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.

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…

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.

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.

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

PubMed

Miyashita, Shuhei; Kishino, Hirohisa

2010-02-01

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

The 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

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. 

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.

Modeling cooperative driving behavior in freeway merges.

DOT National Transportation Integrated Search

2011-11-01

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

Cloud Technology May Widen Genomic Bottleneck - TCGA

Cancer.gov

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

Potential performance bottleneck in Linux TCP

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

Wu, Wenji; Crawford, Matt; /Fermilab

2006-12-01

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

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

NASA Astrophysics Data System (ADS)

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

2018-04-01

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

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

NASA Astrophysics Data System (ADS)

Mishra, Bhavya; Chowdhury, Debashish

2017-06-01

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

Unveiling CO2 heterogeneous freezing plumes during champagne cork popping.

PubMed

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

2017-09-14

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

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

PubMed

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

2016-09-07

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

Intermodal freight capacity box : intermodal freight bottleneck measures

DOT National Transportation Integrated Search

2000-09-01

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

Advances and bottlenecks in microbial hydrogen production.

PubMed

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

2017-09-01

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

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

DOT National Transportation Integrated Search

2011-07-31

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

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

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

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

2010-09-01

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

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

PubMed Central

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

2015-01-01

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

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

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

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.

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.

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…

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

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

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.

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

PubMed Central

Brenowitz, Eliot A.; Zakon, Harold H.

2015-01-01

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

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

PubMed

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

2018-05-25

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

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.

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.

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.

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.

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.

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

PubMed

Brenowitz, Eliot A; Zakon, Harold H

2015-05-01

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

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.

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

PubMed

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

2013-02-01

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

Airport security inspection process model and optimization based on GSPN

NASA Astrophysics Data System (ADS)

Mao, Shuainan

2018-04-01

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

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.

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.

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

PubMed

Chater, Nick; Christiansen, Morten H

2016-01-01

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

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

NASA Astrophysics Data System (ADS)

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

2018-05-01

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

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

PubMed

Knysh, Sergey

2016-08-05

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

Nonbolometric bottleneck in electron-phonon relaxation in ultrathin WSi films

NASA Astrophysics Data System (ADS)

Sidorova, Mariia V.; Kozorezov, A. G.; Semenov, A. V.; Korneeva, Yu. P.; Mikhailov, M. Yu.; Devizenko, A. Yu.; Korneev, A. A.; Chulkova, G. M.; Goltsman, G. N.

2018-05-01

We developed the model of the internal phonon bottleneck to describe the energy exchange between the acoustically soft ultrathin metal film and acoustically rigid substrate. Discriminating phonons in the film into two groups, escaping and nonescaping, we show that electrons and nonescaping phonons may form a unified subsystem, which is cooled down only due to interactions with escaping phonons, either due to direct phonon conversion or indirect sequential interaction with an electronic system. Using an amplitude-modulated absorption of the sub-THz radiation technique, we studied electron-phonon relaxation in ultrathin disordered films of tungsten silicide. We found an experimental proof of the internal phonon bottleneck. The experiment and simulation based on the proposed model agree well, resulting in τe -ph˜14 0 -19 0 ps at TC=3.4 K , supporting the results of earlier measurements by independent techniques.

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.

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

Architecture studies and system demonstrations for optical parallel processor for AI and NI

NASA Astrophysics Data System (ADS)

Lee, Sing H.

1988-03-01

In solving deterministic AI problems the data search for matching the arguments of a PROLOG expression causes serious bottleneck when implemented sequentially by electronic systems. To overcome this bottleneck we have developed the concepts for an optical expert system based on matrix-algebraic formulation, which will be suitable for parallel optical implementation. The optical AI system based on matrix-algebraic formation will offer distinct advantages for parallel search, adult learning, etc.

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.

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.

Differential clonal evolution in oesophageal cancers in response to neo-adjuvant chemotherapy.

PubMed

Findlay, John M; Castro-Giner, Francesc; Makino, Seiko; Rayner, Emily; Kartsonaki, Christiana; Cross, William; Kovac, Michal; Ulahannan, Danny; Palles, Claire; Gillies, Richard S; MacGregor, Thomas P; Church, David; Maynard, Nicholas D; Buffa, Francesca; Cazier, Jean-Baptiste; Graham, Trevor A; Wang, Lai-Mun; Sharma, Ricky A; Middleton, Mark; Tomlinson, Ian

2016-04-05

How chemotherapy affects carcinoma genomes is largely unknown. Here we report whole-exome and deep sequencing of 30 paired oesophageal adenocarcinomas sampled before and after neo-adjuvant chemotherapy. Most, but not all, good responders pass through genetic bottlenecks, a feature associated with higher mutation burden pre-treatment. Some poor responders pass through bottlenecks, but re-grow by the time of surgical resection, suggesting a missed therapeutic opportunity. Cancers often show major changes in driver mutation presence or frequency after treatment, owing to outgrowth persistence or loss of sub-clones, copy number changes, polyclonality and/or spatial genetic heterogeneity. Post-therapy mutation spectrum shifts are also common, particularly C>A and TT>CT changes in good responders or bottleneckers. Post-treatment samples may also acquire mutations in known cancer driver genes (for example, SF3B1, TAF1 and CCND2) that are absent from the paired pre-treatment sample. Neo-adjuvant chemotherapy can rapidly and profoundly affect the oesophageal adenocarcinoma genome. Monitoring molecular changes during treatment may be clinically useful.

Improving the delivery of global tobacco control.

PubMed

Bitton, Asaf; Green, Carol; Colbert, James

2011-01-01

Tobacco control must remain a critical global health priority given the growing burden of tobacco-induced disease in the developing world. Insights from the emerging field of global health delivery suggest that tobacco control could be improved through a systematic, granular analysis of the processes through which it is promoted, implemented, and combated. Using this framework, a critical bottleneck to the delivery of proven health promotion emerges in the role that the tobacco industry plays in promoting tobacco use and blocking effective tobacco-control policies. This "corporate bottleneck" can also be understood as a root cause of massive disease and suffering upon vulnerable populations worldwide, for the goal of maximizing corporate profit. Naming, understanding, and responding to this corporate bottleneck is crucial to the success of tobacco-control policies. Three case studies of tobacco-control policy--South Africa, the Framework Convention on Tobacco Control, and Uruguay--are presented to explore and understand the implications of this analysis. © 2011 Mount Sinai School of Medicine.

Understanding of empty container movement: A study on a bottleneck at an off-dock depot

NASA Astrophysics Data System (ADS)

Zain, Rosmaizura Mohd; Rahman, Mohd Nizam Ab; Nopiah, Zulkifli Mohd; Saibani, Nizaroyani

2014-09-01

Port not only function as connections between marine and land transportation but also as core business areas. In a port terminal, available space is limited, but the influx of container is growing. The off-dock depot is one of the key supply chain players that hold empty containers in the inventory. Therefore, this paper aims to identify the main factors of bottlenecks or congestion that hinder the rapid movement of empty containers from the off-dock depot to the customers. Thirty interviews were conducted with individuals who are key players in the container supply chain. The data were analyzed using Atlas.ti software and the analytic hierarchy process to rank the priority factors of bottlenecks. Findings show that several pertinent factors act as barriers to the key players in the container movement in the day-to-day operations. In future studies, strategies to overcome fragmentation in the container supply chain and logistics must be determined.

STEPS: lean thinking, theory of constraints and identifying bottlenecks in an emergency department.

PubMed

Ryan, A; Hunter, K; Cunningham, K; Williams, J; O'Shea, H; Rooney, P; Hickey, F

2013-04-01

This study aimed to identify the bottlenecks in patients' journeys through an emergency department (ED). For each stage of the patient journey, the average times were compared between two groups divided according to the four hour time frame and disproportionate delays were identified using a significance test These bottlenecks were evaluated with reference to a lean thinking value-stream map and the five focusing steps of the theory of constraints. A total of 434 (72.5%) ED patients were tracked over one week. Logistic regression showed that patients who had radiological tests, blood tests or who were admitted were 4.4, 4.1 and 7.7 times more likely, respectively, to stay over four hours in the ED than those who didn't The stages that were significantly delayed were the time spent waiting for radiology (p = 0.001), waiting for the in-patient team (p = 0.004), waiting for a bed (p < 0.001) and ED doctor turnaround time (p < 0.001).

Are all intertidal wetlands naturally created equal? Bottlenecks, thresholds and knowledge gaps to mangrove and saltmarsh ecosystems

USGS Publications Warehouse

Friess, Daniel A.; Krauss, Ken W.; Horstman, Erik M.; Balke, Thorsten; Bouma, Tjeerd J.; Galli, Demis; Webb, Edward L.

2011-01-01

Intertidal wetlands such as saltmarshes and mangroves provide numerous important ecological functions, though they are in rapid and global decline. To better conserve and restore these wetland ecosystems, we need an understanding of the fundamental natural bottlenecks and thresholds to their establishment and long-term ecological maintenance. Despite inhabiting similar intertidal positions, the biological traits of these systems differ markedly in structure, phenology, life history, phylogeny and dispersal, suggesting large differences in biophysical interactions. By providing the first systematic comparison between saltmarshes and mangroves, we unravel how the interplay between species-specific life-history traits, biophysical interactions and biogeomorphological feedback processes determine where, when and what wetland can establish, the thresholds to long-term ecosystem stability, and constraints to genetic connectivity between intertidal wetland populations at the landscape level. To understand these process interactions, research into the constraints to wetland development, and biological adaptations to overcome these critical bottlenecks and thresholds requires a truly interdisciplinary approach.

Impact of memory bottleneck on the performance of graphics processing units

NASA Astrophysics Data System (ADS)

Son, Dong Oh; Choi, Hong Jun; Kim, Jong Myon; Kim, Cheol Hong

2015-12-01

Recent graphics processing units (GPUs) can process general-purpose applications as well as graphics applications with the help of various user-friendly application programming interfaces (APIs) supported by GPU vendors. Unfortunately, utilizing the hardware resource in the GPU efficiently is a challenging problem, since the GPU architecture is totally different to the traditional CPU architecture. To solve this problem, many studies have focused on the techniques for improving the system performance using GPUs. In this work, we analyze the GPU performance varying GPU parameters such as the number of cores and clock frequency. According to our simulations, the GPU performance can be improved by 125.8% and 16.2% on average as the number of cores and clock frequency increase, respectively. However, the performance is saturated when memory bottleneck problems incur due to huge data requests to the memory. The performance of GPUs can be improved as the memory bottleneck is reduced by changing GPU parameters dynamically.

Helical bottleneck effect in 3D homogeneous isotropic turbulence

NASA Astrophysics Data System (ADS)

Stepanov, Rodion; Golbraikh, Ephim; Frick, Peter; Shestakov, Alexander

2018-02-01

We present the results of modelling the development of homogeneous and isotropic turbulence with a large-scale source of energy and a source of helicity distributed over scales. We use the shell model for numerical simulation of the turbulence at high Reynolds number. The results show that the helicity injection leads to a significant change in the behavior of the energy and helicity spectra in scales larger and smaller than the energy injection scale. We suggest the phenomenology for direct turbulent cascades with the helicity effect, which reduces the efficiency of the spectral energy transfer. Therefore the energy is accumulated and redistributed so that non-linear interactions will be sufficient to provide a constant energy flux. It can be interpreted as the ‘helical bottleneck effect’ which, depending on the parameters of the injection helicity, reminds one of the well-known bottleneck effect at the end of inertial range. Simulations which included the infrared part of the spectrum show that the inverse cascade hardly develops under distributed helicity forcing.

Selective Bottlenecks Shape Evolutionary Pathways Taken during Mammalian Adaptation of a 1918-like Avian Influenza Virus.

PubMed

Moncla, Louise H; Zhong, Gongxun; Nelson, Chase W; Dinis, Jorge M; Mutschler, James; Hughes, Austin L; Watanabe, Tokiko; Kawaoka, Yoshihiro; Friedrich, Thomas C

2016-02-10

Avian influenza virus reassortants resembling the 1918 human pandemic virus can become transmissible among mammals by acquiring mutations in hemagglutinin (HA) and polymerase. Using the ferret model, we trace the evolutionary pathway by which an avian-like virus evolves the capacity for mammalian replication and airborne transmission. During initial infection, within-host HA diversity increased drastically. Then, airborne transmission fixed two polymerase mutations that do not confer a detectable replication advantage. In later transmissions, selection fixed advantageous HA1 variants. Transmission initially involved a "loose" bottleneck, which became strongly selective after additional HA mutations emerged. The stringency and evolutionary forces governing between-host bottlenecks may therefore change throughout host adaptation. Mutations occurred in multiple combinations in transmitted viruses, suggesting that mammalian transmissibility can evolve through multiple genetic pathways despite phenotypic constraints. Our data provide a glimpse into avian influenza virus adaptation in mammals, with broad implications for surveillance on potentially zoonotic viruses. Copyright © 2016 Elsevier Inc. All rights reserved.

A novel cell autolysis system for cost-competitive downstream processing.

PubMed

Hajnal, Ivan; Chen, Xiangbin; Chen, Guo-Qiang

2016-11-01

The industrial production of low value-added biological products poses significant challenges due to cost pressures. In recent years, it has been argued that synthetic biology approaches will lead to breakthroughs that eliminate price bottlenecks for the production of a wide range of biological products including bioplastics and biofuels. One significant bottleneck lies in the necessity to break the tough cell walls of microbes in order to release intracellular products. We here report the implementation of the first synthetic biology standard part based on the lambda phage SRRz genes and a synthetic ribosome binding site (RBS) that works in Escherichia coli and Halomonas campaniensis, which enables the producer strains to induce lysis after the addition of small amounts (1-5 %) of solvents or to spontaneously lyse during the stresses of downstream processing, and thus has the potential to eliminate the mechanical cell disruption step as both an efficiency bottleneck and a significant capex barrier when implementing downstream bioprocesses.

Room-Temperature Coherent Optical Phonon in 2D Electronic Spectra of CH 3NH 3PbI 3 Perovskite as a Possible Cooling Bottleneck

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

Monahan, Daniele M.; Guo, Liang; Lin, Jia

2017-06-29

A hot phonon bottleneck may be responsible for slow hot carrier cooling in methylammonium lead iodide hybrid perovskite, creating the potential for more efficient hot carrier photovoltaics. In room-temperature 2D electronic spectra near the band edge, we observe in this paper amplitude oscillations due to a remarkably long lived 0.9 THz coherent phonon population at room temperature. This phonon (or set of phonons) is assigned to angular distortions of the Pb–I lattice, not coupled to cation rotations. The strong coupling between the electronic transition and the 0.9 THz mode(s), together with relative isolation from other phonon modes, makes it likelymore » to cause a phonon bottleneck. Finally, the pump frequency resolution of the 2D spectra also enables independent observation of photoinduced absorptions and bleaches independently and confirms that features due to band gap renormalization are longer-lived than in transient absorption spectra.« less

The Suite for Embedded Applications and Kernels

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

2016-05-10

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

Physics of automated driving in framework of three-phase traffic theory.

PubMed

Kerner, Boris S

2018-04-01

We have revealed physical features of automated driving in the framework of the three-phase traffic theory for which there is no fixed time headway to the preceding vehicle. A comparison with the classical model approach to automated driving for which an automated driving vehicle tries to reach a fixed (desired or "optimal") time headway to the preceding vehicle has been made. It turns out that automated driving in the framework of the three-phase traffic theory can exhibit the following advantages in comparison with the classical model of automated driving: (i) The absence of string instability. (ii) Considerably smaller speed disturbances at road bottlenecks. (iii) Automated driving vehicles based on the three-phase theory can decrease the probability of traffic breakdown at the bottleneck in mixed traffic flow consisting of human driving and automated driving vehicles; on the contrary, even a single automated driving vehicle based on the classical approach can provoke traffic breakdown at the bottleneck in mixed traffic flow.

Physics of automated driving in framework of three-phase traffic theory

NASA Astrophysics Data System (ADS)

Kerner, Boris S.

2018-04-01

We have revealed physical features of automated driving in the framework of the three-phase traffic theory for which there is no fixed time headway to the preceding vehicle. A comparison with the classical model approach to automated driving for which an automated driving vehicle tries to reach a fixed (desired or "optimal") time headway to the preceding vehicle has been made. It turns out that automated driving in the framework of the three-phase traffic theory can exhibit the following advantages in comparison with the classical model of automated driving: (i) The absence of string instability. (ii) Considerably smaller speed disturbances at road bottlenecks. (iii) Automated driving vehicles based on the three-phase theory can decrease the probability of traffic breakdown at the bottleneck in mixed traffic flow consisting of human driving and automated driving vehicles; on the contrary, even a single automated driving vehicle based on the classical approach can provoke traffic breakdown at the bottleneck in mixed traffic flow.

Bayesian inference of a historical bottleneck in a heavily exploited marine mammal.

PubMed

Hoffman, J I; Grant, S M; Forcada, J; Phillips, C D

2011-10-01

Emerging Bayesian analytical approaches offer increasingly sophisticated means of reconstructing historical population dynamics from genetic data, but have been little applied to scenarios involving demographic bottlenecks. Consequently, we analysed a large mitochondrial and microsatellite dataset from the Antarctic fur seal Arctocephalus gazella, a species subjected to one of the most extreme examples of uncontrolled exploitation in history when it was reduced to the brink of extinction by the sealing industry during the late eighteenth and nineteenth centuries. Classical bottleneck tests, which exploit the fact that rare alleles are rapidly lost during demographic reduction, yielded ambiguous results. In contrast, a strong signal of recent demographic decline was detected using both Bayesian skyline plots and Approximate Bayesian Computation, the latter also allowing derivation of posterior parameter estimates that were remarkably consistent with historical observations. This was achieved using only contemporary samples, further emphasizing the potential of Bayesian approaches to address important problems in conservation and evolutionary biology. © 2011 Blackwell Publishing Ltd.

