The Role of Host and Microbial Factors in the Pathogenesis of Pneumococcal Bacteraemia Arising from a Single Bacterial Cell Bottleneck

PubMed Central

Furi, Leonardo; Braccini, Tiziana; Manso, Ana Sousa; Pammolli, Andrea; Wang, Bo; Vivi, Antonio; Tassini, Maria; van Rooijen, Nico; Pozzi, Gianni; Ricci, Susanna; Andrew, Peter W.; Koedel, Uwe; Moxon, E. Richard; Oggioni, Marco R.

2014-01-01

The pathogenesis of bacteraemia after challenge with one million pneumococci of three isogenic variants was investigated. Sequential analyses of blood samples indicated that most episodes of bacteraemia were monoclonal events providing compelling evidence for a single bacterial cell bottleneck at the origin of invasive disease. With respect to host determinants, results identified novel properties of splenic macrophages and a role for neutrophils in early clearance of pneumococci. Concerning microbial factors, whole genome sequencing provided genetic evidence for the clonal origin of the bacteraemia and identified SNPs in distinct sub-units of F0/F1 ATPase in the majority of the ex vivo isolates. When compared to parental organisms of the inoculum, ex-vivo pneumococci with mutant alleles of the F0/F1 ATPase had acquired the capacity to grow at low pH at the cost of the capacity to grow at high pH. Although founded by a single cell, the genotypes of pneumococci in septicaemic mice indicate strong selective pressure for fitness, emphasising the within-host complexity of the pathogenesis of invasive disease. PMID:24651834

Integrated driver modelling considering state transition feature for individual adaptation of driver assistance systems

NASA Astrophysics Data System (ADS)

Raksincharoensak, Pongsathorn; Khaisongkram, Wathanyoo; Nagai, Masao; Shimosaka, Masamichi; Mori, Taketoshi; Sato, Tomomasa

2010-12-01

This paper describes the modelling of naturalistic driving behaviour in real-world traffic scenarios, based on driving data collected via an experimental automobile equipped with a continuous sensing drive recorder. This paper focuses on the longitudinal driving situations which are classified into five categories - car following, braking, free following, decelerating and stopping - and are referred to as driving states. Here, the model is assumed to be represented by a state flow diagram. Statistical machine learning of driver-vehicle-environment system model based on driving database is conducted by a discriminative modelling approach called boosting sequential labelling method.

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

Ripple gate drive circuit for fast operation of series connected IGBTs

DOEpatents

Rockot, Joseph H.; Murray, Thomas W.; Bass, Kevin C.

2005-09-20

A ripple gate drive circuit includes a plurality of transistors having their power terminals connected in series across an electrical potential. A plurality of control circuits, each associated with one of the transistors, is provided. Each control circuit is responsive to a control signal and an optical signal received from at least one other control circuit for controlling the conduction of electrical current through the power terminals of the associated transistor. The control circuits are responsive to a first state of the control circuit for causing each transistor in series to turn on sequentially and responsive to a second state of the control signal for causing each transistor in series to turn off sequentially.

Operations management tools to be applied for textile

NASA Astrophysics Data System (ADS)

Maralcan, A.; Ilhan, I.

2017-10-01

In this paper, basic concepts of process analysis such as flow time, inventory, bottleneck, labour cost and utilization are illustrated first. The effect of bottleneck on the results of a business are especially emphasized. In the next section, tools on productivity measurement; KPI (Key Performance Indicators) Tree, OEE (Overall Equipment Effectiveness) and Takt Time are introduced and exemplified. KPI tree is a diagram on which we can visualize all the variables of an operation which are driving financial results through cost and profit. OEE is a tool to measure a potential extra capacity of an equipment or an employee. Takt time is a tool to determine the process flow rate according to the customer demand. KPI tree is studied through the whole process while OEE is exemplified for a stenter frame machine which is the most important machine (and usually the bottleneck) and the most expensive investment in a finishing plant. Takt time is exemplified for the quality control department. Finally quality tools, six sigma, control charts and jidoka are introduced. Six sigma is a tool to measure process capability and by the way probability of a defect. Control chart is a powerful tool to monitor the process. The idea of jidoka (detect, stop and alert) is about alerting the people that there is a problem in the process.

Brain Dynamics in Predicting Driving Fatigue Using a Recurrent Self-Evolving Fuzzy Neural Network.

PubMed

Liu, Yu-Ting; Lin, Yang-Yin; Wu, Shang-Lin; Chuang, Chun-Hsiang; Lin, Chin-Teng

2016-02-01

This paper proposes a generalized prediction system called a recurrent self-evolving fuzzy neural network (RSEFNN) that employs an on-line gradient descent learning rule to address the electroencephalography (EEG) regression problem in brain dynamics for driving fatigue. The cognitive states of drivers significantly affect driving safety; in particular, fatigue driving, or drowsy driving, endangers both the individual and the public. For this reason, the development of brain-computer interfaces (BCIs) that can identify drowsy driving states is a crucial and urgent topic of study. Many EEG-based BCIs have been developed as artificial auxiliary systems for use in various practical applications because of the benefits of measuring EEG signals. In the literature, the efficacy of EEG-based BCIs in recognition tasks has been limited by low resolutions. The system proposed in this paper represents the first attempt to use the recurrent fuzzy neural network (RFNN) architecture to increase adaptability in realistic EEG applications to overcome this bottleneck. This paper further analyzes brain dynamics in a simulated car driving task in a virtual-reality environment. The proposed RSEFNN model is evaluated using the generalized cross-subject approach, and the results indicate that the RSEFNN is superior to competing models regardless of the use of recurrent or nonrecurrent structures.

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.

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

Sequential reconstruction of driving-forces from nonlinear nonstationary dynamics

NASA Astrophysics Data System (ADS)

Güntürkün, Ulaş

2010-07-01

This paper describes a functional analysis-based method for the estimation of driving-forces from nonlinear dynamic systems. The driving-forces account for the perturbation inputs induced by the external environment or the secular variations in the internal variables of the system. The proposed algorithm is applicable to the problems for which there is too little or no prior knowledge to build a rigorous mathematical model of the unknown dynamics. We derive the estimator conditioned on the differentiability of the unknown system’s mapping, and smoothness of the driving-force. The proposed algorithm is an adaptive sequential realization of the blind prediction error method, where the basic idea is to predict the observables, and retrieve the driving-force from the prediction error. Our realization of this idea is embodied by predicting the observables one-step into the future using a bank of echo state networks (ESN) in an online fashion, and then extracting the raw estimates from the prediction error and smoothing these estimates in two adaptive filtering stages. The adaptive nature of the algorithm enables to retrieve both slowly and rapidly varying driving-forces accurately, which are illustrated by simulations. Logistic and Moran-Ricker maps are studied in controlled experiments, exemplifying chaotic state and stochastic measurement models. The algorithm is also applied to the estimation of a driving-force from another nonlinear dynamic system that is stochastic in both state and measurement equations. The results are judged by the posterior Cramer-Rao lower bounds. The method is finally put into test on a real-world application; extracting sun’s magnetic flux from the sunspot time series.

Sea Fighter Analysis

DTIC Science & Technology

2007-02-01

which is used by the model to drive the normal activities of the crew (Figure C.1-2). These routines consist of a sequential list of high- level...separately. Figure C.1-3: Resources & Logic Sheet C.1.1.4 Scenario The scenario that is performed during a model run is a sequential list of all...were marked with a white fore and aft lineup stripe on both landing spots. Current Sea Fighter design does not provide a hangar; however, there

HIT'nDRIVE: patient-specific multidriver gene prioritization for precision oncology

PubMed Central

Hodzic, Ermin; Sauerwald, Thomas; Dao, Phuong; Wang, Kendric; Yeung, Jake; Anderson, Shawn; Vandin, Fabio; Haffari, Gholamreza; Collins, Colin C.; Sahinalp, S. Cenk

2017-01-01

Prioritizing molecular alterations that act as drivers of cancer remains a crucial bottleneck in therapeutic development. Here we introduce HIT'nDRIVE, a computational method that integrates genomic and transcriptomic data to identify a set of patient-specific, sequence-altered genes, with sufficient collective influence over dysregulated transcripts. HIT'nDRIVE aims to solve the “random walk facility location” (RWFL) problem in a gene (or protein) interaction network, which differs from the standard facility location problem by its use of an alternative distance measure: “multihitting time,” the expected length of the shortest random walk from any one of the set of sequence-altered genes to an expression-altered target gene. When applied to 2200 tumors from four major cancer types, HIT'nDRIVE revealed many potentially clinically actionable driver genes. We also demonstrated that it is possible to perform accurate phenotype prediction for tumor samples by only using HIT'nDRIVE-seeded driver gene modules from gene interaction networks. In addition, we identified a number of breast cancer subtype-specific driver modules that are associated with patients’ survival outcome. Furthermore, HIT'nDRIVE, when applied to a large panel of pan-cancer cell lines, accurately predicted drug efficacy using the driver genes and their seeded gene modules. Overall, HIT'nDRIVE may help clinicians contextualize massive multiomics data in therapeutic decision making, enabling widespread implementation of precision oncology. PMID:28768687

Nonlinear interferometry approach to photonic sequential logic

NASA Astrophysics Data System (ADS)

Mabuchi, Hideo

2011-10-01

Motivated by rapidly advancing capabilities for extensive nanoscale patterning of optical materials, I propose an approach to implementing photonic sequential logic that exploits circuit-scale phase coherence for efficient realizations of fundamental components such as a NAND-gate-with-fanout and a bistable latch. Kerr-nonlinear optical resonators are utilized in combination with interference effects to drive the binary logic. Quantum-optical input-output models are characterized numerically using design parameters that yield attojoule-scale energy separation between the latch states.

Design and evaluation of a hybrid storage system in HEP environment

NASA Astrophysics Data System (ADS)

Xu, Qi; Cheng, Yaodong; Chen, Gang

2017-10-01

Nowadays, the High Energy Physics experiments produce a large amount of data. These data are stored in mass storage systems which need to balance the cost, performance and manageability. In this paper, a hybrid storage system including SSDs (Solid-state Drive) and HDDs (Hard Disk Drive) is designed to accelerate data analysis and maintain a low cost. The performance of accessing files is a decisive factor for the HEP computing system. A new deployment model of Hybrid Storage System in High Energy Physics is proposed which is proved to have higher I/O performance. The detailed evaluation methods and the evaluations about SSD/HDD ratio, and the size of the logic block are also given. In all evaluations, sequential-read, sequential-write, random-read and random-write are all tested to get the comprehensive results. The results show the Hybrid Storage System has good performance in some fields such as accessing big files in HEP.

VLSI design of lossless frame recompression using multi-orientation prediction

NASA Astrophysics Data System (ADS)

Lee, Yu-Hsuan; You, Yi-Lun; Chen, Yi-Guo

2016-01-01

Pursuing an experience of high-end visual quality drives human to demand a higher display resolution and a higher frame rate. Hence, a lot of powerful coding tools are aggregated together in emerging video coding standards to improve coding efficiency. This also makes video coding standards suffer from two design challenges: heavy computation and tremendous memory bandwidth. The first issue can be properly solved by a careful hardware architecture design with advanced semiconductor processes. Nevertheless, the second one becomes a critical design bottleneck for a modern video coding system. In this article, a lossless frame recompression using multi-orientation prediction technique is proposed to overcome this bottleneck. This work is realised into a silicon chip with the technology of TSMC 0.18 µm CMOS process. Its encoding capability can reach full-HD (1920 × 1080)@48 fps. The chip power consumption is 17.31 mW@100 MHz. Core area and chip area are 0.83 × 0.83 mm2 and 1.20 × 1.20 mm2, respectively. Experiment results demonstrate that this work exhibits an outstanding performance on lossless compression ratio with a competitive hardware performance.

Bottlenecks drive temporal and spatial genetic changes in alpine caddisfly metapopulations.

PubMed

Shama, Lisa N S; Kubow, Karen B; Jokela, Jukka; Robinson, Christopher T

2011-09-27

Extinction and re-colonisation of local populations is common in ephemeral habitats such as temporary streams. In most cases, such population turnover leads to reduced genetic diversity within populations and increased genetic differentiation among populations due to stochastic founder events, genetic drift, and bottlenecks associated with re-colonisation. Here, we examined the spatio-temporal genetic structure of 8 alpine caddisfly populations inhabiting permanent and temporary streams from four valleys in two regions of the Swiss Alps in years before and after a major stream drying event, the European heat wave in summer 2003. We found that population turnover after 2003 led to a loss of allelic richness and gene diversity but not to significant changes in observed heterozygosity. Within all valleys, permanent and temporary streams in any given year were not differentiated, suggesting considerable gene flow and admixture between streams with differing hydroperiods. Large changes in allele frequencies after 2003 resulted in a substantial increase in genetic differentiation among valleys within one to two years (1-2 generations) driven primarily by drift and immigration. Signatures of genetic bottlenecks were detected in all 8 populations after 2003 using the M-ratio method, but in no populations when using a heterozygosity excess method, indicating differential sensitivity of bottleneck detection methods. We conclude that genetic differentiation among A. uncatus populations changed markedly both temporally and spatially in response to the extreme climate event in 2003. Our results highlight the magnitude of temporal population genetic changes in response to extreme events. More specifically, our results show that extreme events can cause rapid genetic divergence in metapopulations. Further studies are needed to determine if recovery from this perturbation through gradual mixing of diverged populations by migration and gene flow leads to the pre-climate event state, or whether the observed changes represent a new genetic equilibrium.

Evolutionary bottlenecks in brackish water habitats drive the colonization of fresh water by stingrays.

PubMed

Kirchhoff, K N; Hauffe, T; Stelbrink, B; Albrecht, C; Wilke, T

2017-08-01

Species richness in freshwater bony fishes depends on two main processes: the transition into and the diversification within freshwater habitats. In contrast to bony fishes, only few cartilaginous fishes, mostly stingrays (Myliobatoidei), were able to colonize fresh water. Respective transition processes have been mainly assessed from a physiological and morphological perspective, indicating that the freshwater lifestyle is strongly limited by the ability to perform osmoregulatory adaptations. However, the transition history and the effect of physiological constraints on the diversification in stingrays remain poorly understood. Herein, we estimated the geographic pathways of freshwater colonization and inferred the mode of habitat transitions. Further, we assessed habitat-related speciation rates in a time-calibrated phylogenetic framework to understand factors driving the transition of stingrays into and the diversification within fresh water. Using South American and Southeast Asian freshwater taxa as model organisms, we found one independent freshwater colonization event by stingrays in South America and at least three in Southeast Asia. We revealed that vicariant processes most likely caused freshwater transition during the time of major marine incursions. The habitat transition rates indicate that brackish water species switch preferably back into marine than forth into freshwater habitats. Moreover, our results showed significantly lower diversification rates in brackish water lineages, whereas freshwater and marine lineages exhibit similar rates. Thus, brackish water habitats may have functioned as evolutionary bottlenecks for the colonization of fresh water by stingrays, probably because of the higher variability of environmental conditions in brackish water. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

Multi-function magnetic jack control drive mechanism

DOEpatents

Bollinger, L.R.; Crawford, D.C.

1983-10-06

A multi-function magnetic jack control drive mechanism for controlling a nuclear reactor is provided. The mechanism includes an elongate pressure housing in which a plurality of closely spaced drive rods are located. Each drive rod is connected to a rod which is insertable in the reactor core. An electromechanical stationary latch device is provided which is actuatable to hold each drive rod stationary with respect to the pressure housing. An electromechanical movable latch device is also provided for each one of the drive rods. Each movable latch device is provided with a base and is actuatable to hold a respective drive rod stationary with respect to the base. An electromechanical lift device is further provided for each base which is actuatable for moving a respective base longitudinally along the pressure housing. In this manner, one or more drive rods can be moved in the pressure housing by sequentially and repetitively operating the electromechanical devices. Preferably, each latch device includes a pair of opposed latches which grip teeth located on the respective drive rod. Two, three, or four drive rods can be located symmetrically about the longitudinal axis of the pressure housing.

Multi-function magnetic jack control drive mechanism

DOEpatents

Bollinger, Lawrence R.; Crawford, Donald C.

1986-01-01

A multi-function magnetic jack control drive mechanism for controlling a nuclear reactor is provided. The mechanism includes an elongate pressure housing in which a plurality of closely spaced drive rods are located. Each drive rod is connected to a rod which is insertable in the reactor core. An electromechanical stationary latch device is provided which is actuatable to hold each drive rod stationary with respect to the pressure housing. An electromechanical movable latch device is also provided for each one of the drive rods. Each movable latch device is provided with a base and is actuatable to hold a respective drive rod stationary with respect to the base. An electromechanical lift device is further provided for each base which is actuatable for moving a respective base longitudinally along the pressure housing. In this manner, one or more drive rods can be moved in the pressure housing by sequentially and repetitively operating the electromechanical devices. Preferably, each latch device includes a pair of opposed latches which grip teeth located on the respective drive rod. Two, three, or four drive rods can be located symmetrically about the longitudinal axis of the pressure housing.

Implementation of Temperature Sequential Controller on Variable Speed Drive

NASA Astrophysics Data System (ADS)

Cheong, Z. X.; Barsoum, N. N.

2008-10-01

There are many pump and motor installations with quite extensive speed variation, such as Sago conveyor, heating, ventilation and air conditioning (HVAC) and water pumping system. A common solution for these applications is to run several fixed speed motors in parallel, with flow control accomplish by turning the motors on and off. This type of control method causes high in-rush current, and adds a risk of damage caused by pressure transients. This paper explains the design and implementation of a temperature speed control system for use in industrial and commercial sectors. Advanced temperature speed control can be achieved by using ABB ACS800 variable speed drive-direct torque sequential control macro, programmable logic controller and temperature transmitter. The principle of direct torque sequential control macro (DTC-SC) is based on the control of torque and flux utilizing the stator flux field orientation over seven preset constant speed. As a result of continuous comparison of ambient temperature to the references temperatures; electromagnetic torque response is particularly fast to the motor state and it is able maintain constant speeds. Experimental tests have been carried out by using ABB ACS800-U1-0003-2, to validate the effectiveness and dynamic respond of ABB ACS800 against temperature variation, loads, and mechanical shocks.

Process Model of A Fusion Fuel Recovery System for a Direct Drive IFE Power Reactor

NASA Astrophysics Data System (ADS)

Natta, Saswathi; Aristova, Maria; Gentile, Charles

2008-11-01

A task has been initiated to develop a detailed representative model for the fuel recovery system (FRS) in the prospective direct drive inertial fusion energy (IFE) reactor. As part of the conceptual design phase of the project, a chemical process model is developed in order to observe the interaction of system components. This process model is developed using FEMLAB Multiphysics software with the corresponding chemical engineering module (CEM). Initially, the reactants, system structure, and processes are defined using known chemical species of the target chamber exhaust. Each step within the Fuel recovery system is modeled compartmentally and then merged to form the closed loop fuel recovery system. The output, which includes physical properties and chemical content of the products, is analyzed after each step of the system to determine the most efficient and productive system parameters. This will serve to attenuate possible bottlenecks in the system. This modeling evaluation is instrumental in optimizing and closing the fusion fuel cycle in a direct drive IFE power reactor. The results of the modeling are presented in this paper.

Analytical investigation of the faster-is-slower effect with a simplified phenomenological model

NASA Astrophysics Data System (ADS)

Suzuno, K.; Tomoeda, A.; Ueyama, D.

2013-11-01

We investigate the mechanism of the phenomenon called the “faster-is-slower”effect in pedestrian flow studies analytically with a simplified phenomenological model. It is well known that the flow rate is maximized at a certain strength of the driving force in simulations using the social force model when we consider the discharge of self-driven particles through a bottleneck. In this study, we propose a phenomenological and analytical model based on a mechanics-based modeling to reveal the mechanism of the phenomenon. We show that our reduced system, with only a few degrees of freedom, still has similar properties to the original many-particle system and that the effect comes from the competition between the driving force and the nonlinear friction from the model. Moreover, we predict the parameter dependences on the effect from our model qualitatively, and they are confirmed numerically by using the social force model.

Development of a drive system for a sequential space camera

NASA Technical Reports Server (NTRS)

Sharpsteen, J. T.; Solheim, C. D.; Stoap, L. J.

1976-01-01

Breadboard models of single and dual motor drives for the shutter, claw and magazine of a space camera system were designed and tested. The single motor technique utilizes a single electronically commutated motor to drive the claw and shutter without resorting to a solenoid actuated clutch for pulse operation. Shutter speed is established by a combination of the cinemode speed and the opening of the conventional DAC two piece shutter. Pulse mode operation is obtained by applying power at a fixed clock rate and removing power at an appropriate point in the mechanical cycle such that the motor comes to rest by system friction. The dual motor approach utilizes a stepper motor to drive the shutter and an electronically commutated dc motor to drive the claw and magazine functions. The motors are synchronized electronically.

Development of a drive system for a sequential space camera

NASA Technical Reports Server (NTRS)

Sharpsteen, J. T.; Solheim, C. D.; Stoap, L. J.

1976-01-01

An electronically commutated dc motor is reported for driving the camera claw and magazine, and a stepper motor is described for driving the shutter with the two motors synchronized electrically. Subsequent tests on the breadboard positively proved the concept, but further development beyond this study should be done. The breadboard testing also established that the electronically commutated motor can control speed over a wide dynamic range, and has a high torque capability for accelerating loads. This performance suggested the possibility of eliminating the clutch from the system while retaining all of the other mechanical features of the DAC, if the requirement for independent shutter speeds and frame rates can be removed. Therefore, as a final step in the study, the breadboard shutter and shutter drive were returned to the original DAC configuration, while retaining the brushless dc motor drive.

Principles of cell-free genetic circuit assembly.

PubMed

Noireaux, Vincent; Bar-Ziv, Roy; Libchaber, Albert

2003-10-28

Cell-free genetic circuit elements were constructed in a transcription-translation extract. We engineered transcriptional activation and repression cascades, in which the protein product of each stage is the input required to drive or block the following stage. Although we can find regions of linear response for single stages, cascading to subsequent stages requires working in nonlinear regimes. Substantial time delays and dramatic decreases in output production are incurred with each additional stage because of a bottleneck at the translation machinery. Faster turnover of RNA message can relieve competition between genes and stabilize output against variations in input and parameters.

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.

A suppression hierarchy among competing motor programs drives sequential grooming in Drosophila

PubMed Central

Seeds, Andrew M; Ravbar, Primoz; Chung, Phuong; Hampel, Stefanie; Midgley, Frank M; Mensh, Brett D; Simpson, Julie H

2014-01-01

Motor sequences are formed through the serial execution of different movements, but how nervous systems implement this process remains largely unknown. We determined the organizational principles governing how dirty fruit flies groom their bodies with sequential movements. Using genetically targeted activation of neural subsets, we drove distinct motor programs that clean individual body parts. This enabled competition experiments revealing that the motor programs are organized into a suppression hierarchy; motor programs that occur first suppress those that occur later. Cleaning one body part reduces the sensory drive to its motor program, which relieves suppression of the next movement, allowing the grooming sequence to progress down the hierarchy. A model featuring independently evoked cleaning movements activated in parallel, but selected serially through hierarchical suppression, was successful in reproducing the grooming sequence. This provides the first example of an innate motor sequence implemented by the prevailing model for generating human action sequences. DOI: http://dx.doi.org/10.7554/eLife.02951.001 PMID:25139955

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

An Experimental Approach for Restoration of Salmon River Ecosystems

NASA Astrophysics Data System (ADS)

Stanford, J. A.

2005-05-01

River ecosystem theory predicts that dynamic, nonlinear physical and biological processes linking water, heat and materials (biota, sediment, plant-growth nutrients) flux and retention to fluvial landscape change in a habitat mosaic context drive salmon life histories and productivity in freshwater. Multidisciplinary studies and cross-site comparisons within a network of pristine salmon river observatories around the north Pacific Rim support these predictions. Billions of dollars have been spent on salmon-river restoration worldwide to little avail, mainly because salmon biology, rather than ecosystem process boundaries and bottlenecks, is driving restoration goals. I argue that entire river catchment restoration, in relation to these dynamic processes and bottlenecks and also coherent with the estuarine and marine implications of salmon life history parameters, is the only possibility for sustaining or restoring natural productivity and life history (genetic) diversity in salmon rivers. This can be done only in a few places owing to the continual press of human demands on river ecosystems, the morass of legal challenges to proactive salmon river restoration strategies and insufficient understanding of freshwater and marine linkages. The Elwha and Yakima Rivers in Washington, among a few others that I will name, offer real opportunities to restore entire watersheds for wild salmon. These restorations should be viewed as experimental manipulations in which outcomes may be evaluated against norms measured in the salmon river observatory network. Bias from hatcheries and harvest, among other anthropogenic interferences, must be eliminated for such experiments to be evaluated in light of contemporary river ecosystem theory. And, a much more synthetic understanding of freshwater and marine linkages must be forthcoming in concert with a much more robust general theory of river restoration.

Embedded optical interconnect technology in data storage systems

NASA Astrophysics Data System (ADS)

Pitwon, Richard C. A.; Hopkins, Ken; Milward, Dave; Muggeridge, Malcolm

2010-05-01

As both data storage interconnect speeds increase and form factors in hard disk drive technologies continue to shrink, the density of printed channels on the storage array midplane goes up. The dominant interconnect protocol on storage array midplanes is expected to increase to 12 Gb/s by 2012 thereby exacerbating the performance bottleneck in future digital data storage systems. The design challenges inherent to modern data storage systems are discussed and an embedded optical infrastructure proposed to mitigate this bottleneck. The proposed solution is based on the deployment of an electro-optical printed circuit board and active interconnect technology. The connection architecture adopted would allow for electronic line cards with active optical edge connectors to be plugged into and unplugged from a passive electro-optical midplane with embedded polymeric waveguides. A demonstration platform has been developed to assess the viability of embedded electro-optical midplane technology in dense data storage systems and successfully demonstrated at 10.3 Gb/s. Active connectors incorporate optical transceiver interfaces operating at 850 nm and are connected in an in-plane coupling configuration to the embedded waveguides in the midplane. In addition a novel method of passively aligning and assembling passive optical devices to embedded polymer waveguide arrays has also been demonstrated.

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.

Singular spectrum and singular entropy used in signal processing of NC table

NASA Astrophysics Data System (ADS)

Wang, Linhong; He, Yiwen

2011-12-01

NC (numerical control) table is a complex dynamic system. The dynamic characteristics caused by backlash, friction and elastic deformation among each component are so complex that they have become the bottleneck of enhancing the positioning accuracy, tracking accuracy and dynamic behavior of NC table. This paper collects vibration acceleration signals from NC table, analyzes the signals with SVD (singular value decomposition) method, acquires the singular spectrum and calculates the singular entropy of the signals. The signal characteristics and their regulations of NC table are revealed via the characteristic quantities such as singular spectrum, singular entropy etc. The steep degrees of singular spectrums can be used to discriminate complex degrees of signals. The results show that the signals in direction of driving axes are the simplest and the signals in perpendicular direction are the most complex. The singular entropy values can be used to study the indetermination of signals. The results show that the signals of NC table are not simple signal nor white noise, the entropy values in direction of driving axe are lower, the entropy values increase along with the increment of driving speed and the entropy values at the abnormal working conditions such as resonance or creeping etc decrease obviously.

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.

Learning multiple variable-speed sequences in striatum via cortical tutoring.

PubMed

Murray, James M; Escola, G Sean

2017-05-08

Sparse, sequential patterns of neural activity have been observed in numerous brain areas during timekeeping and motor sequence tasks. Inspired by such observations, we construct a model of the striatum, an all-inhibitory circuit where sequential activity patterns are prominent, addressing the following key challenges: (i) obtaining control over temporal rescaling of the sequence speed, with the ability to generalize to new speeds; (ii) facilitating flexible expression of distinct sequences via selective activation, concatenation, and recycling of specific subsequences; and (iii) enabling the biologically plausible learning of sequences, consistent with the decoupling of learning and execution suggested by lesion studies showing that cortical circuits are necessary for learning, but that subcortical circuits are sufficient to drive learned behaviors. The same mechanisms that we describe can also be applied to circuits with both excitatory and inhibitory populations, and hence may underlie general features of sequential neural activity pattern generation in the brain.

A sequential EMT-MET mechanism drives the differentiation of human embryonic stem cells towards hepatocytes.

PubMed

Li, Qiuhong; Hutchins, Andrew P; Chen, Yong; Li, Shengbiao; Shan, Yongli; Liao, Baojian; Zheng, Dejin; Shi, Xi; Li, Yinxiong; Chan, Wai-Yee; Pan, Guangjin; Wei, Shicheng; Shu, Xiaodong; Pei, Duanqing

2017-05-03

Reprogramming has been shown to involve EMT-MET; however, its role in cell differentiation is unclear. We report here that in vitro differentiation of hESCs to hepatic lineage undergoes a sequential EMT-MET with an obligatory intermediate mesenchymal phase. Gene expression analysis reveals that Activin A-induced formation of definitive endoderm (DE) accompanies a synchronous EMT mediated by autocrine TGFβ signalling followed by a MET process. Pharmacological inhibition of TGFβ signalling blocks the EMT as well as DE formation. We then identify SNAI1 as the key EMT transcriptional factor required for the specification of DE. Genetic ablation of SNAI1 in hESCs does not affect the maintenance of pluripotency or neural differentiation, but completely disrupts the formation of DE. These results reveal a critical mesenchymal phase during the acquisition of DE, highlighting a role for sequential EMT-METs in both differentiation and reprogramming.

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.

Inferring human population size and separation history from multiple genome sequences.

PubMed

Schiffels, Stephan; Durbin, Richard

2014-08-01

The availability of complete human genome sequences from populations across the world has given rise to new population genetic inference methods that explicitly model ancestral relationships under recombination and mutation. So far, application of these methods to evolutionary history more recent than 20,000-30,000 years ago and to population separations has been limited. Here we present a new method that overcomes these shortcomings. The multiple sequentially Markovian coalescent (MSMC) analyzes the observed pattern of mutations in multiple individuals, focusing on the first coalescence between any two individuals. Results from applying MSMC to genome sequences from nine populations across the world suggest that the genetic separation of non-African ancestors from African Yoruban ancestors started long before 50,000 years ago and give information about human population history as recent as 2,000 years ago, including the bottleneck in the peopling of the Americas and separations within Africa, East Asia and Europe.

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.

Economical launching and accelerating control strategy for a single-shaft parallel hybrid electric bus

NASA Astrophysics Data System (ADS)

Yang, Chao; Song, Jian; Li, Liang; Li, Shengbo; Cao, Dongpu

2016-08-01

This paper presents an economical launching and accelerating mode, including four ordered phases: pure electrical driving, clutch engagement and engine start-up, engine active charging, and engine driving, which can be fit for the alternating conditions and improve the fuel economy of hybrid electric bus (HEB) during typical city-bus driving scenarios. By utilizing the fast response feature of electric motor (EM), an adaptive controller for EM is designed to realize the power demand during the pure electrical driving mode, the engine starting mode and the engine active charging mode. Concurrently, the smoothness issue induced by the sequential mode transitions is solved with a coordinated control logic for engine, EM and clutch. Simulation and experimental results show that the proposed launching and accelerating mode and its control methods are effective in improving the fuel economy and ensure the drivability during the fast transition between the operation modes of HEB.

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.

Bottlenecks of Motion Processing during a Visual Glance: The Leaky Flask Model

PubMed Central

Öğmen, Haluk; Ekiz, Onur; Huynh, Duong; Bedell, Harold E.; Tripathy, Srimant P.

2013-01-01

Where do the bottlenecks for information and attention lie when our visual system processes incoming stimuli? The human visual system encodes the incoming stimulus and transfers its contents into three major memory systems with increasing time scales, viz., sensory (or iconic) memory, visual short-term memory (VSTM), and long-term memory (LTM). It is commonly believed that the major bottleneck of information processing resides in VSTM. In contrast to this view, we show major bottlenecks for motion processing prior to VSTM. In the first experiment, we examined bottlenecks at the stimulus encoding stage through a partial-report technique by delivering the cue immediately at the end of the stimulus presentation. In the second experiment, we varied the cue delay to investigate sensory memory and VSTM. Performance decayed exponentially as a function of cue delay and we used the time-constant of the exponential-decay to demarcate sensory memory from VSTM. We then decomposed performance in terms of quality and quantity measures to analyze bottlenecks along these dimensions. In terms of the quality of information, two thirds to three quarters of the motion-processing bottleneck occurs in stimulus encoding rather than memory stages. In terms of the quantity of information, the motion-processing bottleneck is distributed, with the stimulus-encoding stage accounting for one third of the bottleneck. The bottleneck for the stimulus-encoding stage is dominated by the selection compared to the filtering function of attention. We also found that the filtering function of attention is operating mainly at the sensory memory stage in a specific manner, i.e., influencing only quantity and sparing quality. These results provide a novel and more complete understanding of information processing and storage bottlenecks for motion processing. PMID:24391806

Bottlenecks of motion processing during a visual glance: the leaky flask model.

PubMed

Öğmen, Haluk; Ekiz, Onur; Huynh, Duong; Bedell, Harold E; Tripathy, Srimant P

2013-01-01

Where do the bottlenecks for information and attention lie when our visual system processes incoming stimuli? The human visual system encodes the incoming stimulus and transfers its contents into three major memory systems with increasing time scales, viz., sensory (or iconic) memory, visual short-term memory (VSTM), and long-term memory (LTM). It is commonly believed that the major bottleneck of information processing resides in VSTM. In contrast to this view, we show major bottlenecks for motion processing prior to VSTM. In the first experiment, we examined bottlenecks at the stimulus encoding stage through a partial-report technique by delivering the cue immediately at the end of the stimulus presentation. In the second experiment, we varied the cue delay to investigate sensory memory and VSTM. Performance decayed exponentially as a function of cue delay and we used the time-constant of the exponential-decay to demarcate sensory memory from VSTM. We then decomposed performance in terms of quality and quantity measures to analyze bottlenecks along these dimensions. In terms of the quality of information, two thirds to three quarters of the motion-processing bottleneck occurs in stimulus encoding rather than memory stages. In terms of the quantity of information, the motion-processing bottleneck is distributed, with the stimulus-encoding stage accounting for one third of the bottleneck. The bottleneck for the stimulus-encoding stage is dominated by the selection compared to the filtering function of attention. We also found that the filtering function of attention is operating mainly at the sensory memory stage in a specific manner, i.e., influencing only quantity and sparing quality. These results provide a novel and more complete understanding of information processing and storage bottlenecks for motion processing.

Comparison of historical bottleneck effects and genetic consequences of re-introduction in a critically endangered island passerine.

PubMed

Bristol, Rachel M; Tucker, Rachel; Dawson, Deborah A; Horsburgh, Gavin; Prys-Jones, Robert P; Frantz, Alain C; Krupa, Andy; Shah, Nirmal J; Burke, Terry; Groombridge, Jim J

2013-09-01

Re-introduction is an important tool for recovering endangered species; however, the magnitude of genetic consequences for re-introduced populations remains largely unknown, in particular the relative impacts of historical population bottlenecks compared to those induced by conservation management. We characterize 14 microsatellite loci developed for the Seychelles paradise flycatcher and use them to quantify temporal and spatial measures of genetic variation across a 134-year time frame encompassing a historical bottleneck that reduced the species to ~28 individuals in the 1960s, through the initial stages of recovery and across a second contemporary conservation-introduction-induced bottleneck. We then evaluate the relative impacts of the two bottlenecks, and finally apply our findings to inform broader re-introduction strategy. We find a temporal trend of significant decrease in standard measures of genetic diversity across the historical bottleneck, but only a nonsignificant downward trend in number of alleles across the contemporary bottleneck. However, accounting for the different timescales of the two bottlenecks (~40 historical generations versus <1 contemporary generation), the loss of genetic diversity per generation is greater across the contemporary bottleneck. Historically, the flycatcher population was genetically structured; however, extinction on four of five islands has resulted in a homogeneous contemporary population. We conclude that severe historical bottlenecks can leave a large footprint in terms of sheer quantity of genetic diversity lost. However, severely depleted genetic diversity does not render a species immune to further genetic erosion upon re-introduction. In some cases, the loss of genetic diversity per generation can, initially at least, be greater across re-introduction-induced bottlenecks. © 2013 John Wiley & Sons Ltd.

Improving Initiation and Tracking of Research Projects at an Academic Health Center: A Case Study.

PubMed

Schmidt, Susanne; Goros, Martin; Parsons, Helen M; Saygin, Can; Wan, Hung-Da; Shireman, Paula K; Gelfond, Jonathan A L

2017-09-01

Research service cores at academic health centers are important in driving translational advancements. Specifically, biostatistics and research design units provide services and training in data analytics, biostatistics, and study design. However, the increasing demand and complexity of assigning appropriate personnel to time-sensitive projects strains existing resources, potentially decreasing productivity and increasing costs. Improving processes for project initiation, assigning appropriate personnel, and tracking time-sensitive projects can eliminate bottlenecks and utilize resources more efficiently. In this case study, we describe our application of lean six sigma principles to our biostatistics unit to establish a systematic continual process improvement cycle for intake, allocation, and tracking of research design and data analysis projects. The define, measure, analyze, improve, and control methodology was used to guide the process improvement. Our goal was to assess and improve the efficiency and effectiveness of operations by objectively measuring outcomes, automating processes, and reducing bottlenecks. As a result, we developed a web-based dashboard application to capture, track, categorize, streamline, and automate project flow. Our workflow system resulted in improved transparency, efficiency, and workload allocation. Using the dashboard application, we reduced the average study intake time from 18 to 6 days, a 66.7% reduction over 12 months (January to December 2015).

Driving delivery vehicles with ultrasound ☆

PubMed Central

Ferrara, Katherine W.

2009-01-01

Therapeutic applications of ultrasound have been considered for over 40 years, with the mild hyperthermia and associated increases in perfusion produced by ultrasound harnessed in many of the earliest treatments. More recently, new mechanisms for ultrasound-based or ultrasound-enhanced therapies have been described, and there is now great momentum and enthusiasm for the clinical translation of these techniques. This dedicated issue of Advanced Drug Delivery Reviews, entitled “Ultrasound for Drug and Gene Delivery,” addresses the mechanisms by which ultrasound can enhance local drug and gene delivery and the applications that have been demonstrated at this time. In this commentary, the identified mechanisms, delivery vehicles, applications and current bottlenecks for translation of these techniques are summarized. PMID:18479775

On-chip phase-change photonic memory and computing

NASA Astrophysics Data System (ADS)

Cheng, Zengguang; Ríos, Carlos; Youngblood, Nathan; Wright, C. David; Pernice, Wolfram H. P.; Bhaskaran, Harish

2017-08-01

The use of photonics in computing is a hot topic of interest, driven by the need for ever-increasing speed along with reduced power consumption. In existing computing architectures, photonic data storage would dramatically improve the performance by reducing latencies associated with electrical memories. At the same time, the rise of `big data' and `deep learning' is driving the quest for non-von Neumann and brain-inspired computing paradigms. To succeed in both aspects, we have demonstrated non-volatile multi-level photonic memory avoiding the von Neumann bottleneck in the existing computing paradigm and a photonic synapse resembling the biological synapses for brain-inspired computing using phase-change materials (Ge2Sb2Te5).

