaving section, as a typical bottleneck, is one source of vehicle conflicts and an accident-prone area. Traffic accident will block lanes and the road capacity will be reduced. Several models have been established to study the dynamics around traffic bottlenecks. However, little attention has been paid to study the complex traffic dynamics influenced by the combined effects of bottleneck and accident. This paper presents a cellular automaton model to characterize accident-induced traffic behavior around the weaving section. Some effective control measures are proposed and verified for traffic management under accident condition. The total flux as a function of inflow rates, the phase diagrams, the spatial-temporal diagrams, and the density and velocity profiles are presented to analyze the impact of accident. It was shown that the proposed control measures for weaving traffic can improve the capacity of weaving section under both normal and accident conditions; the accidents occurring on median lane in the weaving section are more inclined to cause traffic jam and reduce road capacity; the capacity of weaving section will be greatly reduced when the accident happens downstream the weaving section.

Performances of multiprocessor multidisk architectures for continuous media storage

NASA Astrophysics Data System (ADS)

Gennart, Benoit A.; Messerli, Vincent; Hersch, Roger D.

1996-03-01

Multimedia interfaces increase the need for large image databases, capable of storing and reading streams of data with strict synchronicity and isochronicity requirements. In order to fulfill these requirements, we consider a parallel image server architecture which relies on arrays of intelligent disk nodes, each disk node being composed of one processor and one or more disks. This contribution analyzes through bottleneck performance evaluation and simulation the behavior of two multi-processor multi-disk architectures: a point-to-point architecture and a shared-bus architecture similar to current multiprocessor workstation architectures. We compare the two architectures on the basis of two multimedia algorithms: the compute-bound frame resizing by resampling and the data-bound disk-to-client stream transfer. The results suggest that the shared bus is a potential bottleneck despite its very high hardware throughput (400Mbytes/s) and that an architecture with addressable local memories located closely to their respective processors could partially remove this bottleneck. The point- to-point architecture is scalable and able to sustain high throughputs for simultaneous compute- bound and data-bound operations.

Molecular Determinants and Bottlenecks in the Dissociation Dynamics of Biotin-Streptavidin.

PubMed

Tiwary, Pratyush

2017-12-07

Biotin-streptavidin is a very popular system used to gain insight into protein-ligand interactions. In its tetrameric form, it is well-known for its exceptionally high kinetic stability, being one of the strongest known noncovalent interactions in nature, and it is heavily used across the biotechnological industry. In this work, we gain understanding of the molecular determinants and bottlenecks in the dissociation of the dimeric biotin-streptavidin system in wild type and with a point mutation. Using recently proposed enhanced sampling methods with full atomistic resolution, we reproduce the experimentally reported effect of the mutation on the dissociation rate. We also answer a longstanding question regarding cause/effect in the coupled events of bond stretching and bond hydration during dissociation and establish that in this system, it is the bond stretching and not hydration which forms the bottleneck in the early parts of the dissociation process. We believe these calculations represent a step forward in the use of atomistic simulations to study pharmacokinetics. An improved understanding of biotin-streptavidin dissociation dynamics should also have direct benefits in biotechnological and nanobiotechnological applications.

Manufacturing Enhancement through Reduction of Cycle Time using Different Lean Techniques

NASA Astrophysics Data System (ADS)

Suganthini Rekha, R.; Periyasamy, P.; Nallusamy, S.

2017-08-01

In recent manufacturing system the most important parameters in production line are work in process, TAKT time and line balancing. In this article lean tools and techniques were implemented to reduce the cycle time. The aim is to enhance the productivity of the water pump pipe by identifying the bottleneck stations and non value added activities. From the initial time study the bottleneck processes were identified and then necessary expanding processes were also identified for the bottleneck process. Subsequently the improvement actions have been established and implemented using different lean tools like value stream mapping, 5S and line balancing. The current state value stream mapping was developed to describe the existing status and to identify various problem areas. 5S was used to implement the steps to reduce the process cycle time and unnecessary movements of man and material. The improvement activities were implemented with required suggested and the future state value stream mapping was developed. From the results it was concluded that the total cycle time was reduced about 290.41 seconds and the customer demand has been increased about 760 units.