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.

Sequential Bottlenecks Drive Viral Evolution in Early Acute Hepatitis C Virus Infection

PubMed Central

McElroy, Kerensa; Gaudieri, Silvana; Pham, Son T.; Chopra, Abha; Cameron, Barbara; Maher, Lisa; Dore, Gregory J.; White, Peter A.; Lloyd, Andrew R.

2011-01-01

Hepatitis C is a pandemic human RNA virus, which commonly causes chronic infection and liver disease. The characterization of viral populations that successfully initiate infection, and also those that drive progression to chronicity is instrumental for understanding pathogenesis and vaccine design. A comprehensive and longitudinal analysis of the viral population was conducted in four subjects followed from very early acute infection to resolution of disease outcome. By means of next generation sequencing (NGS) and standard cloning/Sanger sequencing, genetic diversity and viral variants were quantified over the course of the infection at frequencies as low as 0.1%. Phylogenetic analysis of reassembled viral variants revealed acute infection was dominated by two sequential bottleneck events, irrespective of subsequent chronicity or clearance. The first bottleneck was associated with transmission, with one to two viral variants successfully establishing infection. The second occurred approximately 100 days post-infection, and was characterized by a decline in viral diversity. In the two subjects who developed chronic infection, this second bottleneck was followed by the emergence of a new viral population, which evolved from the founder variants via a selective sweep with fixation in a small number of mutated sites. The diversity at sites with non-synonymous mutation was higher in predicted cytotoxic T cell epitopes, suggesting immune-driven evolution. These results provide the first detailed analysis of early within-host evolution of HCV, indicating strong selective forces limit viral evolution in the acute phase of infection. PMID:21912520

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

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.

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.

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.

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.

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.

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.

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

Identifying bottlenecks in the iron and folic acid supply chain in Bihar, India: a mixed-methods study.

PubMed

Wendt, Amanda S; Stephenson, Rob; Young, Melissa F; Verma, Pankaj; Srikantiah, Sridhar; Webb-Girard, Amy; Hogue, Carol J; Ramakrishnan, Usha; Martorell, Reynaldo

2018-04-12

Maternal anaemia prevalence in Bihar, India remains high despite government mandated iron supplementation targeting pregnant women. Inadequate supply has been identified as a potential barrier to iron and folic acid (IFA) receipt. Our study objective was to examine the government health system's IFA supply and distribution system and identify bottlenecks contributing to insufficient IFA supply. Primary data collection was conducted in November 2011 and July 2012 across 8 districts in Bihar, India. A cross-sectional, observational, mixed methods approach was utilized. Auxiliary Nurse Midwives were surveyed on current IFA supply and practices. In-depth interviews (n = 59) were conducted with health workers at state, district, block, health sub-centre, and village levels. Overall, 44% of Auxiliary Nurse Midwives were out of IFA stock. Stock levels and supply chain practices varied greatly across districts. Qualitative data revealed specific bottlenecks impacting IFA forecasting, procurement, storage, disposal, lack of personnel, and few training opportunities for key players in the supply chain. Inadequate IFA supply is a major constraint to the IFA supplementation program, the extent of which varies widely across districts. Improvements at all levels of infrastructure, practices, and effective monitoring will be critical to strengthen the IFA supply chain in Bihar.

Engineering metabolic pathways in plants by multigene transformation.

PubMed

Zorrilla-López, Uxue; Masip, Gemma; Arjó, Gemma; Bai, Chao; Banakar, Raviraj; Bassie, Ludovic; Berman, Judit; Farré, Gemma; Miralpeix, Bruna; Pérez-Massot, Eduard; Sabalza, Maite; Sanahuja, Georgina; Vamvaka, Evangelia; Twyman, Richard M; Christou, Paul; Zhu, Changfu; Capell, Teresa

2013-01-01

Metabolic engineering in plants can be used to increase the abundance of specific valuable metabolites, but single-point interventions generally do not improve the yields of target metabolites unless that product is immediately downstream of the intervention point and there is a plentiful supply of precursors. In many cases, an intervention is necessary at an early bottleneck, sometimes the first committed step in the pathway, but is often only successful in shifting the bottleneck downstream, sometimes also causing the accumulation of an undesirable metabolic intermediate. Occasionally it has been possible to induce multiple genes in a pathway by controlling the expression of a key regulator, such as a transcription factor, but this strategy is only possible if such master regulators exist and can be identified. A more robust approach is the simultaneous expression of multiple genes in the pathway, preferably representing every critical enzymatic step, therefore removing all bottlenecks and ensuring completely unrestricted metabolic flux. This approach requires the transfer of multiple enzyme-encoding genes to the recipient plant, which is achieved most efficiently if all genes are transferred at the same time. Here we review the state of the art in multigene transformation as applied to metabolic engineering in plants, highlighting some of the most significant recent advances in the field.

Host-Pathogen Checkpoints and Population Bottlenecks in Persistent and Intracellular Uropathogenic E. coli Bladder Infection

PubMed Central

Hannan, Thomas J.; Totsika, Makrina; Mansfield, Kylie J.; Moore, Kate H.; Schembri, Mark A.; Hultgren, Scott J.

2013-01-01

Bladder infections affect millions of people yearly, and recurrent symptomatic infections (cystitis) are very common. The rapid increase in infections caused by multi-drug resistant uropathogens threatens to make recurrent cystitis an increasingly troubling public health concern. Uropathogenic E. coli (UPEC) cause the vast majority of bladder infections. Upon entry into the lower urinary tract, UPEC face obstacles to colonization that constitute population bottlenecks, reducing diversity and selecting for fit clones. A critical mucosal barrier to bladder infection is the epithelium (urothelium). UPEC bypass this barrier when they invade urothelial cells and form intracellular bacterial communities (IBCs), a process which requires type 1 pili. IBCs are transient in nature, occurring primarily during acute infection. Chronic bladder infection is common and can be either latent, in the form of the Quiescent Intracellular Reservoir (QIR), or active, in the form of asymptomatic bacteriuria (ASB/ABU) or chronic cystitis. In mice, the fate of bladder infection: QIR, ASB, or chronic cystitis, is determined within the first 24 hours of infection and constitutes a putative host-pathogen mucosal checkpoint that contributes to susceptibility to recurrent cystitis. Knowledge of these checkpoints and bottlenecks is critical for our understanding of bladder infection and efforts to devise novel therapeutic strategies. PMID:22404313

Concurrent deployment of visual attention and response selection bottleneck in a dual-task: Electrophysiological and behavioural evidence.

PubMed

Reimer, Christina B; Strobach, Tilo; Schubert, Torsten

2017-12-01

Visual attention and response selection are limited in capacity. Here, we investigated whether visual attention requires the same bottleneck mechanism as response selection in a dual-task of the psychological refractory period (PRP) paradigm. The dual-task consisted of an auditory two-choice discrimination Task 1 and a conjunction search Task 2, which were presented at variable temporal intervals (stimulus onset asynchrony, SOA). In conjunction search, visual attention is required to select items and to bind their features resulting in a serial search process around the items in the search display (i.e., set size). We measured the reaction time of the visual search task (RT2) and the N2pc, an event-related potential (ERP), which reflects lateralized visual attention processes. If the response selection processes in Task 1 influence the visual attention processes in Task 2, N2pc latency and amplitude would be delayed and attenuated at short SOA compared to long SOA. The results, however, showed that latency and amplitude were independent of SOA, indicating that visual attention was concurrently deployed to response selection. Moreover, the RT2 analysis revealed an underadditive interaction of SOA and set size. We concluded that visual attention does not require the same bottleneck mechanism as response selection in dual-tasks.

Studies to reveal the nature of interactions between catalase and curcumin using computational methods and optical techniques.

PubMed

Mofidi Najjar, Fayezeh; Ghadari, Rahim; Yousefi, Reza; Safari, Naser; Sheikhhasani, Vahid; Sheibani, Nader; Moosavi-Movahedi, Ali Akbar

2017-02-01

Curcumin is an important antioxidant compound, and is widely reported as an effective component for reducing complications of many diseases. However, the detailed mechanisms of its activity remain poorly understood. We found that curcumin can significantly increase catalase activity of BLC (bovine liver catalase). The mechanism of curcumin action was investigated using a computational method. We suggested that curcumin may activate BLC by modifying the bottleneck of its narrow channel. The molecular dynamic simulation data showed that placing curcumin on the structure of enzyme can increase the size of the bottleneck in the narrow channel of BLC, and readily allow the access of substrate to the active site. Because of the increase of the distance between amino acids of the bottleneck in the presence of curcumin, the entrance space of substrate increased from 250Å 3 to 440Å 3 . In addition, the increase in emission of intrinsic fluorescence of BLC in presence of curcumin demonstrated changes in tertiary structure of catalase, and possibility of less quenching. We also used circular dichroism (CD) spectropolarimetry to determine how curcumin may alter the enzyme secondary structure. Catalase spectra in the presence of various concentrations of curcumin showed an increase in the amount of α-helix content. Copyright © 2016 Elsevier B.V. All rights reserved.

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.

A Simulation Study of Paced TCP

NASA Technical Reports Server (NTRS)

Kulik, Joanna; Coulter, Robert; Rockwell, Dennis; Partridge, Craig

2000-01-01

In this paper, we study the performance of paced TCP, a modified version of TCP designed especially for high delay- bandwidth networks. In typical networks, TCP optimizes its send-rate by transmitting increasingly large bursts, or windows, of packets, one burst per round-trip time, until it reaches a maximum window-size, which corresponds to the full capacity of the network. In a network with a high delay-bandwidth product, however, Transmission Control Protocol's (TCPs) maximum window-size may be larger than the queue size of the intermediate routers, and routers will begin to drop packets as soon as the windows become too large for the router queues. The TCP sender then concludes that the bottleneck capacity of the network has been reached, and it limits its send-rate accordingly. Partridge proposed paced TCP as a means of solving the problem of queueing bottlenecks. A sender using paced TCP would release packets in multiple, small bursts during a round-trip time in which ordinary TCP would release a single, large burst of packets. This approach allows the sender to increase its send-rate to the maximum window size without encountering queueing bottlenecks. This paper describes the performance of paced TCP in a simulated network and discusses implementation details that can affect the performance of paced TCP.

Reconstruction of the astaxanthin biosynthesis pathway in rice endosperm reveals a metabolic bottleneck at the level of endogenous β-carotene hydroxylase activity.

PubMed

Bai, Chao; Berman, Judit; Farre, Gemma; Capell, Teresa; Sandmann, Gerhard; Christou, Paul; Zhu, Changfu

2017-02-01

Astaxanthin is a high-value ketocarotenoid rarely found in plants. It is derived from β-carotene by the 3-hydroxylation and 4-ketolation of both ionone end groups, in reactions catalyzed by β-carotene hydroxylase and β-carotene ketolase, respectively. We investigated the feasibility of introducing an extended carotenoid biosynthesis pathway into rice endosperm to achieve the production of astaxanthin. This allowed us to identify potential metabolic bottlenecks that have thus far prevented the accumulation of this valuable compound in storage tissues such as cereal grains. Rice endosperm does not usually accumulate carotenoids because phytoene synthase, the enzyme responsible for the first committed step in the pathway, is not present in this tissue. We therefore expressed maize phytoene synthase 1 (ZmPSY1), Pantoea ananatis phytoene desaturase (PaCRTI) and a synthetic Chlamydomonas reinhardtii β-carotene ketolase (sCrBKT) in transgenic rice plants under the control of endosperm-specific promoters. The resulting grains predominantly accumulated the diketocarotenoids canthaxanthin, adonirubin and astaxanthin as well as low levels of monoketocarotenoids. The predominance of canthaxanthin and adonirubin indicated the presence of a hydroxylation bottleneck in the ketocarotenoid pathway. This final rate-limiting step must therefore be overcome to maximize the accumulation of astaxanthin, the end product of the pathway.

Decoupled systems on trial: Eliminating bottlenecks to improve aquaponic processes

PubMed Central

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. PMID:28957357

Mapping the yeast host cell response to recombinant membrane protein production: relieving the biological bottlenecks.

PubMed

Ashe, Mark P; Bill, Roslyn M

2011-06-01

Understanding the structures and functions of membrane proteins is an active area of research within bioscience. Membrane proteins are key players in essential cellular processes such as the uptake of nutrients, the export of waste products, and the way in which cells communicate with their environment. It is therefore not surprising that membrane proteins are targeted by over half of all prescription drugs. Since most membrane proteins are not abundant in their native membranes, it is necessary to produce them in recombinant host cells to enable further structural and functional studies. Unfortunately, achieving the required yields of functional recombinant membrane proteins is still a bottleneck in contemporary bioscience. This has highlighted the need for defined and rational optimization strategies based upon experimental observation rather than relying on trial and error. We have published a transcriptome and subsequent genetic analysis that has identified genes implicated in high-yielding yeast cells. These results have highlighted a role for alterations to a cell's protein synthetic capacity in the production of high yields of recombinant membrane protein: paradoxically, reduced protein synthesis favors higher yields. These results highlight a potential bottleneck at the protein folding or translocation stage of protein production. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Genome sequencing highlights the dynamic early history of dogs.

PubMed

Freedman, Adam H; Gronau, Ilan; Schweizer, Rena M; Ortega-Del Vecchyo, Diego; Han, Eunjung; Silva, Pedro M; Galaverni, Marco; Fan, Zhenxin; Marx, Peter; Lorente-Galdos, Belen; Beale, Holly; Ramirez, Oscar; Hormozdiari, Farhad; Alkan, Can; Vilà, Carles; Squire, Kevin; Geffen, Eli; Kusak, Josip; Boyko, Adam R; Parker, Heidi G; Lee, Clarence; Tadigotla, Vasisht; Wilton, Alan; Siepel, Adam; Bustamante, Carlos D; Harkins, Timothy T; Nelson, Stanley F; Ostrander, Elaine A; Marques-Bonet, Tomas; Wayne, Robert K; Novembre, John

2014-01-01

To identify genetic changes underlying dog domestication and reconstruct their early evolutionary history, we generated high-quality genome sequences from three gray wolves, one from each of the three putative centers of dog domestication, two basal dog lineages (Basenji and Dingo) and a golden jackal as an outgroup. Analysis of these sequences supports a demographic model in which dogs and wolves diverged through a dynamic process involving population bottlenecks in both lineages and post-divergence gene flow. In dogs, the domestication bottleneck involved at least a 16-fold reduction in population size, a much more severe bottleneck than estimated previously. A sharp bottleneck in wolves occurred soon after their divergence from dogs, implying that the pool of diversity from which dogs arose was substantially larger than represented by modern wolf populations. We narrow the plausible range for the date of initial dog domestication to an interval spanning 11-16 thousand years ago, predating the rise of agriculture. In light of this finding, we expand upon previous work regarding the increase in copy number of the amylase gene (AMY2B) in dogs, which is believed to have aided digestion of starch in agricultural refuse. We find standing variation for amylase copy number variation in wolves and little or no copy number increase in the Dingo and Husky lineages. In conjunction with the estimated timing of dog origins, these results provide additional support to archaeological finds, suggesting the earliest dogs arose alongside hunter-gathers rather than agriculturists. Regarding the geographic origin of dogs, we find that, surprisingly, none of the extant wolf lineages from putative domestication centers is more closely related to dogs, and, instead, the sampled wolves form a sister monophyletic clade. This result, in combination with dog-wolf admixture during the process of domestication, suggests that a re-evaluation of past hypotheses regarding dog origins is necessary.

Genome Sequencing Highlights the Dynamic Early History of Dogs

PubMed Central

Freedman, Adam H.; Gronau, Ilan; Schweizer, Rena M.; Ortega-Del Vecchyo, Diego; Han, Eunjung; Silva, Pedro M.; Galaverni, Marco; Fan, Zhenxin; Marx, Peter; Lorente-Galdos, Belen; Beale, Holly; Ramirez, Oscar; Hormozdiari, Farhad; Alkan, Can; Vilà, Carles; Squire, Kevin; Geffen, Eli; Kusak, Josip; Boyko, Adam R.; Parker, Heidi G.; Lee, Clarence; Tadigotla, Vasisht; Siepel, Adam; Bustamante, Carlos D.; Harkins, Timothy T.; Nelson, Stanley F.; Ostrander, Elaine A.; Marques-Bonet, Tomas; Wayne, Robert K.; Novembre, John

2014-01-01

To identify genetic changes underlying dog domestication and reconstruct their early evolutionary history, we generated high-quality genome sequences from three gray wolves, one from each of the three putative centers of dog domestication, two basal dog lineages (Basenji and Dingo) and a golden jackal as an outgroup. Analysis of these sequences supports a demographic model in which dogs and wolves diverged through a dynamic process involving population bottlenecks in both lineages and post-divergence gene flow. In dogs, the domestication bottleneck involved at least a 16-fold reduction in population size, a much more severe bottleneck than estimated previously. A sharp bottleneck in wolves occurred soon after their divergence from dogs, implying that the pool of diversity from which dogs arose was substantially larger than represented by modern wolf populations. We narrow the plausible range for the date of initial dog domestication to an interval spanning 11–16 thousand years ago, predating the rise of agriculture. In light of this finding, we expand upon previous work regarding the increase in copy number of the amylase gene (AMY2B) in dogs, which is believed to have aided digestion of starch in agricultural refuse. We find standing variation for amylase copy number variation in wolves and little or no copy number increase in the Dingo and Husky lineages. In conjunction with the estimated timing of dog origins, these results provide additional support to archaeological finds, suggesting the earliest dogs arose alongside hunter-gathers rather than agriculturists. Regarding the geographic origin of dogs, we find that, surprisingly, none of the extant wolf lineages from putative domestication centers is more closely related to dogs, and, instead, the sampled wolves form a sister monophyletic clade. This result, in combination with dog-wolf admixture during the process of domestication, suggests that a re-evaluation of past hypotheses regarding dog origins is necessary. PMID:24453982

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

Linkage Disequilibrium Under Recurrent Bottlenecks

PubMed Central

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

2012-01-01

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

Considering the Influence of Nonadaptive Evolution on Primate Color Vision.