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.

Exploring Teachers' Read-Aloud Book Selections: What Drives the Decision

ERIC Educational Resources Information Center

Ross, Rachael L.

2017-01-01

Reading aloud is a common classroom practice that has many cognitive and affective benefits for students. Early childhood teachers conduct read-aloud events in classrooms across the country on a daily basis. A read-aloud event could not occur without the intentional selection of a book. This exploratory, sequential mixed method study explored the…

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.

Optimal scan strategy for mega-pixel and kilo-gray-level OLED-on-silicon microdisplay.

PubMed

Ji, Yuan; Ran, Feng; Ji, Weigui; Xu, Meihua; Chen, Zhangjing; Jiang, Yuxi; Shen, Weixin

2012-06-10

The digital pixel driving scheme makes the organic light-emitting diode (OLED) microdisplays more immune to the pixel luminance variations and simplifies the circuit architecture and design flow compared to the analog pixel driving scheme. Additionally, it is easily applied in full digital systems. However, the data bottleneck becomes a notable problem as the number of pixels and gray levels grow dramatically. This paper will discuss the digital driving ability to achieve kilogray-levels for megapixel displays. The optimal scan strategy is proposed for creating ultra high gray levels and increasing light efficiency and contrast ratio. Two correction schemes are discussed to improve the gray level linearity. A 1280×1024×3 OLED-on-silicon microdisplay, with 4096 gray levels, is designed based on the optimal scan strategy. The circuit driver is integrated in the silicon backplane chip in the 0.35 μm 3.3 V-6 V dual voltage one polysilicon layer, four metal layers (1P4M) complementary metal-oxide semiconductor (CMOS) process with custom top metal. The design aspects of the optimal scan controller are also discussed. The test results show the gray level linearity of the correction schemes for the optimal scan strategy is acceptable by the human eye.

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...

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.

Driving behavior recognition using EEG data from a simulated car-following experiment.

PubMed

Yang, Liu; Ma, Rui; Zhang, H Michael; Guan, Wei; Jiang, Shixiong

2018-07-01

Driving behavior recognition is the foundation of driver assistance systems, with potential applications in automated driving systems. Most prevailing studies have used subjective questionnaire data and objective driving data to classify driving behaviors, while few studies have used physiological signals such as electroencephalography (EEG) to gather data. To bridge this gap, this paper proposes a two-layer learning method for driving behavior recognition using EEG data. A simulated car-following driving experiment was designed and conducted to simultaneously collect data on the driving behaviors and EEG data of drivers. The proposed learning method consists of two layers. In Layer I, two-dimensional driving behavior features representing driving style and stability were selected and extracted from raw driving behavior data using K-means and support vector machine recursive feature elimination. Five groups of driving behaviors were classified based on these two-dimensional driving behavior features. In Layer II, the classification results from Layer I were utilized as inputs to generate a k-Nearest-Neighbor classifier identifying driving behavior groups using EEG data. Using independent component analysis, a fast Fourier transformation, and linear discriminant analysis sequentially, the raw EEG signals were processed to extract two core EEG features. Classifier performance was enhanced using the adaptive synthetic sampling approach. A leave-one-subject-out cross validation was conducted. The results showed that the average classification accuracy for all tested traffic states was 69.5% and the highest accuracy reached 83.5%, suggesting a significant correlation between EEG patterns and car-following behavior. Copyright © 2017 Elsevier Ltd. All rights reserved.

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.

Drug delivery into the cochlear apex: Improved control to sequentially affect finely spaced regions along the entire length of the cochlear spiral.

PubMed

Lichtenhan, J T; Hartsock, J; Dornhoffer, J R; Donovan, K M; Salt, A N

2016-11-01

Administering pharmaceuticals to the scala tympani of the inner ear is a common approach to study cochlear physiology and mechanics. We present here a novel method for in vivo drug delivery in a controlled manner to sealed ears. Injections of ototoxic solutions were applied from a pipette sealed into a fenestra in the cochlear apex, progressively driving solutions along the length of scala tympani toward the cochlear aqueduct at the base. Drugs can be delivered rapidly or slowly. In this report we focus on slow delivery in which the injection rate is automatically adjusted to account for varying cross sectional area of the scala tympani, therefore driving a solution front at uniform rate. Objective measurements originating from finely spaced, low- to high-characteristic cochlear frequency places were sequentially affected. Comparison with existing methods(s): Controlled administration of pharmaceuticals into the cochlear apex overcomes a number of serious limitations of previously established methods such as cochlear perfusions with an injection pipette in the cochlear base: The drug concentration achieved is more precisely controlled, drug concentrations remain in scala tympani and are not rapidly washed out by cerebrospinal fluid flow, and the entire length of the cochlear spiral can be treated quickly or slowly with time. Controlled administration of solutions into the cochlear apex can be a powerful approach to sequentially effect objective measurements originating from finely spaced cochlear regions and allows, for the first time, the spatial origin of CAPs to be objectively defined. Copyright © 2016 Elsevier B.V. All rights reserved.

Drug delivery into the cochlear apex: Improved control to sequentially affect finely spaced regions along the entire length of the cochlear spiral

PubMed Central

Lichtenhan, JT; Hartsock, J; Dornhoffer, JR; Donovan, KM; Salt, AN

2016-01-01

Background Administering pharmaceuticals to the scala tympani of the inner ear is a common approach to study cochlear physiology and mechanics. We present here a novel method for in vivo drug delivery in a controlled manner to sealed ears. New method Injections of ototoxic solutions were applied from a pipette sealed into a fenestra in the cochlear apex, progressively driving solutions along the length of scala tympani toward the cochlear aqueduct at the base. Drugs can be delivered rapidly or slowly. In this report we focus on slow delivery in which the injection rate is automatically adjusted to account for varying cross sectional area of the scala tympani, therefore driving a solution front at uniform rate. Results Objective measurements originating from finely spaced, low- to high-characteristic cochlear frequency places were sequentially affected. Comparison with existing methods(s): Controlled administration of pharmaceuticals into the cochlear apex overcomes a number of serious limitations of previously established methods such as cochlear perfusions with an injection pipette in the cochlear base: The drug concentration achieved is more precisely controlled, drug concentrations remain in scala tympani and are not rapidly washed out by cerebrospinal fluid flow, and the entire length of the cochlear spiral can be treated quickly or slowly with time. Conclusions Controlled administration of solutions into the cochlear apex can be a powerful approach to sequentially effect objective measurements originating from finely spaced cochlear regions and allows, for the first time, the spatial origin of CAPs to be objectively defined. PMID:27506463

Impaired-driving prevalence among US high school students: associations with substance use and risky driving behaviors.

PubMed

Li, Kaigang; Simons-Morton, Bruce G; Hingson, Ralph

2013-11-01

We examined the prevalence of impaired driving among US high school students and associations with substance use and risky driving behavior. We assessed driving while alcohol or drug impaired (DWI) and riding with alcohol- or drug-impaired drivers (RWI) in a nationally representative sample of 11th-grade US high school students (n = 2431). We examined associations with drinking and binge drinking, illicit drug use, risky driving, and demographic factors using multivariate sequential logistic regression analysis. Thirteen percent of 11th-grade students reported DWI at least 1 of the past 30 days, and 24% reported RWI at least once in the past year. Risky driving was positively associated with DWI (odds ratio [OR] = 1.25; P < .001) and RWI (OR = 1.09; P < .05), controlling for binge drinking (DWI: OR = 3.17; P < .01; RWI: OR = 6.12; P < .001) and illicit drug use (DWI: OR = 5.91; P < .001; RWI: OR = 2.29; P = .05). DWI was higher for adolescents who drove after midnight (OR = 15.7), drove while sleepy or drowsy (OR = 8.6), read text messages (OR = 11.8), sent text messages (OR = 5.0), and made cell phone calls (OR = 3.2) while driving. Our findings suggest the need for comprehensive approaches to the prevention of DWI, RWI, and other risky driving behavior.

Microprocessor control of photovoltaic systems

NASA Technical Reports Server (NTRS)

Millner, A. R.; Kaufman, D. L.

1984-01-01

The present low power CMOS microprocessor controller for photovoltaic power systems possesses three programs, which are respectively intended for (1) conventional battery-charging systems with state-of-charge estimation and sequential shedding of subarrays and loads, (2) maximum power-controlled battery-charging systems, and (3) variable speed dc motor drives. Attention is presently given to the development of this terrestrial equipment for spacecraft use.

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.

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

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

Towards building high performance medical image management system for clinical trials

NASA Astrophysics Data System (ADS)

Wang, Fusheng; Lee, Rubao; Zhang, Xiaodong; Saltz, Joel

2011-03-01

Medical image based biomarkers are being established for therapeutic cancer clinical trials, where image assessment is among the essential tasks. Large scale image assessment is often performed by a large group of experts by retrieving images from a centralized image repository to workstations to markup and annotate images. In such environment, it is critical to provide a high performance image management system that supports efficient concurrent image retrievals in a distributed environment. There are several major challenges: high throughput of large scale image data over the Internet from the server for multiple concurrent client users, efficient communication protocols for transporting data, and effective management of versioning of data for audit trails. We study the major bottlenecks for such a system, propose and evaluate a solution by using a hybrid image storage with solid state drives and hard disk drives, RESTfulWeb Services based protocols for exchanging image data, and a database based versioning scheme for efficient archive of image revision history. Our experiments show promising results of our methods, and our work provides a guideline for building enterprise level high performance medical image management systems.

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

Fully utilizing high power diode lasers by synergizing diode laser light sources and beam shaping micro-optics

NASA Astrophysics Data System (ADS)

Fan, Yingmin; Wang, Jingwei; Cai, Lei; Mitra, Thomas; Hauschild, Dirk; Zah, Chung-En; Liu, Xingsheng

2018-02-01

High power diode lasers (HPDLs) offer the highest wall-plug efficiency, highest specific power (power-to-weight ratio), arguably the lowest cost and highest reliability among all laser types. However, the poor beam quality of commercially HPDLs is the main bottleneck limiting their direct applications requiring high brightness at least in one dimension. In order to expand the applications of HPDLs, beam shaping and optical design are essential. In this work, we report the recent progresses on maximizing applications of HPDLs by synergizing diode laser light source and beam shaping micro-optics. Successful examples of matching of diode laser light sources and beam shaping micro-optics driving new applications are presented.

"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...

Increased genetic variation and evolutionary potential drive the success of an invasive grass.

PubMed

Lavergne, Sébastien; Molofsky, Jane

2007-03-06

Despite the increasing biological and economic impacts of invasive species, little is known about the evolutionary mechanisms that favor geographic range expansion and evolution of invasiveness in introduced species. Here, we focus on the invasive wetland grass Phalaris arundinacea L. and document the evolutionary consequences that resulted from multiple and uncontrolled introductions into North America of genetic material native to different European regions. Continental-scale genetic variation occurring in reed canarygrass' European range has been reshuffled and recombined within North American introduced populations, giving rise to a number of novel genotypes. This process alleviated genetic bottlenecks throughout reed canarygrass' introduced range, including in peripheral populations, where depletion of genetic diversity is expected and is observed in the native range. Moreover, reed canarygrass had higher genetic diversity and heritable phenotypic variation in its invasive range relative to its native range. The resulting high evolutionary potential of invasive populations allowed for rapid selection of genotypes with higher vegetative colonization ability and phenotypic plasticity. Our results show that repeated introductions of a single species may inadvertently create harmful invaders with high adaptive potential. Such invasive species may be able to evolve in response to changing climate, allowing them to have increasing impact on native communities and ecosystems in the future. More generally, multiple immigration events may thus trigger future adaptation and geographic spread of a species population by preventing genetic bottlenecks and generating genetic novelties through recombination.

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

Properties of the numerical algorithms for problems of quantum information technologies: Benefits of deep analysis

NASA Astrophysics Data System (ADS)

Chernyavskiy, Andrey; Khamitov, Kamil; Teplov, Alexey; Voevodin, Vadim; Voevodin, Vladimir

2016-10-01

In recent years, quantum information technologies (QIT) showed great development, although, the way of the implementation of QIT faces the serious difficulties, some of which are challenging computational tasks. This work is devoted to the deep and broad analysis of the parallel algorithmic properties of such tasks. As an example we take one- and two-qubit transformations of a many-qubit quantum state, which are the most critical kernels of many important QIT applications. The analysis of the algorithms uses the methodology of the AlgoWiki project (algowiki-project.org) and consists of two parts: theoretical and experimental. Theoretical part includes features like sequential and parallel complexity, macro structure, and visual information graph. Experimental part was made by using the petascale Lomonosov supercomputer (Moscow State University, Russia) and includes the analysis of locality and memory access, scalability and the set of more specific dynamic characteristics of realization. This approach allowed us to obtain bottlenecks and generate ideas of efficiency improvement.

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.

Estimating soil labile organic carbon and potential turnover rates using a sequential fumigation–incubation procedure.

Treesearch

X.M. Zoua; H.H. Ruanc; Y. Fua; X.D. Yanga; L.Q. Sha

2005-01-01

Labile carbon is the fraction of soil organic carbon with most rapid turnover times and its oxidation drives the flux of CO2 between soils and atmosphere. Available chemical and physical fractionation methods for estimating soil labile organic carbon are indirect and lack a clear biological definition. We have modified the well-established Jenkinson and Powlson’s...

Linear motion device and method for inserting and withdrawing control rods

DOEpatents

Smith, Jay E.

1984-01-01

A linear motion device, more specifically a control rod drive mechanism (CRDM) for inserting and withdrawing control rods into a reactor core, is capable of independently and sequentially positioning two sets of control rods with a single motor stator and rotor. The CRDM disclosed can control more than one control rod lead screw without incurring a substantial increase in the size of the mechanism.

"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...

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.

Street racing video games and risk-taking driving: An Internet survey of automobile enthusiasts.

PubMed

Vingilis, Evelyn; Seeley, Jane; Wiesenthal, David L; Wickens, Christine M; Fischer, Peter; Mann, Robert E

2013-01-01

The purpose of this study was to examine the relationships among risky driving attitudes, self-perceptions as a risky driver, playing of "drive'em up" (which rewarded players for frequent traffic and other violations) and "circuit" racing video games as well as self-reported risky driving through a web-based survey of car and racing club members in relation to a socio-cognitive model of the effects of racing video game playing. An Internet questionnaire was developed and included: (1) self-perceptions as a risky driver scales (Driver Thrill Seeking and Competitive Attitude Toward Driving); (2) attitudes regarding street racing; (3) street racing video game playing, and (4) self-reported risky driving (Risk-Taking Driving Scale). A sequential logistic regression was performed entering age and driving exposure as control variables in the first block, self-perceptions as a risky driver in the second block, attitudes in the third block and playing "drive'em up" and "circuit" racing games in the last block to examine their effects on self-reported risk-taking driving. A total of 503 survey respondents were included in the analyses and only 20% reported any risk-taking driving. Higher score on the Competitive Attitude Toward Driving Scale, more positive attitudes toward street racing, and more frequent reported playing of "drive'em up" video games were associated with higher odds on the self-reported Risk-Taking Driving Scale. However, the Driver Thrill Seeking Scale and "circuit" video game playing failed to predict self-reported risk-taking driving. Self-perceptions as a risky driver, positive attitudes toward risky driving and "drive'em up" street-racing games, but not "circuit" racing games, are associated with increased risk-taking driving. These findings are congruent with experimental studies in which games that reward driving violations increased risk taking, suggesting that risk taking may be a function of type of street racing game played by affecting self-perceptions as a risky driver. Copyright © 2012 Elsevier Ltd. All rights reserved.

Impaired-Driving Prevalence Among US High School Students: Associations With Substance Use and Risky Driving Behaviors

PubMed Central

Li, Kaigang; Simons-Morton, Bruce G.; Hingson, Ralph

2013-01-01

Objectives. We examined the prevalence of impaired driving among US high school students and associations with substance use and risky driving behavior. Methods. We assessed driving while alcohol or drug impaired (DWI) and riding with alcohol- or drug-impaired drivers (RWI) in a nationally representative sample of 11th-grade US high school students (n = 2431). We examined associations with drinking and binge drinking, illicit drug use, risky driving, and demographic factors using multivariate sequential logistic regression analysis. Results. Thirteen percent of 11th-grade students reported DWI at least 1 of the past 30 days, and 24% reported RWI at least once in the past year. Risky driving was positively associated with DWI (odds ratio [OR] = 1.25; P < .001) and RWI (OR = 1.09; P < .05), controlling for binge drinking (DWI: OR = 3.17; P < .01; RWI: OR = 6.12; P < .001) and illicit drug use (DWI: OR = 5.91; P < .001; RWI: OR = 2.29; P = .05). DWI was higher for adolescents who drove after midnight (OR = 15.7), drove while sleepy or drowsy (OR = 8.6), read text messages (OR = 11.8), sent text messages (OR = 5.0), and made cell phone calls (OR = 3.2) while driving. Conclusions. Our findings suggest the need for comprehensive approaches to the prevention of DWI, RWI, and other risky driving behavior. PMID:24028236

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.

α2 Integrin, extracellular matrix metalloproteinase inducer, and matrix metalloproteinase-3 act sequentially to induce differentiation of mouse embryonic stem cells into odontoblast-like cells

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

Ozeki, Nobuaki; Kawai, Rie; Hase, Naoko

We previously reported that interleukin 1β acts via matrix metalloproteinase (MMP)-3 to regulate cell proliferation and suppress apoptosis in α2 integrin-positive odontoblast-like cells differentiated from mouse embryonic stem (ES) cells. Here we characterize the signal cascade underpinning odontoblastic differentiation in mouse ES cells. The expression of α2 integrin, extracellular matrix metalloproteinase inducer (Emmprin), and MMP-3 mRNA and protein were all potently increased during odontoblastic differentiation. Small interfering RNA (siRNA) disruption of the expression of these effectors potently suppressed the expression of the odontoblastic biomarkers dentin sialophosphoprotein, dentin matrix protein-1 and alkaline phosphatase, and blocked odontoblast calcification. Our siRNA, western blotmore » and blocking antibody analyses revealed a unique sequential cascade involving α2 integrin, Emmprin and MMP-3 that drives ES cell differentiation into odontoblasts. This cascade requires the interaction between α2 integrin and Emmprin and is potentiated by exogenous MMP-3. Finally, although odontoblast-like cells potently express α2, α6, αV, β1, and β3, integrins, we confirmed that β1 integrin acts as the trigger for ES cell differentiation, apparently in complex with α2 integrin. These results demonstrate a unique and unanticipated role for an α2 integrin-, Emmprin-, and MMP-3-mediated signaling cascade in driving mouse ES cell differentiation into odontoblast-like cells. - Highlights: • Odontoblast differentiation requires activation of α2 integrin, Emmprin and MMP-3. • α2 integrin, Emmprin and MMP-3 form a sequential signaling cascade. • β1 integrin acts a specific trigger for odontoblast differentiation. • The role of these effectors is highly novel and unanticipated.« less

Electrical field-induced extraction and separation techniques: promising trends in analytical chemistry--a review.

PubMed

Yamini, Yadollah; Seidi, Shahram; Rezazadeh, Maryam

2014-03-03

Sample preparation is an important issue in analytical chemistry, and is often a bottleneck in chemical analysis. So, the major incentive for the recent research has been to attain faster, simpler, less expensive, and more environmentally friendly sample preparation methods. The use of auxiliary energies, such as heat, ultrasound, and microwave, is one of the strategies that have been employed in sample preparation to reach the above purposes. Application of electrical driving force is the current state-of-the-art, which presents new possibilities for simplifying and shortening the sample preparation process as well as enhancing its selectivity. The electrical driving force has scarcely been utilized in comparison with other auxiliary energies. In this review, the different roles of electrical driving force (as a powerful auxiliary energy) in various extraction techniques, including liquid-, solid-, and membrane-based methods, have been taken into consideration. Also, the references have been made available, relevant to the developments in separation techniques and Lab-on-a-Chip (LOC) systems. All aspects of electrical driving force in extraction and separation methods are too specific to be treated in this contribution. However, the main aim of this review is to provide a brief knowledge about the different fields of analytical chemistry, with an emphasis on the latest efforts put into the electrically assisted membrane-based sample preparation systems. The advantages and disadvantages of these approaches as well as the new achievements in these areas have been discussed, which might be helpful for further progress in the future. Copyright © 2013 Elsevier B.V. All rights reserved.

A link between occupant and vehicle accelerations during common driving tasks.

PubMed

Mathias, Anne C; Shibata, Peggy A; Sprague, James K

2014-01-01

When evaluating occupant motions during driving tasks, it is desirable to have a well-established correlation between vehicle and occupant accelerations. Therefore, this study demonstrated a methodology to quantify accelerations experienced by the driver of a passenger vehicle and compare them to associated vehicle motions. Acceleration levels were measured at the seat and the driver’s head, cervical spine, and lumbar spine during six non-collision driving tasks. Tasks included mounting a 127 mm (5 in) -high curb, crossing railroad tracks, driving on a rough road, braking heavily from 13.4 m/s (30 mph), having a 89 mm (3.5 in)-diameter roller sequentially pass under two tires, and dropping one tire from a 171-mm (6.75 in) height. The driver experienced peak resultant accelerations of similar magnitudes across all trials. Peak body accelerations were less than 1.2 g, including 0.82 g lumbar acceleration during heavy braking and 0.88 g head acceleration during the curb mount. These preliminary measurements are comparable to or lower than accelerations experienced during non-driving activities such as sitting quickly. This study contributes to the scientific understanding of accelerations experienced by vehicle occupants and demonstrates the potential to relate vehicle and occupant accelerations during common driving activities that do not involve collisions.

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…

Cellular automata in photonic cavity arrays.

PubMed

Li, Jing; Liew, T C H

2016-10-31

We propose theoretically a photonic Turing machine based on cellular automata in arrays of nonlinear cavities coupled with artificial gauge fields. The state of the system is recorded making use of the bistability of driven cavities, in which losses are fully compensated by an external continuous drive. The sequential update of the automaton layers is achieved automatically, by the local switching of bistable states, without requiring any additional synchronization or temporal control.

A Study of the Ethernet Troughput Performance of the Embedded System

NASA Astrophysics Data System (ADS)

Duan, Zhi-Yu; Zhao, Zhao-Wang

2007-09-01

An ethernet acceleration solution developed for the NIOS II Embedded System in astronomical applications - Mason Express is introduced in this paper. By manually constructing the proper network protocol headers and directly driving the hardware, Mason Express goes around the performance bottleneck of the Light Weighted IP stack (LWIP), and achieves up to 90Mb/s unidirectional data troughput rate from the embedded system board to the data collecting computer. With the LWIP stack, the maximum data rate is about 10.57Mb/s. Mason Express is a total software solution and no hardware changes required, neither does it affect the uCOS II operating system nor the LWIP stack, and can be implemented with or without any embedded operating system. It maximally protects the intelligence investment of the users.

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...

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.

Prototype color field sequential television lens assembly

NASA Technical Reports Server (NTRS)

1974-01-01

The design, development, and evaluation of a prototype modular lens assembly with a self-contained field sequential color wheel is presented. The design of a color wheel of maximum efficiency, the selection of spectral filters, and the design of a quiet, efficient wheel drive system are included. Design tradeoffs considered for each aspect of the modular assembly are discussed. Emphasis is placed on achieving a design which can be attached directly to an unmodified camera, thus permitting use of the assembly in evaluating various candidate camera and sensor designs. A technique is described which permits maintaining high optical efficiency with an unmodified camera. A motor synchronization system is developed which requires only the vertical synchronization signal as a reference frequency input. Equations and tradeoff curves are developed to permit optimizing the filter wheel aperture shapes for a variety of different design conditions.

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.

Efficient Solar Energy Harvesting and Storage through a Robust Photocatalyst Driving Reversible Redox Reactions.

PubMed

Zhou, Yangen; Zhang, Shun; Ding, Yu; Zhang, Leyuan; Zhang, Changkun; Zhang, Xiaohong; Zhao, Yu; Yu, Guihua

2018-06-14

Simultaneous solar energy conversion and storage is receiving increasing interest for better utilization of the abundant yet intermittently available sunlight. Photoelectrodes driving nonspontaneous reversible redox reactions in solar-powered redox cells (SPRCs), which can deliver energy via the corresponding reverse reactions, present a cost-effective and promising approach for direct solar energy harvesting and storage. However, the lack of photoelectrodes having both high conversion efficiency and high durability becomes a bottleneck that hampers practical applications of SPRCs. Here, it is shown that a WO 3 -decorated BiVO 4 photoanode, without the need of extra electrocatalysts, can enable a single-photocatalyst-driven SPRC with a solar-to-output energy conversion efficiency as high as 1.25%. This SPRC presents stable performance over 20 solar energy storage/delivery cycles. The high efficiency and stability are attributed to the rapid redox reactions, the well-matched energy level, and the efficient light harvesting and charge separation of the prepared BiVO 4 . This demonstrated device system represents a potential alternative toward the development of low-cost, durable, and easy-to-implement solar energy technologies. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A three-dimensional model for lubricant depletion under sliding condition on bit patterned media of hard disk drives

NASA Astrophysics Data System (ADS)

Wu, Lin

2018-05-01

In this paper, we model the depletion dynamics of the molecularly thin layer of lubricants on a bit patterned media disk of hard disk drives under a sliding air bearing head. The dominant physics and consequently, the lubricant depletion dynamics on a patterned disk are shown to be significantly different from the well-studied cases of a smooth disk. Our results indicate that the surface tension effect, which is negligible on a flat disk, apparently suppresses depletion by enforcing a bottleneck effect around the disk pattern peak regions to thwart the migration of lubricants. When the disjoining pressure is relatively small, it assists the depletion. But, when the disjoining pressure becomes dominant, the disjoining pressure resists depletion. Disk pattern orientation plays a critical role in the depletion process. The effect of disk pattern orientation on depletion originates from its complex interaction with other intermingled factors of external air shearing stress distribution and lubricant particle trajectory. Patterning a disk surface with nanostructures of high density, large height/pitch ratio, and particular orientation is demonstrated to be one efficient way to alleviate the formation of lubricant depletion tracks.

Isolation driven divergence: speciation in a widespread North American songbird (Aves: Certhiidae)

PubMed Central

Manthey, Joseph D.; Klicka, John; Spellman, Garth M.

2011-01-01

Lineage, or true “species,” trees may differ from gene trees because of stochastic processes in molecular evolution leading to gene-tree heterogeneity. Problems with inferring species trees due to excessive incomplete lineage sorting may be exacerbated in lineages with rapid diversification or recent divergences necessitating the use of multiple loci and individuals. Many recent multilocus studies that investigate divergence times identify lineage splitting to be more recent than single locus studies, forcing the revision of biogeographic scenarios driving divergence. Here we use 21 nuclear loci from regional populations to reevaluate hypotheses identified in an mtDNA phylogeographic study of the Brown Creeper (Certhia americana), as well as identify processes driving divergence. Nuclear phylogeographic analyses identified hierarchical genetic structure, supporting a basal split at roughly 32°N latitude, splitting northern and southern populations, with mixed patterns of genealogical concordance and discordance between datasets within the major lineages. Coalescent-based analyses identify isolation, with little to no gene flow, as the primary driver of divergence between lineages. Recent isolation appears to have caused genetic bottlenecks in populations in the Sierra Madre Oriental and coastal mountain ranges of California, which may be targets for conservation concerns. PMID:21933295

Increased genetic variation and evolutionary potential drive the success of an invasive grass

PubMed Central

Lavergne, Sébastien; Molofsky, Jane

2007-01-01

Despite the increasing biological and economic impacts of invasive species, little is known about the evolutionary mechanisms that favor geographic range expansion and evolution of invasiveness in introduced species. Here, we focus on the invasive wetland grass Phalaris arundinacea L. and document the evolutionary consequences that resulted from multiple and uncontrolled introductions into North America of genetic material native to different European regions. Continental-scale genetic variation occurring in reed canarygrass' European range has been reshuffled and recombined within North American introduced populations, giving rise to a number of novel genotypes. This process alleviated genetic bottlenecks throughout reed canarygrass' introduced range, including in peripheral populations, where depletion of genetic diversity is expected and is observed in the native range. Moreover, reed canarygrass had higher genetic diversity and heritable phenotypic variation in its invasive range relative to its native range. The resulting high evolutionary potential of invasive populations allowed for rapid selection of genotypes with higher vegetative colonization ability and phenotypic plasticity. Our results show that repeated introductions of a single species may inadvertently create harmful invaders with high adaptive potential. Such invasive species may be able to evolve in response to changing climate, allowing them to have increasing impact on native communities and ecosystems in the future. More generally, multiple immigration events may thus trigger future adaptation and geographic spread of a species population by preventing genetic bottlenecks and generating genetic novelties through recombination. PMID:17360447

Consequences of extreme life history traits on population persistence: do short-lived gobies face demographic bottlenecks?

NASA Astrophysics Data System (ADS)

Lefèvre, Carine D.; Nash, Kirsty L.; González-Cabello, Alonso; Bellwood, David R.

2016-06-01

The majority of coral reef goby species are short-lived, with some highly abundant species living less than 100 d. To understand the role and consequences of this extreme life history in shaping coral reef fish populations, we quantitatively documented the structure of small reef fish populations over a 26-month period (>14 short-lived fish generations) at an inshore reef on the Great Barrier Reef, Australia. Most species with life spans >1 yr, such as pomacentrids, exhibited a peak in recruitment during the austral summer, driving seasonal changes in the small fish community composition. In contrast, there were no clear changes in goby community composition, despite the abundance of short-lived, high turnover species. Species of Eviota, the most abundant gobiid genus observed, showed remarkably similar demographic profiles year-round, with consistent densities of adults as well as recently recruited juveniles. Our results demonstrate ongoing recruitment of these small cryptic fishes, which appears to compensate for an exceptionally short life span on the reef. Our results suggest that gobiid populations are able to overcome demographic limitations, and by maintaining reproduction, larval survival and recruitment throughout the year, they may avoid population bottlenecks. These findings also underline the potential trophodynamic importance of these small species; because of this constant turnover, Eviota species and other short-lived fishes may be particularly valuable contributors to the flow of energy on coral reefs, underpinning the year-round trophic structure.

Deadly competition and life-saving predation: the potential for alternative stable states in a stage-structured predator–prey system

PubMed Central

Rombado, Bianca R.; Rudolf, Volker H. W.

2016-01-01

Predators often undergo complete ontogenetic diet shifts, engaging in resource competition with species that become their prey during later developmental stages. Theory posits that this mix of stage-specific competition and predation, termed life-history intraguild predation (LHIGP), can lead to alternative stable states. In one state, prey exclude predators through competition (i.e. juvenile competitive bottleneck), while in the alternative, adult predators control prey density to limit competition and foster coexistence. Nevertheless, the interactions leading to these states have not been demonstrated in an empirical LHIGP system. To address this gap, we manipulated densities of cannibalistic adult cyclopoid copepods (Mesocyclops edax) and their cladoceran prey (Daphnia pulex) in a response-surface design and measured the maturation and survival of juvenile copepods (nauplii). We found that Daphnia reduced and even precluded both nauplii maturation and survival through depletion of a shared food resource. As predicted, adult copepods enhanced nauplii maturation and survival through Daphnia consumption, yet this positive effect was dependent on the relative abundance of Daphnia as well as the absolute density of adult copepods. Adult copepods reduced nauplii survival through cannibalism at low Daphnia densities and at the highest copepod density. This work demonstrates that predation can relax a strong juvenile competitive bottleneck in freshwater zooplankton, though cannibalism can reduce predator recruitment. Thus, our results highlight a key role for cannibalism in LHIGP dynamics and provide evidence for the interactions that drive alternative stable states in such systems. PMID:27581881

Microcomputer Software Engineering, Documentation and Evaluation

DTIC Science & Technology

1981-03-31

local dealer or call for complete specificalons. eAUTOMATIC INC To proceed step by step, we need toUe G T A TOMA IC NC. know where we are going and a...MICROPROCESSOR normal sequence that should be DIRECT MEMORY ACCESS preserved in the documentation. For INTRODUCTION 2.2 DRIVE CONTROLS example, you...with linear, sequential logic (like a computer). It is also the verbal side and controls language. The right side specializes in images, music, pictures

Linear motion device and method for inserting and withdrawing control rods

DOEpatents

Smith, J.E.

Disclosed is a linear motion device and more specifically a control rod drive mechanism (CRDM) for inserting and withdrawing control rods into a reactor core. The CRDM and method disclosed is capable of independently and sequentially positioning two sets of control rods with a single motor stator and rotor. The CRDM disclosed can control more than one control rod lead screw without incurring a substantial increase in the size of the mechanism.

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.

Next-day residual effects of gabapentin, diphenhydramine, and triazolam on simulated driving performance in healthy volunteers: a phase 3, randomized, double-blind, placebo-controlled, crossover trial.

PubMed

Kay, Gary G; Schwartz, Howard I; Wingertzahn, Mark A; Jayawardena, Shyamalie; Rosenberg, Russell P

2016-05-01

Next-day residual effects of a nighttime dose of gabapentin 250 mg were evaluated on simulated driving performance in healthy participants in a randomized, placebo-controlled, double-blind, multicenter, four-period crossover study that included diphenhydramine citrate 76 mg and triazolam 0.5 mg. At treatment visits, participants (n = 59) were dosed at ~23:30, went to bed immediately, and awakened 6.5 h postdose for evaluation. The primary endpoint was the standard deviation of lateral position for the 100-km driving scenario. Additional measures of driving, sleepiness, and cognition were included. Study sensitivity was established with triazolam, which demonstrated significant next-day impairment on all driving endpoints, relative to placebo (p < 0.001). Gabapentin demonstrated noninferiority to placebo on standard deviation of lateral position and speed deviation but not for lane excursions. Diphenhydramine citrate demonstrated significant impairment relative to gabapentin and placebo on speed deviation (p < 0.05). Other comparisons were either nonsignificant or statistically ineligible per planned, sequential comparisons. Secondary endpoints for sleepiness and cognitive performance were supportive of these conclusions. Together, these data suggest that low-dose gabapentin had no appreciable next-day effects on simulated driving performance or cognitive functioning. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

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.

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

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.

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

Continuous Manufacturing of Nitrocellulose by Magnesium Nitrate Method. Volume 1

DTIC Science & Technology

1979-06-01

enters a scrubber . The scrubber removes entrained acid, water, and NC fines from the air before it enters a Roots water sealed (lobe type) vacuum pump...and is exhausted to the atmosphere. The air enters the bottom of the scrubber and is forced (by vacuum) sequentially through two weir arrangements...the panel from left to right, the Eimco dewatering filter drive, vacuum pressure, receiver, vacuum scrubber , and pump controls may be seen along with

Genomic profiling of multiple sequentially acquired tumor metastatic sites from an “exceptional responder” lung adenocarcinoma patient reveals extensive genomic heterogeneity and novel somatic variants driving treatment response. | Center for Cancer Research

Cancer.gov

Biswas et al. describe an “exceptional responder” lung adenocarcinoma patient who survived with metastatic lung adenocarcinoma for 7 years while undergoing single or combination ERBB2-directed therapies. Whole-genome, whole-exome, and high-coverage ion-torrent targeted sequencing were used to demonstrate extreme genomic heterogeneity between the lung and lymph node metastatic

Hazardous Traffic Event Detection Using Markov Blanket and Sequential Minimal Optimization (MB-SMO)

PubMed Central

Yan, Lixin; Zhang, Yishi; He, Yi; Gao, Song; Zhu, Dunyao; Ran, Bin; Wu, Qing

2016-01-01

The ability to identify hazardous traffic events is already considered as one of the most effective solutions for reducing the occurrence of crashes. Only certain particular hazardous traffic events have been studied in previous studies, which were mainly based on dedicated video stream data and GPS data. The objective of this study is twofold: (1) the Markov blanket (MB) algorithm is employed to extract the main factors associated with hazardous traffic events; (2) a model is developed to identify hazardous traffic event using driving characteristics, vehicle trajectory, and vehicle position data. Twenty-two licensed drivers were recruited to carry out a natural driving experiment in Wuhan, China, and multi-sensor information data were collected for different types of traffic events. The results indicated that a vehicle’s speed, the standard deviation of speed, the standard deviation of skin conductance, the standard deviation of brake pressure, turn signal, the acceleration of steering, the standard deviation of acceleration, and the acceleration in Z (G) have significant influences on hazardous traffic events. The sequential minimal optimization (SMO) algorithm was adopted to build the identification model, and the accuracy of prediction was higher than 86%. Moreover, compared with other detection algorithms, the MB-SMO algorithm was ranked best in terms of the prediction accuracy. The conclusions can provide reference evidence for the development of dangerous situation warning products and the design of intelligent vehicles. PMID:27420073

Three-dimensional Simulation and Prediction of Solenoid Valve Failure Mechanism Based on Finite Element Model

NASA Astrophysics Data System (ADS)

Li, Jianfeng; Xiao, Mingqing; Liang, Yajun; Tang, Xilang; Li, Chao

2018-01-01

The solenoid valve is a kind of basic automation component applied widely. It’s significant to analyze and predict its degradation failure mechanism to improve the reliability of solenoid valve and do research on prolonging life. In this paper, a three-dimensional finite element analysis model of solenoid valve is established based on ANSYS Workbench software. A sequential coupling method used to calculate temperature filed and mechanical stress field of solenoid valve is put forward. The simulation result shows the sequential coupling method can calculate and analyze temperature and stress distribution of solenoid valve accurately, which has been verified through the accelerated life test. Kalman filtering algorithm is introduced to the data processing, which can effectively reduce measuring deviation and restore more accurate data information. Based on different driving current, a kind of failure mechanism which can easily cause the degradation of coils is obtained and an optimization design scheme of electro-insulating rubbers is also proposed. The high temperature generated by driving current and the thermal stress resulting from thermal expansion can easily cause the degradation of coil wires, which will decline the electrical resistance of coils and result in the eventual failure of solenoid valve. The method of finite element analysis can be applied to fault diagnosis and prognostic of various solenoid valves and improve the reliability of solenoid valve’s health management.

Hazardous Traffic Event Detection Using Markov Blanket and Sequential Minimal Optimization (MB-SMO).

PubMed

Yan, Lixin; Zhang, Yishi; He, Yi; Gao, Song; Zhu, Dunyao; Ran, Bin; Wu, Qing

2016-07-13

The ability to identify hazardous traffic events is already considered as one of the most effective solutions for reducing the occurrence of crashes. Only certain particular hazardous traffic events have been studied in previous studies, which were mainly based on dedicated video stream data and GPS data. The objective of this study is twofold: (1) the Markov blanket (MB) algorithm is employed to extract the main factors associated with hazardous traffic events; (2) a model is developed to identify hazardous traffic event using driving characteristics, vehicle trajectory, and vehicle position data. Twenty-two licensed drivers were recruited to carry out a natural driving experiment in Wuhan, China, and multi-sensor information data were collected for different types of traffic events. The results indicated that a vehicle's speed, the standard deviation of speed, the standard deviation of skin conductance, the standard deviation of brake pressure, turn signal, the acceleration of steering, the standard deviation of acceleration, and the acceleration in Z (G) have significant influences on hazardous traffic events. The sequential minimal optimization (SMO) algorithm was adopted to build the identification model, and the accuracy of prediction was higher than 86%. Moreover, compared with other detection algorithms, the MB-SMO algorithm was ranked best in terms of the prediction accuracy. The conclusions can provide reference evidence for the development of dangerous situation warning products and the design of intelligent vehicles.