Determination of the mode of occurrence of As, Cr, and Hg in three Chinese coal samples by sequential acid leaching

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

Wang, B.; Li, W.; Wang, G.

2007-07-01

Sequential acid leaching was used to leach minerals and the trace elements they contain. One-step leaching uses concentrated nitric acid as solvent, while three-step leaching uses 5M hydrochloric acid, concentrated hydrofluoric acid, and concentrated hydrochloric acid as solvents. The sequential acid leaching by three-and one-step leach was also examined. The results showed that one-step leaching could leach over 80% of arsenic from coal samples, and also could leach mercury to a certain degree. During one-step leaching, little chromium is removed, but it is available to leach by three-step leaching; and during the sequential acid leaching by three and one-step leaching,more » almost 98% ash is leached. The result of acid leaching could also give detailed information on mode of occurrence of As, Cr, and Hg, which could be classified into: silicate association, pyrite association, organic association, and carbonates and sulfates association. Over half of chromium in the three coals is associated with organic matters and the rest is associated with silicates. The mode of occurrence of arsenic and mercury is mainly associated with different mineral matters depending on the coal samples studied.« less

Sequential and prosodic design of English and Greek non-valenced news receipts.

PubMed

Kaimaki, Marianna

2012-03-01

Results arising from a prosodic and interactional study of the organization of everyday talk in English suggest that news receipts can be grouped into two categories: valenced (e.g., oh good) and non-valenced (e.g., oh really). In-depth investigation of both valenced and non-valenced news receipts shows that differences in their prosodic design do not seem to affect the sequential structure of the news informing sequence. News receipts with falling and rising pitch may have the same uptake and are treated in the same way by co-participants. A preliminary study of a Greek telephone corpus yielded the following receipts of news announcements: a malista, a(h) orea, a ne, a, oh. These are news markers composed of a standalone particle or a particle followed by an adverb or a response token (ne). Analysis of the sequential and prosodic design of Greek news announcement sequences is made to determine any interactional patterns and/or prosodic constraints. By examining the way in which co-participants display their interpretation of these turns I show that the phonological systems of contrast are different depending on the sequential environment, in much the same way that consonantal systems of contrast are not the same syllable initially and finally.

Feature Extraction in Sequential Multimedia Images: with Applications in Satellite Images and On-line Videos

NASA Astrophysics Data System (ADS)

Liang, Yu-Li

Multimedia data is increasingly important in scientific discovery and people's daily lives. Content of massive multimedia is often diverse and noisy, and motion between frames is sometimes crucial in analyzing those data. Among all, still images and videos are commonly used formats. Images are compact in size but do not contain motion information. Videos record motion but are sometimes too big to be analyzed. Sequential images, which are a set of continuous images with low frame rate, stand out because they are smaller than videos and still maintain motion information. This thesis investigates features in different types of noisy sequential images, and the proposed solutions that intelligently combined multiple features to successfully retrieve visual information from on-line videos and cloudy satellite images. The first task is detecting supraglacial lakes above ice sheet in sequential satellite images. The dynamics of supraglacial lakes on the Greenland ice sheet deeply affect glacier movement, which is directly related to sea level rise and global environment change. Detecting lakes above ice is suffering from diverse image qualities and unexpected clouds. A new method is proposed to efficiently extract prominent lake candidates with irregular shapes, heterogeneous backgrounds, and in cloudy images. The proposed system fully automatize the procedure that track lakes with high accuracy. We further cooperated with geoscientists to examine the tracked lakes and found new scientific findings. The second one is detecting obscene content in on-line video chat services, such as Chatroulette, that randomly match pairs of users in video chat sessions. A big problem encountered in such systems is the presence of flashers and obscene content. Because of various obscene content and unstable qualities of videos capture by home web-camera, detecting misbehaving users is a highly challenging task. We propose SafeVchat, which is the first solution that achieves satisfactory detection rate by using facial features and skin color model. To harness all the features in the scene, we further developed another system using multiple types of local descriptors along with Bag-of-Visual Word framework. In addition, an investigation of new contour feature in detecting obscene content is presented.

Learning, memory, and the role of neural network architecture.