PubMed

Jacobs, Rachel L; Bradley, Brenda J

2016-01-01

Color vision in primates is variable across species, and it represents a rare trait in which the genetic mechanisms underlying phenotypic variation are fairly well-understood. Research on primate color vision has largely focused on adaptive explanations for observed variation, but it remains unclear why some species have trichromatic or polymorphic color vision while others are red-green color blind. Lemurs, in particular, are highly variable. While some species are polymorphic, many closely-related species are strictly dichromatic. We provide the first characterization of color vision in a wild population of red-bellied lemurs (Eulemur rubriventer, Ranomafana National Park, Madagascar) with a sample size (87 individuals; NX chromosomes = 134) large enough to detect even rare variants (0.95 probability of detection at ≥ 3% frequency). By sequencing exon 5 of the X-linked opsin gene we identified opsin spectral sensitivity based on known diagnostic sites and found this population to be dichromatic and monomorphic for a long wavelength allele. Apparent fixation of this long allele is in contrast to previously published accounts of Eulemur species, which exhibit either polymorphic color vision or only the medium wavelength opsin. This unexpected result may represent loss of color vision variation, which could occur through selective processes and/or genetic drift (e.g., genetic bottleneck). To indirectly assess the latter scenario, we genotyped 55 adult red-bellied lemurs at seven variable microsatellite loci and used heterozygosity excess and M-ratio tests to assess if this population may have experienced a recent genetic bottleneck. Results of heterozygosity excess but not M-ratio tests suggest a bottleneck might have occurred in this red-bellied lemur population. Therefore, while selection may also play a role, the unique color vision observed in this population might have been influenced by a recent genetic bottleneck. These results emphasize the need to consider adaptive and nonadaptive mechanisms of color vision evolution in primates.

Considering the Influence of Nonadaptive Evolution on Primate Color Vision

PubMed Central

Jacobs, Rachel L.; Bradley, Brenda J.

2016-01-01

Color vision in primates is variable across species, and it represents a rare trait in which the genetic mechanisms underlying phenotypic variation are fairly well-understood. Research on primate color vision has largely focused on adaptive explanations for observed variation, but it remains unclear why some species have trichromatic or polymorphic color vision while others are red-green color blind. Lemurs, in particular, are highly variable. While some species are polymorphic, many closely-related species are strictly dichromatic. We provide the first characterization of color vision in a wild population of red-bellied lemurs (Eulemur rubriventer, Ranomafana National Park, Madagascar) with a sample size (87 individuals; NX chromosomes = 134) large enough to detect even rare variants (0.95 probability of detection at ≥ 3% frequency). By sequencing exon 5 of the X-linked opsin gene we identified opsin spectral sensitivity based on known diagnostic sites and found this population to be dichromatic and monomorphic for a long wavelength allele. Apparent fixation of this long allele is in contrast to previously published accounts of Eulemur species, which exhibit either polymorphic color vision or only the medium wavelength opsin. This unexpected result may represent loss of color vision variation, which could occur through selective processes and/or genetic drift (e.g., genetic bottleneck). To indirectly assess the latter scenario, we genotyped 55 adult red-bellied lemurs at seven variable microsatellite loci and used heterozygosity excess and M-ratio tests to assess if this population may have experienced a recent genetic bottleneck. Results of heterozygosity excess but not M-ratio tests suggest a bottleneck might have occurred in this red-bellied lemur population. Therefore, while selection may also play a role, the unique color vision observed in this population might have been influenced by a recent genetic bottleneck. These results emphasize the need to consider adaptive and nonadaptive mechanisms of color vision evolution in primates. PMID:26959829

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.

Laboratory Colonisation and Genetic Bottlenecks in the Tsetse Fly Glossina pallidipes

PubMed Central

Ciosi, Marc

2014-01-01

Background The IAEA colony is the only one available for mass rearing of Glossina pallidipes, a vector of human and animal African trypanosomiasis in eastern Africa. This colony is the source for Sterile Insect Technique (SIT) programs in East Africa. The source population of this colony is unclear and its genetic diversity has not previously been evaluated and compared to field populations. Methodology/Principal Findings We examined the genetic variation within and between the IAEA colony and its potential source populations in north Zimbabwe and the Kenya/Uganda border at 9 microsatellites loci to retrace the demographic history of the IAEA colony. We performed classical population genetics analyses and also combined historical and genetic data in a quantitative analysis using Approximate Bayesian Computation (ABC). There is no evidence of introgression from the north Zimbabwean population into the IAEA colony. Moreover, the ABC analyses revealed that the foundation and establishment of the colony was associated with a genetic bottleneck that has resulted in a loss of 35.7% of alleles and 54% of expected heterozygosity compared to its source population. Also, we show that tsetse control carried out in the 1990's is likely reduced the effective population size of the Kenya/Uganda border population. Conclusions/Significance All the analyses indicate that the area of origin of the IAEA colony is the Kenya/Uganda border and that a genetic bottleneck was associated with the foundation and establishment of the colony. Genetic diversity associated with traits that are important for SIT may potentially have been lost during this genetic bottleneck which could lead to a suboptimal competitiveness of the colony males in the field. The genetic diversity of the colony is lower than that of field populations and so, studies using colony flies should be interpreted with caution when drawing general conclusions about G. pallidipes biology. PMID:24551260

Simultaneous dual-task performance reveals parallel response selection after practice

NASA Technical Reports Server (NTRS)

Hazeltine, Eliot; Teague, Donald; Ivry, Richard B.

2002-01-01

E. H. Schumacher, T. L. Seymour, J. M. Glass, D. E. Kieras, and D. E. Meyer (2001) reported that dual-task costs are minimal when participants are practiced and give the 2 tasks equal emphasis. The present research examined whether such findings are compatible with the operation of an efficient response selection bottleneck. Participants trained until they were able to perform both tasks simultaneously without interference. Novel stimulus pairs produced no reaction time costs, arguing against the development of compound stimulus-response associations (Experiment 1). Manipulating the relative onsets (Experiments 2 and 4) and durations (Experiments 3 and 4) of response selection processes did not lead to dual-task costs. The results indicate that the 2 tasks did not share a bottleneck after practice.

In vitro replication highlights the mutability of prions.

PubMed

Vanni, Ilaria; Di Bari, Michele Angelo; Pirisinu, Laura; D'Agostino, Claudia; Agrimi, Umberto; Nonno, Romolo

2014-01-01

Prions exist as strains, which are thought to reflect PrP(Sc) conformational variants. Prion strains can mutate and it has been proposed that prion mutability depends on an intrinsic heterogeneity of prion populations that would behave as quasispecies. We investigated in vitro prion mutability of 2 strains, by following PrP(Sc) variations of populations serially propagated in PMCA under constant environmental pressure. Each strain was propagated either at low dilution of the seed, i.e., by large population passages, or at limiting dilution, mimicking bottleneck events. In both strains, PrP(Sc) conformational variants were identified only after large population passages, while repeated bottleneck events caused a rapid decline in amplification rates. These findings support the view that mutability is an intrinsic property of prions.

Genetic bottlenecks and successful biological invasions: the case of a recent Lessepsian migrant.

PubMed

Golani, Daniel; Azzurro, Ernesto; Corsini-Foka, Maria; Falautano, Manuela; Andaloro, Franco; Bernardi, Giacomo

2007-10-22

Our current understanding of the mechanisms that lead to successful biological invasions is limited. Although adaptations play a central role in biological invasions, genetic studies have so far failed to produce a unified theory. The bluespotted cornetfish, a recent Red Sea invader in the Mediterranean Sea via the Suez Canal, provides an ideal case study for research in the mechanisms of invasive genetics. In this study, we show that the invading bluespotted cornetfish underwent a severe population bottleneck that reduced the genetic diversity of this immigrant to only two mitochondrial haplotypes. Although loss of genetic diversity is considered detrimental to the need to adapt to new environments, bluespotted cornetfish experienced an unprecedented success and rapid spread across the Mediterranean.

Photoexcitation Cascade and Quantum-Relativistic Jets in Graphene

NASA Astrophysics Data System (ADS)

Lewandowski, Cyprian; Levitov, L. S.

2018-02-01

In Dirac materials linear band dispersion blocks momentum-conserving interband transitions, creating a bottleneck for electron-hole pair production and carrier multiplication in the photoexcitation cascade. Here we show that the decays are unblocked and the bottleneck is relieved by subtle many-body effects involving multiple off-shell e -h pairs. The decays result from a collective behavior due to simultaneous emission of many soft pairs. We discuss characteristic signatures of the off-shell pathways, in particular the sharp angular distribution of secondary carriers, resembling relativistic jets in high-energy physics. The jets can be directly probed using solid-state equivalent of particle detectors. Collinear scattering enhances carrier multiplication, allowing for emission of as many as ˜10 secondary carriers per single absorbed photon.

Mask manufacturing improvement through capability definition and bottleneck line management

NASA Astrophysics Data System (ADS)

Strott, Al

1994-02-01

In 1989, Intel's internal mask operation limited itself to research and development activities and re-inspection and pellicle application of externally manufactured masks. Recognizing the rising capital cost of mask manufacturing at the leading edge, Intel's Mask Operation management decided to offset some of these costs by manufacturing more masks internally. This was the beginning of the challenge they set to manufacture at least 50% of Intel's mask volume internally, at world class performance levels. The first step in responding to this challenge was the completion of a comprehensive operation capability analysis. A series of bottleneck improvements by focus teams resulted in an average cycle time improvement to less than five days on all product and less than two days on critical products.

Bottleneck Effect on Evolutionary Rate in the Nearly Neutral Mutation Model

PubMed Central

Araki, H.; Tachida, H.

1997-01-01

Variances of evolutionary rates among lineages in some proteins are larger than those expected from simple Poisson processes. This phenomenon is called overdispersion of the molecular clock. If population size N is constant, the overdispersion is observed only in a limited range of 2Nσ under the nearly neutral mutation model, where σ represents the standard deviation of selection coefficients of new mutants. In this paper, we investigated effects of changing population size on the evolutionary rate by computer simulations assuming the nearly neutral mutation model. The size was changed cyclically between two numbers, N(1) and N(2) (N(1) > N(2)), in the simulations. The overdispersion is observed if 2N(2)σ is less than two and the state of reduced size (bottleneck state) continues for more than ~0.1/u generations, where u is the mutation rate. The overdispersion results mainly because the average fitnesses of only a portion of populations go down when the population size is reduced and only in these populations subsequent advantageous substitutions occur after the population size becomes large. Since the fitness reduction after the bottleneck is stochastic, acceleration of the evolutionary rate does not necessarily occur uniformly among loci. From these results, we argue that the nearly neutral mutation model is a candidate mechanism to explain the overdispersed molecular clock. PMID:9335622

Linking crowding, visual span, and reading.

PubMed

He, Yingchen; Legge, Gordon E

2017-09-01

The visual span is hypothesized to be a sensory bottleneck on reading speed with crowding thought to be the major sensory factor limiting the size of the visual span. This proposed linkage between crowding, visual span, and reading speed is challenged by the finding that training to read crowded letters reduced crowding but did not improve reading speed (Chung, 2007). Here, we examined two properties of letter-recognition training that may influence the transfer to improved reading: the spatial arrangement of training stimuli and the presence of flankers. Three groups of nine young adults were trained with different configurations of letter stimuli at 10° in the lower visual field: a flanked-local group (flanked letters localized at one position), a flanked-distributed group (flanked letters distributed across different horizontal locations), and an isolated-distributed group (isolated and distributed letters). We found that distributed training, but not the presence of flankers, appears to be necessary for the training benefit to transfer to increased reading speed. Localized training may have biased attention to one specific, small area in the visual field, thereby failing to improve reading. We conclude that the visual span represents a sensory bottleneck on reading, but there may also be an attentional bottleneck. Reducing the impact of crowding can enlarge the visual span and can potentially facilitate reading, but not when adverse attentional bias is present. Our results clarify the association between crowding, visual span, and reading.

Linking crowding, visual span, and reading

PubMed Central

He, Yingchen; Legge, Gordon E.

2017-01-01

The visual span is hypothesized to be a sensory bottleneck on reading speed with crowding thought to be the major sensory factor limiting the size of the visual span. This proposed linkage between crowding, visual span, and reading speed is challenged by the finding that training to read crowded letters reduced crowding but did not improve reading speed (Chung, 2007). Here, we examined two properties of letter-recognition training that may influence the transfer to improved reading: the spatial arrangement of training stimuli and the presence of flankers. Three groups of nine young adults were trained with different configurations of letter stimuli at 10° in the lower visual field: a flanked-local group (flanked letters localized at one position), a flanked-distributed group (flanked letters distributed across different horizontal locations), and an isolated-distributed group (isolated and distributed letters). We found that distributed training, but not the presence of flankers, appears to be necessary for the training benefit to transfer to increased reading speed. Localized training may have biased attention to one specific, small area in the visual field, thereby failing to improve reading. We conclude that the visual span represents a sensory bottleneck on reading, but there may also be an attentional bottleneck. Reducing the impact of crowding can enlarge the visual span and can potentially facilitate reading, but not when adverse attentional bias is present. Our results clarify the association between crowding, visual span, and reading. PMID:28973564

Instruction-level performance modeling and characterization of multimedia applications

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

Luo, Y.; Cameron, K.W.

1999-06-01

One of the challenges for characterizing and modeling realistic multimedia applications is the lack of access to source codes. On-chip performance counters effectively resolve this problem by monitoring run-time behaviors at the instruction-level. This paper presents a novel technique of characterizing and modeling workloads at the instruction level for realistic multimedia applications using hardware performance counters. A variety of instruction counts are collected from some multimedia applications, such as RealPlayer, GSM Vocoder, MPEG encoder/decoder, and speech synthesizer. These instruction counts can be used to form a set of abstract characteristic parameters directly related to a processor`s architectural features. Based onmore » microprocessor architectural constraints and these calculated abstract parameters, the architectural performance bottleneck for a specific application can be estimated. Meanwhile, the bottleneck estimation can provide suggestions about viable architectural/functional improvement for certain workloads. The biggest advantage of this new characterization technique is a better understanding of processor utilization efficiency and architectural bottleneck for each application. This technique also provides predictive insight of future architectural enhancements and their affect on current codes. In this paper the authors also attempt to model architectural effect on processor utilization without memory influence. They derive formulas for calculating CPI{sub 0}, CPI without memory effect, and they quantify utilization of architectural parameters. These equations are architecturally diagnostic and predictive in nature. Results provide promise in code characterization, and empirical/analytical modeling.« less

Evidence for population bottlenecks and subtle genetic structure in the yellow rail

USGS Publications Warehouse

Popper, Kenneth J.; Miller, Leonard F.; Green, Michael; Haig, Susan M.; Mullins, Thomas D.

2012-01-01

The Yellow Rail (Coturnicops noveboracencis) is among the most enigmatic and least studied North American birds. Nesting exclusively in marshes and wetlands, it breeds largely east of the Rocky Mountains in the northern United States and Canada, but there is an isolated population in southern Oregon once believed extirpated. The degree of connectivity of the Oregon population with the main population is unknown. We used mitochondrial DNA sequences (mtDNA) and six microsatellite loci to characterize the Yellow Rail's genetic structure and diversity patterns in six areas. Our mtDNA-based analyses of genetic structure identified significant population differentiation, but pairwise comparison of regions identified no clear geographic trends. In contrast, microsatellites suggested subtle genetic structure differentiating the Oregon population from those in the five regions sampled in the Yellow Rail's main breeding range. The genetic diversity of the Oregon population was also the lowest of the six regions sampled, and Oregon was one of three regions that demonstrated evidence of recent population bottlenecks. Factors that produced population reductions may include loss of wetlands to development and agricultural conversion, drought, and wildfire. At this time, we are unable to determine if the high percentage (50%) of populations having experienced bottlenecks is representative of the Yellow Rail's entire range. Further genetic data from additional breeding populations will be required for this issue to be addressed.