NanoShuttles: Harnessing Motor Proteins to Transport Cargo in Synthetic Environments

NASA Astrophysics Data System (ADS)

Vogel, V.; Hess, H.

Motors have become a crucial commodity in our daily lives, from transportation to driving conveyor belts that enable the sequential assembly of cars and other industrial machines. For the sequential assembly of building blocks at the nanoscale that would not assemble spontaneously into larger functional systems, however, active transport systems are not yet available. In contrast, cells have evolved sophisticated molecular machinery that drives movement and active transport. Driven by the conversion of chemical into mechanical energy, namely through hydrolysis of the biological fuel ATP, molecular motors enable cells to operate far away from equilibrium by transporting organelles and molecules to designated locations within the cell, often against concentration gradients. Inspired by the biological concept of active transport, major efforts are underway to learn how to build nanoscale transport systems that are driven by molecular motors. Emerging engineering principles are discussed of how to build tracks and junctions to guide such nanoshuttles, how to load them with cargo and control their speed, how to use active transport to assemble mesoscopic structures that would otherwise not assemble spontaneously and what polymeric materials to choose to integrate motors into MEMS and other biohybrid devices. Finally, two applications that exploit the physical properties of microtubules are discussed, surface imaging by a swarm of microtubules and a self-assembled picoNewton force meter to probe receptor-ligand interactions.

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.

Simultaneous activation of parallel sensory pathways promotes a grooming sequence in Drosophila

PubMed Central

Hampel, Stefanie; McKellar, Claire E

2017-01-01

A central model that describes how behavioral sequences are produced features a neural architecture that readies different movements simultaneously, and a mechanism where prioritized suppression between the movements determines their sequential performance. We previously described a model whereby suppression drives a Drosophila grooming sequence that is induced by simultaneous activation of different sensory pathways that each elicit a distinct movement (Seeds et al., 2014). Here, we confirm this model using transgenic expression to identify and optogenetically activate sensory neurons that elicit specific grooming movements. Simultaneous activation of different sensory pathways elicits a grooming sequence that resembles the naturally induced sequence. Moreover, the sequence proceeds after the sensory excitation is terminated, indicating that a persistent trace of this excitation induces the next grooming movement once the previous one is performed. This reveals a mechanism whereby parallel sensory inputs can be integrated and stored to elicit a delayed and sequential grooming response. PMID:28887878

Sinecatechins and imiquimod as proactive sequential therapy of external genital and perianal warts in adults.

PubMed

Schöfer, Helmut; Tatti, Silvio; Lynde, Charles W; Skerlev, Mihael; Hercogová, Jana; Rotaru, Maria; Ballesteros, Juan; Calzavara-Pinton, Piergiacomo

2017-12-01

This review about the proactive sequential therapy (PST) of external genital and perianal warts (EGW) is based on the most current available clinical literature and on the broad clinical experience of a group of international experts, physicians who are well versed in the treatment of human papillomavirus-associated diseases. It provides a practical guide for the treatment of EGW, including epidemiology, etiology, clinical appearance, and diagnostic procedures for these viral infections. Furthermore, the treatment goals and current treatment options, elucidating provider- and patient-applied therapies, and the parameters driving treatment decisions are summarized. Specifically, the mode of action of the topical treatments sinecatechins and imiquimod, as well as the PST for EGW to achieve rapid and sustained clearance is discussed. The group of experts has developed a treatment algorithm giving healthcare providers a practical tool for the treatment of EGW which is very valuable in the presence of many different treatment options.

Dissociating hippocampal and striatal contributions to sequential prediction learning

PubMed Central

Bornstein, Aaron M.; Daw, Nathaniel D.

2011-01-01

Behavior may be generated on the basis of many different kinds of learned contingencies. For instance, responses could be guided by the direct association between a stimulus and response, or by sequential stimulus-stimulus relationships (as in model-based reinforcement learning or goal-directed actions). However, the neural architecture underlying sequential predictive learning is not well-understood, in part because it is difficult to isolate its effect on choice behavior. To track such learning more directly, we examined reaction times (RTs) in a probabilistic sequential picture identification task. We used computational learning models to isolate trial-by-trial effects of two distinct learning processes in behavior, and used these as signatures to analyze the separate neural substrates of each process. RTs were best explained via the combination of two delta rule learning processes with different learning rates. To examine neural manifestations of these learning processes, we used functional magnetic resonance imaging to seek correlates of timeseries related to expectancy or surprise. We observed such correlates in two regions, hippocampus and striatum. By estimating the learning rates best explaining each signal, we verified that they were uniquely associated with one of the two distinct processes identified behaviorally. These differential correlates suggest that complementary anticipatory functions drive each region's effect on behavior. Our results provide novel insights as to the quantitative computational distinctions between medial temporal and basal ganglia learning networks and enable experiments that exploit trial-by-trial measurement of the unique contributions of both hippocampus and striatum to response behavior. PMID:22487032

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

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.

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.

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).

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.

Microwave mode shifting antenna system for regenerating particulate filters

DOEpatents

Gonze, Eugene V [Pinckney, MI; Kirby, Kevin W [Calabasas Hills, CA; Phelps, Amanda [Malibu, CA; Gregoire, Daniel J [Thousand Oaks, CA

2011-04-26

A regeneration system comprises a particulate matter (PM) filter including a microwave energy absorbing surface, and an antenna system comprising N antennas and an antenna driver module that sequentially drives the antenna system in a plurality of transverse modes of the antenna system to heat selected portions of the microwave absorbing surface to regenerate the PM filter, where N is an integer greater than one. The transverse modes may include transverse electric (TE) and/or transverse magnetic (TM) modes.

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.

Selfish Little Circles: Transmission Bias and Evolution of Large Deletion-Bearing Mitochondrial DNA in Caenorhabditis briggsae Nematodes

PubMed Central

Clark, Katie A.; Howe, Dana K.; Gafner, Kristin; Kusuma, Danika; Ping, Sita; Estes, Suzanne; Denver, Dee R.

2012-01-01

Selfish DNA poses a significant challenge to genome stability and organismal fitness in diverse eukaryotic lineages. Although selfish mitochondrial DNA (mtDNA) has known associations with cytoplasmic male sterility in numerous gynodioecious plant species and is manifested as petite mutants in experimental yeast lab populations, examples of selfish mtDNA in animals are less common. We analyzed the inheritance and evolution of mitochondrial DNA bearing large heteroplasmic deletions including nad5 gene sequences (nad5Δ mtDNA), in the nematode Caenorhabditis briggsae. The deletion is widespread in C. briggsae natural populations and is associated with deleterious organismal effects. We studied the inheritance patterns of nad5Δ mtDNA using eight sets of C. briggsae mutation-accumulation (MA) lines, each initiated from a different natural strain progenitor and bottlenecked as single hermaphrodites across generations. We observed a consistent and strong drive toward higher levels of deletion-bearing molecules in the heteroplasmic pool of mtDNA after ten generations of bottlenecking. Our results demonstrate a uniform transmission bias whereby nad5Δ mtDNA accumulates to higher levels relative to intact mtDNA in multiple genetically diverse natural strains of C. briggsae. We calculated an average 1% per-generation transmission bias for deletion-bearing mtDNA relative to intact genomes. Our study, coupled with known deleterious phenotypes associated with high deletion levels, shows that nad5Δ mtDNA are selfish genetic elements that have evolved in natural populations of C. briggsae, offering a powerful new system to study selfish mtDNA dynamics in metazoans. PMID:22859984

Benefits of flexible prioritization in working memory can arise without costs.

PubMed

Myers, Nicholas E; Chekroud, Sammi R; Stokes, Mark G; Nobre, Anna C

2018-03-01

Most recent models conceptualize working memory (WM) as a continuous resource, divided up according to task demands. When an increasing number of items need to be remembered, each item receives a smaller chunk of the memory resource. These models predict that the allocation of attention to high-priority WM items during the retention interval should be a zero-sum game: improvements in remembering cued items come at the expense of uncued items because resources are dynamically transferred from uncued to cued representations. The current study provides empirical data challenging this model. Four precision retrocueing WM experiments assessed cued and uncued items on every trial. This permitted a test for trade-off of the memory resource. We found no evidence for trade-offs in memory across trials. Moreover, robust improvements in WM performance for cued items came at little or no cost to uncued items that were probed afterward, thereby increasing the net capacity of WM relative to neutral cueing conditions. An alternative mechanism of prioritization proposes that cued items are transferred into a privileged state within a response-gating bottleneck, in which an item uniquely controls upcoming behavior. We found evidence consistent with this alternative. When an uncued item was probed first, report of its orientation was biased away from the cued orientation to be subsequently reported. We interpret this bias as competition for behavioral control in the output-driving bottleneck. Other items in WM did not bias each other, making this result difficult to explain with a shared resource model. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

Effects of memory rehearsal on driver performance: experiment and theoretical account.

PubMed

Salvucci, Dario D; Beltowska, Joanna

2008-10-01

We report an experiment and a theoretical analysis concerning the effects of an exclusively cognitive task, specifically a memory rehearsal task, on driver performance. Although recent work on driver distraction has elucidated the sometimes significant effects of cognitive processing on driver performance, these studies have typically mixed cognitive with perceptual and motor processing, making it difficult to isolate the effects of cognitive processing alone. We asked participants to drive in a driving simulator during only the rehearsal stage of a serial-recall memory task while we measured their ability to maintain a central lane position and respond to the illumination of a lead vehicle's brake lights. Memory rehearsal significantly affected drivers' steering performance as measured by lateral deviation from lane center, and it also significantly affected drivers' response time to the braking stimulus for the higher load memory task. These results lend support to a theoretical account of cognitive distraction provided by threaded cognition theory in terms of a cognitive bottleneck in procedural processing, and they also suggest that consideration of task urgency may be important in accounting for performance trade-offs among concurrent tasks. The experiment augments the current understanding of cognitive driver distraction and suggests that even exclusively cognitive secondary tasks may sometimes affect driver performance.

Product reliability and thin-film photovoltaics

NASA Astrophysics Data System (ADS)

Gaston, Ryan; Feist, Rebekah; Yeung, Simon; Hus, Mike; Bernius, Mark; Langlois, Marc; Bury, Scott; Granata, Jennifer; Quintana, Michael; Carlson, Carl; Sarakakis, Georgios; Ogden, Douglas; Mettas, Adamantios

2009-08-01

Despite significant growth in photovoltaics (PV) over the last few years, only approximately 1.07 billion kWhr of electricity is estimated to have been generated from PV in the US during 2008, or 0.27% of total electrical generation. PV market penetration is set for a paradigm shift, as fluctuating hydrocarbon prices and an acknowledgement of the environmental impacts associated with their use, combined with breakthrough new PV technologies, such as thin-film and BIPV, are driving the cost of energy generated with PV to parity or cost advantage versus more traditional forms of energy generation. In addition to reaching cost parity with grid supplied power, a key to the long-term success of PV as a viable energy alternative is the reliability of systems in the field. New technologies may or may not have the same failure modes as previous technologies. Reliability testing and product lifetime issues continue to be one of the key bottlenecks in the rapid commercialization of PV technologies today. In this paper, we highlight the critical need for moving away from relying on traditional qualification and safety tests as a measure of reliability and focus instead on designing for reliability and its integration into the product development process. A drive towards quantitative predictive accelerated testing is emphasized and an industrial collaboration model addressing reliability challenges is proposed.

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.

Improving formaldehyde consumption drives methanol assimilation in engineered E. coli.

PubMed

Woolston, Benjamin M; King, Jason R; Reiter, Michael; Van Hove, Bob; Stephanopoulos, Gregory

2018-06-19

Due to volatile sugar prices, the food vs fuel debate, and recent increases in the supply of natural gas, methanol has emerged as a promising feedstock for the bio-based economy. However, attempts to engineer Escherichia coli to metabolize methanol have achieved limited success. Here, we provide a rigorous systematic analysis of several potential pathway bottlenecks. We show that regeneration of ribulose 5-phosphate in E. coli is insufficient to sustain methanol assimilation, and overcome this by activating the sedoheptulose bisphosphatase variant of the ribulose monophosphate pathway. By leveraging the kinetic isotope effect associated with deuterated methanol as a chemical probe, we further demonstrate that under these conditions overall pathway flux is kinetically limited by methanol dehydrogenase. Finally, we identify NADH as a potent kinetic inhibitor of this enzyme. These results provide direction for future engineering strategies to improve methanol utilization, and underscore the value of chemical biology methodologies in metabolic engineering.

Tree regeneration by seed in bottomland hardwood forests: A review

USGS Publications Warehouse

Kroschel, Whitney A.; King, Sammy L.; Keim, Richard F.

2016-01-01

Bottomland hardwood forests (BLH) are found in temperate, humid regions of the southeastern US, primarily on alluvial floodplains adjacent to rivers. Altered hydrology in rivers and floodplains has caused changes in stand development and species composition of BLHs. We hypothesize that the driving mechanisms behind these changes are related to the regeneration process because of the complexity of recruitment and the vulnerability of species at that age in development. Here we review the state of our understanding regarding BLH regeneration, and identify potential bottlenecks throughout the stages of seed production, seed dispersal, germination, establishment, and survival. Our process-level understanding of regeneration by seed in BLHs is rudimentary, thus limiting our ability to predict the effects of hydrologic alterations on species composition. By focusing future research on the appropriate stages of regeneration, we can better understand the sources of forest-community transitions across the diverse range of BLH systems.

Water Oxidation Mechanisms of Metal Oxide Catalysts by Vibrational Spectroscopy of Transient Intermediates.

PubMed

Zhang, Miao; Frei, Heinz

2017-05-05

Water oxidation is an essential reaction of an artificial photosystem for solar fuel generation because it provides electrons needed to reduce carbon dioxide or protons to a fuel. Earth-abundant metal oxides are among the most attractive catalytic materials for this reaction because of their robustness and scalability, but their efficiency poses a challenge. Knowledge of catalytic surface intermediates gained by vibrational spectroscopy under reaction conditions plays a key role in uncovering kinetic bottlenecks and provides a basis for catalyst design improvements. Recent dynamic infrared and Raman studies reveal the molecular identity of transient surface intermediates of water oxidation on metal oxides. Combined with ultrafast infrared observations of how charges are delivered to active sites of the metal oxide catalyst and drive the multielectron reaction, spectroscopic advances are poised to play a key role in accelerating progress toward improved catalysts for artificial photosynthesis.

A Protein Chimera Strategy Supports Production of a Model "Difficult-to-Express" Recombinant Target.

PubMed

Hussain, Hirra; Fisher, David I; Roth, Robert G; Abbott, W Mark; Carballo-Amador, Manuel Alejandro; Warwicker, Jim; Dickson, Alan J

2018-06-22

Due in part to the needs of the biopharmaceutical industry, there has been an increased drive to generate high quality recombinant proteins in large amounts. However, achieving high yields can be a challenge as the novelty and increased complexity of new targets often makes them 'difficult-to-express'. This study aimed to define the molecular features that restrict the production of a model 'difficult-to-express' recombinant protein, Tissue Inhibitor Metalloproteinase-3 (TIMP-3). Building from experimental data, computational approaches were used to rationalise the re-design of this recombinant target to generate a chimera with enhanced secretion. The results highlight the importance of early identification of unfavourable sequence attributes, enabling the generation of engineered protein forms that bypass 'secretory' bottlenecks and result in efficient recombinant protein production. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Tracing the Trans-Pacific Evolutionary History of a Domesticated Seaweed (Gracilaria chilensis) with Archaeological and Genetic Data

PubMed Central

Guillemin, Marie-Laure; Valero, Myriam; Faugeron, Sylvain; Nelson, Wendy; Destombe, Christophe

2014-01-01

The history of a domesticated marine macroalga is studied using archaeological, phylogeographic and population genetic tools. Phylogeographic and population genetic analyses demonstrated that the cultivated red alga Gracilaria chilensis colonised the Chilean coast from New Zealand. Combining archaeological observations with phylogeographic data provided evidence that exchanges between New Zealand and Chile have occurred at least before the Holocene, likely at the end of the Last Glacial Maximum (LGM) and we suggest that migration probably occurred via rafting. Furthermore, the remarkably low microsatellite diversity found in the Chilean populations compared to those in New Zealand is consistent with a recent genetic bottleneck as a result of over-exploitation of natural populations and/or the process of domestication. Therefore, the aquaculture of this seaweed, based essentially on clonal propagation, is occurring from genetically depressed populations and may be driving the species to an extinction vortex in Chile. PMID:25501717

Role of entropy in the ground state formation of frustrated systems

NASA Astrophysics Data System (ADS)

Sereni, Julian G.

2018-05-01

The absence of magnetic order in Rare Earth-based frustrated compounds allows to recognize the action of the third law of thermodynamics in the low temperature behavior of those systems. One of the most relevant findings is the appearance of a coincident specific heat Cm / T|T→0 ≈ 7 J /molK2 'plateau' in six Yb systems. This characteristic feature occurs after a systematic modification of the thermal trajectory of their entropies Sm (T) in the range of a few hundred milikelvin degrees. Such behavior is explained by the formation of an entropy-bottleneck imposed by the third law constraint (Sm|T→0 ≥ 0), that drives the system into alternative ground states. Based in these finding, three possible approaches to the Sm|T→0 limit observed in real systems are analyzed in terms of the ∂2Sm / ∂T2 dependencies.

Adaptive divergence despite strong genetic drift: genomic analysis of the evolutionary mechanisms causing genetic differentiation in the island fox (Urocyon littoralis)

PubMed Central

FUNK, W. CHRIS; LOVICH, ROBERT E.; HOHENLOHE, PAUL A.; HOFMAN, COURTNEY A.; MORRISON, SCOTT A.; SILLETT, T. SCOTT; GHALAMBOR, CAMERON K.; MALDONADO, JESUS E.; RICK, TORBEN C.; DAY, MITCH D.; POLATO, NICHOLAS R.; FITZPATRICK, SARAH W.; COONAN, TIMOTHY J.; CROOKS, KEVIN R.; DILLON, ADAM; GARCELON, DAVID K.; KING, JULIE L.; BOSER, CHRISTINA L.; GOULD, NICHOLAS; ANDELT, WILLIAM F.

2016-01-01

The evolutionary mechanisms generating the tremendous biodiversity of islands have long fascinated evolutionary biologists. Genetic drift and divergent selection are predicted to be strong on islands and both could drive population divergence and speciation. Alternatively, strong genetic drift may preclude adaptation. We conducted a genomic analysis to test the roles of genetic drift and divergent selection in causing genetic differentiation among populations of the island fox (Urocyon littoralis). This species consists of 6 subspecies, each of which occupies a different California Channel Island. Analysis of 5293 SNP loci generated using Restriction-site Associated DNA (RAD) sequencing found support for genetic drift as the dominant evolutionary mechanism driving population divergence among island fox populations. In particular, populations had exceptionally low genetic variation, small Ne (range = 2.1–89.7; median = 19.4), and significant genetic signatures of bottlenecks. Moreover, islands with the lowest genetic variation (and, by inference, the strongest historical genetic drift) were most genetically differentiated from mainland gray foxes, and vice versa, indicating genetic drift drives genome-wide divergence. Nonetheless, outlier tests identified 3.6–6.6% of loci as high FST outliers, suggesting that despite strong genetic drift, divergent selection contributes to population divergence. Patterns of similarity among populations based on high FST outliers mirrored patterns based on morphology, providing additional evidence that outliers reflect adaptive divergence. Extremely low genetic variation and small Ne in some island fox populations, particularly on San Nicolas Island, suggest that they may be vulnerable to fixation of deleterious alleles, decreased fitness, and reduced adaptive potential. PMID:26992010

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...

A Self-Adaptive Dynamic Recognition Model for Fatigue Driving Based on Multi-Source Information and Two Levels of Fusion

PubMed Central

Sun, Wei; Zhang, Xiaorui; Peeta, Srinivas; He, Xiaozheng; Li, Yongfu; Zhu, Senlai

2015-01-01

To improve the effectiveness and robustness of fatigue driving recognition, a self-adaptive dynamic recognition model is proposed that incorporates information from multiple sources and involves two sequential levels of fusion, constructed at the feature level and the decision level. Compared with existing models, the proposed model introduces a dynamic basic probability assignment (BPA) to the decision-level fusion such that the weight of each feature source can change dynamically with the real-time fatigue feature measurements. Further, the proposed model can combine the fatigue state at the previous time step in the decision-level fusion to improve the robustness of the fatigue driving recognition. An improved correction strategy of the BPA is also proposed to accommodate the decision conflict caused by external disturbances. Results from field experiments demonstrate that the effectiveness and robustness of the proposed model are better than those of models based on a single fatigue feature and/or single-source information fusion, especially when the most effective fatigue features are used in the proposed model. PMID:26393615

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.

The perceptual processing capacity of summary statistics between and within feature dimensions

PubMed Central

Attarha, Mouna; Moore, Cathleen M.

2015-01-01

The simultaneous–sequential method was used to test the processing capacity of statistical summary representations both within and between feature dimensions. Sixteen gratings varied with respect to their size and orientation. In Experiment 1, the gratings were equally divided into four separate smaller sets, one of which with a mean size that was larger or smaller than the other three sets, and one of which with a mean orientation that was tilted more leftward or rightward. The task was to report the mean size and orientation of the oddball sets. This therefore required four summary representations for size and another four for orientation. The sets were presented at the same time in the simultaneous condition or across two temporal frames in the sequential condition. Experiment 1 showed evidence of a sequential advantage, suggesting that the system may be limited with respect to establishing multiple within-feature summaries. Experiment 2 eliminates the possibility that some aspect of the task, other than averaging, was contributing to this observed limitation. In Experiment 3, the same 16 gratings appeared as one large superset, and therefore the task only required one summary representation for size and another one for orientation. Equal simultaneous–sequential performance indicated that between-feature summaries are capacity free. These findings challenge the view that within-feature summaries drive a global sense of visual continuity across areas of the peripheral visual field, and suggest a shift in focus to seeking an understanding of how between-feature summaries in one area of the environment control behavior. PMID:26360153

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

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.

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

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

Spinal interneurons differentiate sequentially from those driving the fastest swimming movements in larval zebrafish to those driving the slowest ones.

PubMed

McLean, David L; Fetcho, Joseph R

2009-10-28

Studies of neuronal networks have revealed few general principles that link patterns of development with later functional roles. While investigating the neural control of movements, we recently discovered a topographic map in the spinal cord of larval zebrafish that relates the position of motoneurons and interneurons to their order of recruitment during swimming. Here, we show that the map reflects an orderly pattern of differentiation of neurons driving different movements. First, we use high-speed filming to show that large-amplitude swimming movements with bending along much of the body appear first, with smaller, regional swimming movements emerging later. Next, using whole-cell patch recordings, we demonstrate that the excitatory circuits that drive large-amplitude, fast swimming movements at larval stages are present and functional early on in embryos. Finally, we systematically assess the orderly emergence of spinal circuits according to swimming speed using transgenic fish expressing the photoconvertible protein Kaede to track neuronal differentiation in vivo. We conclude that a simple principle governs the development of spinal networks in which the neurons driving the fastest, most powerful swimming in larvae develop first with ones that drive increasingly weaker and slower larval movements layered on over time. Because the neurons are arranged by time of differentiation in the spinal cord, the result is a topographic map that represents the speed/strength of movements at which neurons are recruited and the temporal emergence of networks. This pattern may represent a general feature of neuronal network development throughout the brain and spinal cord.

Four dimensional imaging of E. coli nucleoid organization and dynamics in living cells

PubMed Central

Fisher, J. K.; Bourniquel, A.; Witz, G.; Weiner, B.; Prentiss, M.; Kleckner, N.

2013-01-01

Visualization of living E. coli nucleoids, defined by HupA-mCherry, reveals a discrete, dynamic helical ellipsoid. Three basic features emerge. (i) Nucleoid density efficiently coalesces into longitudinal bundles, giving a stiff, low DNA density ellipsoid. (ii) This ellipsoid is radially confined within the cell cylinder. Radial confinement gives helical shape and drives and directs global nucleoid dynamics, including sister segregation. (iii) Longitudinal density waves flux back and forth along the nucleoid, with 5–10% of density shifting within 5s, enhancing internal nucleoid mobility. Furthermore, sisters separate end-to-end in sequential discontinuous pulses, each elongating the nucleoid by 5–15%. Pulses occur at 20min intervals, at defined cell cycle times. This progression is mediated by sequential installation and release of programmed tethers, implying cyclic accumulation and relief of intra-nucleoid mechanical stress. These effects could comprise a chromosome-based cell cycle engine. Overall, the presented results suggest a general conceptual framework for bacterial nucleoid morphogenesis and dynamics. PMID:23623305

Three- α particle correlations in quasi-projectile decay in 12C + 24Mg collisions at 35A MeV

NASA Astrophysics Data System (ADS)

Quattrocchi, L.; Acosta, L.; Amorini, F.; Anzalone, A.; Auditore, L.; Berceanu, I.; Cardella, G.; Chbihi, A.; De Filippo, E.; De Luca, S.; Dell'Aquila, D.; Francalanza, L.; Gnoffo, B.; Grzeszczuk, A.; Lanzalone, G.; Lombardo, I.; Martel, I.; Martorana, N. S.; Minniti, T.; Norella, S.; Pagano, A.; Pagano, E. V.; Papa, M.; Pirrone, S.; Politi, G.; Porto, F.; Rizzo, F.; Rosato, E.; Russotto, P.; Trifirò, A.; Trimarchi, M.; Verde, G.; Veselsky, M.; Vigilante, M.

2017-11-01

Two and multi particle correlations have been studied in peripheral 12C + 24Mg collisions at 35A MeV with CHIMERA 4 π multi detector, in order to explore resonances produced in light nuclei. Correlations techniques have become a tool to explore nuclear structure properties but also to evaluate the competition between simultaneous and sequential channels in decay of light isotopes. The exploration of features such as branching ratios with respect to different decay channels (sequential vs. simultaneous) could provide information on in-medium effects on nuclear structure properties, an important perspective for research on the nuclear interaction. The performed experiment is preliminary to further studies to be performed by coupling of CHIMERA to FARCOS (Femtoscope ARray for COrrelations and Spectroscopy, FARCOS TDR available at https://drive.google.com/file/d/0B5CgGWz8LpOOc3pGTWdOcDBoWFE) array devoted to measurements of two and multi particle correlations with high energy and angular resolutions.

Impact of the HIV-1 genetic background and HIV-1 population size on the evolution of raltegravir resistance.

PubMed

Fun, Axel; Leitner, Thomas; Vandekerckhove, Linos; Däumer, Martin; Thielen, Alexander; Buchholz, Bernd; Hoepelman, Andy I M; Gisolf, Elizabeth H; Schipper, Pauline J; Wensing, Annemarie M J; Nijhuis, Monique

2018-01-05

Emergence of resistance against integrase inhibitor raltegravir in human immunodeficiency virus type 1 (HIV-1) patients is generally associated with selection of one of three signature mutations: Y143C/R, Q148K/H/R or N155H, representing three distinct resistance pathways. The mechanisms that drive selection of a specific pathway are still poorly understood. We investigated the impact of the HIV-1 genetic background and population dynamics on the emergence of raltegravir resistance. Using deep sequencing we analyzed the integrase coding sequence (CDS) in longitudinal samples from five patients who initiated raltegravir plus optimized background therapy at viral loads > 5000 copies/ml. To investigate the role of the HIV-1 genetic background we created recombinant viruses containing the viral integrase coding region from pre-raltegravir samples from two patients in whom raltegravir resistance developed through different pathways. The in vitro selections performed with these recombinant viruses were designed to mimic natural population bottlenecks. Deep sequencing analysis of the viral integrase CDS revealed that the virological response to raltegravir containing therapy inversely correlated with the relative amount of unique sequence variants that emerged suggesting diversifying selection during drug pressure. In 4/5 patients multiple signature mutations representing different resistance pathways were observed. Interestingly, the resistant population can consist of a single resistant variant that completely dominates the population but also of multiple variants from different resistance pathways that coexist in the viral population. We also found evidence for increased diversification after stronger bottlenecks. In vitro selections with low viral titers, mimicking population bottlenecks, revealed that both recombinant viruses and HXB2 reference virus were able to select mutations from different resistance pathways, although typically only one resistance pathway emerged in each individual culture. The generation of a specific raltegravir resistant variant is not predisposed in the genetic background of the viral integrase CDS. Typically, in the early phases of therapy failure the sequence space is explored and multiple resistance pathways emerge and then compete for dominance which frequently results in a switch of the dominant population over time towards the fittest variant or even multiple variants of similar fitness that can coexist in the viral population.

Mine countermeasures (MCM) sensor technology drivers

NASA Astrophysics Data System (ADS)

Skinner, David P.

1995-06-01

In recent years, MCM has moved to the forefront of the Navy's attention. This paper describes the general problems that drive the technology requirements of classical sea mine countermeasure (MCM) sensors for those working outside of this specialized area. Sensor requirements for MCM are compared with those for antisubmarine warfare. This highlights the unique environmental issues and crucial false target problems. The elimination of false targets, not mine detection, is the principal driver of MCM sensor requirements and places special emphasis on the technologies needed for the sequential operations of detection, classification, and identification.

Practical method and device for enhancing pulse contrast ratio for lasers and electron accelerators

DOEpatents

Zhang, Shukui; Wilson, Guy

2014-09-23

An apparatus and method for enhancing pulse contrast ratios for drive lasers and electron accelerators. The invention comprises a mechanical dual-shutter system wherein the shutters are placed sequentially in series in a laser beam path. Each shutter of the dual shutter system has an individually operated trigger for opening and closing the shutter. As the triggers are operated individually, the delay between opening and closing first shutter and opening and closing the second shutter is variable providing for variable differential time windows and enhancement of pulse contrast ratio.

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.

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

Robust Electrical Transfer System (RETS) for Solar Array Drive Mechanism SlipRing Assembly

NASA Astrophysics Data System (ADS)

Bommottet, Daniel; Bossoney, Luc; Schnyder, Ralph; Howling, Alan; Hollenstein, Christoph

2013-09-01

Demands for robust and reliable power transmission systems for sliprings for SADM (Solar Array Drive Mechanism) are increasing steadily. As a consequence, it is required to know their performances regarding the voltage breakdown limit.An understanding of the overall shape of the breakdown voltage versus pressure curve is established, based on experimental measurements of DC (Direct Current) gas breakdown in complex geometries compared with a numerical simulation model.In addition a detailed study was made of the functional behaviour of an entire wing of satellite in a like- operational mode, comprising the solar cells, the power transmission lines, the SRA (SlipRing Assembly), the power S3R (Sequential Serial/shunt Switching Regulators) and the satellite load to simulate the electrical power consumption.A test bench able to measure automatically the: a)breakdown voltage versus pressure curve and b)the functional switching performances, was developed and validated.

Fast nanoscale addressability of nitrogen-vacancy spins via coupling to a dynamic ferromagnetic vortex

PubMed Central

Wolf, M. S.; Badea, R.; Berezovsky, J.

2016-01-01

The core of a ferromagnetic vortex domain creates a strong, localized magnetic field, which can be manipulated on nanosecond timescales, providing a platform for addressing and controlling individual nitrogen-vacancy centre spins in diamond at room temperature, with nanometre-scale resolution. Here, we show that the ferromagnetic vortex can be driven into proximity with a nitrogen-vacancy defect using small applied magnetic fields, inducing significant nitrogen-vacancy spin splitting. We also find that the magnetic field gradient produced by the vortex is sufficient to address spins separated by nanometre-length scales. By applying a microwave-frequency magnetic field, we drive both the vortex and the nitrogen-vacancy spins, resulting in enhanced coherent rotation of the spin state. Finally, we demonstrate that by driving the vortex on fast timescales, sequential addressing and coherent manipulation of spins is possible on ∼100 ns timescales. PMID:27296550

Fast nanoscale addressability of nitrogen-vacancy spins via coupling to a dynamic ferromagnetic vortex

DOE PAGES

Wolf, M. S.; Badea, R.; Berezovsky, J.

2016-06-14

The core of a ferromagnetic vortex domain creates a strong, localized magnetic field, which can be manipulated on nanosecond timescales, providing a platform for addressing and controlling individual nitrogen-vacancy centre spins in diamond at room temperature, with nanometre-scale resolution. Here, we show that the ferromagnetic vortex can be driven into proximity with a nitrogen-vacancy defect using small applied magnetic fields, inducing significant nitrogen-vacancy spin splitting. We also find that the magnetic field gradient produced by the vortex is sufficient to address spins separated by nanometre-length scales. By applying a microwave-frequency magnetic field, we drive both the vortex and the nitrogen-vacancymore » spins, resulting in enhanced coherent rotation of the spin state. Lastly, we demonstrate that by driving the vortex on fast timescales, sequential addressing and coherent manipulation of spins is possible on ~ 100 ns timescales.« less

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

PREMER: a Tool to Infer Biological Networks.

PubMed

Villaverde, Alejandro F; Becker, Kolja; Banga, Julio R

2017-10-04

Inferring the structure of unknown cellular networks is a main challenge in computational biology. Data-driven approaches based on information theory can determine the existence of interactions among network nodes automatically. However, the elucidation of certain features - such as distinguishing between direct and indirect interactions or determining the direction of a causal link - requires estimating information-theoretic quantities in a multidimensional space. This can be a computationally demanding task, which acts as a bottleneck for the application of elaborate algorithms to large-scale network inference problems. The computational cost of such calculations can be alleviated by the use of compiled programs and parallelization. To this end we have developed PREMER (Parallel Reverse Engineering with Mutual information & Entropy Reduction), a software toolbox that can run in parallel and sequential environments. It uses information theoretic criteria to recover network topology and determine the strength and causality of interactions, and allows incorporating prior knowledge, imputing missing data, and correcting outliers. PREMER is a free, open source software tool that does not require any commercial software. Its core algorithms are programmed in FORTRAN 90 and implement OpenMP directives. It has user interfaces in Python and MATLAB/Octave, and runs on Windows, Linux and OSX (https://sites.google.com/site/premertoolbox/).

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

[Application of extended exergy method in driving mechanism and efficiency of regional eco-economy].

PubMed

Fan, Xin Gang; Mi, Wen Bao; Hou, Jing Wei

2017-01-01

To analyze social-economic causes of the regional ecological degradation, and avoid such problems as the complex circulation network and difficulty to identify laws caused by extended exergy analysis (EEA) previously applied at the national scale, this paper reduced spatial scale to the county scale and took Pengyang County in Ningxia as an example. Eco-economic system in Peng-yang County was divided into seven interrelated sectors. The exergy value of circulations in the eco-economic system including materials, labor and capital were calculated respectively to analyze the extended exergy characteristics of the driving sectors, factors and paths and evaluate their ecological efficiency. The results showed that agriculture and households were the main driving sectors of the eco-economic system in Pengyang County. The average exergy value of 31 flow paths among the sectors was 0.80 PJ. There were only 8 flow paths whose exergy values were higher than the average value. Eco-economic system in Pengyang County development was driven by two continuous flow paths, labor output of the households sector and demands of the households sector supported by other sectors. The mineral resources were massively exploited, and then directly exported to the outside, which could not promote the local development from the inside, but, on the contrary, increase the ecological environment pressure because of the over-exploitation. The eco-efficiency of Pengyang County in 2014 was 68.1%, almost equivalent to the by-level of the national scale at home and abroad ten years ago, mainly because of the lower eco-efficiencies of the service sector and households sector. EEA had the advantage of networking and structuring, could specify the sectors, factors and driven paths, and break through the bottleneck of driving mechanism research of the eco-economic system. EEA had certain adaptability to explore the operational principle and optimal pattern of the regional eco-economic system. Compared with the national scale, EEA at the regional scale could more easily identify the driving mechanism of eco-economic system, and could clearly guide the regional administrative department to reduce the ecological environment pressure.

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...

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.

Retinal vascular segmentation using superpixel-based line operator and its application to vascular topology estimation.

PubMed

Na, Tong; Xie, Jianyang; Zhao, Yitian; Zhao, Yifan; Liu, Yue; Wang, Yongtian; Liu, Jiang

2018-05-09

Automatic methods of analyzing of retinal vascular networks, such as retinal blood vessel detection, vascular network topology estimation, and arteries/veins classification are of great assistance to the ophthalmologist in terms of diagnosis and treatment of a wide spectrum of diseases. We propose a new framework for precisely segmenting retinal vasculatures, constructing retinal vascular network topology, and separating the arteries and veins. A nonlocal total variation inspired Retinex model is employed to remove the image intensity inhomogeneities and relatively poor contrast. For better generalizability and segmentation performance, a superpixel-based line operator is proposed as to distinguish between lines and the edges, thus allowing more tolerance in the position of the respective contours. The concept of dominant sets clustering is adopted to estimate retinal vessel topology and classify the vessel network into arteries and veins. The proposed segmentation method yields competitive results on three public data sets (STARE, DRIVE, and IOSTAR), and it has superior performance when compared with unsupervised segmentation methods, with accuracy of 0.954, 0.957, and 0.964, respectively. The topology estimation approach has been applied to five public databases (DRIVE,STARE, INSPIRE, IOSTAR, and VICAVR) and achieved high accuracy of 0.830, 0.910, 0.915, 0.928, and 0.889, respectively. The accuracies of arteries/veins classification based on the estimated vascular topology on three public databases (INSPIRE, DRIVE and VICAVR) are 0.90.9, 0.910, and 0.907, respectively. The experimental results show that the proposed framework has effectively addressed crossover problem, a bottleneck issue in segmentation and vascular topology reconstruction. The vascular topology information significantly improves the accuracy on arteries/veins classification. © 2018 American Association of Physicists in Medicine.

Adaptive divergence despite strong genetic drift: genomic analysis of the evolutionary mechanisms causing genetic differentiation in the island fox (Urocyon littoralis).

PubMed

Funk, W Chris; Lovich, Robert E; Hohenlohe, Paul A; Hofman, Courtney A; Morrison, Scott A; Sillett, T Scott; Ghalambor, Cameron K; Maldonado, Jesus E; Rick, Torben C; Day, Mitch D; Polato, Nicholas R; Fitzpatrick, Sarah W; Coonan, Timothy J; Crooks, Kevin R; Dillon, Adam; Garcelon, David K; King, Julie L; Boser, Christina L; Gould, Nicholas; Andelt, William F

2016-05-01

The evolutionary mechanisms generating the tremendous biodiversity of islands have long fascinated evolutionary biologists. Genetic drift and divergent selection are predicted to be strong on islands and both could drive population divergence and speciation. Alternatively, strong genetic drift may preclude adaptation. We conducted a genomic analysis to test the roles of genetic drift and divergent selection in causing genetic differentiation among populations of the island fox (Urocyon littoralis). This species consists of six subspecies, each of which occupies a different California Channel Island. Analysis of 5293 SNP loci generated using Restriction-site Associated DNA (RAD) sequencing found support for genetic drift as the dominant evolutionary mechanism driving population divergence among island fox populations. In particular, populations had exceptionally low genetic variation, small Ne (range = 2.1-89.7; median = 19.4), and significant genetic signatures of bottlenecks. Moreover, islands with the lowest genetic variation (and, by inference, the strongest historical genetic drift) were most genetically differentiated from mainland grey foxes, and vice versa, indicating genetic drift drives genome-wide divergence. Nonetheless, outlier tests identified 3.6-6.6% of loci as high FST outliers, suggesting that despite strong genetic drift, divergent selection contributes to population divergence. Patterns of similarity among populations based on high FST outliers mirrored patterns based on morphology, providing additional evidence that outliers reflect adaptive divergence. Extremely low genetic variation and small Ne in some island fox populations, particularly on San Nicolas Island, suggest that they may be vulnerable to fixation of deleterious alleles, decreased fitness and reduced adaptive potential. © 2016 John Wiley & Sons Ltd.