PubMed

Hermundstad, Ann M; Brown, Kevin S; Bassett, Danielle S; Carlson, Jean M

2011-06-01

The performance of information processing systems, from artificial neural networks to natural neuronal ensembles, depends heavily on the underlying system architecture. In this study, we compare the performance of parallel and layered network architectures during sequential tasks that require both acquisition and retention of information, thereby identifying tradeoffs between learning and memory processes. During the task of supervised, sequential function approximation, networks produce and adapt representations of external information. Performance is evaluated by statistically analyzing the error in these representations while varying the initial network state, the structure of the external information, and the time given to learn the information. We link performance to complexity in network architecture by characterizing local error landscape curvature. We find that variations in error landscape structure give rise to tradeoffs in performance; these include the ability of the network to maximize accuracy versus minimize inaccuracy and produce specific versus generalizable representations of information. Parallel networks generate smooth error landscapes with deep, narrow minima, enabling them to find highly specific representations given sufficient time. While accurate, however, these representations are difficult to generalize. In contrast, layered networks generate rough error landscapes with a variety of local minima, allowing them to quickly find coarse representations. Although less accurate, these representations are easily adaptable. The presence of measurable performance tradeoffs in both layered and parallel networks has implications for understanding the behavior of a wide variety of natural and artificial learning systems.

Large scale nonlinear programming for the optimization of spacecraft trajectories

NASA Astrophysics Data System (ADS)

Arrieta-Camacho, Juan Jose

Despite the availability of high fidelity mathematical models, the computation of accurate optimal spacecraft trajectories has never been an easy task. While simplified models of spacecraft motion can provide useful estimates on energy requirements, sizing, and cost; the actual launch window and maneuver scheduling must rely on more accurate representations. We propose an alternative for the computation of optimal transfers that uses an accurate representation of the spacecraft dynamics. Like other methodologies for trajectory optimization, this alternative is able to consider all major disturbances. In contrast, it can handle explicitly equality and inequality constraints throughout the trajectory; it requires neither the derivation of costate equations nor the identification of the constrained arcs. The alternative consist of two steps: (1) discretizing the dynamic model using high-order collocation at Radau points, which displays numerical advantages, and (2) solution to the resulting Nonlinear Programming (NLP) problem using an interior point method, which does not suffer from the performance bottleneck associated with identifying the active set, as required by sequential quadratic programming methods; in this way the methodology exploits the availability of sound numerical methods, and next generation NLP solvers. In practice the methodology is versatile; it can be applied to a variety of aerospace problems like homing, guidance, and aircraft collision avoidance; the methodology is particularly well suited for low-thrust spacecraft trajectory optimization. Examples are presented which consider the optimization of a low-thrust orbit transfer subject to the main disturbances due to Earth's gravity field together with Lunar and Solar attraction. Other example considers the optimization of a multiple asteroid rendezvous problem. In both cases, the ability of our proposed methodology to consider non-standard objective functions and constraints is illustrated. Future research directions are identified, involving the automatic scheduling and optimization of trajectory correction maneuvers. The sensitivity information provided by the methodology is expected to be invaluable in such research pursuit. The collocation scheme and nonlinear programming algorithm presented in this work, complement other existing methodologies by providing reliable and efficient numerical methods able to handle large scale, nonlinear dynamic models.

Design and construction of a double inversion recombination switch for heritable sequential genetic memory.

PubMed

Ham, Timothy S; Lee, Sung K; Keasling, Jay D; Arkin, Adam P

2008-07-30

Inversion recombination elements present unique opportunities for computing and information encoding in biological systems. They provide distinct binary states that are encoded into the DNA sequence itself, allowing us to overcome limitations posed by other biological memory or logic gate systems. Further, it is in theory possible to create complex sequential logics by careful positioning of recombinase recognition sites in the sequence. In this work, we describe the design and synthesis of an inversion switch using the fim and hin inversion recombination systems to create a heritable sequential memory switch. We have integrated the two inversion systems in an overlapping manner, creating a switch that can have multiple states. The switch is capable of transitioning from state to state in a manner analogous to a finite state machine, while encoding the state information into DNA. This switch does not require protein expression to maintain its state, and "remembers" its state even upon cell death. We were able to demonstrate transition into three out of the five possible states showing the feasibility of such a switch. We demonstrate that a heritable memory system that encodes its state into DNA is possible, and that inversion recombination system could be a starting point for more complex memory circuits. Although the circuit did not fully behave as expected, we showed that a multi-state, temporal memory is achievable.