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

NASA Astrophysics Data System (ADS)

van Rooijen, Wim-Jan; Rodriguez, Ben

2002-12-01

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

Applying Unique Molecular Identifiers in Next Generation Sequencing Reveals a Constrained Viral Quasispecies Evolution under Cross-Reactive Antibody Pressure Targeting Long Alpha Helix of Hemagglutinin

PubMed Central

Hauck, Nastasja C.; Kirpach, Josiane; Kiefer, Christina; Farinelle, Sophie; Morris, Stephen A.; Muller, Claude P.; Lu, I-Na

2018-01-01

To overcome yearly efforts and costs for the production of seasonal influenza vaccines, new approaches for the induction of broadly protective and long-lasting immune responses have been developed in the past decade. To warrant safety and efficacy of the emerging crossreactive vaccine candidates, it is critical to understand the evolution of influenza viruses in response to these new immune pressures. Here we applied unique molecular identifiers in next generation sequencing to analyze the evolution of influenza quasispecies under in vivo antibody pressure targeting the hemagglutinin (HA) long alpha helix (LAH). Our vaccine targeting LAH of hemagglutinin elicited significant seroconversion and protection against homologous and heterologous influenza virus strains in mice. The vaccine not only significantly reduced lung viral titers, but also induced a well-known bottleneck effect by decreasing virus diversity. In contrast to the classical bottleneck effect, here we showed a significant increase in the frequency of viruses with amino acid sequences identical to that of vaccine targeting LAH domain. No escape mutant emerged after vaccination. These results not only support the potential of a universal influenza vaccine targeting the conserved LAH domains, but also clearly demonstrate that the well-established bottleneck effect on viral quasispecies evolution does not necessarily generate escape mutants. PMID:29587397

Conservation genetics of the alligator snapping turtle: cytonuclear evidence of range-wide bottleneck effects and unusually pronounced geographic structure

USGS Publications Warehouse

Echelle, A.A.; Hackler, J.C.; Lack, Justin B.; Ballard, S. R.; Roman, J.; Fox, S. F.; Leslie,, David M.; Van Den Bussche, Ronald A.

2010-01-01

A previous mtDNA study indicated that female-mediated gene flow was extremely rare among alligator snapping turtle populations in different drainages of the Gulf of Mexico. In this study, we used variation at seven microsatellite DNA loci to assess the possibility of male-mediated gene flow, we augmented the mtDNA survey with additional sampling of the large Mississippi River System, and we evaluated the hypothesis that the consistently low within-population mtDNA diversity reflects past population bottlenecks. The results show that dispersal between drainages of the Gulf of Mexico is rare (F STmsat  = 0.43, ΦSTmtDNA = 0.98). Past range-wide bottlenecks are indicated by several genetic signals, including low diversity for microsatellites (1.1–3.9 alleles/locus; H e = 0.06–0.53) and mtDNA (h = 0.00 for most drainages; π = 0.000–0.001). Microsatellite data reinforce the conclusion from mtDNA that the Suwannee River population might eventually be recognized as a distinct taxonomic unit. It was the only population showing fixation or near fixation for otherwise rare microsatellite alleles. Six evolutionarily significant units are recommended on the basis of reciprocal mtDNA monophyly and high levels of microsatellite DNA divergence.

Complexity of spatiotemporal traffic phenomena in flow of identical drivers: Explanation based on fundamental hypothesis of three-phase theory

NASA Astrophysics Data System (ADS)

Kerner, Boris S.

2012-03-01

Based on numerical simulations of a stochastic three-phase traffic flow model, we reveal the physics of the fundamental hypothesis of three-phase theory that, in contrast with a fundamental diagram of classical traffic flow theories, postulates the existence of a two-dimensional (2D) region of steady states of synchronized flow where a driver makes an arbitrary choice of a space gap (time headway) to the preceding vehicle. We find that macroscopic and microscopic spatiotemporal effects of the entire complexity of traffic congestion observed up to now in real measured traffic data can be explained by simulations of traffic flow consisting of identical drivers and vehicles, if a microscopic model used in these simulations incorporates the fundamental hypothesis of three-phase theory. It is shown that the driver's choice of space gaps within the 2D region of synchronized flow associated with the fundamental hypothesis of three-phase theory can qualitatively change types of congested patterns that can emerge at a highway bottleneck. In particular, if drivers choose long enough spaces gaps associated with the fundamental hypothesis, then general patterns, which consist of synchronized flow and wide moving jams, do not emerge independent of the flow rates and bottleneck characteristics: Even at a heavy bottleneck leading to a very low speed within congested patterns, only synchronized flow patterns occur in which no wide moving jams emerge spontaneously.

Complexity of spatiotemporal traffic phenomena in flow of identical drivers: explanation based on fundamental hypothesis of three-phase theory.

PubMed

Kerner, Boris S

2012-03-01

Based on numerical simulations of a stochastic three-phase traffic flow model, we reveal the physics of the fundamental hypothesis of three-phase theory that, in contrast with a fundamental diagram of classical traffic flow theories, postulates the existence of a two-dimensional (2D) region of steady states of synchronized flow where a driver makes an arbitrary choice of a space gap (time headway) to the preceding vehicle. We find that macroscopic and microscopic spatiotemporal effects of the entire complexity of traffic congestion observed up to now in real measured traffic data can be explained by simulations of traffic flow consisting of identical drivers and vehicles, if a microscopic model used in these simulations incorporates the fundamental hypothesis of three-phase theory. It is shown that the driver's choice of space gaps within the 2D region of synchronized flow associated with the fundamental hypothesis of three-phase theory can qualitatively change types of congested patterns that can emerge at a highway bottleneck. In particular, if drivers choose long enough spaces gaps associated with the fundamental hypothesis, then general patterns, which consist of synchronized flow and wide moving jams, do not emerge independent of the flow rates and bottleneck characteristics: Even at a heavy bottleneck leading to a very low speed within congested patterns, only synchronized flow patterns occur in which no wide moving jams emerge spontaneously.

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

PubMed

Christiansen, Morten H; Chater, Nick

2016-01-01

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

Conscious Connections: Phenomenology and Decoding the Disciplines

ERIC Educational Resources Information Center

Currie, Genevieve

2017-01-01

This chapter describes how seven disciplinary bottlenecks from four diverse disciplines were analyzed using a phenomenological perspective and includes a discussion of embodied knowing and implications for educators.

Final Report - Freight Facilities and System Inventory

DOT National Transportation Integrated Search

1995-09-01

This report describes the general physical and operational characteristics and : bottlenecks to the efficient operation of intermodal terminals and systems in the New York metropolitan area and its vicinity.

The information science of microbial ecology.

PubMed

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

2016-06-01

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

Renaissance of protein crystallization and precipitation in biopharmaceuticals purification.

PubMed

Dos Santos, Raquel; Carvalho, Ana Luísa; Roque, A Cecília A

The current chromatographic approaches used in protein purification are not keeping pace with the increasing biopharmaceutical market demand. With the upstream improvements, the bottleneck shifted towards the downstream process. New approaches rely in Anything But Chromatography methodologies and revisiting former techniques with a bioprocess perspective. Protein crystallization and precipitation methods are already implemented in the downstream process of diverse therapeutic biological macromolecules, overcoming the current chromatographic bottlenecks. Promising work is being developed in order to implement crystallization and precipitation in the purification pipeline of high value therapeutic molecules. This review focuses in the role of these two methodologies in current industrial purification processes, and highlights their potential implementation in the purification pipeline of high value therapeutic molecules, overcoming chromatographic holdups. Copyright © 2016 Elsevier Inc. All rights reserved.

Skewed segregation of the mtDNA nt 8993 (T-->G) mutation in human oocytes.

PubMed Central

Blok, R B; Gook, D A; Thorburn, D R; Dahl, H H

1997-01-01

Rapid changes in mtDNA variants between generations have led to the bottleneck theory, which proposes a dramatic reduction in mtDNA numbers during early oogenesis. We studied oocytes from a woman with heteroplasmic expression of the mtDNA nt 8993 (T-->G) mutation. Of seven oocytes analyzed, one showed no evidence of the mutation, and the remaining six had a mutant load > 95%. This skewed expression of the mutation in oocytes is not compatible with the conventional bottleneck theory. A possible explanation is that, during amplification of mtDNA in the developing oocyte, mtDNA from one mitochondrion is preferentially amplified. Thus, subsequent mature oocytes may contain predominantly wild-type or mutant mitochondrial genomes. Images Figure 2 Figure 3 PMID:9199572

Highlight on Bottlenecks in Food Allergen Analysis: Detection and Quantification by Mass Spectrometry.

PubMed

Planque, Mélanie; Arnould, Thierry; Renard, Patricia; Delahaut, Philippe; Dieu, Marc; Gillard, Nathlie

2017-07-01

Food laboratories have developed methods for testing allergens in foods. The efficiency of qualitative and quantitative methods is of prime importance in protecting allergic populations. Unfortunately, food laboratories encounter barriers to developing efficient methods. Bottlenecks include the lack of regulatory thresholds, delays in the emergence of reference materials and guidelines, and the need to detect processed allergens. In this study, ultra-HPLC coupled to tandem MS was used to illustrate difficulties encountered in determining method performances. We measured the major influences of both processing and matrix effects on the detection of egg, milk, soy, and peanut allergens in foodstuffs. The main goals of this work were to identify difficulties that food laboratories still encounter in detecting and quantifying allergens and to sensitize researchers to them.

[Innovation in pharmaceutical and health biotechnology industries: challenges for a virtuous agenda].

PubMed

Vargas, Marco; Gadelha, Carlos Augusto Grabois; Costa, Laís Silveira; Maldonado, José

2012-12-01

Pharmaceutical and biotechnology industries comprise a major production subsystem of the health industrial complex in Brazil. It stands out for both its economic importance and its prominent role in developing new technologies in strategic areas. Strengthening the local production of generic drugs in the last decade has significantly increased the number of Brazilian companies in the local pharmaceutical market and has been an important turning point for this industry's growth. However, there remain major structural bottlenecks both in terms of production and continuous innovation. These bottlenecks reveal the high vulnerability of the Brazilian National Health System and point to the need of public policies that promote strengthening the production base and innovation in the pharmaceutical industry and that at the same time meet health-related social demands in health in Brazil.

Hydrogen gas storage in fluorinated ultramicroporous tunnel crystal

NASA Astrophysics Data System (ADS)

Kataoka, Keisuke; Katagiri, Toshimasa

2012-07-01

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

Connected vehicle freeway speed harmonization systems.

DOT National Transportation Integrated Search

2016-03-15

The capacity drop phenomenon, which reduces the maximum bottleneck discharge rate following the onset of congestion, is a critical restriction in transportation networks that causes additional traffic congestion. Consequently, preventing or reducing ...

Speed harmonization

DOT National Transportation Integrated Search

2015-01-01

Speed harmonization is a method to reduce congestion and improve traffic performance. This method is applied at points where lanes merge and form bottlenecks, the greatest cause of congestion nationwide. The strategy involves gradually lowering speed...

Advanced Photon Source Upgrade Project - Materials

ScienceCinema

Gibbson, Murray

2018-03-02

An upgrade to Advanced Photon Source announced by DOE - http://go.usa.gov/ivZ -- will help scientists break through bottlenecks in materials design in order to develop materials with desirable functions.

Advanced software development workstation project: Engineering scripting language. Graphical editor

NASA Technical Reports Server (NTRS)

1992-01-01

Software development is widely considered to be a bottleneck in the development of complex systems, both in terms of development and in terms of maintenance of deployed systems. Cost of software development and maintenance can also be very high. One approach to reducing costs and relieving this bottleneck is increasing the reuse of software designs and software components. A method for achieving such reuse is a software parts composition system. Such a system consists of a language for modeling software parts and their interfaces, a catalog of existing parts, an editor for combining parts, and a code generator that takes a specification and generates code for that application in the target language. The Advanced Software Development Workstation is intended to be an expert system shell designed to provide the capabilities of a software part composition system.

Design, Optimization and Application of Small Molecule Biosensor in Metabolic Engineering.

PubMed

Liu, Yang; Liu, Ye; Wang, Meng

2017-01-01

The development of synthetic biology and metabolic engineering has painted a great future for the bio-based economy, including fuels, chemicals, and drugs produced from renewable feedstocks. With the rapid advance of genome-scale modeling, pathway assembling and genome engineering/editing, our ability to design and generate microbial cell factories with various phenotype becomes almost limitless. However, our lack of ability to measure and exert precise control over metabolite concentration related phenotypes becomes a bottleneck in metabolic engineering. Genetically encoded small molecule biosensors, which provide the means to couple metabolite concentration to measurable or actionable outputs, are highly promising solutions to the bottleneck. Here we review recent advances in the design, optimization and application of small molecule biosensor in metabolic engineering, with particular focus on optimization strategies for transcription factor (TF) based biosensors.

First Results at ultra-high Rλ in a wind tunnel

NASA Astrophysics Data System (ADS)

Kuechler, Christian; Bodenschatz, Eberhard; Bewley, Gregory P.

2017-11-01

With a new active grid installed, the Variable Density Turbulence Tunnel (VDTT) at the Max-Planck-Institute for Dynamics and Self-Organization produced homogeneous turbulence at Reynolds numbers up to Rλ 7500 . The active grid consisted of 111 individually controllable flaps that produced more intense turbulence than classical fixed grids. We varied the Reynolds number by changing the pressure of sulfur hexafluoride gas in the tunnel between 0.5 and 15 bar, which changes the viscosity of the gas. With hot wire probes called NSTAPs that were 30 microns long, we measured velocity spectra and structure functions. While a bottleneck is present in the spectra at Reynolds numbers up to Rλ < 3000 , the bottleneck weakens and disappears at higher Rλ. We compare this observation with measurements made in the field and with computer simulations.

Design, Optimization and Application of Small Molecule Biosensor in Metabolic Engineering

PubMed Central

Liu, Yang; Liu, Ye; Wang, Meng

2017-01-01

The development of synthetic biology and metabolic engineering has painted a great future for the bio-based economy, including fuels, chemicals, and drugs produced from renewable feedstocks. With the rapid advance of genome-scale modeling, pathway assembling and genome engineering/editing, our ability to design and generate microbial cell factories with various phenotype becomes almost limitless. However, our lack of ability to measure and exert precise control over metabolite concentration related phenotypes becomes a bottleneck in metabolic engineering. Genetically encoded small molecule biosensors, which provide the means to couple metabolite concentration to measurable or actionable outputs, are highly promising solutions to the bottleneck. Here we review recent advances in the design, optimization and application of small molecule biosensor in metabolic engineering, with particular focus on optimization strategies for transcription factor (TF) based biosensors. PMID:29089935

Maintenance of Genetic Diversity in an Introduced Island Population of Guanacos after Seven Decades and Two Severe Demographic Bottlenecks: Implications for Camelid Conservation

PubMed Central

von Borries, Rainer; Johnson, Warren E.; Franklin, William L.; Marín, Juan C.

2014-01-01

Fifteen guanacos were introduced to Staats Island in the Falklands/Malvinas archipelago from Patagonia in the 1930s. Twenty five years later, the population was culled from 300 to 10–20 individuals, but quickly rebounded to a population of almost 400 animals that today retain the genetic signature of the founding event and later bottleneck. The goals of this study were to (i) make a genetic assessment of this island population through comparisons with mainland populations and simulations, and (ii) assess the likely source-population of the introduced guanacos. Genetic variation was estimated from 513 bp of mitochondrial DNA sequence and 15 microsatellite loci among 154 guanacos collected from eight localities, including the adjacent mainland and the islands of Tierra del Fuego and Staats Island. Of the 23 haplotypes observed among our samples, the Staats Island population only contained three haplotypes, all of which were shared with the coastal Monte Leon population in southern Patagonia. Mitochondrial DNA and microsatellite variations on Staats Island were comparable to most mainland populations and greater than those observed on Tierra del Fuego. Patterns of genetic structure suggest that the Staats Island guanaco population was founded with animals from southern Patagonia (as opposed to northern Patagonia or Tierra del Fuego), but that effective reductions in population size lasted only a few generations and that surviving animals were a random sample of the pre-bottleneck genetic variation. PMID:24663026

Genetic depletion at adaptive but not neutral loci in an endangered bird species.

PubMed

Hartmann, Stefanie A; Schaefer, H Martin; Segelbacher, Gernot

2014-12-01

Many endangered species suffer from the loss of genetic diversity, but some populations may be able to thrive even if genetically depleted. To investigate the underlying genetic processes of population bottlenecks, we apply an innovative approach for assessing genetic diversity in the last known population of the endangered Pale-headed Brushfinch (Atlapetes pallidiceps) in Ecuador. First, we measure genetic diversity at eleven neutral microsatellite loci and adaptive SNP variation in five Toll-like receptor (TLR) immune system genes. Bottleneck tests confirm genetic drift as the main force shaping genetic diversity in this species and indicate a 99 % reduction in population size dating back several hundred years. Second, we compare contemporary microsatellite diversity with historic museum samples of A. pallidiceps, finding no change in genetic diversity. Third, we compare genetic diversity in the Pale-headed Brushfinch with two co-occurring-related brushfinch species (Atlapetes latinuchus, Buarremon torquatus), finding a reduction of up to 91% diversity in the immune system genes but not in microsatellites. High TLR diversity is linked to decreased survival probabilities in A. pallidiceps. Low TLR diversity is thus probably an adaptation to the specific selection regime within its currently very restricted distribution (approximately 200 ha), but could severely restrict the adaptive potential of the species in the long run. Our study illustrates the importance of investigating both neutral and adaptive markers to assess the effect of population bottlenecks and for recommending specific management plans in endangered species. © 2014 John Wiley & Sons Ltd.

Maintenance of genetic diversity in an introduced island population of guanacos after seven decades and two severe demographic bottlenecks: implications for camelid conservation.