Mapping supply chain risk by network analysis of product platforms

DOE PAGES

Nuss, Philip; Graedel, T. E.; Alonso, Elisa; ...

2016-10-15

Modern technology makes use of a variety of materials to allow for its proper functioning. Here, to explore in detail the relationships connecting materials to the products that require them, we map supply chains for five product platforms (a cadmium telluride solar cell, a germanium solar cell, a turbine blade, a lead acid battery, and a hard drive (HD) magnet) using a data ontology that specifies the supply chain actors (nodes) and linkages (e.g., material exchange and contractual relationships) among them. We then propose a set of network indicators (product complexity, producer diversity, supply chain length, and potential bottlenecks) tomore » assess the situation for each platform in the overall supply chain networks. Among the results of interest are the following: (1) the turbine blade displays a high product complexity, defined by the material linkages to the platform; (2) the germanium solar cell is produced by only a few manufacturers globally and requires more physical transformation steps than do the other project platforms; (3) including production quantity and sourcing countries in the assessment shows that a large portion of nodes of the supply chain of the hard-drive magnet are located in potentially unreliable countries. Finally, we conclude by discussing how the network analysis of supply chains could be combined with criticality and scenario analyses of abiotic raw materials to comprise a comprehensive picture of product platform risk.« less

Driving simulator evaluation of drivers' response to intersections with dynamic use of exit-lanes for left-turn.

PubMed

Zhao, Jing; Yun, Meiping; Zhang, H Michael; Yang, Xiaoguang

2015-08-01

With the worsening of urban traffic congestion in large cities around the world, researchers have been looking for unconventional designs and/or controls to squeeze more capacity out of intersections, the most common bottlenecks of the road network. One of these innovative intersection designs, known as the exit-lanes for left-turn (EFL), opens up exit-lanes to be used by left-turn traffic with the help of an additional traffic light installed at the median opening (the pre-signal). This paper studies how drivers respond to EFL intersections with a series of driving simulator experiments. In our experiments, 64 drivers were recruited and divided into two groups. One group is trained to use the EFL while the other group is not. In addition, four scenarios were considered with different sign and marking designs and traffic conditions in the experiments. Results indicate that drivers show certain amount of confusion and hesitation when encountering an EFL intersection for the first time. They can be overcome, however, by increasing exposure through driver education or by cue provided from other vehicles. Moreover, drivers unfamiliar with EFL operation can make a left turn using the conventional left-turn lanes as usual. The EFL operation is not likely to pose any serious safety risk of the intersection in real life operations. Copyright © 2015 Elsevier Ltd. All rights reserved.

Mapping supply chain risk by network analysis of product platforms

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

Nuss, Philip; Graedel, T. E.; Alonso, Elisa

Modern technology makes use of a variety of materials to allow for its proper functioning. Here, to explore in detail the relationships connecting materials to the products that require them, we map supply chains for five product platforms (a cadmium telluride solar cell, a germanium solar cell, a turbine blade, a lead acid battery, and a hard drive (HD) magnet) using a data ontology that specifies the supply chain actors (nodes) and linkages (e.g., material exchange and contractual relationships) among them. We then propose a set of network indicators (product complexity, producer diversity, supply chain length, and potential bottlenecks) tomore » assess the situation for each platform in the overall supply chain networks. Among the results of interest are the following: (1) the turbine blade displays a high product complexity, defined by the material linkages to the platform; (2) the germanium solar cell is produced by only a few manufacturers globally and requires more physical transformation steps than do the other project platforms; (3) including production quantity and sourcing countries in the assessment shows that a large portion of nodes of the supply chain of the hard-drive magnet are located in potentially unreliable countries. Finally, we conclude by discussing how the network analysis of supply chains could be combined with criticality and scenario analyses of abiotic raw materials to comprise a comprehensive picture of product platform risk.« less

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.

Bottlenecks in the implementation of essential screening tests in antenatal care: Syphilis, HIV, and anemia testing in rural Tanzania and Uganda.

PubMed

Baker, Ulrika; Okuga, Monica; Waiswa, Peter; Manzi, Fatuma; Peterson, Stefan; Hanson, Claudia

2015-06-01

To identify and compare implementation bottlenecks for effective coverage of screening for syphilis, HIV, and anemia in antenatal care in rural Tanzania and Uganda; and explore the underlying determinants and perceived solutions to overcome these bottlenecks. In this multiple case study, we analyzed data collected as part of the Expanded Quality Management Using Information Power (EQUIP) project between November 2011 and April 2014. Indicators from household interviews (n=4415 mothers) and health facility surveys (n=122) were linked to estimate coverage in stages of implementation between which bottlenecks can be identified. Key informant interviews (n=15) were conducted to explore underlying determinants and analyzed using a framework approach. Large differences in implementation were found within and between countries. Availability and effective coverage was significantly lower for all tests in Uganda compared with Tanzania. Syphilis screening had the lowest availability and effective coverage in both countries. The main implementation bottleneck was poor availability of tests and equipment. Key informant interviews validated these findings and perceived solutions included the need for improved procurement at the central level. Our findings reinforce essential screening as a missed opportunity, caused by a lack of integration of funding and support for comprehensive antenatal care programs. Copyright © 2015 International Federation of Gynecology and Obstetrics. Published by Elsevier Ireland Ltd. All rights reserved.

Design and model for the giant magnetostrictive actuator used on an electronic controlled injector

NASA Astrophysics Data System (ADS)

Xue, Guangming; Zhang, Peilin; He, Zhongbo; Li, Ben; Rong, Ce

2017-05-01

Giant magnetostrictive actuator (GMA) may be a promising candidate actuator to drive an electronic controlled injector as giant magnetostrictive material (GMM) has excellent performances as large output, fast response and high operating stability etc. To meet the driving requirement of the injector, the GMA should produce maximal shortening displacement when energized. An unbiased GMA with a ‘T’ shaped output rod is designed to reach the target. Furthermore, an open-hold-fall type driving voltage is exerted on the actuator coil to accelerate the response speed of the coil current. The actuator displacement is modeled from establishing the sub-models of coil current, magnetic field within GMM rod, magnetization and magnetostrictive strain sequentially. Two modifications are done to make the model more accurate. Firstly, consider the model fails to compute the transient-state response precisely, a dead-zone and delay links are embedded into the coil current sub-model. Secondly, as the magnetization and magnetostrictive strain sub-models just influence the change rule of the transient-state response the linear magnetostrictive strain-magnetic field sub-model is introduced. From experimental results, the modified model with linear magnetostrictive stain expression can predict the actuator displacement quite effectively.

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…

High-speed reference-beam-angle control technique for holographic memory drive

NASA Astrophysics Data System (ADS)

Yamada, Ken-ichiro; Ogata, Takeshi; Hosaka, Makoto; Fujita, Koji; Okuyama, Atsushi

2016-09-01

We developed a holographic memory drive for next-generation optical memory. In this study, we present the key technology for achieving a high-speed transfer rate for reproduction, that is, a high-speed control technique for the reference beam angle. In reproduction in a holographic memory drive, there is the issue that the optimum reference beam angle during reproduction varies owing to distortion of the medium. The distortion is caused by, for example, temperature variation, beam irradiation, and moisture absorption. Therefore, a reference-beam-angle control technique to position the reference beam at the optimum angle is crucial. We developed a new optical system that generates an angle-error-signal to detect the optimum reference beam angle. To achieve the high-speed control technique using the new optical system, we developed a new control technique called adaptive final-state control (AFSC) that adds a second control input to the first one derived from conventional final-state control (FSC) at the time of angle-error-signal detection. We established an actual experimental system employing AFSC to achieve moving control between each page (Page Seek) within 300 µs. In sequential multiple Page Seeks, we were able to realize positioning to the optimum angles of the reference beam that maximize the diffracted beam intensity. We expect that applying the new control technique to the holographic memory drive will enable a giga-bit/s-class transfer rate.

Mechanical model for filament buckling and growth by phase ordering.

PubMed

Rey, Alejandro D; Abukhdeir, Nasser M

2008-02-05

A mechanical model of open filament shape and growth driven by phase ordering is formulated. For a given phase-ordering driving force, the model output is the filament shape evolution and the filament end-point kinematics. The linearized model for the slope of the filament is the Cahn-Hilliard model of spinodal decomposition, where the buckling corresponds to concentration fluctuations. Two modes are predicted: (i) sequential growth and buckling and (ii) simultaneous buckling and growth. The relation among the maximum buckling rate, filament tension, and matrix viscosity is given. These results contribute to ongoing work in smectic A filament buckling.

Timing of recent accelerations of Pine Island Glacier, Antarctica

USGS Publications Warehouse

Joughin, I.; Rignot, E.; Rosanova, C.E.; Lucchitta, B.K.; Bohlander, J.

2003-01-01

We have used Interferometric Synthetic Aperture Radar (InSAR) data and sequential Landsat imagery to identify and temporally constrain two acceleration events on Pine Island Glacier (PIG). These two events are separated by a period of at least seven years (1987 - 1994). The change in discharge between two flux gates indicates that the majority of the increase in discharge associated with the second acceleration originates well inland (>80 km) from the grounding line. An analysis indicates that changes in driving stress consistent with observed thinning rates are sufficient in magnitude to explain much of the acceleration.

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…

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.

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

Strong photon antibunching in weakly nonlinear two-dimensional exciton-polaritons

NASA Astrophysics Data System (ADS)

Ryou, Albert; Rosser, David; Saxena, Abhi; Fryett, Taylor; Majumdar, Arka

2018-06-01

A deterministic and scalable array of single photon nonlinearities in the solid state holds great potential for both fundamental physics and technological applications, but its realization has proved extremely challenging. Despite significant advances, leading candidates such as quantum dots and group III-V quantum wells have yet to overcome their respective bottlenecks in random positioning and weak nonlinearity. Here we consider a hybrid light-matter platform, marrying an atomically thin two-dimensional material to a photonic crystal cavity, and analyze its second-order coherence function. We identify several mechanisms for photon antibunching under different system parameters, including one characterized by large dissipation and weak nonlinearity. Finally, we show that by patterning the two-dimensional material into different sizes, we can drive our system dynamics from a coherent state into a regime of strong antibunching with second-order coherence function g(2 )(0 ) ˜10-3 , opening a possible route to scalable, on-chip quantum simulations with correlated photons.

All-integrated terahertz modulators

NASA Astrophysics Data System (ADS)

Degl'Innocenti, Riccardo; Kindness, Stephen J.; Beere, Harvey E.; Ritchie, David A.

2018-01-01

Terahertz (0.1-10 THz corresponding to vacuum wavelengths between 30 μm and 3 mm) research has experienced impressive progress in the last few decades. The importance of this frequency range stems from unique applications in several fields, including spectroscopy, communications, and imaging. THz emitters have experienced great development recently with the advent of the quantum cascade laser, the improvement in the frequency range covered by electronic-based sources, and the increased performance and versatility of time domain spectroscopic systems based on full-spectrum lasers. However, the lack of suitable active optoelectronic devices has hindered the ability of THz technologies to fulfill their potential. The high demand for fast, efficient integrated optical components, such as amplitude, frequency, and polarization modulators, is driving one of the most challenging research areas in photonics. This is partly due to the inherent difficulties in using conventional integrated modulation techniques. This article aims to provide an overview of the different approaches and techniques recently employed in order to overcome this bottleneck.

Eddies in a bottleneck: an arbitrary Debye length theory for capillary electroosmosis.

PubMed

Park, Stella Y; Russo, Christopher J; Branton, Daniel; Stone, Howard A

2006-05-15

Using an applied electrical field to drive fluid flows becomes desirable as channels become smaller. Although most discussions of electroosmosis treat the case of thin Debye layers, here electroosmotic flow (EOF) through a constricted cylinder is presented for arbitrary Debye lengths (kappa(-1)) using a long wavelength perturbation of the cylinder radius. The analysis uses the approximation of small potentials. The varying diameter of the cylinder produces radially and axially varying effective electric fields, as well as an induced pressure gradient. We predict the existence of eddies for certain constricted geometries and propose the possibility of electrokinetic trapping in these regions. We also present a leading-order criterion which predicts central eddies in very narrow constrictions at the scale of the Debye length. Eddies can be found both in the center of the channel and along the perimeter, and the presence of the eddies is a consequence of the induced pressure gradient that accompanies electrically driven flow into a narrow constriction.

Eddies in a Bottleneck: An Arbitrary Debye Length Theory for Capillary Electroosmosis

PubMed Central

Park, Stella Y.; Russo, Christopher J.; Branton, Daniel; Stone, Howard A.

2011-01-01

Using an applied electrical field to drive fluid flows becomes desirable as channels become smaller. Although most discussions of electroosmosis treat the case of thin Debye layers, here electroosmotic flow (EOF) through a constricted cylinder is presented for arbitrary Debye lengths (κ−1) using a long wavelength perturbation of the cylinder radius. The analysis uses the approximation of small potentials. The varying diameter of the cylinder produces radially and axially varying effective electric fields, as well as an induced pressure gradient. We predict the existence of eddies for certain constricted geometries and propose the possibility of electrokinetic trapping in these regions. We also present a leading-order criterion which predicts central eddies in very narrow constrictions at the scale of the Debye length. Eddies can be found both in the center of the channel and along the perimeter, and the presence of the eddies is a consequence of the induced pressure gradient that accompanies electrically driven flow into a narrow constriction. PMID:16376361

Homogeneity of Powassan virus populations in naturally infected Ixodes scapularis

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

Brackney, Doug E.; Brown, Ivy K.; Nofchissey, Robert A.

2010-07-05

Powassan virus (POWV, Flaviviridae: Flavivirus) is the sole North American member of the tick-borne encephalitis complex and consists of two distinct lineages that are maintained in ecologically discrete enzootic transmission cycles. The underlying genetic mechanisms that lead to niche partitioning in arboviruses are poorly understood. Therefore, intra- and interhost genetic diversity was analyzed to determine if POWV exists as a quasispecies in nature and quantify selective pressures within and between hosts. In contrast to previous reports for West Nile virus (WNV), significant intrahost genetic diversity was not observed. However, pN (0.238) and d{sub N}/d{sub S} ratios (0.092) for interhost diversitymore » were similar to those of WNV. Combined, these data suggest that purifying selection and/or population bottlenecks constrain quasispecies diversity within ticks. These same selective and stochastic mechanisms appear to drive minor sequence changes between ticks. Moreover, Powassan virus populations seem not to be structured as quasispecies in naturally infected adult deer ticks.« less

IOPA: I/O-aware parallelism adaption for parallel programs

PubMed Central

Liu, Tao; Liu, Yi; Qian, Chen; Qian, Depei

2017-01-01

With the development of multi-/many-core processors, applications need to be written as parallel programs to improve execution efficiency. For data-intensive applications that use multiple threads to read/write files simultaneously, an I/O sub-system can easily become a bottleneck when too many of these types of threads exist; on the contrary, too few threads will cause insufficient resource utilization and hurt performance. Therefore, programmers must pay much attention to parallelism control to find the appropriate number of I/O threads for an application. This paper proposes a parallelism control mechanism named IOPA that can adjust the parallelism of applications to adapt to the I/O capability of a system and balance computing resources and I/O bandwidth. The programming interface of IOPA is also provided to programmers to simplify parallel programming. IOPA is evaluated using multiple applications with both solid state and hard disk drives. The results show that the parallel applications using IOPA can achieve higher efficiency than those with a fixed number of threads. PMID:28278236

Nanoscale cross-point diode array accessing embedded high density PCM

NASA Astrophysics Data System (ADS)

Wang, Heng; Liu, Yan; Liu, Bo; Gao, Dan; Xu, Zhen; Zhan, Yipeng; Song, Zhitang; Feng, Songlin

2017-08-01

The main bottlenecks in the development of current embedded phase change memory (PCM) technology are the current density and data storage density. In this paper, we present a PCM with 4F2 cross-point diode selector and blade-type bottom electrode contact (BEC). A blade TiN BEC with a cross-sectional area of 630 nm2 (10 nm × 63 nm) reduces the reset current down to about 750 μA. The optimized diode array could supply this 750 μA reset current at about 1.7 V and low off-current 1 × 10-4 μA at about -5.05 V. The on-off ratio of this device is 7.5 × 106. The proposed nanoscale PCM device simultaneously exhibits an operation voltage as low as 3 V and a high density drive current with an ultra small cell size of 4F2 (108 nm × 108 nm). Over 106 cycling endurance properties guarantee that it can work effectively on the embedded memory.

Technologies for Beneficial Microorganisms Inocula Used as Biofertilizers

PubMed Central

Malusá, E.; Sas-Paszt, L.; Ciesielska, J.

2012-01-01

The increasing need for environmentaly friendly agricultural practices is driving the use of fertilizers based on beneficial microorganisms. The latter belong to a wide array of genera, classes, and phyla, ranging from bacteria to yeasts and fungi, which can support plant nutrition with different mechanisms. Moreover, studies on the interactions between plant, soil, and the different microorganisms are shedding light on their interrelationships thus providing new possible ways to exploit them for agricultural purposes. However, even though the inoculation of plants with these microorganisms is a well-known practice, the formulation of inocula with a reliable and consistent effect under field conditions is still a bottleneck for their wider use. The choice of the technology for inocula production and of the carrier for the formulation is key to their successful application. This paper focuses on how inoculation issues can be approached to improve the performance of beneficial microorganisms used as a tool for enhancing plant growth and yield. PMID:22547984

Homogeneity of Powassan virus populations in naturally infected Ixodes scapularis.

PubMed

Brackney, Doug E; Brown, Ivy K; Nofchissey, Robert A; Fitzpatrick, Kelly A; Ebel, Gregory D

2010-07-05

Powassan virus (POWV, Flaviviridae: Flavivirus) is the sole North American member of the tick-borne encephalitis complex and consists of two distinct lineages that are maintained in ecologically discrete enzootic transmission cycles. The underlying genetic mechanisms that lead to niche partitioning in arboviruses are poorly understood. Therefore, intra- and interhost genetic diversity was analyzed to determine if POWV exists as a quasispecies in nature and quantify selective pressures within and between hosts. In contrast to previous reports for West Nile virus (WNV), significant intrahost genetic diversity was not observed. However, pN (0.238) and d(N)/d(S) ratios (0.092) for interhost diversity were similar to those of WNV. Combined, these data suggest that purifying selection and/or population bottlenecks constrain quasispecies diversity within ticks. These same selective and stochastic mechanisms appear to drive minor sequence changes between ticks. Moreover, Powassan virus populations seem not to be structured as quasispecies in naturally infected adult deer ticks. Copyright 2010 Elsevier Inc. All rights reserved.

HOMOGENEITY OF POWASSAN VIRUS POPULATIONS IN NATURALLY INFECTED IXODES SCAPULARIS

PubMed Central

Brackney, Doug E.; Brown, Ivy K.; Nofchissey, Robert A.; Fitzpatrick, Kelly A.; Ebel, Gregory D.

2010-01-01

Powassan virus (POWV, Flaviviridae: Flavivirus) is the sole North American member of the tick-borne encephalitis complex and consists of two distinct lineages that are maintained in ecologically discrete enzootic transmission cycles. The underlying genetic mechanisms that lead to niche partitioning in arboviruses are poorly understood. Therefore, intra- and interhost genetic diversity was analyzed to determine if POWV exists as a quasispecies in nature and quantify selective pressures within and between hosts. In contrast to previous reports for West Nile virus (WNV), significant intrahost genetic diversity was not observed. However, pN (0.238) and dN/dS ratios (0.092) for interhost diversity were similar to those of WNV. Combined, these data suggest that purifying selection and/or population bottlenecks constrain quasispecies diversity within ticks. These same selective and stochastic mechanisms appear to drive minor sequence changes between ticks. Moreover, Powassan virus populations seem not to be structured as quasispecies in naturally infected adult deer ticks. PMID:20434750

Low-power, transparent optical network interface for high bandwidth off-chip interconnects.

PubMed

Liboiron-Ladouceur, Odile; Wang, Howard; Garg, Ajay S; Bergman, Keren

2009-04-13

The recent emergence of multicore architectures and chip multiprocessors (CMPs) has accelerated the bandwidth requirements in high-performance processors for both on-chip and off-chip interconnects. For next generation computing clusters, the delivery of scalable power efficient off-chip communications to each compute node has emerged as a key bottleneck to realizing the full computational performance of these systems. The power dissipation is dominated by the off-chip interface and the necessity to drive high-speed signals over long distances. We present a scalable photonic network interface approach that fully exploits the bandwidth capacity offered by optical interconnects while offering significant power savings over traditional E/O and O/E approaches. The power-efficient interface optically aggregates electronic serial data streams into a multiple WDM channel packet structure at time-of-flight latencies. We demonstrate a scalable optical network interface with 70% improvement in power efficiency for a complete end-to-end PCI Express data transfer.

IOPA: I/O-aware parallelism adaption for parallel programs.

PubMed

Liu, Tao; Liu, Yi; Qian, Chen; Qian, Depei

2017-01-01

With the development of multi-/many-core processors, applications need to be written as parallel programs to improve execution efficiency. For data-intensive applications that use multiple threads to read/write files simultaneously, an I/O sub-system can easily become a bottleneck when too many of these types of threads exist; on the contrary, too few threads will cause insufficient resource utilization and hurt performance. Therefore, programmers must pay much attention to parallelism control to find the appropriate number of I/O threads for an application. This paper proposes a parallelism control mechanism named IOPA that can adjust the parallelism of applications to adapt to the I/O capability of a system and balance computing resources and I/O bandwidth. The programming interface of IOPA is also provided to programmers to simplify parallel programming. IOPA is evaluated using multiple applications with both solid state and hard disk drives. The results show that the parallel applications using IOPA can achieve higher efficiency than those with a fixed number of threads.

The Molecular Industrial Revolution: Automated Synthesis of Small Molecules.

PubMed

Trobe, Melanie; Burke, Martin D

2018-04-09

Today we are poised for a transition from the highly customized crafting of specific molecular targets by hand to the increasingly general and automated assembly of different types of molecules with the push of a button. Creating machines that are capable of making many different types of small molecules on demand, akin to that which has been achieved on the macroscale with 3D printers, is challenging. Yet important progress is being made toward this objective with two complementary approaches: 1) Automation of customized synthesis routes to different targets by machines that enable the use of many reactions and starting materials, and 2) automation of generalized platforms that make many different targets using common coupling chemistry and building blocks. Continued progress in these directions has the potential to shift the bottleneck in molecular innovation from synthesis to imagination, and thereby help drive a new industrial revolution on the molecular scale. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

An Orthogonal and pH-Tunable Sensor-Selector for Muconic Acid Biosynthesis in Yeast.

PubMed

Snoek, Tim; Romero-Suarez, David; Zhang, Jie; Ambri, Francesca; Skjoedt, Mette L; Sudarsan, Suresh; Jensen, Michael K; Keasling, Jay D

2018-04-20

Microbes offer enormous potential for production of industrially relevant chemicals and therapeutics, yet the rapid identification of high-producing microbes from large genetic libraries is a major bottleneck in modern cell factory development. Here, we develop and apply a synthetic selection system in Saccharomyces cerevisiae that couples the concentration of muconic acid, a plastic precursor, to cell fitness by using the prokaryotic transcriptional regulator BenM driving an antibiotic resistance gene. We show that the sensor-selector does not affect production nor fitness, and find that tuning pH of the cultivation medium limits the rise of nonproducing cheaters. We apply the sensor-selector to selectively enrich for best-producing variants out of a large library of muconic acid production strains, and identify an isolate that produces more than 2 g/L muconic acid in a bioreactor. We expect that this sensor-selector can aid the development of other synthetic selection systems based on allosteric transcription factors.

Study of data I/O performance on distributed disk system in mask data preparation

NASA Astrophysics Data System (ADS)

Ohara, Shuichiro; Odaira, Hiroyuki; Chikanaga, Tomoyuki; Hamaji, Masakazu; Yoshioka, Yasuharu

2010-09-01

Data volume is getting larger every day in Mask Data Preparation (MDP). In the meantime, faster data handling is always required. MDP flow typically introduces Distributed Processing (DP) system to realize the demand because using hundreds of CPU is a reasonable solution. However, even if the number of CPU were increased, the throughput might be saturated because hard disk I/O and network speeds could be bottlenecks. So, MDP needs to invest a lot of money to not only hundreds of CPU but also storage and a network device which make the throughput faster. NCS would like to introduce new distributed processing system which is called "NDE". NDE could be a distributed disk system which makes the throughput faster without investing a lot of money because it is designed to use multiple conventional hard drives appropriately over network. NCS studies I/O performance with OASIS® data format on NDE which contributes to realize the high throughput in this paper.

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.

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.

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.

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

A Hybrid Shared-Memory Parallel Max-Tree Algorithm for Extreme Dynamic-Range Images.

PubMed

Moschini, Ugo; Meijster, Arnold; Wilkinson, Michael H F

2018-03-01

Max-trees, or component trees, are graph structures that represent the connected components of an image in a hierarchical way. Nowadays, many application fields rely on images with high-dynamic range or floating point values. Efficient sequential algorithms exist to build trees and compute attributes for images of any bit depth. However, we show that the current parallel algorithms perform poorly already with integers at bit depths higher than 16 bits per pixel. We propose a parallel method combining the two worlds of flooding and merging max-tree algorithms. First, a pilot max-tree of a quantized version of the image is built in parallel using a flooding method. Later, this structure is used in a parallel leaf-to-root approach to compute efficiently the final max-tree and to drive the merging of the sub-trees computed by the threads. We present an analysis of the performance both on simulated and actual 2D images and 3D volumes. Execution times are about better than the fastest sequential algorithm and speed-up goes up to on 64 threads.

Attosecond Spectroscopy Probing Electron Correlation Dynamics

NASA Astrophysics Data System (ADS)

Winney, Alexander H.

Electrons are the driving force behind every chemical reaction. The exchange, ionization, or even relaxation of electrons is behind every bond broken or formed. According to the Bohr model of the atom, it takes an electron 150 as to orbit a proton[6]. With this as a unit time scale for an electron, it is clear that a pulse duration of several femtoseconds will not be sufficient to understanding electron dynamics. Our work demonstrates both technical and scientific achievements that push the boundaries of attosecond dynamics. TDSE studies show that amplification the yield of high harmonic generation (HHG) may be possible with transverse confinement of the electron. XUV-pump-XUV-probe shows that the yield of APT train can be sufficient for 2-photon double ionization studies. A zero dead-time detection system allows for the measurement of state-resolved double ionization for the first time. Exploiting attosecond angular streaking[7] probes sequential and non-sequential double ionization via electron-electron correlations with attosecond time resolution. Finally, using recoil frame momentum correlation, the fast dissociation of CH 3I reveals important orbital ionization dynamics of non-dissociative & dissociative, single & double ionization.

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.

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.

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…

Saccadic Eye Movements Impose a Natural Bottleneck on Visual Short-Term Memory

ERIC Educational Resources Information Center

Ohl, Sven; Rolfs, Martin

2017-01-01

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…

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.

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.

Evasion of cell senescence in SHH medulloblastoma.

PubMed

Tamayo-Orrego, Lukas; Swikert, Shannon M; Charron, Frédéric

2016-08-17

The mechanisms leading to brain tumor formation are poorly understood. Using Ptch1 +/- mice as a medulloblastoma model, sequential mutations were found to shape tumor evolution. Initially, medulloblastoma preneoplastic lesions display loss of heterozygosity of the Ptch1 wild-type allele, an event associated with cell senescence in preneoplasia. Subsequently, p53 mutations lead to senescence evasion and progression from preneoplasia to medulloblastoma. These findings are consistent with a model where high levels of Hedgehog signaling caused by the loss of the tumor suppressor Ptch1 lead to oncogene-induced senescence and drive p53 mutations. Thus, cell senescence is an important characteristic of a subset of SHH medulloblastoma and might explain the acquisition of somatic TP53 mutations in human medulloblastoma. This mode of medulloblastoma formation contrasts with the one characterizing Li-Fraumeni patients with medulloblastoma, where TP53 germ-line mutations cause chromothriptic genomic instability and lead to mutations in Hedgehog signaling genes, which drive medulloblastoma growth. Here we discuss in detail these 2 alternative mechanisms leading to medulloblastoma tumorigenesis.

Evasion of cell senescence in SHH medulloblastoma

PubMed Central

Tamayo-Orrego, Lukas; Swikert, Shannon M.; Charron, Frédéric

2016-01-01

ABSTRACT The mechanisms leading to brain tumor formation are poorly understood. Using Ptch1+/− mice as a medulloblastoma model, sequential mutations were found to shape tumor evolution. Initially, medulloblastoma preneoplastic lesions display loss of heterozygosity of the Ptch1 wild-type allele, an event associated with cell senescence in preneoplasia. Subsequently, p53 mutations lead to senescence evasion and progression from preneoplasia to medulloblastoma. These findings are consistent with a model where high levels of Hedgehog signaling caused by the loss of the tumor suppressor Ptch1 lead to oncogene-induced senescence and drive p53 mutations. Thus, cell senescence is an important characteristic of a subset of SHH medulloblastoma and might explain the acquisition of somatic TP53 mutations in human medulloblastoma. This mode of medulloblastoma formation contrasts with the one characterizing Li-Fraumeni patients with medulloblastoma, where TP53 germ-line mutations cause chromothriptic genomic instability and lead to mutations in Hedgehog signaling genes, which drive medulloblastoma growth. Here we discuss in detail these 2 alternative mechanisms leading to medulloblastoma tumorigenesis. PMID:27229128

Chamber identity programs drive early functional partitioning of the heart.

PubMed

Mosimann, Christian; Panáková, Daniela; Werdich, Andreas A; Musso, Gabriel; Burger, Alexa; Lawson, Katy L; Carr, Logan A; Nevis, Kathleen R; Sabeh, M Khaled; Zhou, Yi; Davidson, Alan J; DiBiase, Anthony; Burns, Caroline E; Burns, C Geoffrey; MacRae, Calum A; Zon, Leonard I

2015-08-26

The vertebrate heart muscle (myocardium) develops from the first heart field (FHF) and expands by adding second heart field (SHF) cells. While both lineages exist already in teleosts, the primordial contributions of FHF and SHF to heart structure and function remain incompletely understood. Here we delineate the functional contribution of the FHF and SHF to the zebrafish heart using the cis-regulatory elements of the draculin (drl) gene. The drl reporters initially delineate the lateral plate mesoderm, including heart progenitors. Subsequent myocardial drl reporter expression restricts to FHF descendants. We harnessed this unique feature to uncover that loss of tbx5a and pitx2 affect relative FHF versus SHF contributions to the heart. High-resolution physiology reveals distinctive electrical properties of each heart field territory that define a functional boundary within the single zebrafish ventricle. Our data establish that the transcriptional program driving cardiac septation regulates physiologic ventricle partitioning, which successively provides mechanical advantages of sequential contraction.

A Sequential Shifting Algorithm for Variable Rotor Speed Control

NASA Technical Reports Server (NTRS)

Litt, Jonathan S.; Edwards, Jason M.; DeCastro, Jonathan A.

2007-01-01

A proof of concept of a continuously variable rotor speed control methodology for rotorcraft is described. Variable rotor speed is desirable for several reasons including improved maneuverability, agility, and noise reduction. However, it has been difficult to implement because turboshaft engines are designed to operate within a narrow speed band, and a reliable drive train that can provide continuous power over a wide speed range does not exist. The new methodology proposed here is a sequential shifting control for twin-engine rotorcraft that coordinates the disengagement and engagement of the two turboshaft engines in such a way that the rotor speed may vary over a wide range, but the engines remain within their prescribed speed bands and provide continuous torque to the rotor; two multi-speed gearboxes facilitate the wide rotor speed variation. The shifting process begins when one engine slows down and disengages from the transmission by way of a standard freewheeling clutch mechanism; the other engine continues to apply torque to the rotor. Once one engine disengages, its gear shifts, the multi-speed gearbox output shaft speed resynchronizes and it re-engages. This process is then repeated with the other engine. By tailoring the sequential shifting, the rotor may perform large, rapid speed changes smoothly, as demonstrated in several examples. The emphasis of this effort is on the coordination and control aspects for proof of concept. The engines, rotor, and transmission are all simplified linear models, integrated to capture the basic dynamics of the problem.

White-light-emitting organic electroluminescent devices based on interlayer sequential energy transfer

NASA Astrophysics Data System (ADS)

Deshpande, R. S.; Bulović, V.; Forrest, S. R.

1999-08-01

We demonstrate efficient, molecular organic white-light-emitting devices using vacuum-deposited thin films of red luminescent [2-methyl-6-[2-(2,3,6,7-tetrahydro-1H, 5H-benzo [ij] quinolizin-9-yl) ethenyl]-4H-pyran-4-ylidene] propane-dinitrile (DCM2), doped into blue-emitting 4, 4' bis [N-1-napthyl-N-phenyl-amino]biphenyl (α-NPD), and green-emitting tris-(8-hydroxyquinolinato) aluminum(III) (AlQ3). The luminescent layers are separated by a hole-blocking layer of 2,9-dimethyl, 4,7-diphenyl, 1,10-phenanthroline (BCP), whose thickness is on the order of a typical Förster transfer radius of 30-40 Å. Excitons formed on α-NPD sequentially transfer their energy via a Förster mechanism to AlQ3 across the BCP layer, and from AlQ3 to DCM2. This interlayer sequential energy transfer results in partial excitation of all three molecular species, thereby producing white light emission. The thickness of the blocking layer and the concentration of DCM2 in α-NPD permit the tuning of the device spectrum to achieve a balanced white emission with Commission Internationale d'Eclairage chromaticity coordinates of (0.33, 0.33). The spectrum is largely insensitive to the drive current, and the devices have a maximum luminance of 13 500 cd/m2. At a luminance of 100 cd/m2, the quantum and power efficiencies are 0.5% and 0.35 lm/W, respectively.

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.

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

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.

Driver Gaze Behavior Is Different in Normal Curve Driving and when Looking at the Tangent Point

PubMed Central

Itkonen, Teemu; Pekkanen, Jami; Lappi, Otto

2015-01-01

Several steering models in the visual science literature attempt to capture the visual strategies in curve driving. Some of them are based on steering points on the future path (FP), others on tangent points (TP). It is, however, challenging to differentiate between the models’ predictions in real–world contexts. Analysis of optokinetic nystagmus (OKN) parameters is one useful measure, as the different strategies predict measurably different OKN patterns. Here, we directly test this prediction by asking drivers to either a) “drive as they normally would” or b) to “look at the TP”. The design of the experiment is similar to a previous study by Kandil et al., but uses more sophisticated methods of eye–movement analysis. We find that the eye-movement patterns in the “normal” condition are indeed markedly different from the “tp” condition, and consistent with drivers looking at waypoints on the future path. This is the case for both overall fixation distribution, as well as the more informative fixation–by–fixation analysis of OKN. We find that the horizontal gaze speed during OKN corresponds well to the quantitative prediction of the future path models. The results also definitively rule out the alternative explanation that the OKN is produced by an involuntary reflex even while the driver is “trying” to look at the TP. The results are discussed in terms of the sequential organization of curve driving. PMID:26287914

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.

Demonstration of fully enabled data center subsystem with embedded optical interconnect

NASA Astrophysics Data System (ADS)

Pitwon, Richard; Worrall, Alex; Stevens, Paul; Miller, Allen; Wang, Kai; Schmidtke, Katharine

2014-03-01

The evolution of data storage communication protocols and corresponding in-system bandwidth densities is set to impose prohibitive cost and performance constraints on future data storage system designs, fuelling proposals for hybrid electronic and optical architectures in data centers. The migration of optical interconnect into the system enclosure itself can substantially mitigate the communications bottlenecks resulting from both the increase in data rate and internal interconnect link lengths. In order to assess the viability of embedding optical links within prevailing data storage architectures, we present the design and assembly of a fully operational data storage array platform, in which all internal high speed links have been implemented optically. This required the deployment of mid-board optical transceivers, an electro-optical midplane and proprietary pluggable optical connectors for storage devices. We present the design of a high density optical layout to accommodate the midplane interconnect requirements of a data storage enclosure with support for 24 Small Form Factor (SFF) solid state or rotating disk drives and the design of a proprietary optical connector and interface cards, enabling standard drives to be plugged into an electro-optical midplane. Crucially, we have also modified the platform to accommodate longer optical interconnect lengths up to 50 meters in order to investigate future datacenter architectures based on disaggregation of modular subsystems. The optically enabled data storage system has been fully validated for both 6 Gb/s and 12 Gb/s SAS data traffic conveyed along internal optical links.

Memory effects in microscopic traffic models and wide scattering in flow-density data

NASA Astrophysics Data System (ADS)

Treiber, Martin; Helbing, Dirk

2003-10-01

By means of microscopic simulations we show that noninstantaneous adaptation of the driving behavior to the traffic situation together with the conventional method to measure flow-density data provides a possible explanation for the observed inverse-λ shape and the wide scattering of flow-density data in “synchronized” congested traffic. We model a memory effect in the response of drivers to the traffic situation for a wide class of car-following models by introducing an additional dynamical variable (the “subjective level of service”) describing the adaptation of drivers to the surrounding traffic situation during the past few minutes and couple this internal state to parameters of the underlying model that are related to the driving style. For illustration, we use the intelligent-driver model (IDM) as the underlying model, characterize the level of service solely by the velocity, and couple the internal variable to the IDM parameter “time gap” to model an increase of the time gap in congested traffic (“frustration effect”), which is supported by single-vehicle data. We simulate open systems with a bottleneck and obtain flow-density data by implementing “virtual detectors.” The shape, relative size, and apparent “stochasticity” of the region of the scattered data points agree nearly quantitatively with empirical data. Wide scattering is even observed for identical vehicles, although the proposed model is a time-continuous, deterministic, single-lane car-following model with a unique fundamental diagram.

Quasistationary Plasma Predator-Prey System of Coupled Turbulence, Drive, and Sheared E × B Flow During High Performance DIII-D Tokamak Discharges [A New, Quasi-stationary Plasma Predator-Prey System of Coupled Turbulence, Drive, and Sheared E × B Flow During High Performance DIII-D Tokamak Discharges

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

Barada, Kshitish; Rhodes, Terry L.; Burrell, Keith H.