Design and Construction of a Double Inversion Recombination Switch for Heritable Sequential Genetic Memory

PubMed Central

Ham, Timothy S.; Lee, Sung K.; Keasling, Jay D.; Arkin, Adam P.

2008-01-01

Background Inversion recombination elements present unique opportunities for computing and information encoding in biological systems. They provide distinct binary states that are encoded into the DNA sequence itself, allowing us to overcome limitations posed by other biological memory or logic gate systems. Further, it is in theory possible to create complex sequential logics by careful positioning of recombinase recognition sites in the sequence. Methodology/Principal Findings In this work, we describe the design and synthesis of an inversion switch using the fim and hin inversion recombination systems to create a heritable sequential memory switch. We have integrated the two inversion systems in an overlapping manner, creating a switch that can have multiple states. The switch is capable of transitioning from state to state in a manner analogous to a finite state machine, while encoding the state information into DNA. This switch does not require protein expression to maintain its state, and “remembers” its state even upon cell death. We were able to demonstrate transition into three out of the five possible states showing the feasibility of such a switch. Conclusions/Significance We demonstrate that a heritable memory system that encodes its state into DNA is possible, and that inversion recombination system could be a starting point for more complex memory circuits. Although the circuit did not fully behave as expected, we showed that a multi-state, temporal memory is achievable. PMID:18665232

SYNERGISMS IN SEQUENTIAL DISINFECTION OF CRYPTOSPORIDIUM PARVUM. (R826830)

EPA Science Inventory

The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Concl...

Real-time validation of receiver state information in optical space-time block code systems.

PubMed

Alamia, John; Kurzweg, Timothy

2014-06-15

Free space optical interconnect (FSOI) systems are a promising solution to interconnect bottlenecks in high-speed systems. To overcome some sources of diminished FSOI performance caused by close proximity of multiple optical channels, multiple-input multiple-output (MIMO) systems implementing encoding schemes such as space-time block coding (STBC) have been developed. These schemes utilize information pertaining to the optical channel to reconstruct transmitted data. The STBC system is dependent on accurate channel state information (CSI) for optimal system performance. As a result of dynamic changes in optical channels, a system in operation will need to have updated CSI. Therefore, validation of the CSI during operation is a necessary tool to ensure FSOI systems operate efficiently. In this Letter, we demonstrate a method of validating CSI, in real time, through the use of moving averages of the maximum likelihood decoder data, and its capacity to predict the bit error rate (BER) of the system.

Compressing climate model simulations: reducing storage burden while preserving information

NASA Astrophysics Data System (ADS)

Hammerling, Dorit; Baker, Allison; Xu, Haiying; Clyne, John; Li, Samuel

2017-04-01

Climate models, which are run at high spatial and temporal resolutions, generate massive quantities of data. As our computing capabilities continue to increase, storing all of the generated data is becoming a bottleneck, which negatively affects scientific progress. It is thus important to develop methods for representing the full datasets by smaller compressed versions, which still preserve all the critical information and, as an added benefit, allow for faster read and write operations during analysis work. Traditional lossy compression algorithms, as for example used for image files, are not necessarily ideally suited for climate data. While visual appearance is relevant, climate data has additional critical features such as the preservation of extreme values and spatial and temporal gradients. Developing alternative metrics to quantify information loss in a manner that is meaningful to climate scientists is an ongoing process still in its early stages. We will provide an overview of current efforts to develop such metrics to assess existing algorithms and to guide the development of tailored compression algorithms to address this pressing challenge.