PubMed

González, Benito A; Orozco-Terwengel, Pablo; von Borries, Rainer; Johnson, Warren E; Franklin, William L; Marín, Juan C

2014-01-01

Fifteen guanacos were introduced to Staats Island in the Falklands/Malvinas archipelago from Patagonia in the 1930s. Twenty five years later, the population was culled from 300 to 10-20 individuals, but quickly rebounded to a population of almost 400 animals that today retain the genetic signature of the founding event and later bottleneck. The goals of this study were to (i) make a genetic assessment of this island population through comparisons with mainland populations and simulations, and (ii) assess the likely source-population of the introduced guanacos. Genetic variation was estimated from 513 bp of mitochondrial DNA sequence and 15 microsatellite loci among 154 guanacos collected from eight localities, including the adjacent mainland and the islands of Tierra del Fuego and Staats Island. Of the 23 haplotypes observed among our samples, the Staats Island population only contained three haplotypes, all of which were shared with the coastal Monte Leon population in southern Patagonia. Mitochondrial DNA and microsatellite variations on Staats Island were comparable to most mainland populations and greater than those observed on Tierra del Fuego. Patterns of genetic structure suggest that the Staats Island guanaco population was founded with animals from southern Patagonia (as opposed to northern Patagonia or Tierra del Fuego), but that effective reductions in population size lasted only a few generations and that surviving animals were a random sample of the pre-bottleneck genetic variation.

Genetic patterns of domestication in pigeonpea (Cajanus cajan (L.) Millsp.) and wild Cajanus relatives.

PubMed

Kassa, Mulualem T; Penmetsa, R Varma; Carrasquilla-Garcia, Noelia; Sarma, Birinchi K; Datta, Subhojit; Upadhyaya, Hari D; Varshney, Rajeev K; von Wettberg, Eric J B; Cook, Douglas R

2012-01-01

Pigeonpea (Cajanus cajan) is an annual or short-lived perennial food legume of acute regional importance, providing significant protein to the human diet in less developed regions of Asia and Africa. Due to its narrow genetic base, pigeonpea improvement is increasingly reliant on introgression of valuable traits from wild forms, a practice that would benefit from knowledge of its domestication history and relationships to wild species. Here we use 752 single nucleotide polymorphisms (SNPs) derived from 670 low copy orthologous genes to clarify the evolutionary history of pigeonpea (79 accessions) and its wild relatives (31 accessions). We identified three well-supported lineages that are geographically clustered and congruent with previous nuclear and plastid sequence-based phylogenies. Among all species analyzed Cajanus cajanifolius is the most probable progenitor of cultivated pigeonpea. Multiple lines of evidence suggest recent gene flow between cultivated and non-cultivated forms, as well as historical gene flow between diverged but sympatric species. Evidence supports that primary domestication occurred in India, with a second and more recent nested population bottleneck focused in tropical regions that is the likely consequence of pigeonpea breeding. We find abundant allelic variation and genetic diversity among the wild relatives, with the exception of wild species from Australia for which we report a third bottleneck unrelated to domestication within India. Domesticated C. cajan possess 75% less allelic diversity than the progenitor clade of wild Indian species, indicating a severe "domestication bottleneck" during pigeonpea domestication.

Population structure and connectivity in the Mediterranean sponge Ircinia fasciculata are affected by mass mortalities and hybridization

PubMed Central

Riesgo, A; Pérez-Portela, R; Pita, L; Blasco, G; Erwin, P M; López-Legentil, S

2016-01-01

Recent episodes of mass mortalities in the Mediterranean Sea have been reported for the closely related marine sponges Ircinia fasciculata and Ircinia variabilis that live in sympatry. In this context, the assessment of the genetic diversity, bottlenecks and connectivity of these sponges has become urgent in order to evaluate the potential effects of mass mortalities on their latitudinal range. Our study aims to establish (1) the genetic structure, connectivity and signs of bottlenecks across the populations of I. fasciculata and (2) the hybridization levels between I. fasciculata and I. variabilis. To accomplish the first objective, 194 individuals of I. fasciculata from 12 locations across the Mediterranean were genotyped at 14 microsatellite loci. For the second objective, mitochondrial cytochrome c oxidase subunit I sequences of 16 individuals from both species were analyzed along with genotypes at 12 microsatellite loci of 40 individuals coexisting in 3 Mediterranean populations. We detected strong genetic structure along the Mediterranean for I. fasciculata, with high levels of inbreeding in all locations and bottleneck signs in most locations. Oceanographic barriers like the Almeria-Oran front, North-Balearic front and the Ligurian-Thyrrenian barrier seem to be impeding gene flow for I. fasciculata, adding population divergence to the pattern of isolation by distance derived from the low dispersal abilities of sponge larvae. Hybridization between both species occurred in some populations that might be increasing genetic diversity and somewhat palliating the genetic loss caused by population decimation in I. fasciculata. PMID:27599575

Identification and Validation of Ifit1 as an Important Innate Immune Bottleneck

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

McDermott, Jason E.; Vartanian, Keri B.; Mitchell, Hugh D.

The innate immune system plays important roles in a number of disparate processes. Foremost, innate immunity is a first responder to invasion by pathogens and triggers early defensive responses and recruits the adaptive immune system. The innate immune system also responds to endogenous damage signals that arise from tissue injury. Recently it has been found that innate immunity plays an important role in neuroprotection against ischemic stroke through the activation of the primary innate immune receptors, Toll-like receptors (TLRs). Using several large-scale transcriptomic data sets from mouse and mouse macrophage studies we identified targets predicted to be important in controllingmore » innate immune processes initiated by TLR activation. Targets were identified as genes with high betweenness centrality, so-called bottlenecks, in networks inferred from statistical associations between gene expression patterns. A small set of putative bottlenecks were identified in each of the data sets investigated including interferon-stimulated genes (Ifit1, Ifi47, Tgtp and Oasl2) as well as genes uncharacterized in immune responses (Axud1 and Ppp1r15a). We further validated one of these targets, Ifit1, in mouse macrophages by showing that silencing it suppresses induction of predicted downstream genes by lipopolysaccharide (LPS)-mediated TLR4 activation through an unknown direct or indirect mechanism. Our study demonstrates the utility of network analysis for identification of interesting targets related to innate immune function, and highlights that Ifit1 can exert a positive regulatory effect on downstream genes.« less

An approximate classical unimolecular reaction rate theory

NASA Astrophysics Data System (ADS)

Zhao, Meishan; Rice, Stuart A.

1992-05-01

We describe a classical theory of unimolecular reaction rate which is derived from the analysis of Davis and Gray by use of simplifying approximations. These approximations concern the calculation of the locations of, and the fluxes of phase points across, the bottlenecks to fragmentation and to intramolecular energy transfer. The bottleneck to fragment separation is represented as a vibration-rotation state dependent separatrix, which approximation is similar to but extends and improves the approximations for the separatrix introduced by Gray, Rice, and Davis and by Zhao and Rice. The novel feature in our analysis is the representation of the bottlenecks to intramolecular energy transfer as dividing surfaces in phase space; the locations of these dividing surfaces are determined by the same conditions as locate the remnants of robust tori with frequency ratios related to the golden mean (in a two degree of freedom system these are the cantori). The flux of phase points across each dividing surface is calculated with an analytic representation instead of a stroboscopic mapping. The rate of unimolecular reaction is identified with the net rate at which phase points escape from the region of quasiperiodic bounded motion to the region of free fragment motion by consecutively crossing the dividing surfaces for intramolecular energy exchange and the separatrix. This new theory generates predictions of the rates of predissociation of the van der Waals molecules HeI2, NeI2 and ArI2 which are in very good agreement with available experimental data.

How Influenza Vaccination Policy May affect Vaccine Logistics

PubMed Central

Assi, Tina-Marie; Rookkapan, Korngamon; Rajgopal, Jayant; Sornsrivichai, Vorasith; Brown, Shawn T.; Welling, Joel S.; Norman, Bryan A.; Connor, Diana L.; Chen, Sheng-I; Slayton, Rachel B.; Laosiritaworn, Yongjua; Wateska, Angela R.; Wisniewski, Stephen R.; Lee, Bruce Y.

2012-01-01

Background When policymakers make decision about the target populations and timing of influenza vaccination, they may not consider the impact on the vaccine supply chains, which may in turn affect vaccine availability. Purpose Our goal is to explore the effects on the Thailand vaccine supply chain of introducing influenza vaccines and varying the target populations and immunization time-frames. Methods Utilized our custom-designed software HERMES (Highly Extensible Resource for Modeling Supply Chains), we developed a detailed, computational discrete-event simulation model of the Thailand's National Immunization Program (NIP) supply chain in Trang Province, Thailand., A suite of experiments simulated introducing influenza vaccines for different target populations and over different time-frames prior to and during the annual influenza season. Results Introducing influenza vaccines creates bottlenecks that reduce the availability of both influenza vaccines as well as the other NIP vaccines, with provincial to district transport capacity being the primary constraint. Even covering only 25% of the Advisory Committee on Immunization Practice-recommended population while administering the vaccine over six months hinders overall vaccine availability so that only 62% of arriving patients can receive vaccines. Increasing the target population from 25% to 100% progressively worsens these bottlenecks, while increasing influenza vaccination time - frame from 1 to 6 months decreases these bottlenecks. Conclusion Since the choice of target populations for influenza vaccination and the time-frame to deliver this vaccine can substantially affect the flow of all vaccines, policy-makers may want to consider supply chain effects when choosing target populations for a vaccine. PMID:22537993

Freeway bottleneck removals : workshop enhancement and technology transfer.

DOT National Transportation Integrated Search

2009-12-01

As transportation improvement projects become increasingly costly and complex and as funding sources are not : keeping pace with needs in highly urbanized areas, it becomes critical that existing freeway systems be finetuned to : maximize capacity...

Multimodal and corridor applications of travel time reliability.

DOT National Transportation Integrated Search

2012-03-30

Congestion is all too familiar in Floridas cities. Traditionally, agencies have tried to mitigate recurring congestion by comparing demand and capacity during peak periods and alleviating bottlenecks. However, congestion is often due to nonrecurri...

Multimodal and corridor applications of travel time reliability : [summary].

DOT National Transportation Integrated Search

2012-01-01

Congestion is all too familiar in Floridas cities. Traditionally, agencies have tried to mitigate recurring congestion by comparing demand and capacity during peak periods and alleviating bottlenecks. However, congestion is often due to nonrecurri...

Optimized active traffic management and speed harmonization in work zones.

DOT National Transportation Integrated Search

2014-01-01

Traffic and demand management are major strategies to control delay and congestion in : highway bottlenecks including work zones. The Federal Highway Administration (FHWA) : introduced innovative strategies, called Active Traffic and Demand Managemen...

Practical Doping Principles

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

Zunger, A.

2003-05-01

'Theoretical investigations of doping of several wide-gap materials suggest a number of rather general, practical"doping principles" that may help guide experimental strategies of overcoming doping bottlenecks. This paper will be published as a journal article in the future.

Addressing MAP-21 freight objectives using GPS data.

DOT National Transportation Integrated Search

2016-12-01

Freight planning and operation perspectives of Moving Ahead for Progress in the 21st Century Act (MAP-21) includes development of a national freight plan to address freight congestion bottlenecks, connectivity enhancement of major intermodal centers,...

Towards transformational change: UNDP's work in environment and sustainable development 2008-2012

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

Mordt, Matilde; Hildebrandt, Laura; Iyer, Devika

2013-03-15

This report highlights significant advances in sustainable development from almost 60 country reports and underscores the challenges and bottlenecks to moving beyond the economic-led growth strategies of the past 20 years.

Efficient access pricing for rail bottlenecks

DOT National Transportation Integrated Search

2000-06-01

This study, which is posted online, was undertaken at the request of the Federal Railroad Administration (FRA), specifically the Office of the Associate Administrator for Policy and Program Development. The FRA Policy Office asked for a review of som...

Determining queue and congestion in highway work zone bottlenecks.

DOT National Transportation Integrated Search

2011-03-11

Construction zones, though required for infrastructure maintenance, have become congestion choke points on most highway systems in the US. The congestion may create potentially unsafe driving conditions for approaching motorists that do not expect qu...

Determining Queue and Congestion in Highway Work Zone Bottlenecks

DOT National Transportation Integrated Search

2011-03-11

Construction zones, though required for infrastructure maintenance, have become congestion choke points on most highway systems in the US. The congestion may create potentially unsafe driving conditions for approaching motorists that do not expect qu...

Environment construction and bottleneck breakthrough in the improvement of wisdom exhibition

NASA Astrophysics Data System (ADS)

Zhang, Jiankang

2017-08-01

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

Museum samples reveal rapid evolution by wild honey bees exposed to a novel parasite

PubMed Central

Mikheyev, Alexander S.; Tin, Mandy M. Y.; Arora, Jatin; Seeley, Thomas D.

2015-01-01

Understanding genetic changes caused by novel pathogens and parasites can reveal mechanisms of adaptation and genetic robustness. Using whole-genome sequencing of museum and modern specimens, we describe the genomic changes in a wild population of honey bees in North America following the introduction of the ectoparasitic mite, Varroa destructor. Even though colony density in the study population is the same today as in the past, a major loss of haplotypic diversity occurred, indicative of a drastic mitochondrial bottleneck, caused by massive colony mortality. In contrast, nuclear genetic diversity did not change, though hundreds of genes show signs of selection. The genetic diversity within each bee colony, particularly as a consequence of polyandry by queens, may enable preservation of genetic diversity even during population bottlenecks. These findings suggest that genetically diverse honey bee populations can recover from introduced diseases by evolving rapid tolerance, while maintaining much of the standing genetic variation. PMID:26246313

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

PubMed Central

Marois, René

2014-01-01

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

Using fragmentation trees and mass spectral trees for identifying unknown compounds in metabolomics.

PubMed

Vaniya, Arpana; Fiehn, Oliver

2015-06-01

Identification of unknown metabolites is the bottleneck in advancing metabolomics, leaving interpretation of metabolomics results ambiguous. The chemical diversity of metabolism is vast, making structure identification arduous and time consuming. Currently, comprehensive analysis of mass spectra in metabolomics is limited to library matching, but tandem mass spectral libraries are small compared to the large number of compounds found in the biosphere, including xenobiotics. Resolving this bottleneck requires richer data acquisition and better computational tools. Multi-stage mass spectrometry (MSn) trees show promise to aid in this regard. Fragmentation trees explore the fragmentation process, generate fragmentation rules and aid in sub-structure identification, while mass spectral trees delineate the dependencies in multi-stage MS of collision-induced dissociations. This review covers advancements over the past 10 years as a tool for metabolite identification, including algorithms, software and databases used to build and to implement fragmentation trees and mass spectral annotations.

Critical steps in learning from incidents: using learning potential in the process from reporting an incident to accident prevention.

PubMed

Drupsteen, Linda; Groeneweg, Jop; Zwetsloot, Gerard I J M

2013-01-01

Many incidents have occurred because organisations have failed to learn from lessons of the past. This means that there is room for improvement in the way organisations analyse incidents, generate measures to remedy identified weaknesses and prevent reoccurrence: the learning from incidents process. To improve that process, it is necessary to gain insight into the steps of this process and to identify factors that hinder learning (bottlenecks). This paper presents a model that enables organisations to analyse the steps in a learning from incidents process and to identify the bottlenecks. The study describes how this model is used in a survey and in 3 exploratory case studies in The Netherlands. The results show that there is limited use of learning potential, especially in the evaluation stage. To improve learning, an approach that considers all steps is necessary.

Museum samples reveal rapid evolution by wild honey bees exposed to a novel parasite.

PubMed

Mikheyev, Alexander S; Tin, Mandy M Y; Arora, Jatin; Seeley, Thomas D

2015-08-06

Understanding genetic changes caused by novel pathogens and parasites can reveal mechanisms of adaptation and genetic robustness. Using whole-genome sequencing of museum and modern specimens, we describe the genomic changes in a wild population of honey bees in North America following the introduction of the ectoparasitic mite, Varroa destructor. Even though colony density in the study population is the same today as in the past, a major loss of haplotypic diversity occurred, indicative of a drastic mitochondrial bottleneck, caused by massive colony mortality. In contrast, nuclear genetic diversity did not change, though hundreds of genes show signs of selection. The genetic diversity within each bee colony, particularly as a consequence of polyandry by queens, may enable preservation of genetic diversity even during population bottlenecks. These findings suggest that genetically diverse honey bee populations can recover from introduced diseases by evolving rapid tolerance, while maintaining much of the standing genetic variation.

DistMap: a toolkit for distributed short read mapping on a Hadoop cluster.