A new, long-lived limit cycle oscillation (LCO) regime has been observed in the edge of near zero torque high-performance DIII-D tokamak plasma discharges. These LCOs are localized and comprised of density turbulence, gradient drives, and E X B velocity shear damping ( E and B are the local radial electric and total magnetic fields). Density turbulence sequentially acts as a predator (via turbulence transport) of profile gradients and a prey (via shear suppression) to the E X B velocity shear. Reported here for the first time, a unique spatiotemporal variation of the local E X B velocity which is foundmore » to be essential for the existence of this system. The LCO system is quasi-stationary, existing from 3 to 12 plasma energy confinement times (~30 to 900 LCO cycles) limited by hardware constraints. In conclusion, this plasma system appears to contribute strongly to the edge transport in these high-performance and transient-free plasmas as evident from oscillations in transport relevant edge parameters at LCO timescale.« less

Age- and cohort-related variance of type-A behavior over 24 years: the Young Finns Study.

PubMed

Hintsa, Taina; Jokela, Markus; Pulkki-Råback, Laura; Keltikangas-Järvinen, Liisa

2014-12-01

Over the recent decades, the incidence of cardiovascular and heart diseases has decreased while levels of type-A behavior, i.e., a potential risk factor, appear to have increased. However, the long-term developmental patterns of type-A behavior is poorly understood. Both age- and cohort-related changes may be involved in these developments. The purpose of this study was to examine an age- and cohort-related changes of Hunter-Wolf type-A behavior from adolescence to adulthood. Type-A behavior and its components (aggressiveness, leadership, hard driving, and eagerness energy) were assessed using the Hunter-Wolf A-B rating scale at five time points (1983, 1986, 1989, 2001, and 2007) in a population-based sample consisting of six birth cohorts born between 1962 and 1977 (n = 3,341, a total of 10,506 person observations). Development of type-A behavior and its components was examined with cohort-sequential multilevel modeling. Aggressiveness decreased with age, eagerness energy, hard driving, and global type-A behavior increased, and leadership exhibited no mean level changes. Younger cohorts had higher aggressiveness, lower hard driving, and global type-A behavior. The findings suggest that in order to understand the health consequences of type-A behavior, both life span and societal changes should be considered.

Quasistationary Plasma Predator-Prey System of Coupled Turbulence, Drive, and Sheared E × B Flow During High Performance DIII-D Tokamak Discharges [A New, Quasi-stationary Plasma Predator-Prey System of Coupled Turbulence, Drive, and Sheared E × B Flow During High Performance DIII-D Tokamak Discharges

DOE PAGES

Barada, Kshitish; Rhodes, Terry L.; Burrell, Keith H.; ...

2018-03-27

A new, long-lived limit cycle oscillation (LCO) regime has been observed in the edge of near zero torque high-performance DIII-D tokamak plasma discharges. These LCOs are localized and comprised of density turbulence, gradient drives, and E X B velocity shear damping ( E and B are the local radial electric and total magnetic fields). Density turbulence sequentially acts as a predator (via turbulence transport) of profile gradients and a prey (via shear suppression) to the E X B velocity shear. Reported here for the first time, a unique spatiotemporal variation of the local E X B velocity which is foundmore » to be essential for the existence of this system. The LCO system is quasi-stationary, existing from 3 to 12 plasma energy confinement times (~30 to 900 LCO cycles) limited by hardware constraints. In conclusion, this plasma system appears to contribute strongly to the edge transport in these high-performance and transient-free plasmas as evident from oscillations in transport relevant edge parameters at LCO timescale.« less

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.

Peripheral chemoreceptors tune inspiratory drive via tonic expiratory neuron hubs in the medullary ventral respiratory column network.

PubMed

Segers, L S; Nuding, S C; Ott, M M; Dean, J B; Bolser, D C; O'Connor, R; Morris, K F; Lindsey, B G

2015-01-01

Models of brain stem ventral respiratory column (VRC) circuits typically emphasize populations of neurons, each active during a particular phase of the respiratory cycle. We have proposed that "tonic" pericolumnar expiratory (t-E) neurons tune breathing during baroreceptor-evoked reductions and central chemoreceptor-evoked enhancements of inspiratory (I) drive. The aims of this study were to further characterize the coordinated activity of t-E neurons and test the hypothesis that peripheral chemoreceptors also modulate drive via inhibition of t-E neurons and disinhibition of their inspiratory neuron targets. Spike trains of 828 VRC neurons were acquired by multielectrode arrays along with phrenic nerve signals from 22 decerebrate, vagotomized, neuromuscularly blocked, artificially ventilated adult cats. Forty-eight of 191 t-E neurons fired synchronously with another t-E neuron as indicated by cross-correlogram central peaks; 32 of the 39 synchronous pairs were elements of groups with mutual pairwise correlations. Gravitational clustering identified fluctuations in t-E neuron synchrony. A network model supported the prediction that inhibitory populations with spike synchrony reduce target neuron firing probabilities, resulting in offset or central correlogram troughs. In five animals, stimulation of carotid chemoreceptors evoked changes in the firing rates of 179 of 240 neurons. Thirty-two neuron pairs had correlogram troughs consistent with convergent and divergent t-E inhibition of I cells and disinhibitory enhancement of drive. Four of 10 t-E neurons that responded to sequential stimulation of peripheral and central chemoreceptors triggered 25 cross-correlograms with offset features. The results support the hypothesis that multiple afferent systems dynamically tune inspiratory drive in part via coordinated t-E neurons. Copyright © 2015 the American Physiological Society.

Peripheral chemoreceptors tune inspiratory drive via tonic expiratory neuron hubs in the medullary ventral respiratory column network

PubMed Central

Segers, L. S.; Nuding, S. C.; Ott, M. M.; Dean, J. B.; Bolser, D. C.; O'Connor, R.; Morris, K. F.

2014-01-01

Models of brain stem ventral respiratory column (VRC) circuits typically emphasize populations of neurons, each active during a particular phase of the respiratory cycle. We have proposed that “tonic” pericolumnar expiratory (t-E) neurons tune breathing during baroreceptor-evoked reductions and central chemoreceptor-evoked enhancements of inspiratory (I) drive. The aims of this study were to further characterize the coordinated activity of t-E neurons and test the hypothesis that peripheral chemoreceptors also modulate drive via inhibition of t-E neurons and disinhibition of their inspiratory neuron targets. Spike trains of 828 VRC neurons were acquired by multielectrode arrays along with phrenic nerve signals from 22 decerebrate, vagotomized, neuromuscularly blocked, artificially ventilated adult cats. Forty-eight of 191 t-E neurons fired synchronously with another t-E neuron as indicated by cross-correlogram central peaks; 32 of the 39 synchronous pairs were elements of groups with mutual pairwise correlations. Gravitational clustering identified fluctuations in t-E neuron synchrony. A network model supported the prediction that inhibitory populations with spike synchrony reduce target neuron firing probabilities, resulting in offset or central correlogram troughs. In five animals, stimulation of carotid chemoreceptors evoked changes in the firing rates of 179 of 240 neurons. Thirty-two neuron pairs had correlogram troughs consistent with convergent and divergent t-E inhibition of I cells and disinhibitory enhancement of drive. Four of 10 t-E neurons that responded to sequential stimulation of peripheral and central chemoreceptors triggered 25 cross-correlograms with offset features. The results support the hypothesis that multiple afferent systems dynamically tune inspiratory drive in part via coordinated t-E neurons. PMID:25343784

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.

Distributional Preferences, Reciprocity-Like Behavior, and Efficiency in Bilateral Exchange

PubMed Central

Benjamin, Daniel J.

2014-01-01

Under what conditions do distributional preferences, such as altruism or a concern for fair outcomes, generate efficient trade? I analyze theoretically a simple bilateral exchange game: each player sequentially takes an action that reduces his own material payoff but increases the other player’s. Each player’s preferences may depend on both his/her own material payoff and the other player’s. I identify two key properties of the second-mover’s preferences: indifference curves kinked around “fair” material-payoff distributions, and materials payoffs entering preferences as “normal goods.” Either property can drive reciprocity-like behavior and generate a Pareto efficient outcome. PMID:25664144

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.

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

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.

Putative human sperm Interactome: a networks study.

PubMed

Ordinelli, Alessandra; Bernabò, Nicola; Orsini, Massimiliano; Mattioli, Mauro; Barboni, Barbara

2018-04-11

For over sixty years, it has been known that mammalian spermatozoa immediately after ejaculation are virtually infertile. They became able to fertilize only after they reside for long time (hours to days) within female genital tract where they complete their functional maturation, the capacitation. This process is finely regulated by the interaction with the female environment and involves, in spermatozoa, a myriad of molecules as messengers and target of signals. Since, to date, a model able to represent the molecular interaction that characterize sperm physiology does not exist, we realized the Human Sperm Interactme Network3.0 (HSIN3.0) and its main component (HSNI3.0_MC), starting from the pathway active in male germ cells. HSIN3.0 and HSIN3.0_MC are scale free networks, adherent to the Barabasi-Albert model, and are characterised by an ultra-small world topology. We found that they are resistant to random attacks and that are designed to respond quickly and specifically to external inputs. In addition, it has been possible to identify the most connected nodes (the hubs) and the bottlenecks nodes. This result allowed us to explore the control mechanisms active in driving sperm biochemical machinery and to verify the different levels of controls: party vs. date hubs and hubs vs. bottlenecks, thanks the availability of data from KO mice. Finally, we found that several key nodes represent molecules specifically involved in function that are thought to be not present or not active in sperm cells, such as control of cell cycle, proteins synthesis, nuclear trafficking, and immune response, thus potentially open new perspectives on the study of sperm biology. For the first time we present a network representing putative human sperm interactome. This result gives very intriguing biological information and could contribute to the knowledge of spermatozoa, either in physiological or pathological conditions.

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.

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.

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

Health systems and noncommunicable diseases in the Asia-Pacific region: a review of the published literature.

PubMed

Mannava, Priya; Abdullah, Asnawi; James, Chris; Dodd, Rebecca; Annear, Peter Leslie

2015-03-01

Addressing the growing burden of noncommunicable diseases (NCDs) in countries of the Asia-Pacific region requires well-functioning health systems. In low- and middle-income countries (LMICs), however, health systems are generally characterized by inadequate financial and human resources, unsuitable service delivery models, and weak information systems. The aims of this review were to identify (a) health systems interventions being implemented to deliver NCD programs and services and their outcomes and (b) the health systems bottlenecks impeding access to or delivery of these programs and services in LMICs of the Asia-Pacific region. A search of 4 databases for literature published between 1990 and 2010 retrieved 36 relevant studies. For each study, information on basic characteristics, type of health systems bottleneck/intervention, and outcome was extracted, and methodological quality appraised. Health systems interventions and bottlenecks were classified as per the World Health Organization health systems building blocks framework. The review identified interventions and bottlenecks in the building blocks of service delivery, health workforce, financing, health information systems, and medical products, vaccines, and technologies. Studies, however, were heterogeneous in methodologies used, and the overall quality was generally low. There are several gaps in the evidence base around NCDs in the Asia-Pacific region that require further investigation. © 2013 APJPH.

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.

"Plate cherry picking": a novel semi-sequential screening paradigm for cheaper, faster, information-rich compound selection.

PubMed

Crisman, Thomas J; Jenkins, Jeremy L; Parker, Christian N; Hill, W Adam G; Bender, Andreas; Deng, Zhan; Nettles, James H; Davies, John W; Glick, Meir

2007-04-01

This work describes a novel semi-sequential technique for in silico enhancement of high-throughput screening (HTS) experiments now employed at Novartis. It is used in situations in which the size of the screen is limited by the readout (e.g., high-content screens) or the amount of reagents or tools (proteins or cells) available. By performing computational chemical diversity selection on a per plate basis (instead of a per compound basis), 25% of the 1,000,000-compound screening was optimized for general initial HTS. Statistical models are then generated from target-specific primary results (percentage inhibition data) to drive the cherry picking and testing from the entire collection. Using retrospective analysis of 11 HTS campaigns, the authors show that this method would have captured on average two thirds of the active compounds (IC(50) < 10 microM) and three fourths of the active Murcko scaffolds while decreasing screening expenditure by nearly 75%. This result is true for a wide variety of targets, including G-protein-coupled receptors, chemokine receptors, kinases, metalloproteinases, pathway screens, and protein-protein interactions. Unlike time-consuming "classic" sequential approaches that require multiple iterations of cherry picking, testing, and building statistical models, here individual compounds are cherry picked just once, based directly on primary screening data. Strikingly, the authors demonstrate that models built from primary data are as robust as models built from IC(50) data. This is true for all HTS campaigns analyzed, which represent a wide variety of target classes and assay types.

Flynn effects on sub-factors of episodic and semantic memory: parallel gains over time and the same set of determining factors.

PubMed

Rönnlund, Michael; Nilsson, Lars-Göran

2009-09-01

The study examined the extent to which time-related gains in cognitive performance, so-called Flynn effects, generalize across sub-factors of episodic memory (recall and recognition) and semantic memory (knowledge and fluency). We conducted time-sequential analyses of data drawn from the Betula prospective cohort study, involving four age-matched samples (35-80 years; N=2996) tested on the same battery of memory tasks on either of four occasions (1989, 1995, 1999, and 2004). The results demonstrate substantial time-related improvements on recall and recognition as well as on fluency and knowledge, with a trend of larger gains on semantic as compared with episodic memory [Rönnlund, M., & Nilsson, L. -G. (2008). The magnitude, generality, and determinants of Flynn effects on forms of declarative memory: Time-sequential analyses of data from a Swedish cohort study. Intelligence], but highly similar gains across the sub-factors. Finally, the association with markers of environmental change was similar, with evidence that historical increases in quantity of schooling was a main driving force behind the gains, both on the episodic and semantic sub-factors. The results obtained are discussed in terms of brain regions involved.

A comparative analysis of sex change in Labridae supports the size advantage hypothesis.

PubMed

Kazancioğlu, Erem; Alonzo, Suzanne H

2010-08-01

The size advantage hypothesis (SAH) predicts that the rate of increase in male and female fitness with size (the size advantage) drives the evolution of sequential hermaphroditism or sex change. Despite qualitative agreement between empirical patterns and SAH, only one comparative study tested SAH quantitatively. Here, we perform the first comparative analysis of sex change in Labridae, a group of hermaphroditic and dioecious (non-sex changer) fish with several model sex-changing species. We also estimate, for the first time, rates of evolutionary transitions between sex change and dioecy. Our analyses support SAH and indicate that the evolution of hermaphroditism is correlated to the size advantage. Furthermore, we find that transitions from sex change to dioecy are less likely under stronger size advantage. We cannot determine, however, how the size advantage affects transitions from dioecy to sex change. Finally, contrary to what is generally expected, we find that transitions from dioecy to sex change are more likely than transitions from sex change to dioecy. The similarity of sexual differentiation in hermaphroditic and dioecious labrids might underlie this pattern. We suggest that elucidating the developmental basis of sex change is critical to predict and explain patterns of the evolutionary history of sequential hermaphroditism.

Context-dependent decision-making: a simple Bayesian model

PubMed Central

Lloyd, Kevin; Leslie, David S.

2013-01-01

Many phenomena in animal learning can be explained by a context-learning process whereby an animal learns about different patterns of relationship between environmental variables. Differentiating between such environmental regimes or ‘contexts’ allows an animal to rapidly adapt its behaviour when context changes occur. The current work views animals as making sequential inferences about current context identity in a world assumed to be relatively stable but also capable of rapid switches to previously observed or entirely new contexts. We describe a novel decision-making model in which contexts are assumed to follow a Chinese restaurant process with inertia and full Bayesian inference is approximated by a sequential-sampling scheme in which only a single hypothesis about current context is maintained. Actions are selected via Thompson sampling, allowing uncertainty in parameters to drive exploration in a straightforward manner. The model is tested on simple two-alternative choice problems with switching reinforcement schedules and the results compared with rat behavioural data from a number of T-maze studies. The model successfully replicates a number of important behavioural effects: spontaneous recovery, the effect of partial reinforcement on extinction and reversal, the overtraining reversal effect, and serial reversal-learning effects. PMID:23427101

Context-dependent decision-making: a simple Bayesian model.

PubMed

Lloyd, Kevin; Leslie, David S

2013-05-06

Many phenomena in animal learning can be explained by a context-learning process whereby an animal learns about different patterns of relationship between environmental variables. Differentiating between such environmental regimes or 'contexts' allows an animal to rapidly adapt its behaviour when context changes occur. The current work views animals as making sequential inferences about current context identity in a world assumed to be relatively stable but also capable of rapid switches to previously observed or entirely new contexts. We describe a novel decision-making model in which contexts are assumed to follow a Chinese restaurant process with inertia and full Bayesian inference is approximated by a sequential-sampling scheme in which only a single hypothesis about current context is maintained. Actions are selected via Thompson sampling, allowing uncertainty in parameters to drive exploration in a straightforward manner. The model is tested on simple two-alternative choice problems with switching reinforcement schedules and the results compared with rat behavioural data from a number of T-maze studies. The model successfully replicates a number of important behavioural effects: spontaneous recovery, the effect of partial reinforcement on extinction and reversal, the overtraining reversal effect, and serial reversal-learning effects.

Photoinduced electron transfer in a molecular dyad by nanosecond pump-pump-probe spectroscopy.

PubMed

Ha-Thi, M-H; Pham, V-T; Pino, T; Maslova, V; Quaranta, A; Lefumeux, C; Leibl, W; Aukauloo, A

2018-06-01

The design of robust and inexpensive molecular photocatalysts for the conversion of abundant stable molecules like H2O and CO2 into an energetic carrier is one of the major fundamental questions for scientists nowadays. The outstanding challenge is to couple single photoinduced charge separation events with the sequential accumulation of redox equivalents at the catalytic unit for performing multielectronic catalytic reactions. Herein, double excitation by nanosecond pump-pump-probe experiments was used to interrogate the photoinduced charge transfer and charge accumulation on a molecular dyad composed of a porphyrin chromophore and a ruthenium-based catalyst in the presence of a reversible electron acceptor. An accumulative charge transfer state is unattainable because of rapid reverse electron transfer to the photosensitizer upon the second excitation and the low driving force of the forward photodriven electron transfer reaction. Such a method allows the fundamental understanding of the relaxation mechanism after two sequential photon absorptions, deciphering the undesired electron transfer reactions that limit the charge accumulation efficiency. This study is a step toward the improvement of synthetic strategies of molecular photocatalysts for light-induced charge accumulation and more generally, for solar energy conversion.

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%.

Linguistics, cognitive psychology, and the Now-or-Never bottleneck.

PubMed

Endress, Ansgar D; Katzir, Roni

2016-01-01

Christiansen & Chater (C&C)'s key premise is that "if linguistic information is not processed rapidly, that information is lost for good" (sect. 1, para. 1). From this "Now-or-Never bottleneck" (NNB), C&C derive "wide-reaching and fundamental implications for language processing, acquisition and change as well as for the structure of language itself" (sect. 2, para. 10). We question both the premise and the consequentiality of its purported implications.

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.

Colloidal crystal grain boundary formation and motion

PubMed Central

Edwards, Tara D.; Yang, Yuguang; Beltran-Villegas, Daniel J.; Bevan, Michael A.

2014-01-01

The ability to assemble nano- and micro- sized colloidal components into highly ordered configurations is often cited as the basis for developing advanced materials. However, the dynamics of stochastic grain boundary formation and motion have not been quantified, which limits the ability to control and anneal polycrystallinity in colloidal based materials. Here we use optical microscopy, Brownian Dynamic simulations, and a new dynamic analysis to study grain boundary motion in quasi-2D colloidal bicrystals formed within inhomogeneous AC electric fields. We introduce “low-dimensional” models using reaction coordinates for condensation and global order that capture first passage times between critical configurations at each applied voltage. The resulting models reveal that equal sized domains at a maximum misorientation angle show relaxation dominated by friction limited grain boundary diffusion; and in contrast, asymmetrically sized domains with less misorientation display much faster grain boundary migration due to significant thermodynamic driving forces. By quantifying such dynamics vs. compression (voltage), kinetic bottlenecks associated with slow grain boundary relaxation are understood, which can be used to guide the temporal assembly of defect-free single domain colloidal crystals. PMID:25139760

A Survey of Solver-Related Geometry and Meshing Issues

NASA Technical Reports Server (NTRS)

Masters, James; Daniel, Derick; Gudenkauf, Jared; Hine, David; Sideroff, Chris

2016-01-01

There is a concern in the computational fluid dynamics community that mesh generation is a significant bottleneck in the CFD workflow. This is one of several papers that will help set the stage for a moderated panel discussion addressing this issue. Although certain general "rules of thumb" and a priori mesh metrics can be used to ensure that some base level of mesh quality is achieved, inadequate consideration is often given to the type of solver or particular flow regime on which the mesh will be utilized. This paper explores how an analyst may want to think differently about a mesh based on considerations such as if a flow is compressible vs. incompressible or hypersonic vs. subsonic or if the solver is node-centered vs. cell-centered. This paper is a high-level investigation intended to provide general insight into how considering the nature of the solver or flow when performing mesh generation has the potential to increase the accuracy and/or robustness of the solution and drive the mesh generation process to a state where it is no longer a hindrance to the analysis process.

Expression of Lactate Dehydrogenase in Aspergillus niger for L-Lactic Acid Production

PubMed Central

Dave, Khyati K.; Punekar, Narayan S.

2015-01-01

Different engineered organisms have been used to produce L-lactate. Poor yields of lactate at low pH and expensive downstream processing remain as bottlenecks. Aspergillus niger is a prolific citrate producer and a remarkably acid tolerant fungus. Neither a functional lactate dehydrogenase (LDH) from nor lactate production by A. niger is reported. Its genome was also investigated for the presence of a functional ldh. The endogenous A. niger citrate synthase promoter relevant to A. niger acidogenic metabolism was employed to drive constitutive expression of mouse lactate dehydrogenase (mldhA). An appraisal of different branches of the A. niger pyruvate node guided the choice of mldhA for heterologous expression. A high copy number transformant C12 strain, displaying highest LDH specific activity, was analyzed under different growth conditions. The C12 strain produced 7.7 g/l of extracellular L-lactate from 60 g/l of glucose, in non-neutralizing minimal media. Significantly, lactate and citrate accumulated under two different growth conditions. Already an established acidogenic platform, A. niger now promises to be a valuable host for lactate production. PMID:26683313

Rectified brownian transport in corrugated channels: Fractional brownian motion and Lévy flights.

PubMed

Ai, Bao-quan; Shao, Zhi-gang; Zhong, Wei-rong

2012-11-07

We study fractional brownian motion and Lévy flights in periodic corrugated channels without any external driving forces. From numerical simulations, we find that both fractional gaussian noise and Lévy-stable noise in asymmetric corrugated channels can break thermodynamical equilibrium and induce directed transport. The rectified mechanisms for fractional brownian motion and Lévy flights are different. The former is caused by non-uniform spectral distribution (low or high frequencies) of fractional gaussian noise, while the latter is due to the nonthermal character (occasional long jumps) of the Lévy-stable noise. For fractional brownian motion, average velocity increases with the Hurst exponent for the persistent case, while for the antipersistent case there exists an optimal value of Hurst exponent at which average velocity takes its maximal value. For Lévy flights, the group velocity decreases monotonically as the Lévy index increases. In addition, for both cases, the optimized periodicity and radius at the bottleneck can facilitate the directed transport. Our results could be implemented in constrained structures with narrow channels and pores where the particles undergo anomalous diffusion.

Towards next generation 3D cameras

NASA Astrophysics Data System (ADS)

Gupta, Mohit

2017-03-01

We are in the midst of a 3D revolution. Robots enabled by 3D cameras are beginning to autonomously drive cars, perform surgeries, and manage factories. However, when deployed in the real-world, these cameras face several challenges that prevent them from measuring 3D shape reliably. These challenges include large lighting variations (bright sunlight to dark night), presence of scattering media (fog, body tissue), and optically complex materials (metal, plastic). Due to these factors, 3D imaging is often the bottleneck in widespread adoption of several key robotics technologies. I will talk about our work on developing 3D cameras based on time-of-flight and active triangulation that addresses these long-standing problems. This includes designing `all-weather' cameras that can perform high-speed 3D scanning in harsh outdoor environments, as well as cameras that recover shape of objects with challenging material properties. These cameras are, for the first time, capable of measuring detailed (<100 microns resolution) scans in extremely demanding scenarios with low-cost components. Several of these cameras are making a practical impact in industrial automation, being adopted in robotic inspection and assembly systems.

Transcending the slow bimolecular recombination in lead-halide perovskites for electroluminescence

PubMed Central

Xing, Guichuan; Wu, Bo; Wu, Xiangyang; Li, Mingjie; Du, Bin; Wei, Qi; Guo, Jia; Yeow, Edwin K. L.; Sum, Tze Chien; Huang, Wei

2017-01-01

The slow bimolecular recombination that drives three-dimensional lead-halide perovskites' outstanding photovoltaic performance is conversely a fundamental limitation for electroluminescence. Under electroluminescence working conditions with typical charge densities lower than 1015 cm−3, defect-states trapping in three-dimensional perovskites competes effectively with the bimolecular radiative recombination. Herein, we overcome this limitation using van-der-Waals-coupled Ruddlesden-Popper perovskite multi-quantum-wells. Injected charge carriers are rapidly localized from adjacent thin few layer (n≤4) multi-quantum-wells to the thick (n≥5) multi-quantum-wells with extremely high efficiency (over 85%) through quantum coupling. Light emission originates from excitonic recombination in the thick multi-quantum-wells at much higher decay rate and efficiency than bimolecular recombination in three-dimensional perovskites. These multi-quantum-wells retain the simple solution processability and high charge carrier mobility of two-dimensional lead-halide perovskites. Importantly, these Ruddlesden-Popper perovskites offer new functionalities unavailable in single phase constituents, permitting the transcendence of the slow bimolecular recombination bottleneck in lead-halide perovskites for efficient electroluminescence. PMID:28239146

Transcending the slow bimolecular recombination in lead-halide perovskites for electroluminescence.

PubMed

Xing, Guichuan; Wu, Bo; Wu, Xiangyang; Li, Mingjie; Du, Bin; Wei, Qi; Guo, Jia; Yeow, Edwin K L; Sum, Tze Chien; Huang, Wei

2017-02-27

The slow bimolecular recombination that drives three-dimensional lead-halide perovskites' outstanding photovoltaic performance is conversely a fundamental limitation for electroluminescence. Under electroluminescence working conditions with typical charge densities lower than 10 15  cm -3 , defect-states trapping in three-dimensional perovskites competes effectively with the bimolecular radiative recombination. Herein, we overcome this limitation using van-der-Waals-coupled Ruddlesden-Popper perovskite multi-quantum-wells. Injected charge carriers are rapidly localized from adjacent thin few layer (n≤4) multi-quantum-wells to the thick (n≥5) multi-quantum-wells with extremely high efficiency (over 85%) through quantum coupling. Light emission originates from excitonic recombination in the thick multi-quantum-wells at much higher decay rate and efficiency than bimolecular recombination in three-dimensional perovskites. These multi-quantum-wells retain the simple solution processability and high charge carrier mobility of two-dimensional lead-halide perovskites. Importantly, these Ruddlesden-Popper perovskites offer new functionalities unavailable in single phase constituents, permitting the transcendence of the slow bimolecular recombination bottleneck in lead-halide perovskites for efficient electroluminescence.

BrAD-seq: Breath Adapter Directional sequencing: a streamlined, ultra-simple and fast library preparation protocol for strand specific mRNA library construction.

PubMed

Townsley, Brad T; Covington, Michael F; Ichihashi, Yasunori; Zumstein, Kristina; Sinha, Neelima R

2015-01-01

Next Generation Sequencing (NGS) is driving rapid advancement in biological understanding and RNA-sequencing (RNA-seq) has become an indispensable tool for biology and medicine. There is a growing need for access to these technologies although preparation of NGS libraries remains a bottleneck to wider adoption. Here we report a novel method for the production of strand specific RNA-seq libraries utilizing the terminal breathing of double-stranded cDNA to capture and incorporate a sequencing adapter. Breath Adapter Directional sequencing (BrAD-seq) reduces sample handling and requires far fewer enzymatic steps than most available methods to produce high quality strand-specific RNA-seq libraries. The method we present is optimized for 3-prime Digital Gene Expression (DGE) libraries and can easily extend to full transcript coverage shotgun (SHO) type strand-specific libraries and is modularized to accommodate a diversity of RNA and DNA input materials. BrAD-seq offers a highly streamlined and inexpensive option for RNA-seq libraries.

Lysophosphatidylcholine Regulates Sexual Stage Differentiation in the Human Malaria Parasite Plasmodium falciparum.

PubMed

Brancucci, Nicolas M B; Gerdt, Joseph P; Wang, ChengQi; De Niz, Mariana; Philip, Nisha; Adapa, Swamy R; Zhang, Min; Hitz, Eva; Niederwieser, Igor; Boltryk, Sylwia D; Laffitte, Marie-Claude; Clark, Martha A; Grüring, Christof; Ravel, Deepali; Blancke Soares, Alexandra; Demas, Allison; Bopp, Selina; Rubio-Ruiz, Belén; Conejo-Garcia, Ana; Wirth, Dyann F; Gendaszewska-Darmach, Edyta; Duraisingh, Manoj T; Adams, John H; Voss, Till S; Waters, Andrew P; Jiang, Rays H Y; Clardy, Jon; Marti, Matthias

2017-12-14

Transmission represents a population bottleneck in the Plasmodium life cycle and a key intervention target of ongoing efforts to eradicate malaria. Sexual differentiation is essential for this process, as only sexual parasites, called gametocytes, are infective to the mosquito vector. Gametocyte production rates vary depending on environmental conditions, but external stimuli remain obscure. Here, we show that the host-derived lipid lysophosphatidylcholine (LysoPC) controls P. falciparum cell fate by repressing parasite sexual differentiation. We demonstrate that exogenous LysoPC drives biosynthesis of the essential membrane component phosphatidylcholine. LysoPC restriction induces a compensatory response, linking parasite metabolism to the activation of sexual-stage-specific transcription and gametocyte formation. Our results reveal that malaria parasites can sense and process host-derived physiological signals to regulate differentiation. These data close a critical knowledge gap in parasite biology and introduce a major component of the sexual differentiation pathway in Plasmodium that may provide new approaches for blocking malaria transmission. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

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.

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.

Polycrystalline semiconductor processing

DOEpatents

Glaeser, Andreas M.; Haggerty, John S.; Danforth, Stephen C.

1983-01-01

A process for forming large-grain polycrystalline films from amorphous films for use as photovoltaic devices. The process operates on the amorphous film and uses the driving force inherent to the transition from the amorphous state to the crystalline state as the force which drives the grain growth process. The resultant polycrystalline film is characterized by a grain size that is greater than the thickness of the film. A thin amorphous film is deposited on a substrate. The formation of a plurality of crystalline embryos is induced in the amorphous film at predetermined spaced apart locations and nucleation is inhibited elsewhere in the film. The crystalline embryos are caused to grow in the amorphous film, without further nucleation occurring in the film, until the growth of the embryos is halted by imgingement on adjacently growing embryos. The process is applicable to both batch and continuous processing techniques. In either type of process, the thin amorphous film is sequentially doped with p and n type dopants. Doping is effected either before or after the formation and growth of the crystalline embryos in the amorphous film, or during a continuously proceeding crystallization step.

Polycrystalline semiconductor processing

DOEpatents

Glaeser, A.M.; Haggerty, J.S.; Danforth, S.C.

1983-04-05

A process is described for forming large-grain polycrystalline films from amorphous films for use as photovoltaic devices. The process operates on the amorphous film and uses the driving force inherent to the transition from the amorphous state to the crystalline state as the force which drives the grain growth process. The resultant polycrystalline film is characterized by a grain size that is greater than the thickness of the film. A thin amorphous film is deposited on a substrate. The formation of a plurality of crystalline embryos is induced in the amorphous film at predetermined spaced apart locations and nucleation is inhibited elsewhere in the film. The crystalline embryos are caused to grow in the amorphous film, without further nucleation occurring in the film, until the growth of the embryos is halted by impingement on adjacently growing embryos. The process is applicable to both batch and continuous processing techniques. In either type of process, the thin amorphous film is sequentially doped with p and n type dopants. Doping is effected either before or after the formation and growth of the crystalline embryos in the amorphous film, or during a continuously proceeding crystallization step. 10 figs.

Quasistationary Plasma Predator-Prey System of Coupled Turbulence, Drive, and Sheared E ×B Flow During High Performance DIII-D Tokamak Discharges

NASA Astrophysics Data System (ADS)

Barada, K.; Rhodes, T. L.; Burrell, K. H.; Zeng, L.; Bardóczi, L.; Chen, Xi; Muscatello, C. M.; Peebles, W. A.

2018-03-01

A new, long-lived limit cycle oscillation (LCO) regime has been observed in the edge of near zero torque high performance DIII-D tokamak plasma discharges. These LCOs are localized and composed of density turbulence, gradient drives, and E ×B velocity shear damping (E and B are the local radial electric and total magnetic fields). Density turbulence sequentially acts as a predator (via turbulence transport) of profile gradients and a prey (via shear suppression) to the E ×B velocity shear. Reported here for the first time is a unique spatiotemporal variation of the local E ×B velocity, which is found to be essential for the existence of this system. The LCO system is quasistationary, existing from 3 to 12 plasma energy confinement times (˜30 - 900 LCO cycles) limited by hardware constraints. This plasma system appears to contribute strongly to the edge transport in these high performance and transient-free plasmas, as evident from oscillations in transport relevant edge parameters at LCO time scale.

Design and manufacturing of the CFRP lightweight telescope structure

NASA Astrophysics Data System (ADS)

Stoeffler, Guenter; Kaindl, Rainer

2000-06-01

Design of earthbound telescopes is normally based on conventional steel constructions. Several years ago thermostable CFRP Telescope and reflector structures were developed and manufacturing for harsh terrestrial environments. The airborne SOFIA TA requires beyond thermostability an excessive stiffness to mass ratio for the structure fulfilling performance and not to exceed mass limitations by the aircraft Boeing 747 SP. Additional integration into A/C drives design of structure subassemblies. Thickness of CFRP Laminates, either filament wound or prepreg manufactured need special attention and techniques to gain high material quality according to aerospace requirements. Sequential shop assembly of the structure subassemblies minimizes risk for assembling TA. Design goals, optimization of layout and manufacturing techniques and results are presented.

A quantum mechanics-based approach to model incident-induced dynamic driver behavior

NASA Astrophysics Data System (ADS)

Sheu, Jiuh-Biing

2008-08-01

A better understanding of the psychological factors influencing drivers, and the resulting driving behavior responding to incident-induced lane traffic phenomena while passing by an incident site is vital to the improvement of road safety. This paper presents a microscopic driver behavior model to explain the dynamics of the instantaneous driver decision process under lane-blocking incidents on adjacent lanes. The proposed conceptual framework decomposes the corresponding driver decision process into three sequential phases: (1) initial stimulus, (2) glancing-around car-following, and (3) incident-induced driving behavior. The theorem of quantum mechanics in optical flows is applied in the first phase to explain the motion-related perceptual phenomena while vehicles approach the incident site in adjacent lanes, followed by the incorporation of the effect of quantum optical flows in modeling the induced glancing-around car-following behavior in the second phase. Then, an incident-induced driving behavior model is formulated to reproduce the dynamics of driver behavior conducted in the process of passing by an incident site in the adjacent lanes. Numerical results of model tests using video-based incident data indicate the validity of the proposed traffic behavior model in analyzing the incident-induced lane traffic phenomena. It is also expected that such a proposed quantum-mechanics based methodology can throw more light if applied to driver psychology and response in anomalous traffic environments in order to improve road safety.

Inbreeding drives maize centromere evolution.

PubMed

Schneider, Kevin L; Xie, Zidian; Wolfgruber, Thomas K; Presting, Gernot G

2016-02-23

Functional centromeres, the chromosomal sites of spindle attachment during cell division, are marked epigenetically by the centromere-specific histone H3 variant cenH3 and typically contain long stretches of centromere-specific tandem DNA repeats (∼1.8 Mb in maize). In 23 inbreds of domesticated maize chosen to represent the genetic diversity of maize germplasm, partial or nearly complete loss of the tandem DNA repeat CentC precedes 57 independent cenH3 relocation events that result in neocentromere formation. Chromosomal regions with newly acquired cenH3 are colonized by the centromere-specific retrotransposon CR2 at a rate that would result in centromere-sized CR2 clusters in 20,000-95,000 y. Three lines of evidence indicate that CentC loss is linked to inbreeding, including (i) CEN10 of temperate lineages, presumed to have experienced a genetic bottleneck, contain less CentC than their tropical relatives; (ii) strong selection for centromere-linked genes in domesticated maize reduced diversity at seven of the ten maize centromeres to only one or two postdomestication haplotypes; and (iii) the centromere with the largest number of haplotypes in domesticated maize (CEN7) has the highest CentC levels in nearly all domesticated lines. Rare recombinations introduced one (CEN2) or more (CEN5) alternate CEN haplotypes while retaining a single haplotype at domestication loci linked to these centromeres. Taken together, this evidence strongly suggests that inbreeding, favored by postdomestication selection for centromere-linked genes affecting key domestication or agricultural traits, drives replacement of the tandem centromere repeats in maize and other crop plants. Similar forces may act during speciation in natural systems.

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.

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).

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.

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.

Control x-ray deformable mirrors with few measurements

NASA Astrophysics Data System (ADS)

Huang, Lei; Xue, Junpeng; Idir, Mourad

2016-09-01

After years of development from a concept to early experimental stage, X-ray Deformable Mirrors (XDMs) are used in many synchrotron/free-electron laser facilities as a standard x-ray optics tool. XDM is becoming an integral part of the present and future large x-ray and EUV projects and will be essential in exploiting the full potential of the new sources currently under construction. The main objective of using XDMs is to correct wavefront errors or to enable variable focus beam sizes at the sample. Due to the coupling among the N actuators of a DM, it is usually necessary to perform a calibration or training process to drive the DM into the target shape. Commonly, in order to optimize the actuators settings to minimize slope/height errors, an initial measurement need to be collected, with all actuators set to 0, and then either N or 2N measurements are necessary learn each actuator behavior sequentially. In total, it means that N+1 or 2N+1 scans are required to perform this learning process. When the actuators number N is important and the actuator response or the necessary metrology is slow then this learning process can be time consuming. In this work, we present a fast and accurate method to drive an x-ray active bimorph mirror to a target shape with only 3 or 4 measurements. Instead of sequentially measuring and calculating the influence functions of all actuators and then predicting the voltages needed for any desired shape, the metrology data are directly used to "guide" the mirror from its current status towards the particular target slope/height via iterative compensations. The feedback for the iteration process is the discrepancy in curvature calculated by using B-spline fitting of the measured height/slope data. In this paper, the feasibility of this simple and effective approach is demonstrated with experiments.

C-terminal amino acid residue loss for deprotonated peptide ions containing glutamic acid, aspartic acid, or serine residues at the C-terminus.