Genetic applications in avian conservation

USGS Publications Warehouse

Haig, Susan M.; Bronaugh, Whitcomb M.; Crowhurst, Rachel S.; D'Elia, Jesse; Eagles-Smith, Collin A.; Epps, Clinton W.; Knaus, Brian; Miller, Mark P.; Moses, Michael L.; Oyler-McCance, Sara; Robinson, W. Douglas; Sidlauskas, Brian

2011-01-01

A fundamental need in conserving species and their habitats is defining distinct entities that range from individuals to species to ecosystems and beyond (Table 1; Ryder 1986, Moritz 1994, Mayden and Wood 1995, Haig and Avise 1996, Hazevoet 1996, Palumbi and Cipriano 1998, Hebert et al. 2004, Mace 2004, Wheeler et al. 2004, Armstrong and Ball 2005, Baker 2008, Ellis et al. 2010, Winker and Haig 2010). Rapid progression in this interdisciplinary field continues at an exponential rate; thus, periodic updates on theory, techniques, and applications are important for informing practitioners and consumers of genetic information. Here, we outline conservation topics for which genetic information can be helpful, provide examples of where genetic techniques have been used best in avian conservation, and point to current technical bottlenecks that prevent better use of genomics to resolve conservation issues related to birds. We hope this review will provide geneticists and avian ecologists with a mutually beneficial dialogue on how this integrated field can solve current and future problems.

A complete solution of cartographic displacement based on elastic beams model and Delaunay triangulation

NASA Astrophysics Data System (ADS)

Liu, Y.; Guo, Q.; Sun, Y.

2014-04-01

In map production and generalization, it is inevitable to arise some spatial conflicts, but the detection and resolution of these spatial conflicts still requires manual operation. It is become a bottleneck hindering the development of automated cartographic generalization. Displacement is the most useful contextual operator that is often used for resolving the conflicts arising between two or more map objects. Automated generalization researches have reported many approaches of displacement including sequential approaches and optimization approaches. As an excellent optimization approach on the basis of energy minimization principles, elastic beams model has been used in resolving displacement problem of roads and buildings for several times. However, to realize a complete displacement solution, techniques of conflict detection and spatial context analysis should be also take into consideration. So we proposed a complete solution of displacement based on the combined use of elastic beams model and constrained Delaunay triangulation (CDT) in this paper. The solution designed as a cyclic and iterative process containing two phases: detection phase and displacement phase. In detection phase, CDT of map is use to detect proximity conflicts, identify spatial relationships and structures, and construct auxiliary structure, so as to support the displacement phase on the basis of elastic beams. In addition, for the improvements of displacement algorithm, a method for adaptive parameters setting and a new iterative strategy are put forward. Finally, we implemented our solution on a testing map generalization platform, and successfully tested it against 2 hand-generated test datasets of roads and buildings respectively.

Self-consistent field for fragmented quantum mechanical model of large molecular systems.

PubMed

Jin, Yingdi; Su, Neil Qiang; Xu, Xin; Hu, Hao

2016-01-30

Fragment-based linear scaling quantum chemistry methods are a promising tool for the accurate simulation of chemical and biomolecular systems. Because of the coupled inter-fragment electrostatic interactions, a dual-layer iterative scheme is often employed to compute the fragment electronic structure and the total energy. In the dual-layer scheme, the self-consistent field (SCF) of the electronic structure of a fragment must be solved first, then followed by the updating of the inter-fragment electrostatic interactions. The two steps are sequentially carried out and repeated; as such a significant total number of fragment SCF iterations is required to converge the total energy and becomes the computational bottleneck in many fragment quantum chemistry methods. To reduce the number of fragment SCF iterations and speed up the convergence of the total energy, we develop here a new SCF scheme in which the inter-fragment interactions can be updated concurrently without converging the fragment electronic structure. By constructing the global, block-wise Fock matrix and density matrix, we prove that the commutation between the two global matrices guarantees the commutation of the corresponding matrices in each fragment. Therefore, many highly efficient numerical techniques such as the direct inversion of the iterative subspace method can be employed to converge simultaneously the electronic structure of all fragments, reducing significantly the computational cost. Numerical examples for water clusters of different sizes suggest that the method shall be very useful in improving the scalability of fragment quantum chemistry methods. © 2015 Wiley Periodicals, Inc.