PubMed

Pandey, Ram Vinay; Schlötterer, Christian

2013-01-01

With the rapid and steady increase of next generation sequencing data output, the mapping of short reads has become a major data analysis bottleneck. On a single computer, it can take several days to map the vast quantity of reads produced from a single Illumina HiSeq lane. In an attempt to ameliorate this bottleneck we present a new tool, DistMap - a modular, scalable and integrated workflow to map reads in the Hadoop distributed computing framework. DistMap is easy to use, currently supports nine different short read mapping tools and can be run on all Unix-based operating systems. It accepts reads in FASTQ format as input and provides mapped reads in a SAM/BAM format. DistMap supports both paired-end and single-end reads thereby allowing the mapping of read data produced by different sequencing platforms. DistMap is available from http://code.google.com/p/distmap/

DistMap: A Toolkit for Distributed Short Read Mapping on a Hadoop Cluster

PubMed Central

Pandey, Ram Vinay; Schlötterer, Christian

2013-01-01

With the rapid and steady increase of next generation sequencing data output, the mapping of short reads has become a major data analysis bottleneck. On a single computer, it can take several days to map the vast quantity of reads produced from a single Illumina HiSeq lane. In an attempt to ameliorate this bottleneck we present a new tool, DistMap - a modular, scalable and integrated workflow to map reads in the Hadoop distributed computing framework. DistMap is easy to use, currently supports nine different short read mapping tools and can be run on all Unix-based operating systems. It accepts reads in FASTQ format as input and provides mapped reads in a SAM/BAM format. DistMap supports both paired-end and single-end reads thereby allowing the mapping of read data produced by different sequencing platforms. DistMap is available from http://code.google.com/p/distmap/ PMID:24009693

Preprinting Microbiology

PubMed Central

2017-01-01

ABSTRACT The field of microbiology has experienced significant growth due to transformative advances in technology and the influx of scientists driven by a curiosity to understand how microbes sustain myriad biochemical processes that maintain Earth. With this explosion in scientific output, a significant bottleneck has been the ability to rapidly disseminate new knowledge to peers and the public. Preprints have emerged as a tool that a growing number of microbiologists are using to overcome this bottleneck. Posting preprints can help to transparently recruit a more diverse pool of reviewers prior to submitting to a journal for formal peer review. Although the use of preprints is still limited in the biological sciences, early indications are that preprints are a robust tool that can complement and enhance peer-reviewed publications. As publishing moves to embrace advances in Internet technology, there are many opportunities for preprints and peer-reviewed journals to coexist in the same ecosystem. PMID:28536284

Preprinting Microbiology.

PubMed

Schloss, Patrick D

2017-05-23

The field of microbiology has experienced significant growth due to transformative advances in technology and the influx of scientists driven by a curiosity to understand how microbes sustain myriad biochemical processes that maintain Earth. With this explosion in scientific output, a significant bottleneck has been the ability to rapidly disseminate new knowledge to peers and the public. Preprints have emerged as a tool that a growing number of microbiologists are using to overcome this bottleneck. Posting preprints can help to transparently recruit a more diverse pool of reviewers prior to submitting to a journal for formal peer review. Although the use of preprints is still limited in the biological sciences, early indications are that preprints are a robust tool that can complement and enhance peer-reviewed publications. As publishing moves to embrace advances in Internet technology, there are many opportunities for preprints and peer-reviewed journals to coexist in the same ecosystem. Copyright © 2017 Schloss.

Keeping mtDNA in Shape between Generations

PubMed Central

Stewart, James B.; Larsson, Nils-Göran

2014-01-01

Since the unexpected discovery that mitochondria contain their own distinct DNA molecules, studies of the mitochondrial DNA (mtDNA) have yielded many surprises. In animals, transmission of the mtDNA genome is explicitly non-Mendelian, with a very high number of genome copies being inherited from the mother after a drastic bottleneck. Recent work has begun to uncover the molecular details of this unusual mode of transmission. Many surprising variations in animal mitochondrial biology are known; however, a series of recent studies have identified a core of evolutionarily conserved mechanisms relating to mtDNA inheritance, e.g., mtDNA bottlenecks during germ cell development, selection against specific mtDNA mutation types during maternal transmission, and targeted destruction of sperm mitochondria. In this review, we outline recent literature on the transmission of mtDNA in animals and highlight the implications for human health and ageing. PMID:25299061

From Bottleneck to Breakthrough: Urbanization and the Future of Biodiversity Conservation.

PubMed

Sanderson, Eric W; Walston, Joseph; Robinson, John G

2018-06-01

For the first time in the Anthropocene, the global demographic and economic trends that have resulted in unprecedented destruction of the environment are now creating the necessary conditions for a possible renaissance of nature. Drawing reasonable inferences from current patterns, we can predict that 100 years from now, the Earth could be inhabited by between 6 and 8 billion people, with very few remaining in extreme poverty, most living in towns and cities, and nearly all participating in a technologically driven, interconnected market economy. Building on the scholarship of others in demography, economics, sociology, and conservation biology, here, we articulate a theory of social-environmental change that describes the simultaneous and interacting effects of urban lifestyles on fertility, poverty alleviation, and ideation. By recognizing the shifting dynamics of these macrodrivers, conservation practice has the potential to transform itself from a discipline managing declines ("bottleneck") to a transformative movement of recovery ("breakthrough").

Fungal Beta-Glucosidases: A Bottleneck in Industrial Use of Lignocellulosic Materials

PubMed Central

Sørensen, Annette; Lübeck, Mette; Lübeck, Peter S.; Ahring, Birgitte K.

2013-01-01

Profitable biomass conversion processes are highly dependent on the use of efficient enzymes for lignocellulose degradation. Among the cellulose degrading enzymes, beta-glucosidases are essential for efficient hydrolysis of cellulosic biomass as they relieve the inhibition of the cellobiohydrolases and endoglucanases by reducing cellobiose accumulation. In this review, we discuss the important role beta-glucosidases play in complex biomass hydrolysis and how they create a bottleneck in industrial use of lignocellulosic materials. An efficient beta-glucosidase facilitates hydrolysis at specified process conditions, and key points to consider in this respect are hydrolysis rate, inhibitors, and stability. Product inhibition impairing yields, thermal inactivation of enzymes, and the high cost of enzyme production are the main obstacles to commercial cellulose hydrolysis. Therefore, this sets the stage in the search for better alternatives to the currently available enzyme preparations either by improving known or screening for new beta-glucosidases. PMID:24970184

Head-of-tide bottleneck of particulate material transport from watersheds to estuaries

NASA Astrophysics Data System (ADS)

Ensign, Scott H.; Noe, Gregory B.; Hupp, Cliff R.; Skalak, Katherine J.

2015-12-01

We measured rates of sediment, C, N, and P accumulation at four floodplain sites spanning the nontidal through oligohaline Choptank and Pocomoke Rivers, Maryland, USA. Ceramic tiles were used to collect sediment for a year and sediment cores were collected to derive decadal sedimentation rates using 137Cs. The results showed highest rates of short- and long-term sediment, C, N, and P accumulation occurred in tidal freshwater forests at the head of tide on the Choptank and the oligohaline marsh of the Pocomoke River, and lowest rates occurred in the downstream tidal freshwater forests in both rivers. Presumably, watershed material was mostly trapped at the head of tide, and estuarine material was trapped in oligohaline marshes. This hydrologic transport bottleneck at the head of tide stores most available watershed sediment, C, N, and P creating a sediment shadow in lower tidal freshwater forests potentially limiting their resilience to sea level rise.

Protein crystallization: Eluding the bottleneck of X-ray crystallography

PubMed Central

Holcomb, Joshua; Spellmon, Nicholas; Zhang, Yingxue; Doughan, Maysaa; Li, Chunying; Yang, Zhe

2017-01-01

To date, X-ray crystallography remains the gold standard for the determination of macromolecular structure and protein substrate interactions. However, the unpredictability of obtaining a protein crystal remains the limiting factor and continues to be the bottleneck in determining protein structures. A vast amount of research has been conducted in order to circumvent this issue with limited success. No single method has proven to guarantee the crystallization of all proteins. However, techniques using antibody fragments, lipids, carrier proteins, and even mutagenesis of crystal contacts have been implemented to increase the odds of obtaining a crystal with adequate diffraction. In addition, we review a new technique using the scaffolding ability of PDZ domains to facilitate nucleation and crystal lattice formation. Although in its infancy, such technology may be a valuable asset and another method in the crystallography toolbox to further the chances of crystallizing problematic proteins. PMID:29051919

Targeted gene disruption in Koji mold Aspergillus oryzae.

PubMed

Maruyama, Jun-Ichi; Kitamoto, Katsuhiko

2011-01-01

Filamentous fungi have received attentions as hosts for heterologous protein production because of their high secretion capability and eukaryotic post-translational modifications. One of the safest hosts for heterologous protein production is Koji mold Aspergillus oryzae since it has been used in the production of Japanese fermented foods for over 1,000 years. The production levels of proteins from higher eukaryotes are much lower than those of homologous (fungal) proteins. Bottlenecks in the heterologous protein production are suggested to be proteolytic degradation of the produced protein in the medium and the secretory pathway. For construction of excellent host strains, many genes causing the bottlenecks should be disrupted rapidly and efficiently. We developed a marker recycling system with the highly efficient gene-targeting background in A. oryzae. By employing this technique, we performed multiple gene disruption of the ten protease genes. The decuple protease gene disruptant showed fourfold production level of a heterologous protein compared with the wild-type strain.

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

Nehm, F., E-mail: frederik.nehm@iapp.de; Müller-Meskamp, L.; Klumbies, H.

A major failure mechanism is identified in electrical calcium corrosion tests for quality assessment of high-end application moisture barriers. Accelerated calcium corrosion is found at the calcium/electrode junction, leading to an electrical bottleneck. This causes test failure not related to overall calcium loss. The likely cause is a difference in electrochemical potential between the aluminum electrodes and the calcium sensor, resulting in a corrosion element. As a solution, a thin, full-area copper layer is introduced below the calcium, shifting the corrosion element to the calcium/copper junction and inhibiting bottleneck degradation. Using the copper layer improves the level of sensitivity formore » the water vapor transmission rate (WVTR) by over one order of magnitude. Thin-film encapsulated samples with 20 nm of atomic layer deposited alumina barriers this way exhibit WVTRs of 6 × 10{sup −5} g(H{sub 2}O)/m{sup 2}/d at 38 °C, 90% relative humidity.« less

Head-of-tide bottleneck of particulate material transport from watersheds to estuaries

USGS Publications Warehouse

Ensign, Scott H.; Noe, Gregory; Hupp, Cliff R.; Skalak, Katherine

2015-01-01

We measured rates of sediment, C, N, and P accumulation at four floodplain sites spanning the nontidal through oligohaline Choptank and Pocomoke Rivers, Maryland, USA. Ceramic tiles were used to collect sediment for a year and sediment cores were collected to derive decadal sedimentation rates using 137Cs. The results showed highest rates of short- and long-term sediment, C, N, and P accumulation occurred in tidal freshwater forests at the head of tide on the Choptank and the oligohaline marsh of the Pocomoke River, and lowest rates occurred in the downstream tidal freshwater forests in both rivers. Presumably, watershed material was mostly trapped at the head of tide, and estuarine material was trapped in oligohaline marshes. This hydrologic transport bottleneck at the head of tide stores most available watershed sediment, C, N, and P creating a sediment shadow in lower tidal freshwater forests potentially limiting their resilience to sea level rise.

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

PubMed Central

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

2011-01-01

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

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

PubMed

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

2017-10-01

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

The recent history and population structure of five Mandarina snail species from subtropical Ogasawara (Bonin Islands, Japan).

PubMed

Davison, Angus; Chiba, Satoshi

2006-09-01

The effect of Pleistocene climate change on the organisms of tropical and subtropical regions is rather poorly understood. We therefore studied the land snail genus Mandarina (Bradybaenidae) of oceanic Ogasawara (Bonin Islands, Japan), with the aim of using population genetic data to understand their recent history. Our analysis of a mitochondrial 16S ribosomal RNA region from more than 600 snails in five ground-living species suggests that populations on the small islands of Mukoujima, Anejima, Imotojima and Meijima, as well as on the low-lying southern and central parts of Hahajima, have probably undergone recent bottlenecks followed by subsequent expansions. Except between the main island of Hahajima and Mukouijima, there is almost no evidence for gene flow among islands even though the islands were connected repeatedly by land bridges through the Pleistocene. Within islands the population structure is severe, suggestive of a long-term, low level of gene flow (F(ST) is frequently greater than 0.5 among geographically close populations). Finally, there is a marked genetic patchiness, meaning that genetically close populations are sometimes separated by genetically distant populations. These patterns could be a consequence of expansion from bottlenecks, low active dispersal and founder effects caused by rare long-distance migrants. Unfortunately, the exact nature of the refugia and bottlenecks remains unknown because the palaeoclimate of this region is poorly understood. Dating the population size changes is also challenging because the molecular clock is uncertain. We suggest, however, that arid conditions or deforestation induced by decreased atmospheric CO(2) may have been the main factor in determining population size.

Multiple bottlenecks in hierarchical control of action sequences: what does "response selection" select in skilled typewriting?

PubMed

Yamaguchi, Motonori; Logan, Gordon D; Li, Vanessa

2013-08-01

Does response selection select words or letters in skilled typewriting? Typing performance involves hierarchically organized control processes: an outer loop that controls word level processing, and an inner loop that controls letter (or keystroke) level processing. The present study addressed whether response selection occurs in the outer loop or the inner loop by using the psychological refractory period (PRP) paradigm in which Task1 required typing single words and Task2 required vocal responses to tones. The number of letters (string length) in the words was manipulated to discriminate selection of words from selection of keystrokes. In Experiment 1, the PRP effect depended on string length of words in Task1, suggesting that response selection occurs in the inner loop. To assess contributions of the outer loop, the influence of string length was examined in a lexical-decision task that also involves word encoding and lexical access (Experiment 2), or to-be-typed words were preexposed so outer-loop processing could finish before typing started (Experiment 3). Response time for Task2 (RT2) did not depend on string length with lexical decision, and RT2 still depended on string length with typing preexposed strings. These results support the inner-loop locus of the PRP effect. In Experiment 4, typing was performed as Task2, and the effect of string length on typing RT interacted with stimulus onset asynchrony superadditively, implying that another bottleneck also exists in the outer loop. We conclude that there are at least two bottleneck processes in skilled typewriting. 2013 APA, all rights reserved

Locating the cortical bottleneck for slow reading in peripheral vision

PubMed Central

Yu, Deyue; Jiang, Yi; Legge, Gordon E.; He, Sheng

2015-01-01

Yu, Legge, Park, Gage, and Chung (2010) suggested that the neural bottleneck for slow peripheral reading is located in nonretinotopic areas. We investigated the potential rate-limiting neural site for peripheral reading using fMRI, and contrasted peripheral reading with recognition of peripherally presented line drawings of common objects. We measured the BOLD responses to both text (three-letter words/nonwords) and line-drawing objects presented either in foveal or peripheral vision (10° lower right visual field) at three presentation rates (2, 4, and 8/second). The statistically significant interaction effect of visual field × presentation rate on the BOLD response for text but not for line drawings provides evidence for distinctive processing of peripheral text. This pattern of results was obtained in all five regions of interest (ROIs). At the early retinotopic cortical areas, the BOLD signal slightly increased with increasing presentation rate for foveal text, and remained fairly constant for peripheral text. In the Occipital Word-Responsive Area (OWRA), Visual Word Form Area (VWFA), and object sensitive areas (LO and PHA), the BOLD responses to text decreased with increasing presentation rate for peripheral but not foveal presentation. In contrast, there was no rate-dependent reduction in BOLD response for line-drawing objects in all the ROIs for either foveal or peripheral presentation. Only peripherally presented text showed a distinctive rate-dependence pattern. Although it is possible that the differentiation starts to emerge at the early retinotopic cortical representation, the neural bottleneck for slower reading of peripherally presented text may be a special property of peripheral text processing in object category selective cortex. PMID:26237299

Blended learning in chemistry laboratory courses: Enhancing learning outcomes and aligning student needs with available resources

NASA Astrophysics Data System (ADS)

Burchett, Shayna Brianne

Freshman science courses are intended to prepare students for the rigor and expectations of subsequent college science. While secondary education aims to prepare students for the college curriculum, many incoming freshman lack the sense of responsibility for their own learning that is essential for success in a college-level course. The freshman general-chemistry laboratory course at Missouri University of Science and Technology (Missouri S&T) was identified as a bottleneck course with a demand beyond accommodation capacity. To address the bottleneck and develop a sense of learner responsibility, a decision was made to investigate laboratory course delivery strategies. As a result of the investigation into delivery strategies, a blended freshman general-chemistry laboratory course was designed and implemented at Missouri S&T, which increased student access to the bottleneck course and improved learner engagement while meeting American Chemical Society (ACS) guidelines. The implementation of the Missouri S&T project and its continued evolution at other institutions have a great potential to provide insight on the impact of blended teaching on learner success. This dissertation describes research and design of a blended laboratory course that economically improves capacity while intentionally focusing pedagogy to support learner success, meet industry expectations, and maintain ACS certification. To evaluate success, the project documented and analyzed student performance during the development of the transformation to a blended freshman chemistry laboratory course at Missouri S&T. The findings support the efficacy of the blended teaching model and offer a structure upon which future courses may build.