PubMed

Li, Zhong; Yalcin, Talat; Cassady, Carolyn J

2006-07-01

Deprotonated peptides containing C-terminal glutamic acid, aspartic acid, or serine residues were studied by sustained off-resonance irradiation collision-induced dissociation (SORI-CID) in a Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer with ion production by electrospray ionization (ESI). Additional studies were performed by post source decay (PSD) in a matrix-assisted laser desorption ionization/time-of-flight (MALDI/TOF) mass spectrometer. This work included both model peptides synthesized in our laboratory and bioactive peptides with more complex sequences. During SORI-CID and PSD, [M - H]- and [M - 2H]2- underwent an unusual cleavage corresponding to the elimination of the C-terminal residue. Two mechanisms are proposed to occur. They involve nucleophilic attack on the carbonyl carbon of the adjacent residue by either the carboxylate group of the C-terminus or the side chain carboxylate group of C-terminal glutamic acid and aspartic acid residues. To confirm the proposed mechanisms, AAAAAD was labelled by 18O specifically on the side chain of the aspartic acid residue. For peptides that contain multiple C-terminal glutamic acid residues, each of these residues can be sequentially eliminated from the deprotonated ions; a driving force may be the formation of a very stable pyroglutamatic acid neutral. For peptides with multiple aspartic acid residues at the C-terminus, aspartic acid residue loss is not sequential. For peptides with multiple serine residues at the C-terminus, C-terminal residue loss is sequential; however, abundant loss of other neutral molecules also occurs. In addition, the presence of basic residues (arginine or lysine) in the sequence has no effect on C-terminal residue elimination in the negative ion mode.

An environmental disinfection odyssey: evaluation of sequential interventions to improve disinfection of Clostridium difficile isolation rooms.

PubMed

Sitzlar, Brett; Deshpande, Abhishek; Fertelli, Dennis; Kundrapu, Sirisha; Sethi, Ajay K; Donskey, Curtis J

2013-05-01

OBJECTIVE. Effective disinfection of hospital rooms after discharge of patients with Clostridium difficile infection (CDI) is necessary to prevent transmission. We evaluated the impact of sequential cleaning and disinfection interventions by culturing high-touch surfaces in CDI rooms after cleaning. DESIGN. Prospective intervention. SETTING. A Veterans Affairs hospital. INTERVENTIONS. During a 21-month period, 3 sequential tiered interventions were implemented: (1) fluorescent markers to provide monitoring and feedback on thoroughness of cleaning facility-wide, (2) addition of an automated ultraviolet radiation device for adjunctive disinfection of CDI rooms, and (3) enhanced standard disinfection of CDI rooms, including a dedicated daily disinfection team and implementation of a process requiring supervisory assessment and clearance of terminally cleaned CDI rooms. To determine the impact of the interventions, cultures were obtained from CDI rooms after cleaning and disinfection. RESULTS. The fluorescent marker intervention improved the thoroughness of cleaning of high-touch surfaces (from 47% to 81% marker removal; P < .0001). Relative to the baseline period, the prevalence of positive cultures from CDI rooms was reduced by 14% (P=.024), 48% (P <.001), and 89% (P=.006) with interventions 1, 2, and 3, respectively. During the baseline period, 67% of CDI rooms had positive cultures after disinfection, whereas during interventions periods 1, 2, and 3 the percentages of CDI rooms with positive cultures after disinfection were reduced to 57%, 35%, and 7%, respectively. CONCLUSIONS. An intervention that included formation of a dedicated daily disinfection team and implementation of a standardized process for clearing CDI rooms achieved consistent CDI room disinfection. Culturing of CDI rooms provides a valuable tool to drive improvements in environmental disinfection.

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

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.

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.

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

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

Sequential Insertion Heuristic with Adaptive Bee Colony Optimisation Algorithm for Vehicle Routing Problem with Time Windows

PubMed Central

Jawarneh, Sana; Abdullah, Salwani

2015-01-01

This paper presents a bee colony optimisation (BCO) algorithm to tackle the vehicle routing problem with time window (VRPTW). The VRPTW involves recovering an ideal set of routes for a fleet of vehicles serving a defined number of customers. The BCO algorithm is a population-based algorithm that mimics the social communication patterns of honeybees in solving problems. The performance of the BCO algorithm is dependent on its parameters, so the online (self-adaptive) parameter tuning strategy is used to improve its effectiveness and robustness. Compared with the basic BCO, the adaptive BCO performs better. Diversification is crucial to the performance of the population-based algorithm, but the initial population in the BCO algorithm is generated using a greedy heuristic, which has insufficient diversification. Therefore the ways in which the sequential insertion heuristic (SIH) for the initial population drives the population toward improved solutions are examined. Experimental comparisons indicate that the proposed adaptive BCO-SIH algorithm works well across all instances and is able to obtain 11 best results in comparison with the best-known results in the literature when tested on Solomon’s 56 VRPTW 100 customer instances. Also, a statistical test shows that there is a significant difference between the results. PMID:26132158

Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses.

PubMed

Lagator, Mato; Colegrave, Nick; Neve, Paul

2014-11-07

In rapidly changing environments, selection history may impact the dynamics of adaptation. Mutations selected in one environment may result in pleiotropic fitness trade-offs in subsequent novel environments, slowing the rates of adaptation. Epistatic interactions between mutations selected in sequential stressful environments may slow or accelerate subsequent rates of adaptation, depending on the nature of that interaction. We explored the dynamics of adaptation during sequential exposure to herbicides with different modes of action in Chlamydomonas reinhardtii. Evolution of resistance to two of the herbicides was largely independent of selection history. For carbetamide, previous adaptation to other herbicide modes of action positively impacted the likelihood of adaptation to this herbicide. Furthermore, while adaptation to all individual herbicides was associated with pleiotropic fitness costs in stress-free environments, we observed that accumulation of resistance mechanisms was accompanied by a reduction in overall fitness costs. We suggest that antagonistic epistasis may be a driving mechanism that enables populations to more readily adapt in novel environments. These findings highlight the potential for sequences of xenobiotics to facilitate the rapid evolution of multiple-drug and -pesticide resistance, as well as the potential for epistatic interactions between adaptive mutations to facilitate evolutionary rescue in rapidly changing environments. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

Distal regulatory regions restrict the expression of cis-linked genes to the tapetal cells.

PubMed

Franco, Luciana O; de O Manes, Carmem Lara; Hamdi, Said; Sachetto-Martins, Gilberto; de Oliveira, Dulce E

2002-04-24

The oleosin glycine-rich protein genes Atgrp-6, Atgrp-7, and Atgrp-8 occur in clusters in the Arabidopsis genome and are expressed specifically in the tapetum cells. The cis-regulatory regions involved in the tissue-specific gene expression were investigated by fusing different segments of the gene cluster to the uidA reporter gene. Common distal regulatory regions were identified that coordinate expression of the sequential genes. At least two of these genes were regulated spatially by proximal and distal sequences. The cis-acting elements (122 bp upstream of the transcriptional start point) drive the uidA expression to floral tissues, whereas distal 5' upstream regions restrict the gene activity to tapetal cells.

Objective analysis of impressed chisel toolmarks

DOE PAGES

Spotts, Ryan; Chumbley, L. Scott

2015-08-06

Historical and recent challenges to the practice of comparative forensic examination have created a driving force for the formation of objective methods for toolmark identification. In this study, fifty sequentially manufactured chisels were used to create impression toolmarks in lead (500 toolmarks total). An algorithm previously used to statistically separate known matching and nonmatching striated screwdriver marks and quasi-striated plier marks was used to evaluate the chisel marks. Impression toolmarks, a more complex form of toolmark, pose a more difficult test for the algorithm that was originally designed for striated toolmarks. Lastly, results show in this instance that the algorithmmore » can separate matching and nonmatching impression marks, providing further validation of the assumption that toolmarks are identifiably unique.« less

Tool setting device

DOEpatents

Brown, Raymond J.

1977-01-01

The present invention relates to a tool setting device for use with numerically controlled machine tools, such as lathes and milling machines. A reference position of the machine tool relative to the workpiece along both the X and Y axes is utilized by the control circuit for driving the tool through its program. This reference position is determined for both axes by displacing a single linear variable displacement transducer (LVDT) with the machine tool through a T-shaped pivotal bar. The use of the T-shaped bar allows the cutting tool to be moved sequentially in the X or Y direction for indicating the actual position of the machine tool relative to the predetermined desired position in the numerical control circuit by using a single LVDT.

A Biomimetic Approach to Discrimination Between Sequential and Concerted Models for the Oxidation of Ubiquinol at the Qo­ site of the Cyt bc1 Complex

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

Cape, Jonathan L.; Forquer, Isaac P.; Bowman, Michael K.

2005-09-26

The cytochrome bc complexes function as quinol:cytochrome c oxidoreductases in the energy conserving membranes of nearly all organisms, where they couple the oxidation of a quinol substrate (QH2) to the pumping of protons across the bioenergetic membrane, resulting in the establishment of a proton motive force, which is used to drive the (C)F0/(C)F1 ATP synthase (Trumpower and Gennis 1994). Among the variety of biological quinols characterized, ubiquinol is the substrate used by most bc-type complexes, and its reactions are of great interest concerning diseases related to oxidative stress and the fundamentals of biological energy transduction.

AFFINE-CORRECTED PARADISE: FREE-BREATHING PATIENT-ADAPTIVE CARDIAC MRI WITH SENSITIVITY ENCODING

PubMed Central

Sharif, Behzad; Bresler, Yoram

2013-01-01

We propose a real-time cardiac imaging method with parallel MRI that allows for free breathing during imaging and does not require cardiac or respiratory gating. The method is based on the recently proposed PARADISE (Patient-Adaptive Reconstruction and Acquisition Dynamic Imaging with Sensitivity Encoding) scheme. The new acquisition method adapts the PARADISE k-t space sampling pattern according to an affine model of the respiratory motion. The reconstruction scheme involves multi-channel time-sequential imaging with time-varying channels. All model parameters are adapted to the imaged patient as part of the experiment and drive both data acquisition and cine reconstruction. Simulated cardiac MRI experiments using the realistic NCAT phantom show high quality cine reconstructions and robustness to modeling inaccuracies. PMID:24390159

Drug injection into fat tissue with a laser based microjet injector

NASA Astrophysics Data System (ADS)

Han, Tae-hee; Hah, Jung-moo; Yoh, Jack J.

2011-05-01

We have investigated a new micro drug jet injector using laser pulse energy. An infrared laser beam of high energy (˜3 J/pulse) is focused inside a driving fluid in a small chamber. The pulse then induces various energy releasing processes, and generates fast microjets through a micronozzle. The elastic membrane of this system plays an important role in transferring mechanical pressure and protecting drug from heat release. In this paper, we offer the sequential images of microjet generation taken by a high speed camera as an evidence of the multiple injections via single pulse. Furthermore, we test the proposed system to penetrate soft animal tissues in order to evaluate its feasibility as an advanced transdermal drug delivery method.

Harnessing Thin-Film Continuous-Flow Assembly Lines.

PubMed

Britton, Joshua; Castle, Jared W; Weiss, Gregory A; Raston, Colin L

2016-07-25

Inspired by nature's ability to construct complex molecules through sequential synthetic transformations, an assembly line synthesis of α-aminophosphonates has been developed. In this approach, simple starting materials are continuously fed through a thin-film reactor where the intermediates accrue molecular complexity as they progress through the flow system. Flow chemistry allows rapid multistep transformations to occur via reaction compartmentalization, an approach not amenable to using conventional flasks. Thin film processing can also access facile in situ solvent exchange to drive reaction efficiency, and through this method, α-aminophosphonate synthesis requires only 443 s residence time to produce 3.22 g h(-1) . Assembly-line synthesis allows unprecedented reaction flexibility and processing efficiency. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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.

­Back-to-back mechanisms drive actomyosin ring closure during Drosophila embryo cleavage

PubMed Central

2016-01-01

Contraction of actomyosin rings during cytokinesis is typically attributed to actin filaments sliding toward each other via Myosin-2 motor activity. However, rings constrict in some cells in the absence of Myosin-2 activity. Thus, ring closure uses Myosin-2–dependent and –independent mechanisms. But what the Myosin-2–independent mechanisms are, and to what extent they are sufficient to drive closure, remains unclear. During cleavage in Drosophila melanogaster embryos, actomyosin rings constrict in two sequential and mechanistically distinct phases. We show that these phases differ in constriction speed and are genetically and pharmacologically separable. Further, Myosin-2 activity is required for slow constriction in “phase 1” but is largely dispensable for fast constriction in “phase 2,” and F-actin disassembly is only required for fast constriction in phase 2. Switching from phase 1 to phase 2 seemingly relies on the spatial organization of F-actin as controlled by Cofilin, Anillin, and Septin. Our work shows that fly embryos present a singular opportunity to compare separable ring constriction mechanisms, with varying Myosin-2 dependencies, in one cell type and in vivo. PMID:27799369

Comparative energetics of carbon storage molecules in green algae

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

McKie-Krisberg, Zaid M.; Laurens, Lieve M. L.; Huang, Andy

Several members of the green algae possess the ability to produce lipids and/or high value compounds in significant quantities. While for several of these green algal species induction of increased lipid production has been shown, and cultivation of species for high value molecules occurs at production scale, the molecular mechanisms governing over-accumulation of molecules synthesized from isoprenoid precursors, carotenoids, for example, have received far less attention. Here, we present a calculation of the required ATP equivalencies per carbon atom and reducing power equivalencies as NADH/NADPH (NAD(P)H) per carbon atom for the isoprenoid molecules ..beta..-carotene (C40), astaxanthin (C40), and squalene (C30).more » We compared energetic requirements of carbohydrates, triacylglycerol, and isoprenoid molecules under a gradient of conditions of cellular stress. Our calculations revealed slightly less ATP and NAD(P)H equivalency per carbon atom between triacylglycerol and the three isoprenoid molecules. Based on our results, we propose that the driving force for differences in accumulation patterns of carotenoids vs. triacylglycerols in algal cells under stress is largely dependent on the presence and regulation of bypass mechanisms at metabolic junction bottlenecks, like pyruvate dehydrogenase (PDH), within particular species. We provide a discussion of several molecular mechanisms that may influence carbon partitioning within different groups of green algae, including metabolic inhibition through accumulation of specific substrates related to ATP and reducing equivalent production (NAD(P)H) as well as cellular compartmentalization. This work contributes to the ongoing discussion of cellular homeostatic regulation during stress, as well as the potential mechanisms driving long-term carbon storage as it relates to energy and redox states within the algal cell.« less

Comparative energetics of carbon storage molecules in green algae

DOE PAGES

McKie-Krisberg, Zaid M.; Laurens, Lieve M. L.; Huang, Andy; ...

2018-02-28

Several members of the green algae possess the ability to produce lipids and/or high value compounds in significant quantities. While for several of these green algal species induction of increased lipid production has been shown, and cultivation of species for high value molecules occurs at production scale, the molecular mechanisms governing over-accumulation of molecules synthesized from isoprenoid precursors, carotenoids, for example, have received far less attention. Here, we present a calculation of the required ATP equivalencies per carbon atom and reducing power equivalencies as NADH/NADPH (NAD(P)H) per carbon atom for the isoprenoid molecules ..beta..-carotene (C40), astaxanthin (C40), and squalene (C30).more » We compared energetic requirements of carbohydrates, triacylglycerol, and isoprenoid molecules under a gradient of conditions of cellular stress. Our calculations revealed slightly less ATP and NAD(P)H equivalency per carbon atom between triacylglycerol and the three isoprenoid molecules. Based on our results, we propose that the driving force for differences in accumulation patterns of carotenoids vs. triacylglycerols in algal cells under stress is largely dependent on the presence and regulation of bypass mechanisms at metabolic junction bottlenecks, like pyruvate dehydrogenase (PDH), within particular species. We provide a discussion of several molecular mechanisms that may influence carbon partitioning within different groups of green algae, including metabolic inhibition through accumulation of specific substrates related to ATP and reducing equivalent production (NAD(P)H) as well as cellular compartmentalization. This work contributes to the ongoing discussion of cellular homeostatic regulation during stress, as well as the potential mechanisms driving long-term carbon storage as it relates to energy and redox states within the algal cell.« less

Are habitat fragmentation, local adaptation and isolation-by-distance driving population divergence in wild rice Oryza rufipogon?

PubMed

Zhao, Yao; Vrieling, Klaas; Liao, Hui; Xiao, Manqiu; Zhu, Yongqing; Rong, Jun; Zhang, Wenju; Wang, Yuguo; Yang, Ji; Chen, Jiakuan; Song, Zhiping

2013-11-01

Habitat fragmentation weakens the connection between populations and is accompanied with isolation by distance (IBD) and local adaptation (isolation by adaptation, IBA), both leading to genetic divergence between populations. To understand the evolutionary potential of a population and to formulate proper conservation strategies, information on the roles of IBD and IBA in driving population divergence is critical. The putative ancestor of Asian cultivated rice (Oryza sativa) is endangered in China due to habitat loss and fragmentation. We investigated the genetic variation in 11 Chinese Oryza rufipogon populations using 79 microsatellite loci to infer the effects of habitat fragmentation, IBD and IBA on genetic structure. Historical and current gene flows were found to be rare (mh  = 0.0002-0.0013, mc  = 0.007-0.029), indicating IBD and resulting in a high level of population divergence (FST  = 0.343). High within-population genetic variation (HE  = 0.377-0.515), relatively large effective population sizes (Ne  = 96-158), absence of bottlenecks and limited gene flow were found, demonstrating little impact of recent habitat fragmentation on these populations. Eleven gene-linked microsatellite loci were identified as outliers, indicating local adaptation. Hierarchical AMOVA and partial Mantel tests indicated that population divergence of Chinese O. rufipogon was significantly correlated with environmental factors, especially habitat temperature. Common garden trials detected a significant adaptive population divergence associated with latitude. Collectively, these findings imply that IBD due to historical rather than recent fragmentation, followed by local adaptation, has driven population divergence in O. rufipogon. © 2013 John Wiley & Sons Ltd.

Inbreeding drives maize centromere evolution

PubMed Central

Schneider, Kevin L.; Xie, Zidian; Wolfgruber, Thomas K.; Presting, Gernot G.

2016-01-01

Functional centromeres, the chromosomal sites of spindle attachment during cell division, are marked epigenetically by the centromere-specific histone H3 variant cenH3 and typically contain long stretches of centromere-specific tandem DNA repeats (∼1.8 Mb in maize). In 23 inbreds of domesticated maize chosen to represent the genetic diversity of maize germplasm, partial or nearly complete loss of the tandem DNA repeat CentC precedes 57 independent cenH3 relocation events that result in neocentromere formation. Chromosomal regions with newly acquired cenH3 are colonized by the centromere-specific retrotransposon CR2 at a rate that would result in centromere-sized CR2 clusters in 20,000–95,000 y. Three lines of evidence indicate that CentC loss is linked to inbreeding, including (i) CEN10 of temperate lineages, presumed to have experienced a genetic bottleneck, contain less CentC than their tropical relatives; (ii) strong selection for centromere-linked genes in domesticated maize reduced diversity at seven of the ten maize centromeres to only one or two postdomestication haplotypes; and (iii) the centromere with the largest number of haplotypes in domesticated maize (CEN7) has the highest CentC levels in nearly all domesticated lines. Rare recombinations introduced one (CEN2) or more (CEN5) alternate CEN haplotypes while retaining a single haplotype at domestication loci linked to these centromeres. Taken together, this evidence strongly suggests that inbreeding, favored by postdomestication selection for centromere-linked genes affecting key domestication or agricultural traits, drives replacement of the tandem centromere repeats in maize and other crop plants. Similar forces may act during speciation in natural systems. PMID:26858403

Cloud services on an astronomy data center

NASA Astrophysics Data System (ADS)

Solar, Mauricio; Araya, Mauricio; Farias, Humberto; Mardones, Diego; Wang, Zhong

2016-08-01

The research on computational methods for astronomy performed by the first phase of the Chilean Virtual Observatory (ChiVO) led to the development of functional prototypes, implementing state-of-the-art computational methods and proposing new algorithms and techniques. The ChiVO software architecture is based on the use of the IVOA protocols and standards. These protocols and standards are grouped in layers, with emphasis on the application and data layers, because their basic standards define the minimum operation that a VO should conduct. As momentary verification, the current implementation works with a set of data, with 1 TB capacity, which comes from the reduction of the cycle 0 of ALMA. This research was mainly focused on spectroscopic data cubes coming from the cycle 0 ALMA's public data. As the dataset size increases when the cycle 1 ALMA's public data is also increasing every month, data processing is becoming a major bottleneck for scientific research in astronomy. When designing the ChiVO, we focused on improving both computation and I/ O costs, and this led us to configure a data center with 424 high speed cores of 2,6 GHz, 1 PB of storage (distributed in hard disk drives-HDD and solid state drive-SSD) and high speed communication Infiniband. We are developing a cloud based e-infrastructure for ChiVO services, in order to have a coherent framework for developing novel web services for on-line data processing in the ChiVO. We are currently parallelizing these new algorithms and techniques using HPC tools to speed up big data processing, and we will report our results in terms of data size, data distribution, number of cores and response time, in order to compare different processing and storage configurations.

The Molecular Industrial Revolution: Automated Synthesis of Small Molecules

PubMed Central

Trobe, Melanie; Burke, Martin D.

2018-01-01

The eighteenth and nineteenth centuries marked a sweeping transition from manual to automated manufacturing on the macroscopic scale. This enabled an unmatched period of human innovation that helped drive the Industrial Revolution. The impact on society was transformative, ultimately yielding substantial improvements in living conditions and lifespan in many parts of the world. During the same time period, the first manual syntheses of organic molecules was achieved. Now, two centuries later, we are poised for an analogous transition from highly customized crafting of specific molecular targets by hand to the increasingly general and automated assembly of many different types of molecules with the push of a button. Automation of customized small molecule synthesis pathways is already enabling safer, more reproducible, and readily scalable production of specific targets, and general machines now exist for the synthesis of a wide range of different peptides, oligonucleotides, and oligosaccharides. Creating general machines that are similarly capable of making many different types of small molecules on-demand, akin to that which has been achieved on the macroscopic scale with 3D printers, has proven to be substantially more challenging. Yet important progress is being made toward this potentially transformative objective with two complementary approaches: (1) automation of customized synthesis routes to different targets via machines that enable use of many different reactions and starting materials, and (2) automation of generalized platforms that make many different targets using common coupling chemistry and building blocks. Continued progress in these exciting directions has the potential to shift the bottleneck in molecular innovation from synthesis to imagination, and thereby help drive a new industrial revolution on the molecular scale. PMID:29513400

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.

Perceived risk and other predictors and correlates of teenagers' safety belt use during the first year of licensure.

PubMed

Ouimet, Marie Claude; Morton, Bruce G Simons; Noelcke, Elizabeth A; Williams, Allan F; Leaf, William A; Preusser, David F; Hartos, Jessica L

2008-03-01

Teenagers have the lowest rate of safety belt use and the highest crash rate compared to other age groups. Past studies on teenagers' belt use have mostly been cross-sectional. The first goals of this study were to examine, at licensure, teenagers' and parents' perceptions of risk of crash/injury for newly licensed teenagers when driving unbelted and teenagers' perceived and parents' intended consequences for safety belt rule violations. In addition, the comparability of these variables to other risky driving behaviors was explored. The second goal was to evaluate the importance of these variables in the prediction of teenagers' belt use during the first year of licensure, relative to other factors related to belt use, including demographics and substance use. More than 2,000 parent-teenager dyads were interviewed by telephone, parents at permit and licensure and teenagers at permit, licensure, and 3, 6, and 12 months after licensure. Approximately a third of the teenagers reported at least once at 3, 6, or 12 months post-licensure not always using their safety belt in the past week. At licensure, participants' perceived risk of safety belt non-use was high and ranked among the behaviors most related to crash/injury for newly licensed teenagers, behind driving under the influence of alcohol or drugs. Parent-imposed consequences for safety belt rule violations were not as highly rated as parent-imposed consequences for driving under the influence of alcohol or drugs. Sequential logistic regression modeled the relationship between safety belt use and perceived risk and consequences of non-use, as well as other prospective predictors assessed at permit and licensure, and driving correlates measured after licensure. Teenagers' extreme perceived risk and parents' intended sure consequences for non-use were significant prospective predictors of regular use during the first year of licensure. Other significant predictors and correlates were race (White), high school grade average of "A," not smoking cigarettes, driving a passenger vehicle, and never receiving a traffic citation or engaging in risky driving behaviors, including driving under the influence of alcohol or drugs and running a red light. While the effect size was small for perceived risk of non-use, it is a modifiable factor and focused intervention contrived to enhance perceived risk could increase teenagers' belt use. Perceived risk is discussed as a target for intervention in relation to the Protection Motivation Theory. This theory appears helpful in guiding future research into the modifiable factors studied here as well as other factors, including perceived rewards and costs associated with non-use.

Efficiency of Adaptive Temperature-Based Replica Exchange for Sampling Large-Scale Protein Conformational Transitions.

PubMed

Zhang, Weihong; Chen, Jianhan

2013-06-11

Temperature-based replica exchange (RE) is now considered a principal technique for enhanced sampling of protein conformations. It is also recognized that existence of sharp cooperative transitions (such as protein folding/unfolding) can lead to temperature exchange bottlenecks and significantly reduce the sampling efficiency. Here, we revisit two adaptive temperature-based RE protocols, namely, exchange equalization (EE) and current maximization (CM), that were previously examined using atomistic simulations (Lee and Olson, J. Chem. Physics2011, 134, 24111). Both protocols aim to overcome exchange bottlenecks by adaptively adjusting the simulation temperatures, either to achieve uniform exchange rates (in EE) or to maximize temperature diffusion (CM). By designing a realistic yet computationally tractable coarse-grained protein model, one can sample many reversible folding/unfolding transitions using conventional constant temperature molecular dynamics (MD), standard REMD, EE-REMD, and CM-REMD. This allows rigorous evaluation of the sampling efficiency, by directly comparing the rates of folding/unfolding transitions and convergence of various thermodynamic properties of interest. The results demonstrate that both EE and CM can indeed enhance temperature diffusion compared to standard RE, by ∼3- and over 10-fold, respectively. Surprisingly, the rates of reversible folding/unfolding transitions are similar in all three RE protocols. The convergence rates of several key thermodynamic properties, including the folding stability and various 1D and 2D free energy surfaces, are also similar. Therefore, the efficiency of RE protocols does not appear to be limited by temperature diffusion, but by the inherent rates of spontaneous large-scale conformational rearrangements. This is particularly true considering that virtually all RE simulations of proteins in practice involve exchange attempt frequencies (∼ps(-1)) that are several orders of magnitude faster than the slowest protein motions (∼μs(-1)). Our results also suggest that the efficiency of RE will not likely be improved by other protocols that aim to accelerate exchange or temperature diffusion. Instead, protocols with some types of guided tempering will likely be necessary to drive faster large-scale conformational transitions.

Data transfer nodes and demonstration of 100-400 Gbps wide area throughput using the Caltech SDN testbed

NASA Astrophysics Data System (ADS)

Mughal, A.; Newman, H.

2017-10-01

We review and demonstrate the design of efficient data transfer nodes (DTNs), from the perspective of the highest throughput over both local and wide area networks, as well as the highest performance per unit cost. A careful system-level design is required for the hardware, firmware, OS and software components. Furthermore, additional tuning of these components, and the identification and elimination of any remaining bottlenecks is needed once the system is assembled and commissioned, in order to obtain optimal performance. For high throughput data transfers, specialized software is used to overcome the traditional limits in performance caused by the OS, file system, file structures used, etc. Concretely, we will discuss and present the latest results using Fast Data Transfer (FDT), developed by Caltech. We present and discuss the design choices for three generations of Caltech DTNs. Their transfer capabilities range from 40 Gbps to 400 Gbps. Disk throughput is still the biggest challenge in the current generation of available hardware. However, new NVME drives combined with RDMA and a new NVME network fabric are expected to improve the overall data-transfer throughput and simultaneously reduce the CPU load on the end nodes.

A multiply-add engine with monolithically integrated 3D memristor crossbar/CMOS hybrid circuit.

PubMed

Chakrabarti, B; Lastras-Montaño, M A; Adam, G; Prezioso, M; Hoskins, B; Payvand, M; Madhavan, A; Ghofrani, A; Theogarajan, L; Cheng, K-T; Strukov, D B

2017-02-14

Silicon (Si) based complementary metal-oxide semiconductor (CMOS) technology has been the driving force of the information-technology revolution. However, scaling of CMOS technology as per Moore's law has reached a serious bottleneck. Among the emerging technologies memristive devices can be promising for both memory as well as computing applications. Hybrid CMOS/memristor circuits with CMOL (CMOS + "Molecular") architecture have been proposed to combine the extremely high density of the memristive devices with the robustness of CMOS technology, leading to terabit-scale memory and extremely efficient computing paradigm. In this work, we demonstrate a hybrid 3D CMOL circuit with 2 layers of memristive crossbars monolithically integrated on a pre-fabricated CMOS substrate. The integrated crossbars can be fully operated through the underlying CMOS circuitry. The memristive devices in both layers exhibit analog switching behavior with controlled tunability and stable multi-level operation. We perform dot-product operations with the 2D and 3D memristive crossbars to demonstrate the applicability of such 3D CMOL hybrid circuits as a multiply-add engine. To the best of our knowledge this is the first demonstration of a functional 3D CMOL hybrid circuit.

Bio-rescue of marine environments: On the track of microbially-based metal/metalloid remediation.

PubMed

Marques, Catarina R

2016-09-15

The recent awareness of the huge relevance of marine resources and ecological services is driving regulatory demands for their protection from overwhelming contaminants, such as metals/metalloids. These contaminants enter and accumulate in different marine niches, hence deeply compromising their quality and integrity. Bioremediation has been flourishing to counteract metal/metalloid impacts, since it provides cost-effective and sustainable options by relying on ecology-based technologies. The potential of marine microbes for metal/metalloid bioremediation is the core of many studies, due to their high plasticity to overcome successive environmental hurdles. However, any thorough review on the advances of metal/metalloid bioremediation in marine environments was so far unveiled. This review is designed to (i) outline the characteristics and potential of marine microbes for metal/metalloid bioremediation, (ii) describe the underlying pathways of resistance and detoxification, as well as useful methodologies for their characterization, (iii) identify major bottlenecks on metal/metalloid bioremediation with marine microbes, (iv) present alternative strategies based on microbial consortia and engineered microbes for enhanced bioremediation, and (v) propose key research avenues to keep pace with a changing society, science and economy in a sustainable manner. Copyright © 2016 Elsevier B.V. All rights reserved.

Physiology limits commercially viable photoautotrophic production of microalgal biofuels.

PubMed

Kenny, Philip; Flynn, Kevin J

2017-01-01

Algal biofuels have been offered as an alternative to fossil fuels, based on claims that microalgae can provide a highly productive source of compounds as feedstocks for sustainable transport fuels. Life cycle analyses identify algal productivity as a critical factor affecting commercial and environmental viability. Here, we use mechanistic modelling of the biological processes driving microalgal growth to explore optimal production scenarios in an industrial setting, enabling us to quantify limits to algal biofuels potential. We demonstrate how physiological and operational trade-offs combine to restrict the potential for solar-powered algal-biodiesel production in open ponds to a ceiling of ca. 8000 L ha -1 year -1 . For industrial-scale operations, practical considerations limit production to ca. 6000 L ha -1 year -1 . According to published economic models and life cycle analyses, such production rates cannot support long-term viable commercialisation of solar-powered cultivation of natural microalgae strains exclusively as feedstock for biofuels. The commercial viability of microalgal biofuels depends critically upon limitations in microalgal physiology (primarily in rates of C-fixation); we discuss the scope for addressing this bottleneck concluding that even deployment of genetically modified microalgae with radically enhanced characteristics would leave a very significant logistical if not financial burden.

Plasmonic Control of Multi-Electron Transfer and C-C Coupling in Visible-Light-Driven CO2 Reduction on Au Nanoparticles.

PubMed

Yu, Sungju; Wilson, Andrew J; Heo, Jaeyoung; Jain, Prashant K

2018-04-11

Artificial photosynthesis relies on the availability of synthetic photocatalysts that can drive CO 2 reduction in the presence of water and light. From the standpoint of solar fuel production, it is desirable that these photocatalysts perform under visible light and produce energy-rich hydrocarbons from CO 2 reduction. However, the multistep nature of CO 2 -to-hydrocarbon conversion poses a significant kinetic bottleneck when compared to CO production and H 2 evolution. Here, we show that plasmonic Au nanoparticle photocatalysts can harvest visible light for multielectron, multiproton reduction of CO 2 to yield C 1 (methane) and C 2 (ethane) hydrocarbons. The light-excitation attributes influence the C 2 and C 1 selectivity. The observed trends in activity and selectivity follow Poisson statistics of electron harvesting. Higher photon energies and flux favor simultaneous harvesting of more than one electron from the photocharged Au nanoparticle catalyst, inducing the C-C coupling required for C 2 production. These findings elucidate the nature of plasmonic photocatalysis, which involves strong light-matter coupling, and set the stage for the controlled chemical bond formation by light excitation.

Enhanced intelligent driver model to access the impact of driving strategies on traffic capacity.

PubMed

Kesting, Arne; Treiber, Martin; Helbing, Dirk

2010-10-13

With an increasing number of vehicles equipped with adaptive cruise control (ACC), the impact of such vehicles on the collective dynamics of traffic flow becomes relevant. By means of simulation, we investigate the influence of variable percentages of ACC vehicles on traffic flow characteristics. For simulating the ACC vehicles, we propose a new car-following model that also serves as the basis of an ACC implementation in real cars. The model is based on the intelligent driver model (IDM) and inherits its intuitive behavioural parameters: desired velocity, acceleration, comfortable deceleration and desired minimum time headway. It eliminates, however, the sometimes unrealistic behaviour of the IDM in cut-in situations with ensuing small gaps that regularly are caused by lane changes of other vehicles in dense or congested traffic. We simulate the influence of different ACC strategies on the maximum capacity before breakdown and the (dynamic) bottleneck capacity after breakdown. With a suitable strategy, we find sensitivities of the order of 0.3, i.e. 1 per cent more ACC vehicles will lead to an increase in the capacities by about 0.3 per cent. This sensitivity multiplies when considering travel times at actual breakdowns.

Perceptual learning: top to bottom.

PubMed

Amitay, Sygal; Zhang, Yu-Xuan; Jones, Pete R; Moore, David R

2014-06-01

Perceptual learning has traditionally been portrayed as a bottom-up phenomenon that improves encoding or decoding of the trained stimulus. Cognitive skills such as attention and memory are thought to drive, guide and modulate learning but are, with notable exceptions, not generally considered to undergo changes themselves as a result of training with simple perceptual tasks. Moreover, shifts in threshold are interpreted as shifts in perceptual sensitivity, with no consideration for non-sensory factors (such as response bias) that may contribute to these changes. Accumulating evidence from our own research and others shows that perceptual learning is a conglomeration of effects, with training-induced changes ranging from the lowest (noise reduction in the phase locking of auditory signals) to the highest (working memory capacity) level of processing, and includes contributions from non-sensory factors that affect decision making even on a "simple" auditory task such as frequency discrimination. We discuss our emerging view of learning as a process that increases the signal-to-noise ratio associated with perceptual tasks by tackling noise sources and inefficiencies that cause performance bottlenecks, and present some implications for training populations other than young, smart, attentive and highly-motivated college students. Crown Copyright © 2013. Published by Elsevier Ltd. All rights reserved.

A multiply-add engine with monolithically integrated 3D memristor crossbar/CMOS hybrid circuit

PubMed Central

Chakrabarti, B.; Lastras-Montaño, M. A.; Adam, G.; Prezioso, M.; Hoskins, B.; Cheng, K.-T.; Strukov, D. B.

2017-01-01

Silicon (Si) based complementary metal-oxide semiconductor (CMOS) technology has been the driving force of the information-technology revolution. However, scaling of CMOS technology as per Moore’s law has reached a serious bottleneck. Among the emerging technologies memristive devices can be promising for both memory as well as computing applications. Hybrid CMOS/memristor circuits with CMOL (CMOS + “Molecular”) architecture have been proposed to combine the extremely high density of the memristive devices with the robustness of CMOS technology, leading to terabit-scale memory and extremely efficient computing paradigm. In this work, we demonstrate a hybrid 3D CMOL circuit with 2 layers of memristive crossbars monolithically integrated on a pre-fabricated CMOS substrate. The integrated crossbars can be fully operated through the underlying CMOS circuitry. The memristive devices in both layers exhibit analog switching behavior with controlled tunability and stable multi-level operation. We perform dot-product operations with the 2D and 3D memristive crossbars to demonstrate the applicability of such 3D CMOL hybrid circuits as a multiply-add engine. To the best of our knowledge this is the first demonstration of a functional 3D CMOL hybrid circuit. PMID:28195239

Stimulated Motion Suppression (STMS): a New Approach to Break the Resolution Barrier for Ion Trap Mass Spectrometry

NASA Astrophysics Data System (ADS)

Zhou, Xiaoyu; Liu, Xinwei; Chiang, Spencer; Cao, Wenbo; Li, Ming; Ouyang, Zheng

2018-05-01

Ion trap is an excellent platform to perform tandem mass spectrometry (MS/MS), but has an intrinsic drawback in resolving power. Using ion resonant ejection as an example, the resolution degradation can be largely attributed to the broadening of the resonant frequency band (RFB) between ion motion and driving alternative-current (AC). To solve this problem, stimulated motion suppression (STMS) was developed. The key idea of STMS is the use of two suppression alternative-current (SAC) signals, which both have reversed initial phases to the main AC. The SACs can block the unexpected sideband ion resonances (or ejections), therefore playing a key role in sharpening the RFB. The proof-of-concept has been demonstrated through ion trajectory simulations and validated experimentally. STMS provides a new and versatile means for the improvement of the ion trap resolution, which for a long time has reached the bottleneck through conventional methods, e.g., increasing the radio-frequency (RF) voltage and decreasing the mass scan rate. At the end, it is worth noting that the idea of STMS is very general and principally can be applied in any RF device for the purposes of high-resolution mass analysis and ion isolation.

Glucose Synthesis in a Protein-Based Artificial Photosynthesis System.

PubMed

Lu, Hao; Yuan, Wenqiao; Zhou, Jack; Chong, Parkson Lee-Gau

2015-09-01

The objective of this study was to understand glucose synthesis of a protein-based artificial photosynthesis system affected by operating conditions, including the concentrations of reactants, reaction temperature, and illumination. Results from non-vesicle-based glyceraldehyde-3-phosphate (GAP) and glucose synthesis showed that the initial concentrations of ribulose-1,5-bisphosphate (RuBP) and adenosine triphosphate (ATP), lighting source, and temperature significantly affected glucose synthesis. Higher initial concentrations of RuBP and ATP significantly enhanced GAP synthesis, which was linearly correlated to glucose synthesis, confirming the proper functions of all catalyzing enzymes in the system. White fluorescent light inhibited artificial photosynthesis and reduced glucose synthesis by 79.2 % compared to in the dark. The reaction temperature of 40 °C was optimum, whereas lower or higher temperature reduced glucose synthesis. Glucose synthesis in the vesicle-based artificial photosynthesis system reconstituted with bacteriorhodopsin, F 0 F 1 ATP synthase, and polydimethylsiloxane-methyloxazoline-polydimethylsiloxane triblock copolymer was successfully demonstrated. This system efficiently utilized light-induced ATP to drive glucose synthesis, and 5.2 μg ml(-1) glucose was synthesized in 0.78-ml reaction buffer in 7 h. Light-dependent reactions were found to be the bottleneck of the studied artificial photosynthesis system.