Epigenetic and genetic variation among three separate introductions of the house sparrow (Passer domesticus) into Australia

PubMed Central

Schrey, A.; Ragsdale, A.; Griffith, S. C.

2018-01-01

Invasive populations are often associated with low levels of genetic diversity owing to population bottlenecks at the initial stages of invasion. Despite this, the ability of invasive species to adapt rapidly in response to novel environments is well documented. Epigenetic mechanisms have recently been proposed to facilitate the success of invasive species by compensating for reduced levels of genetic variation. Here, we use methylation sensitive-amplification fragment length polymorphism and microsatellite analyses to compare levels of epigenetic and genetic diversity and differentiation across 15 sites in the introduced Australian house sparrow population. We find patterns of epigenetic and genetic differentiation that are consistent with historical descriptions of three distinct, introductions events. However unlike genetic differentiation, epigenetic differentiation was higher among sample sites than among invasion clusters, suggesting that patterns of epigenetic variation are more strongly influenced by local environmental stimuli or sequential founder events than the initial diversity in the introduction population. Interestingly, we fail to detect correlations between pairwise site comparisons of epigenetic and genetic differentiation, suggesting that some of the observed epigenetic variation has arisen independently of genetic variation. We also fail to detect the potentially compensatory relationship between epigenetic and genetic diversity that has been detected in a more recent house sparrow invasion in Africa. We discuss the potential for this relationship to be obscured by recovered genetic diversity in more established populations, and highlight the importance of incorporating introduction history into population-wide epigenetic analyses. PMID:29765671

Implementing controlled-unitary operations over the butterfly network

NASA Astrophysics Data System (ADS)

Soeda, Akihito; Kinjo, Yoshiyuki; Turner, Peter S.; Murao, Mio

2014-12-01

We introduce a multiparty quantum computation task over a network in a situation where the capacities of both the quantum and classical communication channels of the network are limited and a bottleneck occurs. Using a resource setting introduced by Hayashi [1], we present an efficient protocol for performing controlled-unitary operations between two input nodes and two output nodes over the butterfly network, one of the most fundamental networks exhibiting the bottleneck problem. This result opens the possibility of developing a theory of quantum network coding for multiparty quantum computation, whereas the conventional network coding only treats multiparty quantum communication.

A first packet processing subdomain cluster model based on SDN

NASA Astrophysics Data System (ADS)

Chen, Mingyong; Wu, Weimin

2017-08-01

For the current controller cluster packet processing performance bottlenecks and controller downtime problems. An SDN controller is proposed to allocate the priority of each device in the SDN (Software Defined Network) network, and the domain contains several network devices and Controller, the controller is responsible for managing the network equipment within the domain, the switch performs data delivery based on the load of the controller, processing network equipment data. The experimental results show that the model can effectively solve the risk of single point failure of the controller, and can solve the performance bottleneck of the first packet processing.

Implementing controlled-unitary operations over the butterfly network

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

Soeda, Akihito; Kinjo, Yoshiyuki; Turner, Peter S.

2014-12-04

We introduce a multiparty quantum computation task over a network in a situation where the capacities of both the quantum and classical communication channels of the network are limited and a bottleneck occurs. Using a resource setting introduced by Hayashi [1], we present an efficient protocol for performing controlled-unitary operations between two input nodes and two output nodes over the butterfly network, one of the most fundamental networks exhibiting the bottleneck problem. This result opens the possibility of developing a theory of quantum network coding for multiparty quantum computation, whereas the conventional network coding only treats multiparty quantum communication.

Evaluation of Swift Start TCP in Long-Delay Environment

NASA Technical Reports Server (NTRS)

Lawas-Grodek, Frances J.; Tran, Diepchi T.

2004-01-01

This report presents the test results of the Swift Start algorithm in single-flow and multiple-flow testbeds under the effects of high propagation delays, various slow bottlenecks, and small queue sizes. Although this algorithm estimates capacity and implements packet pacing, the findings were that in a heavily congested link, the Swift Start algorithm will not be applicable. The reason is that the bottleneck estimation is falsely influenced by timeouts induced by retransmissions and the expiration of delayed acknowledgment (ACK) timers, thus causing the modified Swift Start code to fall back to regular transmission control protocol (TCP).