Elevated Proportions of Deleterious Genetic Variation in Domestic Animals and Plants

PubMed Central

Rubin, Carl-Johan; Carneiro, Miguel; Axelsson, Erik; Andersson, Leif

2018-01-01

Abstract A fraction of genetic variants segregating in any population are deleterious, which negatively impacts individual fitness. The domestication of animals and plants is associated with population bottlenecks and artificial selection, which are predicted to increase the proportion of deleterious variants. However, the extent to which this is a general feature of domestic species is unclear. Here, we examine the effects of domestication on the prevalence of deleterious variation using pooled whole-genome resequencing data from five domestic animal species (dog, pig, rabbit, chicken, and silkworm) and two domestic plant species (rice and soybean) compared with their wild ancestors. We find significantly reduced genetic variation and increased proportion of nonsynonymous amino acid changes in all but one of the domestic species. These differences are observable across a range of allele frequencies, both common and rare. We find proportionally more single nucleotide polymorphisms in highly conserved elements in domestic species and a tendency for domestic species to harbor a higher proportion of changes classified as damaging. Our findings most likely reflect an increased incidence of deleterious variants in domestic species, which is most likely attributable to population bottlenecks that lead to a reduction in the efficacy of selection. An exception to this pattern is displayed by European domestic pigs, which do not show traces of a strong population bottleneck and probably continued to exchange genes with wild boar populations after domestication. The results presented here indicate that an elevated proportion of deleterious variants is a common, but not ubiquitous, feature of domestic species. PMID:29325102

Founding events influence genetic population structure of sockeye salmon (Oncorhynchus nerka) in Lake Clark, Alaska

USGS Publications Warehouse

Ramstad, K.M.; Woody, C.A.; Sage, G.K.; Allendorf, F.W.

2004-01-01

Bottlenecks can have lasting effects on genetic population structure that obscure patterns of contemporary gene flow and drift. Sockeye salmon are vulnerable to bottleneck effects because they are a highly structured species with excellent colonizing abilities and often occupy geologically young habitats. We describe genetic divergence among and genetic variation within spawning populations of sockeye salmon throughout the Lake Clark area of Alaska. Fin tissue was collected from sockeye salmon representing 15 spawning populations of Lake Clark, Six-mile Lake, and Lake Iliamna. Allele frequencies differed significantly at 11 microsatellite loci in 96 of 105 pairwise population comparisons. Pairwise estimates of FST ranged from zero to 0.089. Six-mile Lake and Lake Clark populations have historically been grouped together for management purposes and are geographically proximate. However, Six-mile Lake populations are genetically similar to Lake Iliamna populations and are divergent from Lake Clark populations. The reduced allelic diversity and strong divergence of Lake Clark populations relative to Six-mile Lake and Lake Iliamna populations suggest a bottleneck associated with the colonization of Lake Clark by sockeye salmon. Geographic distance and spawning habitat differences apparently do not contribute to isolation and divergence among populations. However, temporal isolation based on spawning time and founder effects associated with ongoing glacial retreat and colonization of new spawning habitats contribute to the genetic population structure of Lake Clark sock-eye salmon. Nonequilibrium conditions and the strong influence of genetic drift caution against using estimates of divergence to estimate gene flow among populations of Lake Clark sockeye salmon.

Is there any Exciton (bottleneck) in an Excitonic Solar Cell: Revisiting the Prospects of Single-Semiconductor OPV

NASA Astrophysics Data System (ADS)

Alam, Muhammad

2014-03-01

The discovery dye sensitized and bulk heterojunction (BHJ) solar cells in early 1990s introduced a new class of PV technology that rely on (i) distributed photogeneration of excitons, (ii) dissociation of excitons into free carriers by the heterojunction between two organic semiconductors (OSC), and (iii) collection of free carriers through electron and hole transport layers. The success of the approach is undisputed: the highest efficiency OPV cells have all relied on variants of BHJ approach. Yet, three concerns related to the use of a pair of OSCs, namely, low Voc, process sensitivity, and reliability, suggest that the technology may never achieve efficiency-variability-reliability metrics comparable to inorganic solar cells. This encourages a reconsideration of the prospects of Single semiconductor OPV (SS-OPV), a system presumably doomed by the exciton bottleneck. In this talk, we use an inverted SS-OPV to demonstrate how the historical SS-OPV experiments may have been misinterpreted. No one disputes the signature of excitons in polymer under narrowband excitation, but our experiments show that exciton dissociation need not be a bottleneck for OPV under broadband solar illumination. We demonstrate that an alternate collection-limited theory consistently interprets the classical and new experiments, resolves puzzles such as efficiency loss with increasing light intensity, and voltage-dependent reverse photo-current, etc. The theory and experiments suggest a new ``perovskite-like'' strategy to efficiency-variability-reliability of organic solar cells. The work was supported by the Columbia DOE-EFRC (DE-SC0001085) and NSF-NCN (EEC-0228390).

Management of Knowledge Representation Standards Activities

NASA Technical Reports Server (NTRS)

Patil, Ramesh S.

1993-01-01

Ever since the mid-seventies, researchers have recognized that capturing knowledge is the key to building large and powerful AI systems. In the years since, we have also found that representing knowledge is difficult and time consuming. In spite of the tools developed to help with knowledge acquisition, knowledge base construction remains one of the major costs in building an Al system: For almost every system we build, a new knowledge base must be constructed from scratch. As a result, most systems remain small to medium in size. Even if we build several systems within a general area, such as medicine or electronics diagnosis, significant portions of the domain must be represented for every system we create. The cost of this duplication of effort has been high and will become prohibitive as we attempt to build larger and larger systems. To overcome this barrier we must find ways of preserving existing knowledge bases and of sharing, re-using, and building on them. 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.

Impact of historical founder effects and a recent bottleneck on MHC variability in Commander Arctic foxes (Vulpes lagopus)

PubMed Central

Ploshnitsa, Anna I; Goltsman, Mikhail E; Macdonald, David W; Kennedy, Lorna J; Sommer, Simone

2012-01-01

Populations of Arctic foxes (Vulpes lagopus) have been isolated on two of the Commander Islands (Bering and Mednyi) from the circumpolar distributed mainland population since the Pleistocene. In 1970–1980, an epizootic outbreak of mange caused a severe population decline on Mednyi Island. Genes of the major histocompatibility complex (MHC) play a primary role in infectious disease resistance. The main objectives of our study were to compare contemporary variation of MHC class II in mainland and island Arctic foxes, and to document the effects of the isolation and the recent bottleneck on MHC polymorphism by analyzing samples from historical and contemporary Arctic foxes. In 184 individuals, we found 25 unique MHC class II DRB and DQB alleles, and identified evidence of balancing selection maintaining allelic lineages over time at both loci. Twenty different MHC alleles were observed in mainland foxes and eight in Bering Island foxes. The historical Mednyi population contained five alleles and all contemporary individuals were monomorphic at both DRB and DQB. Our data indicate that despite positive and diversifying selection leading to elevated rates of amino acid replacement in functionally important antigen-binding sites, below a certain population size, balancing selection may not be strong enough to maintain genetic diversity in functionally important genes. This may have important fitness consequences and might explain the high pathogen susceptibility in some island populations. This is the first study that compares MHC diversity before and after a bottleneck in a wild canid population using DNA from museum samples. PMID:22408734

The ancient tropical rainforest tree Symphonia globulifera L. f. (Clusiaceae) was not restricted to postulated Pleistocene refugia in Atlantic Equatorial Africa.

PubMed

Budde, K B; González-Martínez, S C; Hardy, O J; Heuertz, M

2013-07-01

Understanding the history of forests and their species' demographic responses to past disturbances is important for predicting impacts of future environmental changes. Tropical rainforests of the Guineo-Congolian region in Central Africa are believed to have survived the Pleistocene glacial periods in a few major refugia, essentially centred on mountainous regions close to the Atlantic Ocean. We tested this hypothesis by investigating the phylogeographic structure of a widespread, ancient rainforest tree species, Symphonia globulifera L. f. (Clusiaceae), using plastid DNA sequences (chloroplast DNA [cpDNA], psbA-trnH intergenic spacer) and nuclear microsatellites (simple sequence repeats, SSRs). SSRs identified four gene pools located in Benin, West Cameroon, South Cameroon and Gabon, and São Tomé. This structure was also apparent at cpDNA. Approximate Bayesian Computation detected recent bottlenecks approximately dated to the last glacial maximum in Benin, West Cameroon and São Tomé, and an older bottleneck in South Cameroon and Gabon, suggesting a genetic effect of Pleistocene cycles of forest contraction. CpDNA haplotype distribution indicated wide-ranging long-term persistence of S. globulifera both inside and outside of postulated forest refugia. Pollen flow was four times greater than that of seed in South Cameroon and Gabon, which probably enabled rapid population recovery after bottlenecks. Furthermore, our study suggested ecotypic differentiation-coastal or swamp vs terra firme-in S. globulifera. Comparison with other tree phylogeographic studies in Central Africa highlighted the relevance of species-specific responses to environmental change in forest trees.

The ancient tropical rainforest tree Symphonia globulifera L. f. (Clusiaceae) was not restricted to postulated Pleistocene refugia in Atlantic Equatorial Africa

PubMed Central

Budde, K B; González-Martínez, S C; Hardy, O J; Heuertz, M

2013-01-01

Understanding the history of forests and their species' demographic responses to past disturbances is important for predicting impacts of future environmental changes. Tropical rainforests of the Guineo-Congolian region in Central Africa are believed to have survived the Pleistocene glacial periods in a few major refugia, essentially centred on mountainous regions close to the Atlantic Ocean. We tested this hypothesis by investigating the phylogeographic structure of a widespread, ancient rainforest tree species, Symphonia globulifera L. f. (Clusiaceae), using plastid DNA sequences (chloroplast DNA [cpDNA], psbA-trnH intergenic spacer) and nuclear microsatellites (simple sequence repeats, SSRs). SSRs identified four gene pools located in Benin, West Cameroon, South Cameroon and Gabon, and São Tomé. This structure was also apparent at cpDNA. Approximate Bayesian Computation detected recent bottlenecks approximately dated to the last glacial maximum in Benin, West Cameroon and São Tomé, and an older bottleneck in South Cameroon and Gabon, suggesting a genetic effect of Pleistocene cycles of forest contraction. CpDNA haplotype distribution indicated wide-ranging long-term persistence of S. globulifera both inside and outside of postulated forest refugia. Pollen flow was four times greater than that of seed in South Cameroon and Gabon, which probably enabled rapid population recovery after bottlenecks. Furthermore, our study suggested ecotypic differentiation—coastal or swamp vs terra firme—in S. globulifera. Comparison with other tree phylogeographic studies in Central Africa highlighted the relevance of species-specific responses to environmental change in forest trees. PMID:23572126

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

PubMed

Moghadam, Saeed Montazeri; Seyyedsalehi, Seyyed Ali

2018-05-31

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

Turtle soup, Prohibition, and the population genetic structure of Diamondback Terrapins (Malaclemys terrapin).

PubMed

Converse, Paul E; Kuchta, Shawn R; Hauswaldt, J Susanne; Roosenburg, Willem M

2017-01-01

Diamondback terrapins (Malaclemys terrapin) were a popular food item in early twentieth century America, and were consumed in soup with sherry. Intense market demand for terrapin meat resulted in population declines, notably along the Atlantic seaboard. Efforts to supply terrapins to markets resulted in translocation events, as individuals were moved about to stock terrapin farms. However, in 1920 the market for turtle soup buckled with the enactment of the eighteenth amendment to the United States' Constitution-which initiated the prohibition of alcoholic drinks-and many terrapin fisheries dumped their stocks into local waters. We used microsatellite data to show that patterns of genetic diversity along the terrapin's coastal range are consistent with historical accounts of translocation and cultivation activities. We identified possible instances of human-mediated dispersal by estimating gene flow over historical and contemporary timescales, Bayesian model testing, and bottleneck tests. We recovered six genotypic clusters along the Gulf and Atlantic coasts with varying degrees of admixture, including increased contemporary gene flow from Texas to South Carolina, from North Carolina to Maryland, and from North Carolina to New York. In addition, Bayesian models incorporating translocation events outperformed stepping-stone models. Finally, we were unable to detect population bottlenecks, possibly due to translocation reintroducing genetic diversity into bottlenecked populations. Our data suggest that current patterns of genetic diversity in the terrapin were altered by the demand for turtle soup followed by the enactment of alcohol prohibition. In addition, our study shows that population genetic tools can elucidate metapopulation dynamics in taxa with complex genetic histories impacted by anthropogenic activities.

Instruction-Level Characterization of Scientific Computing Applications Using Hardware Performance Counters

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

Luo, Y.; Cameron, K.W.

1998-11-24

Workload characterization has been proven an essential tool to architecture design and performance evaluation in both scientific and commercial computing areas. Traditional workload characterization techniques include FLOPS rate, cache miss ratios, CPI (cycles per instruction or IPC, instructions per cycle) etc. With the complexity of sophisticated modern superscalar microprocessors, these traditional characterization techniques are not powerful enough to pinpoint the performance bottleneck of an application on a specific microprocessor. They are also incapable of immediately demonstrating the potential performance benefit of any architectural or functional improvement in a new processor design. To solve these problems, many people rely on simulators,more » which have substantial constraints especially on large-scale scientific computing applications. This paper presents a new technique of characterizing applications at the instruction level using hardware performance counters. It has the advantage of collecting instruction-level characteristics in a few runs virtually without overhead or slowdown. A variety of instruction counts can be utilized to calculate some average abstract workload parameters corresponding to microprocessor pipelines or functional units. Based on the microprocessor architectural constraints and these calculated abstract parameters, the architectural performance bottleneck for a specific application can be estimated. In particular, the analysis results can provide some insight to the problem that only a small percentage of processor peak performance can be achieved even for many very cache-friendly codes. Meanwhile, the bottleneck estimation can provide suggestions about viable architectural/functional improvement for certain workloads. Eventually, these abstract parameters can lead to the creation of an analytical microprocessor pipeline model and memory hierarchy model.« less

EFFECTIVENESS OF SELECTION IN REDUCING THE GENETIC LOAD IN POPULATIONS OF PEROMYSCUS POLIONOTUS DURING GENERATIONS OF INBREEDING.

PubMed

Lacy, Robert C; Ballou, Jonathan D

1998-06-01

It has been hypothesized that natural selection reduces the "genetic load" of deleterious alleles from populations that inbreed during bottlenecks, thereby ameliorating impacts of future inbreeding. We tested the efficiency with which natural selection purges deleterious alleles from three subspecies of Peromyscus polionotus during 10 generations of laboratory inbreeding by monitoring pairing success, litter size, viability, and growth in 3604 litters produced from 3058 pairs. In P. p. subgriseus, there was no reduction across generations in inbreeding depression in any of the fitness components. Strongly deleterious recessive alleles may have been removed previously during episodes of local inbreeding in the wild, and the residual genetic load in this population was not further reduced by selection in the lab. In P. p. rhoadsi, four of seven fitness components did show a reduction of the genetic load with continued inbreeding. The average reduction in the genetic load was as expected if inbreeding depression in this population is caused by highly deleterious recessive alleles that are efficiently removed by selection. For P. p. leucocephalus a population that experiences periodic bottlenecks in the wild, the effect of further inbreeding in the laboratory was to exacerbate rather than reduce the genetic load. Recessive deleterious alleles may have been removed from this population during repeated bottlenecks in the wild; the population may be close to a threshold level of heterozygosity below which fitness declines rapidly. Thus, the effects of selection on inbreeding depression varied substantially among populations, perhaps due to different histories of inbreeding and selection. © 1998 The Society for the Study of Evolution.

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

USGS Publications Warehouse

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

2015-01-01

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

Can health systems be enhanced for optimal health services through disease-specific programs? Results of field studies in Viet Nam and Cambodia.

PubMed

Egami, Y; Fujita, N; Akashi, H; Matsumoto, Y; Ohara, H; Takeuchi, M

2012-02-01

Developing better health systems is the key to delivering optimal health services, although more evidence of effective strategies to do so is needed. Field surveys were conducted in Viet Nam and Cambodia to identify best practices in addressing health system bottlenecks to scale up disease control programs. The two countries were compared over time using a framework for analysis developed by the authors. In Viet Nam, a health system was in place for decades at the central to municipal levels, although it was fragile until the 1990s, when the government started taking measures. In Cambodia, the previous health system had been destroyed during previous internal conflict. In the post-conflict period, the health system was rebuilt with support for programs followed by centralization of health services. In different settings, different measures were taken to deal with similar bottlenecks. In Cambodia, vertical programs were dominant, so the government sought to centralize drug management to deal with shortages of essential drugs, while Viet Nam sought to mobilize resources to ensure drug distribution at all levels. This study shows there is no single successful approach to health systems, and a systemic approach needs to be taken because elimination of one bottleneck may reveal another. Efforts to enhance disease-specific programs may not always contribute to overall enhancement of the health system, and the best possible approach may not be the same in different countries. Further study is needed to explore common issues and principles for effective strategies to enhance health systems in different contexts.

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

PubMed

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

2017-12-01

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

Truck Terminal and Warehouse Survey Results

DOT National Transportation Integrated Search

1996-03-01

The survey of truck terminals and warehouses resulted in locating the highway bottlenecks for truck movements which are more localized in nature than the previous air, marine, and rail surveys performed by the NYMTC Central Staff. However, all of the...

Priority Intelligence Requirements: The Operational Vacuum

DTIC Science & Technology

1990-05-16

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

Solar heating system for recreation building at Scattergood School

NASA Technical Reports Server (NTRS)

Heins, C. F.

1978-01-01

The solar heating facility and the project involved in its construction are described. As such, it has both detailed drawings of the completed system and a section that discusses the bottlenecks that were encountered along the way.

Breeding nursery tissue collection for possible genomic analysis

USDA-ARS?s Scientific Manuscript database

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

Mother-to-Child HIV Transmission Bottleneck Selects for Consensus Virus with Lower Gag-Protease-Driven Replication Capacity

PubMed Central

Naidoo, Vanessa L.; Mann, Jaclyn K.; Noble, Christie; Adland, Emily; Carlson, Jonathan M.; Thomas, Jake; Brumme, Chanson J.; Thobakgale-Tshabalala, Christina F.; Brumme, Zabrina L.; Goulder, Philip J. R.