High gain solar photovoltaics

NASA Astrophysics Data System (ADS)

MacDonald, B.; Finot, M.; Heiken, B.; Trowbridge, T.; Ackler, H.; Leonard, L.; Johnson, E.; Chang, B.; Keating, T.

2009-08-01

Skyline Solar Inc. has developed a novel silicon-based PV system to simultaneously reduce energy cost and improve scalability of solar energy. The system achieves high gain through a combination of high capacity factor and optical concentration. The design approach drives innovation not only into the details of the system hardware, but also into manufacturing and deployment-related costs and bottlenecks. The result of this philosophy is a modular PV system whose manufacturing strategy relies only on currently existing silicon solar cell, module, reflector and aluminum parts supply chains, as well as turnkey PV module production lines and metal fabrication industries that already exist at enormous scale. Furthermore, with a high gain system design, the generating capacity of all components is multiplied, leading to a rapidly scalable system. The product design and commercialization strategy cooperate synergistically to promise dramatically lower LCOE with substantially lower risk relative to materials-intensive innovations. In this paper, we will present the key design aspects of Skyline's system, including aspects of the optical, mechanical and thermal components, revealing the ease of scalability, low cost and high performance. Additionally, we will present performance and reliability results on modules and the system, using ASTM and UL/IEC methodologies.

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.

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.

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 Deterministic Information Bottleneck

NASA Astrophysics Data System (ADS)

Strouse, D. J.; Schwab, David

2015-03-01

A fundamental and ubiquitous task that all organisms face is prediction of the future based on past sensory experience. Since an individual's memory resources are limited and costly, however, there is a tradeoff between memory cost and predictive payoff. The information bottleneck (IB) method (Tishby, Pereira, & Bialek 2000) formulates this tradeoff as a mathematical optimization problem using an information theoretic cost function. IB encourages storing as few bits of past sensory input as possible while selectively preserving the bits that are most predictive of the future. Here we introduce an alternative formulation of the IB method, which we call the deterministic information bottleneck (DIB). First, we argue for an alternative cost function, which better represents the biologically-motivated goal of minimizing required memory resources. Then, we show that this seemingly minor change has the dramatic effect of converting the optimal memory encoder from stochastic to deterministic. Next, we propose an iterative algorithm for solving the DIB problem. Additionally, we compare the IB and DIB methods on a variety of synthetic datasets, and examine the performance of retinal ganglion cell populations relative to the optimal encoding strategy for each problem.

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

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.

Central control of interlimb coordination and speed‐dependent gait expression in quadrupeds

PubMed Central

Danner, Simon M.; Wilshin, Simon D.; Shevtsova, Natalia A.

2016-01-01

Key points Quadrupeds express different gaits depending on speed of locomotion.Central pattern generators (one per limb) within the spinal cord generate locomotor oscillations and control limb movements. Neural interactions between these generators define interlimb coordination and gait.We present a computational model of spinal circuits representing four rhythm generators with left–right excitatory and inhibitory commissural and fore–hind inhibitory interactions within the cord.Increasing brainstem drive to all rhythm generators and excitatory commissural interneurons induces an increasing frequency of locomotor oscillations accompanied by speed‐dependent gait changes from walk to trot and to gallop and bound.The model closely reproduces and suggests explanations for multiple experimental data, including speed‐dependent gait transitions in intact mice and changes in gait expression in mutants lacking certain types of commissural interneurons. The model suggests the possible circuit organization in the spinal cord and proposes predictions that can be tested experimentally. Abstract As speed of locomotion is increasing, most quadrupeds, including mice, demonstrate sequential gait transitions from walk to trot and to gallop and bound. The neural mechanisms underlying these transitions are poorly understood. We propose that the speed‐dependent expression of different gaits results from speed‐dependent changes in the interactions between spinal circuits controlling different limbs and interlimb coordination. As a result, the expression of each gait depends on (1) left–right interactions within the spinal cord mediated by different commissural interneurons (CINs), (2) fore–hind interactions on each side of the spinal cord and (3) brainstem drives to rhythm‐generating circuits and CIN pathways. We developed a computational model of spinal circuits consisting of four rhythm generators (RGs) with bilateral left–right interactions mediated by V0 CINs (V0D and V0V sub‐types) providing left–right alternation, and conditional V3 CINs promoting left–right synchronization. Fore and hind RGs mutually inhibited each other. We demonstrate that linearly increasing excitatory drives to the RGs and V3 CINs can produce a progressive increase in the locomotor speed accompanied by sequential changes of gaits from walk to trot and to gallop and bound. The model closely reproduces and suggests explanations for the speed‐dependent gait expression observed in vivo in intact mice and in mutants lacking V0V or all V0 CINs. Specifically, trot is not expressed after removal of V0V CINs, and only bound is expressed after removal of all V0 CINs. The model provides important insights into the organization of spinal circuits and neural control of locomotion. PMID:27633893

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.

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.

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

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.

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).

High-throughput crystal-optimization strategies in the South Paris Yeast Structural Genomics Project: one size fits all?

PubMed

Leulliot, Nicolas; Trésaugues, Lionel; Bremang, Michael; Sorel, Isabelle; Ulryck, Nathalie; Graille, Marc; Aboulfath, Ilham; Poupon, Anne; Liger, Dominique; Quevillon-Cheruel, Sophie; Janin, Joël; van Tilbeurgh, Herman

2005-06-01

Crystallization has long been regarded as one of the major bottlenecks in high-throughput structural determination by X-ray crystallography. Structural genomics projects have addressed this issue by using robots to set up automated crystal screens using nanodrop technology. This has moved the bottleneck from obtaining the first crystal hit to obtaining diffraction-quality crystals, as crystal optimization is a notoriously slow process that is difficult to automatize. This article describes the high-throughput optimization strategies used in the Yeast Structural Genomics project, with selected successful examples.

Explaining bathymetric diversity patterns in marine benthic invertebrates and demersal fishes: physiological contributions to adaptation of life at depth.

PubMed

Brown, Alastair; Thatje, Sven

2014-05-01

Bathymetric biodiversity patterns of marine benthic invertebrates and demersal fishes have been identified in the extant fauna of the deep continental margins. Depth zonation is widespread and evident through a transition between shelf and slope fauna from the shelf break to 1000 m, and a transition between slope and abyssal fauna from 2000 to 3000 m; these transitions are characterised by high species turnover. A unimodal pattern of diversity with depth peaks between 1000 and 3000 m, despite the relatively low area represented by these depths. Zonation is thought to result from the colonisation of the deep sea by shallow-water organisms following multiple mass extinction events throughout the Phanerozoic. The effects of low temperature and high pressure act across hierarchical levels of biological organisation and appear sufficient to limit the distributions of such shallow-water species. Hydrostatic pressures of bathyal depths have consistently been identified experimentally as the maximum tolerated by shallow-water and upper bathyal benthic invertebrates at in situ temperatures, and adaptation appears required for passage to deeper water in both benthic invertebrates and demersal fishes. Together, this suggests that a hyperbaric and thermal physiological bottleneck at bathyal depths contributes to bathymetric zonation. The peak of the unimodal diversity-depth pattern typically occurs at these depths even though the area represented by these depths is relatively low. Although it is recognised that, over long evolutionary time scales, shallow-water diversity patterns are driven by speciation, little consideration has been given to the potential implications for species distribution patterns with depth. Molecular and morphological evidence indicates that cool bathyal waters are the primary site of adaptive radiation in the deep sea, and we hypothesise that bathymetric variation in speciation rates could drive the unimodal diversity-depth pattern over time. Thermal effects on metabolic-rate-dependent mutation and on generation times have been proposed to drive differences in speciation rates, which result in modern latitudinal biodiversity patterns over time. Clearly, this thermal mechanism alone cannot explain bathymetric patterns since temperature generally decreases with depth. We hypothesise that demonstrated physiological effects of high hydrostatic pressure and low temperature at bathyal depths, acting on shallow-water taxa invading the deep sea, may invoke a stress-evolution mechanism by increasing mutagenic activity in germ cells, by inactivating canalisation during embryonic or larval development, by releasing hidden variation or mutagenic activity, or by activating or releasing transposable elements in larvae or adults. In this scenario, increased variation at a physiological bottleneck at bathyal depths results in elevated speciation rate. Adaptation that increases tolerance to high hydrostatic pressure and low temperature allows colonisation of abyssal depths and reduces the stress-evolution response, consequently returning speciation of deeper taxa to the background rate. Over time this mechanism could contribute to the unimodal diversity-depth pattern. © 2013 Natural Environment Research Council. Biological Reviews published by John Wiley & Sons Ltd on behalf of Cambridge Philosophical Society.

Explaining bathymetric diversity patterns in marine benthic invertebrates and demersal fishes: physiological contributions to adaptation of life at depth

PubMed Central

Brown, Alastair; Thatje, Sven

2014-01-01

Bathymetric biodiversity patterns of marine benthic invertebrates and demersal fishes have been identified in the extant fauna of the deep continental margins. Depth zonation is widespread and evident through a transition between shelf and slope fauna from the shelf break to 1000 m, and a transition between slope and abyssal fauna from 2000 to 3000 m; these transitions are characterised by high species turnover. A unimodal pattern of diversity with depth peaks between 1000 and 3000 m, despite the relatively low area represented by these depths. Zonation is thought to result from the colonisation of the deep sea by shallow-water organisms following multiple mass extinction events throughout the Phanerozoic. The effects of low temperature and high pressure act across hierarchical levels of biological organisation and appear sufficient to limit the distributions of such shallow-water species. Hydrostatic pressures of bathyal depths have consistently been identified experimentally as the maximum tolerated by shallow-water and upper bathyal benthic invertebrates at in situ temperatures, and adaptation appears required for passage to deeper water in both benthic invertebrates and demersal fishes. Together, this suggests that a hyperbaric and thermal physiological bottleneck at bathyal depths contributes to bathymetric zonation. The peak of the unimodal diversity–depth pattern typically occurs at these depths even though the area represented by these depths is relatively low. Although it is recognised that, over long evolutionary time scales, shallow-water diversity patterns are driven by speciation, little consideration has been given to the potential implications for species distribution patterns with depth. Molecular and morphological evidence indicates that cool bathyal waters are the primary site of adaptive radiation in the deep sea, and we hypothesise that bathymetric variation in speciation rates could drive the unimodal diversity–depth pattern over time. Thermal effects on metabolic-rate-dependent mutation and on generation times have been proposed to drive differences in speciation rates, which result in modern latitudinal biodiversity patterns over time. Clearly, this thermal mechanism alone cannot explain bathymetric patterns since temperature generally decreases with depth. We hypothesise that demonstrated physiological effects of high hydrostatic pressure and low temperature at bathyal depths, acting on shallow-water taxa invading the deep sea, may invoke a stress–evolution mechanism by increasing mutagenic activity in germ cells, by inactivating canalisation during embryonic or larval development, by releasing hidden variation or mutagenic activity, or by activating or releasing transposable elements in larvae or adults. In this scenario, increased variation at a physiological bottleneck at bathyal depths results in elevated speciation rate. Adaptation that increases tolerance to high hydrostatic pressure and low temperature allows colonisation of abyssal depths and reduces the stress–evolution response, consequently returning speciation of deeper taxa to the background rate. Over time this mechanism could contribute to the unimodal diversity–depth pattern. PMID:24118851

48. VIEW LOOKING NORTHEAST AT EXCITER RESISTANCE GRIDS LOCATED UNDER ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

48. VIEW LOOKING NORTHEAST AT EXCITER RESISTANCE GRIDS LOCATED UNDER THE CONTROL ROOM ON SOUTH SIDE OF TURBINE HALL. THE GRIDS WERE AN ESSENTIAL PART OF THE CONTROL SYSTEM THAT MAINTAINED CONSTANT VOLTAGE ON THE RAILROAD POWER LINES. TIRRILL VOLTAGE REGULATORS (SEE CT-142A-100) SENSED VOLTAGE VARIATIONS AND INITIATED SWITCHING SEQUENCES TO REGULATE THE VOLTAGE AND MAINTAIN A SYSTEM STANDARD VOLTAGE. THE RESISTANCE GRIDS WERE SEQUENTIALLY ADDED TO OR REMOVED FROM THE GENERATOR FIELD COIL CIRCUITS. THIS RESISTANCE LOAD DISSIPATED EXCITIR GENERATOR POWER AS HEAT. THIS IN TURN WOULD VARY THE STRENGTH OF THE FIELD MAGNET AND CONSEQUENTLY RAISE OR LOWER THE OUTPUT VOLTAGE FROM THE MAIN GENERATOR ARMATURE. - New York, New Haven & Hartford Railroad, Cos Cob Power Plant, Sound Shore Drive, Greenwich, Fairfield County, CT

Automated synthesis and composition of taskblocks for control of manufacturing systems.

PubMed

Holloway, L E; Guan, X; Sundaravadivelu, R; Ashley, J R

2000-01-01

Automated control synthesis methods for discrete-event systems promise to reduce the time required to develop, debug, and modify control software. Such methods must be able to translate high-level control goals into detailed sequences of actuation and sensing signals. In this paper, we present such a technique. It relies on analysis of a system model, defined as a set of interacting components, each represented as a form of condition system Petri net. Control logic modules, called taskblocks, are synthesized from these individual models. These then interact hierarchically and sequentially to drive the system through specified control goals. The resulting controller is automatically converted to executable control code. The paper concludes with a discussion of a set of software tools developed to demonstrate the techniques on a small manufacturing system.

Precision Medicine in Myelodysplastic Syndromes and Leukemias: Lessons from Sequential Mutations.

PubMed

Nazha, Aziz; Sekeres, Mikkael A

2017-01-14

Precision medicine can be simply defined as the identification of personalized treatment that matches patient-specific clinical and genomic characteristics. Since the completion of the Human Genome Project in 2003, significant advances have been made in our understanding of the genetic makeup of diseases, especially cancers. The identification of somatic mutations that can drive cancer has led to the development of therapies that specifically target the abnormal proteins derived from these mutations. This has led to a paradigm shift in our treatment methodology. Although some success has been achieved in targeting some genetic abnormalities, several challenges and limitations exist when applying precision-medicine concepts in leukemia and myelodysplastic syndromes. We review the current understanding of genomics in myelodysplastic syndromes (MDS) and leukemias and the limitations of precision-medicine concepts in MDS.

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

USGS Publications Warehouse

Beissenger, S.R.; Wunderle, J.M.; Meyers, J.M.; Saether, B.-E.; Engen, S.

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 analysis, then examine evidence for the importance of specific processes maintaining the bottleneck using the multiple competing hypotheses approach, and finally integrate these results through a sensitivity analysis of a demographic model using life-stage simulation analysis (LSA) to determine the relative importance of genetic, demographic, environmental, and catastrophic processes on population growth. Annual population growth has been slow and variable (1.0 6 5.2 parrots per year, or an average k?1.05 6 0.19) from 16 parrots (1973) to a high of 40-42 birds (1997-1998). A risk analysis based on population prediction intervals (PPI) indicates great risk and large uncertainty, with a range of 22?83 birds in the 90% PPI only five years into the future. Four primary factors (reduced hatching success due to inbreeding, failure of adults to nest, nest failure due to nongenetic causes, and reduced survival of adults and juveniles) were responsible for maintaining the bottleneck. Egghatchability rates were low (70.6% per egg and 76.8% per pair), and hatchability increased after mate changes, suggesting inbreeding effects. Only an average of 34% of the population nested annually, which was well below the percentage of adults that should have reached an age of first breeding (41-56%). This chronic failure to nest appears to have been caused primarily by environmental and/or behavioral factors, and not by nest-site scarcity or a skewed sex ratio. Nest failure rates from nongenetic causes (i.e., predation, parasitism, and wet cavities) were low (29%) due to active management (protecting nests and fostering captive young into wild nests), diminishing the importance of nest failure as a limiting factor. Annual survival has been periodically reduced by catastrophes (hurricanes), which have greatly constrained population growth, but survival rates were high under non-catastrophic conditions. Although the importance of factors maintaining the Puerto Rican Parrot bottleneck varied throughout the 30-year period of study, we determined their long-term influence using LSA simulations to correlate variation in demographic rates with variation in population growth (k). The bottleneck appears to have been maintained primarily by periodic catastrophes (hurricanes) that reduced adult survival, and secondarily by environmental and/or behavioral factors that resulted in a failure of many adults to nest. The influence of inbreeding through reduced hatching success played a much less significant role, even when additional effects of inbreeding on the production and mortality of young were incorporated into the LSA. Management actions needed to speed recovery include (1) continued nest guarding to minimize the effects of nest failure due to nongenetic causes; (2) creating a second population at another location on the island --a process that was recently initiated--to reduce the chance that hurricane strikes will cause extinction; and (3) determining the causes of the low percentage of breeders in the population and ameliorating them, which would have a large impact on population growth.

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

Identification of bottlenecks in the accumulation of cyclic fatty acids in camelina seed oil

DOE PAGES

Yu, Xiao-Hong; Cahoon, Rebecca E.; Horn, Patrick J.; ...

2017-09-20

Modified fatty acids (mFA) have diverse uses, e.g., cyclopropane fatty acids (CPA) are feedstocks for producing coatings, lubricants, plastics, and cosmetics. The expression of mFA-producing enzymes in crop and model plants generally results in lower levels of mFA accumulation than in their natural-occurring source plants. In order to further our understanding of metabolic bottlenecks that limit mFA accumulation, we generated transgenic Camelina sativa lines co-expressing Escherichia coli cyclopropane synthase (EcCPS) and Sterculia foetida lysophosphatidic acid acyltransferase (SfLPAT). In contrast to transgenic CPA-accumulating Arabidopsis, CPA accumulation in camelina caused only minor changes in seed weight, germination rate, oil accumulation, and seedlingmore » development. CPA accumulated to much higher levels in membrane than storage lipids, comprising more than 60% of total fatty acid in both phosphatidylcholine (PC) and phosphatidylethanolamine (PE) versus 26% in diacylglycerol (DAG) and 12% in triacylglycerol (TAG) indicating bottlenecks in the transfer of CPA from PC to DAG and from DAG to TAG. Upon coexpression of SfLPAT with EcCPS, di-CPA-PC increased by ~50% relative to lines expressing EcCPS alone with the di-CPA-PC primarily observed in the embryonic axis and mono-CPA-PC primarily in cotyledon tissue. EcCPS-SfLPAT lines revealed a redistribution of CPA from the sn-1 to sn-2 positions within PC and PE that was associated with a doubling of CPA accumulation in both DAG and TAG. Finally, the identification of metabolic bottlenecks in acyl transfer between site of synthesis (phospholipids) and deposition in storage oils (TAGs) lays the foundation for the optimizing CPA accumulation through directed engineering of oil synthesis in target crops.« less

The Genetic Bottleneck in Vertical Transmission of Subtype C HIV-1 Is Not Driven by Selection of Especially Neutralization-Resistant Virus from the Maternal Viral Population ▿ †

PubMed Central

Russell, Elizabeth S.; Kwiek, Jesse J.; Keys, Jessica; Barton, Kirston; Mwapasa, Victor; Montefiori, David C.; Meshnick, Steven R.; Swanstrom, Ronald

2011-01-01

Subtype C human immunodeficiency virus type 1 (HIV-1C) continues to cause the majority of new cases of mother-to-child transmission (MTCT), and yet there are limited data on HIV-1C transmission. We amplified env from plasma RNA for 19 HIV-1C MTCT pairs, 10 transmitting in utero (IU) and 9 transmitting intrapartum (IP). There was a strong genetic bottleneck between all mother-infant pairs, with a majority of transmission events involving the transmission of a single virus. env genes of viruses transmitted to infants IP, but not IU, encoded Env proteins that were shorter and had fewer putative N-linked glycosylation sites in the V1-V5 region than matched maternal sequences. Viruses pseudotyped with env clones representative of each maternal and infant population were tested for neutralization sensitivity. The 50% inhibitory concentration of autologous serum was similar against both transmitted (infant) and nontransmitted (maternal) viruses in a paired analysis. Mother and infant Env proteins were also similar in sensitivity to soluble CD4, to a panel of monoclonal antibodies, and to heterologous HIV-1C sera. In addition, there was no difference in the breadth or potency of neutralizing antibodies between sera from 50 nontransmitting and 23 IU and 23 IP transmitting HIV-1C-infected women against four Env proteins from heterologous viruses. Thus, while a strong genetic bottleneck was detected during MCTC, with viruses of shorter and fewer glycosylation sites in env present in IP transmission, our data do not support this bottleneck being driven by selective resistance to antibodies. PMID:21593171

Molecular Population Genetics of the Northern Elephant Seal Mirounga angustirostris.

PubMed

Abadía-Cardoso, Alicia; Freimer, Nelson B; Deiner, Kristy; Garza, John Carlos

2017-09-01

The northern elephant seal, Mirounga angustirostris, was heavily hunted and declared extinct in the 19th century. However, a colony remained on remote Guadalupe Island, Mexico and the species has since repopulated most of its historical distribution. Here, we present a comprehensive evaluation of genetic variation in the species. First, we assess the effect of the demographic bottleneck on microsatellite variability and compare it with that found in other pinnipeds, demonstrating levels of variation similar to that in species that continue to be threatened with extinction. Next, we use sequence data from these markers to demonstrate that some of the limited polymorphism predates the bottleneck. However, most contemporary variation appears to have arisen recently and persisted due to exponential growth. We also describe how we use the range in allele size of microsatellites to estimate ancestral effective population size before the bottleneck, demonstrating a large reduction in effective size. We then employ a classical method for bacteria to estimate the microsatellite mutation rate in the species, deriving an estimate that is extremely similar to that estimated for a similar set of loci in humans, indicating consistency of microsatellite mutation rates in mammals. Finally, we find slight significant structure between some geographically separated colonies, although its biological significance is unclear. This work demonstrates that genetic analysis can be useful for evaluating the population biology of the northern elephant seal, in spite of the bottleneck that removed most genetic variation from the species. Published by Oxford University Press on behalf of The American Genetic Association 2017. This work is written by (a) US Government employee(s) and is in the public domain in the US.

Identification of bottlenecks in the accumulation of cyclic fatty acids in camelina seed oil

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

Yu, Xiao-Hong; Cahoon, Rebecca E.; Horn, Patrick J.

Modified fatty acids (mFA) have diverse uses, e.g., cyclopropane fatty acids (CPA) are feedstocks for producing coatings, lubricants, plastics, and cosmetics. The expression of mFA-producing enzymes in crop and model plants generally results in lower levels of mFA accumulation than in their natural-occurring source plants. In order to further our understanding of metabolic bottlenecks that limit mFA accumulation, we generated transgenic Camelina sativa lines co-expressing Escherichia coli cyclopropane synthase (EcCPS) and Sterculia foetida lysophosphatidic acid acyltransferase (SfLPAT). In contrast to transgenic CPA-accumulating Arabidopsis, CPA accumulation in camelina caused only minor changes in seed weight, germination rate, oil accumulation, and seedlingmore » development. CPA accumulated to much higher levels in membrane than storage lipids, comprising more than 60% of total fatty acid in both phosphatidylcholine (PC) and phosphatidylethanolamine (PE) versus 26% in diacylglycerol (DAG) and 12% in triacylglycerol (TAG) indicating bottlenecks in the transfer of CPA from PC to DAG and from DAG to TAG. Upon coexpression of SfLPAT with EcCPS, di-CPA-PC increased by ~50% relative to lines expressing EcCPS alone with the di-CPA-PC primarily observed in the embryonic axis and mono-CPA-PC primarily in cotyledon tissue. EcCPS-SfLPAT lines revealed a redistribution of CPA from the sn-1 to sn-2 positions within PC and PE that was associated with a doubling of CPA accumulation in both DAG and TAG. Finally, the identification of metabolic bottlenecks in acyl transfer between site of synthesis (phospholipids) and deposition in storage oils (TAGs) lays the foundation for the optimizing CPA accumulation through directed engineering of oil synthesis in target crops.« less

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.

Photocatalytic Conversion of Nitrobenzene to Aniline through Sequential Proton-Coupled One-Electron Transfers from a Cadmium Sulfide Quantum Dot

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

Jensen, Stephen C.; Bettis Homan, Stephanie; Weiss, Emily A.

2016-01-28

This paper describes the use of cadmium sulfide quantum dots (CdS QDs) as visible-light photocatalysts for the reduction of nitrobenzene to aniline through six sequential photoinduced, proton-coupled electron transfers. At pH 3.6–4.3, the internal quantum yield of photons-to-reducing electrons is 37.1% over 54 h of illumination, with no apparent decrease in catalyst activity. Monitoring of the QD exciton by transient absorption reveals that, for each step in the catalytic cycle, the sacrificial reductant, 3-mercaptopropionic acid, scavenges the excitonic hole in ~5 ps to form QD•–; electron transfer to nitrobenzene or the intermediates nitrosobenzene and phenylhydroxylamine then occurs on the nanosecondmore » time scale. The rate constants for the single-electron transfer reactions are correlated with the driving forces for the corresponding proton-coupled electron transfers. This result suggests, but does not prove, that electron transfer, not proton transfer, is rate-limiting for these reactions. Nuclear magnetic resonance analysis of the QD–molecule systems shows that the photoproduct aniline, left unprotonated, serves as a poison for the QD catalyst by adsorbing to its surface. Performing the reaction at an acidic pH not only encourages aniline to desorb but also increases the probability of protonated intermediates; the latter effect probably ensures that recruitment of protons is not rate-limiting.« less

Thin, Soft, Skin-Mounted Microfluidic Networks with Capillary Bursting Valves for Chrono-Sampling of Sweat.

PubMed

Choi, Jungil; Kang, Daeshik; Han, Seungyong; Kim, Sung Bong; Rogers, John A

2017-03-01

Systems for time sequential capture of microliter volumes of sweat released from targeted regions of the skin offer the potential to enable analysis of temporal variations in electrolyte balance and biomarker concentration throughout a period of interest. Current methods that rely on absorbent pads taped to the skin do not offer the ease of use in sweat capture needed for quantitative tracking; emerging classes of electronic wearable sweat analysis systems do not directly manage sweat-induced fluid flows for sample isolation. Here, a thin, soft, "skin-like" microfluidic platform is introduced that bonds to the skin to allow for collection and storage of sweat in an interconnected set of microreservoirs. Pressure induced by the sweat glands drives flow through a network of microchannels that incorporates capillary bursting valves designed to open at different pressures, for the purpose of passively guiding sweat through the system in sequential fashion. A representative device recovers 1.8 µL volumes of sweat each from 0.8 min of sweating into a set of separate microreservoirs, collected from 0.03 cm 2 area of skin with approximately five glands, corresponding to a sweat rate of 0.60 µL min -1 per gland. Human studies demonstrate applications in the accurate chemical analysis of lactate, sodium, and potassium concentrations and their temporal variations. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Spatial and Temporal Variability in Sediment P Distribution and Speciation in Coastal Louisiana

NASA Astrophysics Data System (ADS)

Bowes, K.; White, J. R.; Maiti, K.

2017-12-01

Excess loading of phosphorus (P) and nitrogen (N) into aquatic systems leads to degradation of water quality and diminished important ecosystem services. In the Northern Gulf of Mexico (NGOM), excess P and N loading has led to a seasonally present hypoxic area with less than 2 mg/L O2 in bottom waters, approximating 26,000 km2 in 2017. A sequential extraction (SEDEX) method was performed on surficial sediments from five different coastal and shelf sites as a function of distance from the Mississippi River mouth in the NGOM. To better quantify temporal variability in P distribution and speciation, samples were collected during both low (August) and high (May) river flow regimes. Sequential extraction techniques have been successful in separating pools of P into exchangeable or loosely sorbed P, Fe-P, Authigenic-P, Detrital-P, and Organic-P. Preliminary results suggest Authigenic-P is approximately 3-6 times more concentrated in NGOM sediments than all other P pools. Fractionation results did not show a consistent trend with sediment depth. Sediment samples had an average moisture content of 58.72% ± 12.06% and an average bulk density of 0.582 ± 0.275 g/cm3. Continued analysis of P speciation and cycling in NGOM sediments is critical in understanding the driving force behind coastal eutrophication and informing effective nutrient management strategies.

Sequential phosphorylation of CST subunits by different cyclin-Cdk1 complexes orchestrate telomere replication.

PubMed

Gopalakrishnan, Veena; Tan, Cherylin Ruiling; Li, Shang

2017-07-03

Telomeres are nucleoprotein structures that cap the ends of linear chromosomes. Telomere homeostasis is central to maintaining genomic integrity. In budding yeast, Cdk1 phosphorylates the telomere-specific binding protein, Cdc13, promoting the recruitment of telomerase to telomere and thereby telomere elongation. Cdc13 is also an integral part of the CST (Cdc13-Stn1-Ten1) complex that is essential for telomere capping and counteracting telomerase-dependent telomere elongation. Therefore, telomere length homeostasis is a balance between telomerase-extendable and CST-unextendable states. In our earlier work, we showed that Cdk1 also phosphorylates Stn1 which occurs sequentially following Cdc13 phosphorylation during cell cycle progression. This stabilizes the CST complex at the telomere and results in telomerase inhibition. Hence Cdk1-dependent phosphorylations of Stn1 acts like a molecular switch that drives Cdc13 to complex with Stn1-Ten1 rather than with telomerase. However, the underlying mechanism of how a single cyclin-dependent kinase phosphorylates Cdc13 and Stn1 in temporally distinct windows is largely unclear. Here, we show that S phase cyclins are necessary for telomere maintenance. The S phase and mitotic cyclins facilitate Cdc13 and Stn1 phosphorylation respectively, to exert opposing outcomes at the telomere. Thus, our results highlight a previously unappreciated role for cyclins in telomere replication.

Excited state intramolecular charge transfer reaction in nonaqueous electrolyte solutions: Temperature dependence

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

Pradhan, Tuhin; Gazi, Harun Al Rasid; Biswas, Ranjit

2009-08-07

Temperature dependence of the excited state intramolecular charge transfer reaction of 4-(1-azetidinyl)benzonitrile (P4C) in ethyl acetate (EA), acetonitrile (ACN), and ethanol at several concentrations of lithium perchlorate (LiClO{sub 4}) has been investigated by using the steady state and time resolved fluorescence spectroscopic techniques. The temperature range considered is 267-343 K. The temperature dependent spectral peak shifts and reaction driving force (-{Delta}G{sub r}) in electrolyte solutions of these solvents can be explained qualitatively in terms of interaction between the reactant molecule and ion-atmosphere. Time resolved studies indicate that the decay kinetics of P4C is biexponential, regardless of solvents, LiClO{sub 4} concentrations,more » and temperatures considered. Except at higher electrolyte concentrations in EA, reaction rates in solutions follow the Arrhenius-type temperature dependence where the estimated activation energy exhibits substantial electrolyte concentration dependence. The average of the experimentally measured activation energies in these three neat solvents is found to be in very good agreement with the predicted value based on data in room temperature solvents. While the rate constant in EA shows a electrolyte concentration induced parabolic dependence on reaction driving force (-{Delta}G{sub r}), the former in ethanol and ACN increases only linearly with the increase in driving force (-{Delta}G{sub r}). The data presented here also indicate that the step-wise increase in solvent reorganization energy via sequential addition of electrolyte induces the ICT reaction in weakly polar solvents to crossover from the Marcus inverted region to the normal region.« less

Estimating endogenous changes in task performance from EEG

PubMed Central

Touryan, Jon; Apker, Gregory; Lance, Brent J.; Kerick, Scott E.; Ries, Anthony J.; McDowell, Kaleb

2014-01-01

Brain wave activity is known to correlate with decrements in behavioral performance as individuals enter states of fatigue, boredom, or low alertness.Many BCI technologies are adversely affected by these changes in user state, limiting their application and constraining their use to relatively short temporal epochs where behavioral performance is likely to be stable. Incorporating a passive BCI that detects when the user is performing poorly at a primary task, and adapts accordingly may prove to increase overall user performance. Here, we explore the potential for extending an established method to generate continuous estimates of behavioral performance from ongoing neural activity; evaluating the extended method by applying it to the original task domain, simulated driving; and generalizing the method by applying it to a BCI-relevant perceptual discrimination task. Specifically, we used EEG log power spectra and sequential forward floating selection (SFFS) to estimate endogenous changes in behavior in both a simulated driving task and a perceptual discrimination task. For the driving task the average correlation coefficient between the actual and estimated lane deviation was 0.37 ± 0.22 (μ ± σ). For the perceptual discrimination task we generated estimates of accuracy, reaction time, and button press duration for each participant. The correlation coefficients between the actual and estimated behavior were similar for these three metrics (accuracy = 0.25 ± 0.37, reaction time = 0.33 ± 0.23, button press duration = 0.36 ± 0.30). These findings illustrate the potential for modeling time-on-task decrements in performance from concurrent measures of neural activity. PMID:24994968

Meth math: modeling temperature responses to methamphetamine.

PubMed

Molkov, Yaroslav I; Zaretskaia, Maria V; Zaretsky, Dmitry V

2014-04-15

Methamphetamine (Meth) can evoke extreme hyperthermia, which correlates with neurotoxicity and death in laboratory animals and humans. The objective of this study was to uncover the mechanisms of a complex dose dependence of temperature responses to Meth by mathematical modeling of the neuronal circuitry. On the basis of previous studies, we composed an artificial neural network with the core comprising three sequentially connected nodes: excitatory, medullary, and sympathetic preganglionic neuronal (SPN). Meth directly stimulated the excitatory node, an inhibitory drive targeted the medullary node, and, in high doses, an additional excitatory drive affected the SPN node. All model parameters (weights of connections, sensitivities, and time constants) were subject to fitting experimental time series of temperature responses to 1, 3, 5, and 10 mg/kg Meth. Modeling suggested that the temperature response to the lowest dose of Meth, which caused an immediate and short hyperthermia, involves neuronal excitation at a supramedullary level. The delay in response after the intermediate doses of Meth is a result of neuronal inhibition at the medullary level. Finally, the rapid and robust increase in body temperature induced by the highest dose of Meth involves activation of high-dose excitatory drive. The impairment in the inhibitory mechanism can provoke a life-threatening temperature rise and makes it a plausible cause of fatal hyperthermia in Meth users. We expect that studying putative neuronal sites of Meth action and the neuromediators involved in a detailed model of this system may lead to more effective strategies for prevention and treatment of hyperthermia induced by amphetamine-like stimulants.

Meth math: modeling temperature responses to methamphetamine

PubMed Central

Molkov, Yaroslav I.; Zaretskaia, Maria V.

2014-01-01

Methamphetamine (Meth) can evoke extreme hyperthermia, which correlates with neurotoxicity and death in laboratory animals and humans. The objective of this study was to uncover the mechanisms of a complex dose dependence of temperature responses to Meth by mathematical modeling of the neuronal circuitry. On the basis of previous studies, we composed an artificial neural network with the core comprising three sequentially connected nodes: excitatory, medullary, and sympathetic preganglionic neuronal (SPN). Meth directly stimulated the excitatory node, an inhibitory drive targeted the medullary node, and, in high doses, an additional excitatory drive affected the SPN node. All model parameters (weights of connections, sensitivities, and time constants) were subject to fitting experimental time series of temperature responses to 1, 3, 5, and 10 mg/kg Meth. Modeling suggested that the temperature response to the lowest dose of Meth, which caused an immediate and short hyperthermia, involves neuronal excitation at a supramedullary level. The delay in response after the intermediate doses of Meth is a result of neuronal inhibition at the medullary level. Finally, the rapid and robust increase in body temperature induced by the highest dose of Meth involves activation of high-dose excitatory drive. The impairment in the inhibitory mechanism can provoke a life-threatening temperature rise and makes it a plausible cause of fatal hyperthermia in Meth users. We expect that studying putative neuronal sites of Meth action and the neuromediators involved in a detailed model of this system may lead to more effective strategies for prevention and treatment of hyperthermia induced by amphetamine-like stimulants. PMID:24500434

Suppression of surface microstructure evolution in W and W-Ta alloys during simultaneous and sequential He and D ion irradiation in fusion relevant conditions

NASA Astrophysics Data System (ADS)

Gonderman, S.; Tripathi, J. K.; Sizyuk, T.; Hassanein, A.

2017-08-01

Tungsten (W) has been selected as the divertor material in ITER based on its promising thermal and mechanical properties. Despite these advantages, continued investigation has revealed W to undergo extreme surface morphology evolution in response to relevant fusion operating conditions. These complications spur the need for further exploration of W and other innovative plasma facing components (PFCs) for future fusion devices. Recent literature has shown that alloying of W with other refractory metals, such as tantalum (Ta), results in the enhancement of key PFC properties including, but not limited to, ductility, hydrogen isotope retention, and helium ion (He+) radiation tolerance. In the present study, pure W and W-Ta alloys are exposed to simultaneous and sequential low energy, He+ and deuterium (D+) ion beam irradiations at high (1223 K) and low (523 K) temperatures. The goal of this study is to cultivate a complete understanding of the synergistic effects induced by dual and sequential ion irradiation on W and W-Ta alloy surface morphology evolution. For the dual ion beam experiments, W and W-Ta samples were subjected to four different He+: D+ ion ratios (100% He+, 60% D+  +  40% He+, 90% D+  +  10% He+ and 100% D+) having a total constant He+ fluence of 6  ×  1024 ion m-2. The W and W-Ta samples both exhibit the expected damaged surfaces under the 100% He+ irradiation, but as the ratio of D+/He+ ions increases there is a clear suppression of the surface morphology at high temperatures. This observation is supported by the sequential experiments, which show a similar suppression of surface morphology when W and W-Ta samples are first exposed to low energy He+ irradiation and then exposed to subsequent low energy D+ irradiation at high temperatures. Interestingly, this morphology suppression is not observed at low temperatures, implying there is a D-W interaction mechanism which is dependent on temperature that is driving the suppression of the microstructure evolution in both the pure W and W-Ta alloys. Minor irradiation tolerance enhancement in the performance of the W-Ta samples is also observed.

Validity and reliability of naturalistic driving scene categorization Judgments from crowdsourcing.

PubMed

Cabrall, Christopher D D; Lu, Zhenji; Kyriakidis, Miltos; Manca, Laura; Dijksterhuis, Chris; Happee, Riender; de Winter, Joost

2018-05-01

A common challenge with processing naturalistic driving data is that humans may need to categorize great volumes of recorded visual information. By means of the online platform CrowdFlower, we investigated the potential of crowdsourcing to categorize driving scene features (i.e., presence of other road users, straight road segments, etc.) at greater scale than a single person or a small team of researchers would be capable of. In total, 200 workers from 46 different countries participated in 1.5days. Validity and reliability were examined, both with and without embedding researcher generated control questions via the CrowdFlower mechanism known as Gold Test Questions (GTQs). By employing GTQs, we found significantly more valid (accurate) and reliable (consistent) identification of driving scene items from external workers. Specifically, at a small scale CrowdFlower Job of 48 three-second video segments, an accuracy (i.e., relative to the ratings of a confederate researcher) of 91% on items was found with GTQs compared to 78% without. A difference in bias was found, where without GTQs, external workers returned more false positives than with GTQs. At a larger scale CrowdFlower Job making exclusive use of GTQs, 12,862 three-second video segments were released for annotation. Infeasible (and self-defeating) to check the accuracy of each at this scale, a random subset of 1012 categorizations was validated and returned similar levels of accuracy (95%). In the small scale Job, where full video segments were repeated in triplicate, the percentage of unanimous agreement on the items was found significantly more consistent when using GTQs (90%) than without them (65%). Additionally, in the larger scale Job (where a single second of a video segment was overlapped by ratings of three sequentially neighboring segments), a mean unanimity of 94% was obtained with validated-as-correct ratings and 91% with non-validated ratings. Because the video segments overlapped in full for the small scale Job, and in part for the larger scale Job, it should be noted that such reliability reported here may not be directly comparable. Nonetheless, such results are both indicative of high levels of obtained rating reliability. Overall, our results provide compelling evidence for CrowdFlower, via use of GTQs, being able to yield more accurate and consistent crowdsourced categorizations of naturalistic driving scene contents than when used without such a control mechanism. Such annotations in such short periods of time present a potentially powerful resource in driving research and driving automation development. Copyright © 2017 Elsevier Ltd. All rights reserved.

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.

Car accidents induced by a bottleneck

NASA Astrophysics Data System (ADS)

Marzoug, Rachid; Echab, Hicham; Ez-Zahraouy, Hamid

2017-12-01

Based on the Nagel-Schreckenberg model (NS) we study the probability of car accidents to occur (Pac) at the entrance of the merging part of two roads (i.e. junction). The simulation results show that the existence of non-cooperative drivers plays a chief role, where it increases the risk of collisions in the intermediate and high densities. Moreover, the impact of speed limit in the bottleneck (Vb) on the probability Pac is also studied. This impact depends strongly on the density, where, the increasing of Vb enhances Pac in the low densities. Meanwhile, it increases the road safety in the high densities. The phase diagram of the system is also constructed.

A model of airport security work flow based on petri net

NASA Astrophysics Data System (ADS)

Dong, Xinming

2017-09-01

Extremely long lines at airports in the United States have been sharply criticized. In order to find out the bottleneck in the existing security system and put forward reasonable improvement plans and proposal, the Petri net model and the Markov Chain are introduced in this paper. This paper uses data collected by transportation Security Agency (TSA), assuming the data can represent the average level of all airports in the Unites States, to analysis the performance of security check system. By calculating the busy probabilities and the utilization probabilities, the bottleneck is found. Moreover, recommendation is given based on the parameters’ modification in Petri net model.

Low worldwide genetic diversity in the killer whale (Orcinus orca): implications for demographic history.

PubMed Central

Hoelzel, A Rus; Natoli, Ada; Dahlheim, Marilyn E; Olavarria, Carlos; Baird, Robin W; Black, Nancy A

2002-01-01

A low level of genetic variation in mammalian populations where the census population size is relatively large has been attributed to various factors, such as a naturally small effective population size, historical bottlenecks and social behaviour. The killer whale (Orcinus orca) is an abundant, highly social species with reduced genetic variation. We find no consistent geographical pattern of global diversity and no mtDNA variation within some regional populations. The regional lack of variation is likely to be due to the strict matrilineal expansion of local populations. The worldwide pattern and paucity of diversity may indicate a historical bottleneck as an additional factor. PMID:12137576

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

Changes in variation at the MHC class II DQA locus during the final demise of the woolly mammoth

NASA Astrophysics Data System (ADS)

Pečnerová, Patrícia; Díez-Del-Molino, David; Vartanyan, Sergey; Dalén, Love

2016-05-01

According to the nearly-neutral theory of evolution, the relative strengths of selection and drift shift in favour of drift at small population sizes. Numerous studies have analysed the effect of bottlenecks and small population sizes on genetic diversity in the MHC, which plays a central role in pathogen recognition and immune defense and is thus considered a model example for the study of adaptive evolution. However, to understand changes in genetic diversity at loci under selection, it is necessary to compare the genetic diversity of a population before and after the bottleneck. In this study, we analyse three fragments of the MHC DQA gene in woolly mammoth samples radiocarbon dated to before and after a well-documented bottleneck that took place about ten thousand years ago. Our results indicate a decrease in observed heterozygosity and number of alleles, suggesting that genetic drift had an impact on the variation on MHC. Based on coalescent simulations, we found no evidence of balancing selection maintaining MHC diversity during the Holocene. However, strong trans-species polymorphism among mammoths and elephants points to historical effects of balancing selection on the woolly mammoth lineage.

Resistance of virus to extinction on bottleneck passages: study of a decaying and fluctuating pattern of fitness loss

NASA Technical Reports Server (NTRS)

Lazaro, Ester; Escarmis, Cristina; Perez-Mercader, Juan; Manrubia, Susanna C.; Domingo, Esteban

2003-01-01

RNA viruses display high mutation rates and their populations replicate as dynamic and complex mutant distributions, termed viral quasispecies. Repeated genetic bottlenecks, which experimentally are carried out through serial plaque-to-plaque transfers of the virus, lead to fitness decrease (measured here as diminished capacity to produce infectious progeny). Here we report an analysis of fitness evolution of several low fitness foot-and-mouth disease virus clones subjected to 50 plaque-to-plaque transfers. Unexpectedly, fitness decrease, rather than being continuous and monotonic, displayed a fluctuating pattern, which was influenced by both the virus and the state of the host cell as shown by effects of recent cell passage history. The amplitude of the fluctuations increased as fitness decreased, resulting in a remarkable resistance of virus to extinction. Whereas the frequency distribution of fitness in control (independent) experiments follows a log-normal distribution, the probability of fitness values in the evolving bottlenecked populations fitted a Weibull distribution. We suggest that multiple functions of viral genomic RNA and its encoded proteins, subjected to high mutational pressure, interact with cellular components to produce this nontrivial, fluctuating pattern.

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

Recurrent bottlenecks in the malaria life cycle obscure signals of positive selection.

PubMed

Chang, Hsiao-Han; Hartl, Daniel L

2015-02-01

Detecting signals of selection in the genome of malaria parasites is a key to identify targets for drug and vaccine development. Malaria parasites have a unique life cycle alternating between vector and host organism with a population bottleneck at each transition. These recurrent bottlenecks could influence the patterns of genetic diversity and the power of existing population genetic tools to identify sites under positive selection. We therefore simulated the site-frequency spectrum of a beneficial mutant allele through time under the malaria life cycle. We investigated the power of current population genetic methods to detect positive selection based on the site-frequency spectrum as well as temporal changes in allele frequency. We found that a within-host selective advantage is difficult to detect using these methods. Although a between-host transmission advantage could be detected, the power is decreased when compared with the classical Wright-Fisher (WF) population model. Using an adjusted null site-frequency spectrum that takes the malaria life cycle into account, the power of tests based on the site-frequency spectrum to detect positive selection is greatly improved. Our study demonstrates the importance of considering the life cycle in genetic analysis, especially in parasites with complex life cycles.

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

Decoupled systems on trial: Eliminating bottlenecks to improve aquaponic processes.

PubMed

Monsees, Hendrik; Kloas, Werner; Wuertz, Sven

2017-01-01

In classical aquaponics (coupled aquaponic systems, 1-loop systems) the production of fish in recirculating aquaculture systems (RAS) and plants in hydroponics are combined in a single loop, entailing systemic compromises on the optimal production parameters (e.g. pH). Recently presented decoupled aquaponics (2-loop systems) have been awarded for eliminating major bottlenecks. In a pilot study, production in an innovative decoupled aquaponic system was compared with a coupled system and, as a control, a conventional RAS, assessing growth parameters of fish (FCR, SGR) and plants over an experimental period of 5 months. Soluble nutrients (NO3--N, NO2--N, NH4+-N, PO43-, K+, Ca2+, Mg2+, SO42-, Cl2- and Fe2+), elemental composition of plants, fish and sludge (N, P, K, Ca, Mg, Na, C), abiotic factors (temperature, pH, oxygen, and conductivity), fertilizer and water consumption were determined. Fruit yield was 36% higher in decoupled aquaponics and pH and fertilizer management was more effective, whereas fish production was comparable in both systems. The results of this pilot study clearly illustrate the main advantages of decoupled, two-loop aquaponics and demonstrate how bottlenecks commonly encountered in coupled aquaponics can be managed to promote application in aquaculture.

Engineering of protein folding and secretion-strategies to overcome bottlenecks for efficient production of recombinant proteins.

PubMed

Delic, Marizela; Göngrich, Rebecca; Mattanovich, Diethard; Gasser, Brigitte

2014-07-20

Recombinant protein production has developed into a huge market with enormous positive implications for human health and for the future direction of a biobased economy. Limitations in the economic and technical feasibility of production processes are often related to bottlenecks of in vivo protein folding. Based on cell biological knowledge, some major bottlenecks have been overcome by the overexpression of molecular chaperones and other folding related proteins, or by the deletion of deleterious pathways that may lead to misfolding, mistargeting, or degradation. While important success could be achieved by this strategy, the list of reported unsuccessful cases is disappointingly long and obviously dependent on the recombinant protein to be produced. Singular engineering of protein folding steps may not lead to desired results if the pathway suffers from several limitations. In particular, the connection between folding quality control and proteolytic degradation needs further attention. Based on recent understanding that multiple steps in the folding and secretion pathways limit productivity, synergistic combinations of the cell engineering approaches mentioned earlier need to be explored. In addition, systems biology-based whole cell analysis that also takes energy and redox metabolism into consideration will broaden the knowledge base for future rational engineering strategies.

Mosquito bottlenecks alter viral mutant swarm in a tissue and time-dependent manner with contraction and expansion of variant positions and diversity.

PubMed

Patterson, Edward I; Khanipov, Kamil; Rojas, Mark M; Kautz, Tiffany F; Rockx-Brouwer, Dedeke; Golovko, Georgiy; Albayrak, Levent; Fofanov, Yuriy; Forrester, Naomi L

2018-01-01

Viral diversity is theorized to play a significant role during virus infections, particularly for arthropod-borne viruses (arboviruses) that must infect both vertebrate and invertebrate hosts. To determine how viral diversity influences mosquito infection and dissemination Culex taeniopus mosquitoes were infected with the Venezuelan equine encephalitis virus endemic strain 68U201. Bodies and legs/wings of the mosquitoes were collected individually and subjected to multi-parallel sequencing. Virus sequence diversity was calculated for each tissue. Greater diversity was seen in mosquitoes with successful dissemination versus those with no dissemination. Diversity across time revealed that bottlenecks influence diversity following dissemination to the legs/wings, but levels of diversity are restored by Day 12 post-dissemination. Specific minority variants were repeatedly identified across the mosquito cohort, some in nearly every tissue and time point, suggesting that certain variants are important in mosquito infection and dissemination. This study demonstrates that the interaction between the mosquito and the virus results in changes in diversity and the mutational spectrum and may be essential for successful transition of the bottlenecks associated with arbovirus infection.

Fuel system for rotary distributor fuel injection pump

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

Klopfer, K.H.; Kelly, W.W.

1993-06-01

In a fuel injection pump having a drive shaft, a pump rotor driven by the drive shaft, reciprocating pumping means with periodic intake and pumping strokes to periodically receive an intake charge of fuel and deliver fuel at high pressure for fuel injection is described; a distributor head with a plurality of angularly spaced distributor outlets, the pump rotor providing a distributor rotor with a distributor port connected to the pumping means, the distributor rotor being rotatably mounted in the distributor head for sequential registration of the distributor port with the distributor outlets for distributing said high pressure delivery ofmore » fuel thereto; a fuel system for supplying fuel to the pumping means, having an end chamber at one end of the pump rotor and a fuel supply pump driven by the drive shaft and having an inlet and outlet, the supply pump outlet being connected to the end chamber for supplying fuel thereto, and a pressure regulator for regulating the fuel pressure in the end chamber; and a control valve connected between the pumping means and the end chamber and selectively opened during the intake strokes to supply fuel to the pumping means from the end chamber and during the pumping strokes to spill fuel from the pumping means into the end chamber to terminate said high pressure delivery of fuel; the improvement wherein the fuel system comprises a fuel return passage connected in series with the end chamber downstream thereof, wherein the pressure regulator is mounted in the return passage for regulating the upstream fuel pressure, including the upstream fuel pressure within the end chamber, and is connected for conducting excess fuel for return to the supply pump inlet, and wherein the supply pump is driven by the drive shaft to supply fuel at a rate exceeding the rate of said high pressure delivery of fuel for fuel injection and to provide excess fuel flow continuously through the end chamber and return passage to the pressure regulator.« less

Lifetime of dielectric elastomer stack actuators

NASA Astrophysics Data System (ADS)

Lotz, Peter; Matysek, Marc; Schlaak, Helmut F.

2011-04-01

Dielectric elastomer stack actuators (DESA) are well suited for the use in mobile devices, fluidic applications and small electromechanical systems. Despite many improvements during the last years the long term behavior of dielectric elastomer actuators in general is not known or has not been published. The first goal of the study is to characterize the overall lifetime under laboratory conditions and to identify potential factors influencing lifetime. For this we have designed a test setup to examine 16 actuators at once. The actuators are subdivided into 4 groups each with a separate power supply and driving signal. To monitor the performance of the actuators driving voltage and current are measured continuously and additionally, the amplitude of the deformations of each actuator is measured sequentially. From our first results we conclude that lifetime of these actuators is mainly influenced by the contact material between feeding line and multilayer electrodes. So far, actuators themselves are not affected by long term actuation. With the best contact material actuators can be driven for more than 2700 h at 200 Hz with an electrical field strength of 20 V/μm. This results in more than 3 billion cycles. Actually, there are further actuators driven at 10 Hz for more than 4000 hours and still working.

Early-life sexual segregation: ontogeny of isotopic niche differentiation in the Antarctic fur seal

NASA Astrophysics Data System (ADS)

Kernaléguen, L.; Arnould, J. P. Y.; Guinet, C.; Cazelles, B.; Richard, P.; Cherel, Y.

2016-09-01

Investigating the ontogeny of niche differentiation enables to determine at which life-stages sexual segregation arises, providing insights into the main factors driving resource partitioning. We investigated the ontogeny of foraging ecology in Antarctic fur seals (Arctocephalus gazella), a highly dimorphic species with contrasting breeding strategies between sexes. Sequential δ13C and δ15N values of whiskers provided a longitudinal proxy of the foraging niche throughout the whole life of seals, from weaning, when size dimorphism is minimal to the age of 5. Females exhibited an early-life ontogenetic shift, from a total segregation during their first year at-sea, to a similar isotopic niche as breeding females as early as age 2. In contrast, males showed a progressive change in isotopic niche throughout their development such that 5-year-old males did not share the same niche as territorial bulls. Interestingly, males and females segregated straight after weaning with males appearing to feed in more southerly habitats than females. This spatial segregation was of similar amplitude as observed in breeding adults and was maintained throughout development. Such early-life niche differentiation is an unusual pattern and indicates size dimorphism and breeding constraints do not directly drive sexual segregation contrary to what has been assumed in otariid seals.

A cycloidal wobble motor driven by shape memory alloy wires

NASA Astrophysics Data System (ADS)

Hwang, Donghyun; Higuchi, Toshiro

2014-05-01

A cycloidal wobble motor driven by shape memory alloy (SMA) wires is proposed. In realizing a motor driving mechanism well known as a type of reduction system, a cycloidal gear mechanism is utilized. It facilitates the achievement of bidirectional continuous rotation with high-torque capability, based on its high efficiency and high reduction ratio. The applied driving mechanism consists of a pin/roller based annular gear as a wobbler, a cycloidal disc as a rotor, and crankshafts to guide the eccentric wobbling motion. The wobbling motion of the annular gear is generated by sequential activation of radially phase-symmetrically placed SMA wires. Consequently the cycloidal disc is rotated by rolling contact based cycloidal gearing between the wobbler and the rotor. In designing the proposed motor, thermomechanical characterization of an SMA wire biased by extension springs is experimentally performed. Then, a simplified geometric model for the motor is devised to conduct theoretical assessment of design parametric effects on structural features and working performance. With consideration of the results from parametric analysis, a functional prototype three-phase motor is fabricated to carry out experimental verification of working performance. The observed experimental results including output torque, rotational speed, bidirectional positioning characteristic, etc obviously demonstrate the practical applicability and potentiality of the wobble motor.

The evolutionary dynamics of variant antigen genes in Babesia reveal a history of genomic innovation underlying host–parasite interaction

PubMed Central

Jackson, Andrew P.; Otto, Thomas D.; Darby, Alistair; Ramaprasad, Abhinay; Xia, Dong; Echaide, Ignacio Eduardo; Farber, Marisa; Gahlot, Sunayna; Gamble, John; Gupta, Dinesh; Gupta, Yask; Jackson, Louise; Malandrin, Laurence; Malas, Tareq B.; Moussa, Ehab; Nair, Mridul; Reid, Adam J.; Sanders, Mandy; Sharma, Jyotsna; Tracey, Alan; Quail, Mike A.; Weir, William; Wastling, Jonathan M.; Hall, Neil; Willadsen, Peter; Lingelbach, Klaus; Shiels, Brian; Tait, Andy; Berriman, Matt; Allred, David R.; Pain, Arnab

2014-01-01

Babesia spp. are tick-borne, intraerythrocytic hemoparasites that use antigenic variation to resist host immunity, through sequential modification of the parasite-derived variant erythrocyte surface antigen (VESA) expressed on the infected red blood cell surface. We identified the genomic processes driving antigenic diversity in genes encoding VESA (ves1) through comparative analysis within and between three Babesia species, (B. bigemina, B. divergens and B. bovis). Ves1 structure diverges rapidly after speciation, notably through the evolution of shortened forms (ves2) from 5′ ends of canonical ves1 genes. Phylogenetic analyses show that ves1 genes are transposed between loci routinely, whereas ves2 genes are not. Similarly, analysis of sequence mosaicism shows that recombination drives variation in ves1 sequences, but less so for ves2, indicating the adoption of different mechanisms for variation of the two families. Proteomic analysis of the B. bigemina PR isolate shows that two dominant VESA1 proteins are expressed in the population, whereas numerous VESA2 proteins are co-expressed, consistent with differential transcriptional regulation of each family. Hence, VESA2 proteins are abundant and previously unrecognized elements of Babesia biology, with evolutionary dynamics consistently different to those of VESA1, suggesting that their functions are distinct. PMID:24799432

Developmental aspects of the interaction between narcissism, self-esteem and object relations.

PubMed

Dare, C; Holder, A

1981-01-01

This paper reviews the history, within psycho-analysis, of narcissism and shows that it cannot be understood as a unitary concept. This is reflected in much of the extensive literature on the topic. The definition of narcissism solely in terms of the libidinal drive cathexis of the self representation is rejected. Instead, narcissism is defined as the sum of the positively-coloured feeling states attached to the self-representation. By pursuing a developmental investigation of narcissistic and opposing phenomena, the multiple sources which contribute to or detract from the overall level of self-esteem are demonstrated. Such an investigation clarifies the close relationship between the concepts of self-esteem, well-being and narcissism, and differentiating definitions are put forward. The term 'counter-narcissistic' is introduced to denote the negative contributions to self-esteem which detract from the narcissistic input. The interplay between the contributions to the overall quality of self-esteem, deriving on the one hand from somatic and instinctual drive sources, and on the other from object relationships, exemplifies the multiple origins of its qualities at any one time. This interplay is pursued through the sequential developmental phases from infancy to the oedipal level in order to show the complex epigenesis of narcissism, counter-narcissism and self-esteem.

Sympathetic restraint of respiratory sinus arrhythmia: implications for vagal-cardiac tone assessment in humans

NASA Technical Reports Server (NTRS)

Taylor, J. A.; Myers, C. W.; Halliwill, J. R.; Seidel, H.; Eckberg, D. L.

2001-01-01

Clinicians and experimentalists routinely estimate vagal-cardiac nerve traffic from respiratory sinus arrhythmia. However, evidence suggests that sympathetic mechanisms may also modulate respiratory sinus arrhythmia. Our study examined modulation of respiratory sinus arrhythmia by sympathetic outflow. We measured R-R interval spectral power in 10 volunteers that breathed sequentially at 13 frequencies, from 15 to 3 breaths/min, before and after beta-adrenergic blockade. We fitted changes of respiratory frequency R-R interval spectral power with a damped oscillator model: frequency-dependent oscillations with a resonant frequency, generated by driving forces and modified by damping influences. beta-Adrenergic blockade enhanced respiratory sinus arrhythmia at all frequencies (at some, fourfold). The damped oscillator model fit experimental data well (39 of 40 ramps; r = 0.86 +/- 0.02). beta-Adrenergic blockade increased respiratory sinus arrhythmia by amplifying respiration-related driving forces (P < 0.05), without altering resonant frequency or damping influences. Both spectral power data and the damped oscillator model indicate that cardiac sympathetic outflow markedly reduces heart period oscillations at all frequencies. This challenges the notion that respiratory sinus arrhythmia is mediated simply by vagal-cardiac nerve activity. These results have important implications for clinical and experimental estimation of human vagal cardiac tone.

Prdm1a and miR-499 act sequentially to restrict Sox6 activity to the fast-twitch muscle lineage in the zebrafish embryo.

PubMed

Wang, XinGang; Ono, Yosuke; Tan, Swee Chuan; Chai, Ruth JinFen; Parkin, Caroline; Ingham, Philip W

2011-10-01

Sox6 has been proposed to play a conserved role in vertebrate skeletal muscle fibre type specification. In zebrafish, sox6 transcription is repressed in slow-twitch progenitors by the Prdm1a transcription factor. Here we identify sox6 cis-regulatory sequences that drive fast-twitch-specific expression in a Prdm1a-dependent manner. We show that sox6 transcription subsequently becomes derepressed in slow-twitch fibres, whereas Sox6 protein remains restricted to fast-twitch fibres. We find that translational repression of sox6 is mediated by miR-499, the slow-twitch-specific expression of which is in turn controlled by Prdm1a, forming a regulatory loop that initiates and maintains the slow-twitch muscle lineage.

Defocused Imaging of UV-Driven Surface-Bound Molecular Motors.

PubMed

Krajnik, Bartosz; Chen, Jiawen; Watson, Matthew A; Cockroft, Scott L; Feringa, Ben L; Hofkens, Johan

2017-05-31

Synthetic molecular motors continue to attract great interest due to their ability to transduce energy into nanomechanical motion, the potential to do work and drive systems out-of-equilibrium. Of particular interest are unidirectional rotary molecular motors driven by chemical fuel or light. Probing the mechanistic details of their operation at the single-molecule level is hampered by the diffraction limit, which prevents the collection of dynamic positional information by traditional optical methods. Here, we use defocused wide-field imaging to examine the unidirectional rotation of individual molecular rotary motors on a quartz surface in unprecedented detail. The sequential occupation of nanomechanical states during the UV and heat-induced cycle of rotation are directly imaged in real-time. The approach will undoubtedly prove important in elucidating the mechanistic details and assessing the utility of novel synthetic molecular motors in the future.

Simple electronics for inertial and Pan-type piezoelectric positioners used in scanning probe microscopes

NASA Astrophysics Data System (ADS)

Chen, LeuJen; Kim, Seong Heon; Lee, Alfred K. H.; de Lozanne, Alex

2012-01-01

We describe a new type of circuit designed for driving piezoelectric positioners that rely on the stick-slip phenomenon. The circuit can be used for inertial positioners that have only one piezoelectric element (or multiple elements that are moved simultaneously) or for designs using a sequential movement of independent piezoelectric elements. A relay switches the piezoelectric elements between a high voltage source and ground, thus creating a fast voltage step followed by a slow ramp produced by the exponential discharging of the piezoelectric elements through a series resistor. A timing cascade is generated by having each relay power the next relay in the sequence. This design is simple and inexpensive. While it was developed for scanning probe microscopes, it may be useful for any piezoelectric motor based on a fast jump followed by a slow relaxation.

Variable-Speed Simulation of a Dual-Clutch Gearbox Tiltrotor Driveline

NASA Technical Reports Server (NTRS)

DeSmidt, Hans; Wang, Kon-Well; Smith, Edward C.; Lewicki, David G.

2012-01-01

This investigation explores the variable-speed operation and shift response of a prototypical two-speed dual-clutch transmission tiltrotor driveline in forward flight. Here, a Comprehensive Variable-Speed Rotorcraft Propulsion System Modeling (CVSRPM) tool developed under a NASA funded NRA program is utilized to simulate the drive system dynamics. In this study, a sequential shifting control strategy is analyzed under a steady forward cruise condition. This investigation attempts to build upon previous variable-speed rotorcraft propulsion studies by 1) including a fully nonlinear transient gas-turbine engine model, 2) including clutch stick-slip friction effects, 3) including shaft flexibility, 4) incorporating a basic flight dynamics model to account for interactions with the flight control system. Through exploring the interactions between the various subsystems, this analysis provides important insights into the continuing development of variable-speed rotorcraft propulsion systems.

A self-powered, one-step chip for rapid, quantitative and multiplexed detection of proteins from pinpricks of whole blood.

PubMed

Wang, Jun; Ahmad, Habib; Ma, Chao; Shi, Qihui; Vermesh, Ophir; Vermesh, Udi; Heath, James

2010-11-21

We describe an automated, self-powered chip based on lateral flow immunoassay for rapid, quantitative, and multiplex protein detection from pinpricks of whole blood. The device incorporates on-chip purification of blood plasma by employing inertial forces to focus blood cells away from the assay surface, where plasma proteins are captured and detected on antibody "barcode" arrays. Power is supplied from the capillary action of a piece of adsorbent paper, and sequentially drives, over a 40 minute period, the four steps required to capture serum proteins and then develop a multiplex immunoassay. An 11 protein panel is assayed from whole blood, with high sensitivity and high reproducibility. This inexpensive, self-contained, and easy to operate chip provides a useful platform for point-of-care diagnoses, particularly in resource-limited settings.

Imaging pediatric magnet ingestion with surgical-pathological correlation.

PubMed

Otjen, Jeffrey P; Rohrmann, Charles A; Iyer, Ramesh S

2013-07-01

Foreign body ingestion is a common problem in the pediatric population and a frequent cause for emergency room visits. Magnets are common household objects that when ingested can bring about severe, possibly fatal gastrointestinal complications. Radiography is an integral component of the management of these children. Pediatric and emergency radiologists alike must be aware of imaging manifestations of magnet ingestion, as their identification drives decision-making for consulting surgeons and gastroenterologists. Radiology can thus substantially augment the clinical history and physical exam, facilitating appropriate management. This manuscript sequentially presents cases of magnet ingestion featuring imaging findings coupled with surgical and pathological correlation. Each case is presented to highlight ways in which the radiologist can make impactful contributions to diagnosis and management. Clinical overview with pitfalls of magnet ingestion imaging and an imaging decision tree will also be presented.

Foreword to the theme issue on geospatial computer vision

NASA Astrophysics Data System (ADS)

Wegner, Jan Dirk; Tuia, Devis; Yang, Michael; Mallet, Clement

2018-06-01

Geospatial Computer Vision has become one of the most prevalent emerging fields of investigation in Earth Observation in the last few years. In this theme issue, we aim at showcasing a number of works at the interface between remote sensing, photogrammetry, image processing, computer vision and machine learning. In light of recent sensor developments - both from the ground as from above - an unprecedented (and ever growing) quantity of geospatial data is available for tackling challenging and urgent tasks such as environmental monitoring (deforestation, carbon sequestration, climate change mitigation), disaster management, autonomous driving or the monitoring of conflicts. The new bottleneck for serving these applications is the extraction of relevant information from such large amounts of multimodal data. This includes sources, stemming from multiple sensors, that exhibit distinct physical nature of heterogeneous quality, spatial, spectral and temporal resolutions. They are as diverse as multi-/hyperspectral satellite sensors, color cameras on drones, laser scanning devices, existing open land-cover geodatabases and social media. Such core data processing is mandatory so as to generate semantic land-cover maps, accurate detection and trajectories of objects of interest, as well as by-products of superior added-value: georeferenced data, images with enhanced geometric and radiometric qualities, or Digital Surface and Elevation Models.

Epigenetic Potential as a Mechanism of Phenotypic Plasticity in Vertebrate Range Expansions.

PubMed

Kilvitis, Holly J; Hanson, Haley; Schrey, Aaron W; Martin, Lynn B

2017-08-01

During range expansions, organisms are often exposed to multiple pressures, including novel enemies (i.e., predators, competitors and/or parasites) and unfamiliar or limited resources. Additionally, small propagule sizes at range edges can result in genetic founder effects and bottlenecks, which can affect phenotypic diversity and thus selection. Despite these obstacles, individuals in expanding populations often thrive at the periphery of a range, and this success may be mediated by phenotypic plasticity. Increasing evidence suggests that epigenetic mechanisms may underlie such plasticity because they allow for more rapid phenotypic responses to novel environments than are possible via the accumulation of genetic variation. Here, we review how molecular epigenetic mechanisms could facilitate plasticity in range-expanding organisms, emphasizing the roles of DNA methylation and other epigenetic marks in the physiological regulatory networks that drive whole-organism performance. We focus on the hypothalamic-pituitary-adrenal (HPA) axis, arguing that epigenetically-mediated plasticity in the regulation of glucocorticoids in particular might strongly impact range expansions. We hypothesize that novel environments release and/or select for epigenetic potential in HPA variation and hence organismal performance and ultimately fitness. © The Author 2017. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology. All rights reserved. For permissions please email: journals.permissions@oup.com.

Simple cellular automaton model for traffic breakdown, highway capacity, and synchronized flow.

PubMed

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

2011-10-01

We present a simple cellular automaton (CA) model for two-lane roads explaining the physics of traffic breakdown, highway capacity, and synchronized flow. The model consists of the rules "acceleration," "deceleration," "randomization," and "motion" of the Nagel-Schreckenberg CA model as well as "overacceleration through lane changing to the faster lane," "comparison of vehicle gap with the synchronization gap," and "speed adaptation within the synchronization gap" of Kerner's three-phase traffic theory. We show that these few rules of the CA model can appropriately simulate fundamental empirical features of traffic breakdown and highway capacity found in traffic data measured over years in different countries, like characteristics of synchronized flow, the existence of the spontaneous and induced breakdowns at the same bottleneck, and associated probabilistic features of traffic breakdown and highway capacity. Single-vehicle data derived in model simulations show that synchronized flow first occurs and then self-maintains due to a spatiotemporal competition between speed adaptation to a slower speed of the preceding vehicle and passing of this slower vehicle. We find that the application of simple dependences of randomization probability and synchronization gap on driving situation allows us to explain the physics of moving synchronized flow patterns and the pinch effect in synchronized flow as observed in real traffic data.

Livestock Helminths in a Changing Climate: Approaches and Restrictions to Meaningful Predictions.

PubMed

Fox, Naomi J; Marion, Glenn; Davidson, Ross S; White, Piran C L; Hutchings, Michael R

2012-03-06

Climate change is a driving force for livestock parasite risk. This is especially true for helminths including the nematodes Haemonchus contortus, Teladorsagia circumcincta, Nematodirus battus, and the trematode Fasciola hepatica, since survival and development of free-living stages is chiefly affected by temperature and moisture. The paucity of long term predictions of helminth risk under climate change has driven us to explore optimal modelling approaches and identify current bottlenecks to generating meaningful predictions. We classify approaches as correlative or mechanistic, exploring their strengths and limitations. Climate is one aspect of a complex system and, at the farm level, husbandry has a dominant influence on helminth transmission. Continuing environmental change will necessitate the adoption of mitigation and adaptation strategies in husbandry. Long term predictive models need to have the architecture to incorporate these changes. Ultimately, an optimal modelling approach is likely to combine mechanistic processes and physiological thresholds with correlative bioclimatic modelling, incorporating changes in livestock husbandry and disease control. Irrespective of approach, the principal limitation to parasite predictions is the availability of active surveillance data and empirical data on physiological responses to climate variables. By combining improved empirical data and refined models with a broad view of the livestock system, robust projections of helminth risk can be developed.

Hepatic differentiation potential of commercially available human mesenchymal stem cells.

PubMed

Ong, Shin-Yeu; Dai, Hui; Leong, Kam W

2006-12-01

The ready availability and low immunogenicity of commercially available mesenchymal stem cells (MSC) render them a potential cell source for the development of therapeutic products. With cell source a major bottleneck in hepatic tissue engineering, we investigated whether commercially available human MSC (hMSC) can transdifferentiate into the hepatic lineage. Based on previous studies that find rapid gain of hepatic genes in bone marrow-derived stem cells cocultured with liver tissue, we used a similar approach to drive hepatic differentiation by coculturing the hMSC with rat livers treated or untreated with gadolinium chloride (GdCl(3)). After a 24-hour coculture period with liver tissue injured by GdCl(3) in a Transwell configuration, approximately 34% of the cells differentiated into albumin-expressing cells. Cocultured cells were subsequently maintained with growth factors to complete the hepatic differentiation. Cocultured cells expressed more hepatic gene markers, and had higher metabolic functions and P450 activity than cells that were only differentiated with growth factors. In conclusion, commercially available hMSC do show hepatic differentiation potential, and a liver microenvironment in culture can provide potent cues to accelerate and deepen the differentiation. The ability to generate hepatocyte-like cells from a commercially available cell source would find interesting applications in liver tissue engineering.

How we used a patient visit tracker tool to advance experiential learning in systems-based practice and quality improvement in a medical student clinic.

PubMed

Chen, Chen Amy; Park, Ryan J; Hegde, John V; Jun, Tomi; Christman, Mitalee P; Yoo, Sun M; Yamasaki, Alisa; Berhanu, Aaron; Vohra-Khullar, Pamela; Remus, Kristin; Schwartzstein, Richard M; Weinstein, Amy R

2016-01-01

Poorly designed healthcare systems increase costs and preventable medical errors. To address these issues, systems-based practice (SBP) education provides future physicians with the tools to identify systemic errors and implement quality improvement (QI) initiatives to enhance the delivery of cost-effective, safe and multi-disciplinary care. Although SBP education is being implemented in residency programs and is mandated by the Accreditation Council for Graduate Medical Education (ACGME) as one of its core competencies, it has largely not been integrated into undergraduate medical education. We propose that Medical Student-Faculty Collaborative Clinics (MSFCCs) may be the ideal environment in which to train medical students in SBPs and QI initiatives, as they allow students to play pivotal roles in project development, administration, and management. Here we describe a process of experiential learning that was developed within a newly established MSFCC, which challenged students to identify inefficiencies, implement interventions, and track the results. After identifying bottlenecks in clinic operations, our students designed a patient visit tracker tool to monitor clinic flow and implemented solutions to decrease patient visit times. Our model allowed students to drive their own active learning in a practical clinical setting, providing early and unique training in crucial QI skills.

Mapping patient flow in a regional Australian emergency department: a model driven approach.

PubMed

Martin, Mary; Champion, Robert; Kinsman, Leigh; Masman, Kevin

2011-04-01

Unified Modelling Language (UML) models of the patient journey in a regional Australian emergency department (ED) were used to develop an accurate, complete representation of ED processes and drive the collection of comprehensive quantitative and qualitative service delivery and patient treatment data as an evidence base for hospital service planning. The focus was to identify bottle-necks that contribute to over-crowding. Data was collected entirely independently of the routine hospital data collection system. The greatest source of delay in patient flow was the waiting time from a bed request to exit from the ED for hospital admission. It represented 61% of the time that these patients occupied ED cubicles. The physical layout of the triage area was identified as counterproductive to efficient triaging, and the results of investigations were often observed to be available for some time before clinical staff became aware. The use of independent primary data to construct UML models of the patient journey was effective in identifying sources of delay in patient flow, and aspects of ED activity that could be improved. The findings contributed to recent department re-design and informed an initiative to develop a business intelligence system for predicting impending occurrence of access block. Copyright © 2010 Elsevier Ltd. All rights reserved.

The MICRO-BOSS scheduling system: Current status and future efforts

NASA Technical Reports Server (NTRS)

Sadeh, Norman M.

1993-01-01

In this paper, a micro-opportunistic approach to factory scheduling was described that closely monitors the evolution of bottlenecks during the construction of the schedule, and continuously redirects search towards the bottleneck that appears to be most critical. This approach differs from earlier opportunistic approaches, as it does not require scheduling large resource subproblems or large job subproblems before revising the current scheduling strategy. This micro-opportunistic approach was implemented in the context of the MICRO-BOSS factory scheduling system. A study comparing MICRO-BOSS against a macro-opportunistic scheduler suggests that the additional flexibility of the micro-opportunistic approach to scheduling generally yields important reductions in both tardiness and inventory.

An integrated decision support system for diagnosing and managing patients with community-acquired pneumonia.

PubMed Central

Aronsky, D.; Haug, P. J.

1999-01-01

Decision support systems that integrate guidelines have become popular applications to reduce variation and deliver cost-effective care. However, adverse characteristics of decision support systems, such as additional and time-consuming data entry or manually identifying eligible patients, result in a "behavioral bottleneck" that prevents decision support systems to become part of the clinical routine. This paper describes the design and the implementation of an integrated decision support system that explores a novel approach for bypassing the behavioral bottleneck. The real-time decision support system does not require health care providers to enter additional data and consists of a diagnostic and a management component. Images Fig. 1 Fig. 2 Fig. 3 PMID:10566348

Production of bioproducts by endophytic fungi: chemical ecology, biotechnological applications, bottlenecks, and solutions.

PubMed

Yan, Lu; Zhao, Haobin; Zhao, Xixi; Xu, Xiaoguang; Di, Yichao; Jiang, Chunmei; Shi, Junling; Shao, Dongyan; Huang, Qingsheng; Yang, Hui; Jin, Mingliang

2018-05-29

Endophytes are microorganisms that colonize the interior of host plants without causing apparent disease. They have been widely studied for their ability to modulate relationships between plants and biotic/abiotic stresses, often producing valuable secondary metabolites that can affect host physiology. Owing to the advantages of microbial fermentation over plant/cell cultivation and chemical synthesis, endophytic fungi have received significant attention as a mean for secondary metabolite production. This article summarizes currently reported results on plant-endophyte interaction hypotheses and highlights the biotechnological applications of endophytic fungi and their metabolites in agriculture, environment, biomedicine, energy, and biocatalysts. Current bottlenecks in industrial development and commercial applications as well as possible solutions are also discussed.

Bioethanol from Lignocellulosic Biomass: Current Findings Determine Research Priorities

PubMed Central

Kang, Qian; Appels, Lise; Tan, Tianwei

2014-01-01

“Second generation” bioethanol, with lignocellulose material as feedstock, is a promising alternative for first generation bioethanol. This paper provides an overview of the current status and reveals the bottlenecks that hamper its implementation. The current literature specifies a conversion of biomass to bioethanol of 30 to ~50% only. Novel processes increase the conversion yield to about 92% of the theoretical yield. New combined processes reduce both the number of operational steps and the production of inhibitors. Recent advances in genetically engineered microorganisms are promising for higher alcohol tolerance and conversion efficiency. By combining advanced systems and by intensive additional research to eliminate current bottlenecks, second generation bioethanol could surpass the traditional first generation processes. PMID:25614881

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