2017-01-01

ABSTRACT In the large majority of cases, HIV infection is established by a single variant, and understanding the characteristics of successfully transmitted variants is relevant to prevention strategies. Few studies have investigated the viral determinants of mother-to-child transmission. To determine the impact of Gag-protease-driven viral replication capacity on mother-to-child transmission, the replication capacities of 148 recombinant viruses encoding plasma-derived Gag-protease from 53 nontransmitter mothers, 48 transmitter mothers, and 47 infected infants were assayed in an HIV-1-inducible green fluorescent protein reporter cell line. All study participants were infected with HIV-1 subtype C. There was no significant difference in replication capacities between the nontransmitter (n = 53) and transmitter (n = 44) mothers (P = 0.48). Infant-derived Gag-protease NL4-3 recombinant viruses (n = 41) were found to have a significantly lower Gag-protease-driven replication capacity than that of viruses derived from the mothers (P < 0.0001 by a paired t test). High percent similarities to consensus subtype C Gag, p17, p24, and protease sequences were also found in the infants (n = 28) in comparison to their mothers (P = 0.07, P = 0.002, P = 0.03, and P = 0.02, respectively, as determined by a paired t test). These data suggest that of the viral quasispecies found in mothers, the HIV mother-to-child transmission bottleneck favors the transmission of consensus-like viruses with lower viral replication capacities. IMPORTANCE Understanding the characteristics of successfully transmitted HIV variants has important implications for preventative interventions. Little is known about the viral determinants of HIV mother-to-child transmission (MTCT). We addressed the role of viral replication capacity driven by Gag, a major structural protein that is a significant determinant of overall viral replicative ability and an important target of the host immune response, in the MTCT bottleneck. This study advances our understanding of the genetic bottleneck in MTCT by revealing that viruses transmitted to infants have a lower replicative ability as well as a higher similarity to the population consensus (in this case HIV subtype C) than those of their mothers. Furthermore, the observation that “consensus-like” virus sequences correspond to lower in vitro replication abilities yet appear to be preferentially transmitted suggests that viral characteristics favoring transmission are decoupled from those that enhance replicative capacity. PMID:28637761

EPA'S NEW EMISSIONS MODELING FRAMEWORK

EPA Science Inventory

EPA's Office of Air Quality Planning and Standards is building a new Emissions Modeling Framework that will solve many of the long-standing difficulties of emissions modeling. The goals of the Framework are to (1) prevent bottlenecks and errors caused by emissions modeling activi...

Evaluating Environmental Impact of Traffic Congestion in Real Time Based on Sparse Mobile Crowd-sourced Data

DOT National Transportation Integrated Search

2018-02-02

Traffic congestion at arterial intersections and freeway bottlenecks degrades the air quality and threatens the public health. Conventionally, air pollutants are monitored by sparsely-distributed Quality Assurance Air Monitoring Sites. Sparse mobile ...

Genome-environment associations in sorghum landraces predict adaptive traits

USDA-ARS?s Scientific Manuscript database

Improving environmental adaptation in crops is essential for food security under global change, but phenotyping adaptive traits remains a major bottleneck. If associations between single-nucleotide polymorphism (SNP) alleles and environment of origin in crop landraces reflect adaptation, then these ...

A simplified close range photogrammetry method for soil erosion assessment

USDA-ARS?s Scientific Manuscript database

With the increased affordability of consumer grade cameras and the development of powerful image processing software, digital photogrammetry offers a competitive advantage as a tool for soil erosion estimation compared to other technologies. One bottleneck of digital photogrammetry is its dependency...

Applying new technologies to transform blueberry harvesting

USDA-ARS?s Scientific Manuscript database

The growth of the blueberry industry in the past three decades has been remarkable. However, labor shortage for hand harvesting, increasingly high labor costs, and low harvest efficiencies are becoming bottlenecks for sustainable development of the fresh market blueberry production. In this study ...

Upgrading a CD-ROM Network for Multimedia Applications.

ERIC Educational Resources Information Center

Sylvia, Margaret

1995-01-01

Addresses issues to consider when upgrading library CD-ROM networks for multimedia applications. Topics includes security issues; workstation requirements such as soundboards and monitors; local area network configurations that avoid bottlenecks: Asynchronous Transfer Mode, Ethernet, and Integrated Services Digital Network; server performance…

Constraint-Based Scheduling System

NASA Technical Reports Server (NTRS)

Zweben, Monte; Eskey, Megan; Stock, Todd; Taylor, Will; Kanefsky, Bob; Drascher, Ellen; Deale, Michael; Daun, Brian; Davis, Gene

1995-01-01

Report describes continuing development of software for constraint-based scheduling system implemented eventually on massively parallel computer. Based on machine learning as means of improving scheduling. Designed to learn when to change search strategy by analyzing search progress and learning general conditions under which resource bottleneck occurs.

AN INTELLIGENT REPRODUCTIVE AND DEVELOPMENTAL TESTING PARADIGM FOR THE 21ST CENTURY

EPA Science Inventory

Addressing the chemical evaluation bottleneck that currently exists can only be achieved through progressive changes to the current testing paradigm. The primary resources for addressing these issues lie in computational toxicology, a field enriched by recent advances in computer...

Policing the Information Highway.

ERIC Educational Resources Information Center

McClure, Ben

1996-01-01

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

X-ray scattering data and structural genomics

NASA Astrophysics Data System (ADS)

Doniach, Sebastian

2003-03-01

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

Augmenting Transport versus Increasing Cold Storage to Improve Vaccine Supply Chains

PubMed Central

Haidari, Leila A.; Connor, Diana L.; Wateska, Angela R.; Brown, Shawn T.; Mueller, Leslie E.; Norman, Bryan A.; Schmitz, Michelle M.; Paul, Proma; Rajgopal, Jayant; Welling, Joel S.; Leonard, Jim; Chen, Sheng-I; Lee, Bruce Y.

2013-01-01

Background When addressing the urgent task of improving vaccine supply chains, especially to accommodate the introduction of new vaccines, there is often a heavy emphasis on stationary storage. Currently, donations to vaccine supply chains occur largely in the form of storage equipment. Methods This study utilized a HERMES-generated detailed, dynamic, discrete event simulation model of the Niger vaccine supply chain to compare the impacts on vaccine availability of adding stationary cold storage versus transport capacity at different levels and to determine whether adding stationary storage capacity alone would be enough to relieve potential bottlenecks when pneumococcal and rotavirus vaccines are introduced by 2015. Results Relieving regional level storage bottlenecks increased vaccine availability (by 4%) more than relieving storage bottlenecks at the district (1% increase), central (no change), and clinic (no change) levels alone. Increasing transport frequency (or capacity) yielded far greater gains (e.g., 15% increase in vaccine availability when doubling transport frequency to the district level and 18% when tripling). In fact, relieving all stationary storage constraints could only increase vaccine availability by 11%, whereas doubling the transport frequency throughout the system led to a 26% increase and tripling the frequency led to a 30% increase. Increasing transport frequency also reduced the amount of stationary storage space needed in the supply chain. The supply chain required an additional 61,269L of storage to relieve constraints with the current transport frequency, 55,255L with transport frequency doubled, and 51,791L with transport frequency tripled. Conclusions When evaluating vaccine supply chains, it is important to understand the interplay between stationary storage and transport. The HERMES-generated dynamic simulation model showed how augmenting transport can result in greater gains than only augmenting stationary storage and can reduce stationary storage needs. PMID:23717590

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.

Augmenting transport versus increasing cold storage to improve vaccine supply chains.

PubMed

Haidari, Leila A; Connor, Diana L; Wateska, Angela R; Brown, Shawn T; Mueller, Leslie E; Norman, Bryan A; Schmitz, Michelle M; Paul, Proma; Rajgopal, Jayant; Welling, Joel S; Leonard, Jim; Chen, Sheng-I; Lee, Bruce Y

2013-01-01

When addressing the urgent task of improving vaccine supply chains, especially to accommodate the introduction of new vaccines, there is often a heavy emphasis on stationary storage. Currently, donations to vaccine supply chains occur largely in the form of storage equipment. This study utilized a HERMES-generated detailed, dynamic, discrete event simulation model of the Niger vaccine supply chain to compare the impacts on vaccine availability of adding stationary cold storage versus transport capacity at different levels and to determine whether adding stationary storage capacity alone would be enough to relieve potential bottlenecks when pneumococcal and rotavirus vaccines are introduced by 2015. Relieving regional level storage bottlenecks increased vaccine availability (by 4%) more than relieving storage bottlenecks at the district (1% increase), central (no change), and clinic (no change) levels alone. Increasing transport frequency (or capacity) yielded far greater gains (e.g., 15% increase in vaccine availability when doubling transport frequency to the district level and 18% when tripling). In fact, relieving all stationary storage constraints could only increase vaccine availability by 11%, whereas doubling the transport frequency throughout the system led to a 26% increase and tripling the frequency led to a 30% increase. Increasing transport frequency also reduced the amount of stationary storage space needed in the supply chain. The supply chain required an additional 61,269L of storage to relieve constraints with the current transport frequency, 55,255L with transport frequency doubled, and 51,791L with transport frequency tripled. When evaluating vaccine supply chains, it is important to understand the interplay between stationary storage and transport. The HERMES-generated dynamic simulation model showed how augmenting transport can result in greater gains than only augmenting stationary storage and can reduce stationary storage needs.

Reactive transport under stress: Permeability evolution in deformable porous media

NASA Astrophysics Data System (ADS)

Roded, R.; Paredes, X.; Holtzman, R.

2018-07-01

We study reactive transport in a stressed porous media, where dissolution of the solid matrix causes two simultaneous, competing effects: pore enlargement due to chemical deformation, and pore compaction due to mechanical weakening. We use a novel, mechanistic pore-scale model to simulate flooding of a sample under fixed confining stress. Our simulations show that increasing the stress inhibits the permeability enhancement, increasing the injected volume required to reach a certain permeability, in agreement with recent experiments. We explain this behavior by stress concentration downstream, in the less dissolved (hence stiffer) outlet region. As this region is also less conductive, even its small compaction has a strong bottleneck effect that curbs the permeability. Our results also elucidate that the impact of stress depends on the dissolution regime. Under wormholing conditions (slow injection, i.e. high Damkohler number, Da), the development of a sharp dissolution front and high porosity contrast accentuates the bottleneck effect. This reduces transport heterogeneity, promoting wormhole competition. Once the outlet starts eroding, the extreme focusing of transport and hence dissolution-characteristic of wormholing-becomes dominant, diminishing the bottleneck effect and hence the impact of stress at breakthrough. In contrast, at high flow rates (low Da), incomplete reaction upstream allows some of the reactant to traverse the sample, causing a more uniform dissolution. The continuous dissolution and its partial counteraction by compaction at the outlet provides a steady, gradual increase in the effect of stress. Consequently, the impact of stress is more pronounced at high Da during early stages (low permeability), and at low Da close breakthrough. Our work promotes understanding of the interplay between dissolution and compaction and its effect on the hydromechanical property evolution, with important implications for processes ranging from diagenesis and weathering of rocks, to well stimulation and carbon sequestration.

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.

Allelic differences within and among sister spores of the arbuscular mycorrhizal fungus Glomus etunicatum suggest segregation at sporulation.

PubMed

Boon, Eva; Zimmerman, Erin; St-Arnaud, Marc; Hijri, Mohamed

2013-01-01

Arbuscular mycorrhizal fungi (AMF) are root-inhabiting fungi that form mutualistic symbioses with their host plants. AMF are made up of coenocytic networks of hyphae through which nuclei and organelles can freely migrate. In this study, we investigated the possibility of a genetic bottleneck and segregation of allelic variation at sporulation for a low-copy Polymerase1-like gene, PLS. Specifically, our objectives were (1) to estimate what allelic diversity is passed on to a single spore (2) to determine whether this diversity is less than the total amount of variation found in all spores (3) to investigate whether there is any differential segregation of allelic variation. We inoculated three tomato plants with a single spore of Glomus etunicatum each and after six months sampled between two and three daughter spores per tomato plant. Pyrosequencing PLS amplicons in eight spores revealed high levels of allelic diversity; between 43 and 152 alleles per spore. We corroborated the spore pyrosequencing results with Sanger- and pyrosequenced allele distributions from the original parent isolate. Both sequencing methods retrieved the most abundant alleles from the offspring spore allele distributions. Our results indicate that individual spores contain only a subset of the total allelic variation from the pooled spores and parent isolate. Patterns of allele diversity between spores suggest the possibility for segregation of PLS alleles among spores. We conclude that a genetic bottleneck could potentially occur during sporulation in AMF, with resulting differences in genetic variation among sister spores. We suggest that the effects of this bottleneck may be countered by anastomosis (hyphal fusion) between related hyphae.

Molecular Population Genetic Structure in the Piping Plover

USGS Publications Warehouse

Miller, Mark P.; Haig, Susan M.; Gratto-Trevor, Cheri L.; Mullins, Thomas D.

2009-01-01

The Piping Plover (Charadrius melodus) is a migratory shorebird currently listed as Endangered in Canada and the U.S. Great Lakes, and threatened throughout the remainder of its U.S. breeding and winter range. In this study, we undertook the first comprehensive molecular genetic-based investigation of Piping Plovers. Our primary goals were to (1) address higher level subspecific taxonomic issues, (2) characterize population genetic structure, and (3) make inferences regarding past bottlenecks or population expansions that have occurred within this species. Our analyses included samples of individuals from 23 U.S. States and Canadian Provinces, and were based on mitochondrial DNA sequences (580 bp, n = 245 individuals) and eight nuclear microsatellite loci (n = 229 individuals). Our findings illustrate strong support for separate Atlantic and Interior Piping Plover subspecies (C. m. melodus and C. m. circumcinctus, respectively). Birds from the Great Lakes region were allied with the Interior subspecies group and should be taxonomically referred to as C. m. circumcinctus. Population genetic analyses suggested that genetic structure was stronger among Atlantic birds relative to the Interior group. This pattern indicates that natal and breeding site fidelity may be reduced among Interior birds. Furthermore, analyses suggested that Interior birds have previously experienced genetic bottlenecks, whereas no evidence for such patterns existed among the Atlantic subspecies. Likewise, genetic analyses indicated that the Great Lakes region has experienced a population expansion. This finding may be interpreted as population growth following a previous bottleneck event. No genetic evidence for population expansions was found for Atlantic, Prairie Canada, or U.S. Northern Great Plains individuals. We interpret our population history insights in light of 25 years of Piping Plover census data. Overall, differences observed between Interior and Atlantic birds may reflect differences in spatiotemporal stability of Piping Plover nesting habitat between regions.

Ancient and Contemporary DNA Reveal a Pre-Human Decline but No Population Bottleneck Associated with Recent Human Persecution in the Kea (Nestor notabilis)

PubMed Central

Dussex, Nicolas; Rawlence, Nicolas J.; Robertson, Bruce C.

2015-01-01

The impact of population bottlenecks is an important factor to consider when assessing species survival. Population declines can considerably limit the evolutionary potential of species and make them more susceptible to stochastic events. New Zealand has a well documented history of decline of endemic avifauna related to human colonization. Here, we investigate the genetic effects of a recent population decline in the endangered kea (Nestor notabilis). Kea have undergone a long-lasting persecution between the late 1800s to 1970s where an estimated 150,000 kea were culled under a governmental bounty scheme. Kea now number 1,000–5,000 individuals in the wild and it is likely that the recent population decline may have reduced the genetic diversity of the species. Comparison of contemporary (n = 410), historical (n = 15) and fossil samples (n = 4) showed a loss of mitochondrial diversity since the end of the last glaciation (Otiran Glacial) but no loss of overall genetic diversity associated with the cull. Microsatellite data indicated a recent bottleneck for only one population and a range-wide decline in Ne dating back some 300 – 6,000 years ago, a period predating European arrival in NZ. These results suggest that despite a recent human persecution, kea might have experienced a large population decline before stabilizing in numbers prior to human settlement of New Zealand in response to Holocene changes in habitat distribution. Our study therefore highlights the need to understand the respective effects of climate change and human activities on endangered species dynamics when proposing conservation guidelines. PMID:25719752

Protein-protein interaction analysis of Alzheimer`s disease and NAFLD based on systems biology methods unhide common ancestor pathways.

PubMed

Karbalaei, Reza; Allahyari, Marzieh; Rezaei-Tavirani, Mostafa; Asadzadeh-Aghdaei, Hamid; Zali, Mohammad Reza

2018-01-01

Analysis reconstruction networks from two diseases, NAFLD and Alzheimer`s diseases and their relationship based on systems biology methods. NAFLD and Alzheimer`s diseases are two complex diseases, with progressive prevalence and high cost for countries. There are some reports on relation and same spreading pathways of these two diseases. In addition, they have some similar risk factors, exclusively lifestyle such as feeding, exercises and so on. Therefore, systems biology approach can help to discover their relationship. DisGeNET and STRING databases were sources of disease genes and constructing networks. Three plugins of Cytoscape software, including ClusterONE, ClueGO and CluePedia, were used to analyze and cluster networks and enrichment of pathways. An R package used to define best centrality method. Finally, based on degree and Betweenness, hubs and bottleneck nodes were defined. Common genes between NAFLD and Alzheimer`s disease were 190 genes that used construct a network with STRING database. The resulting network contained 182 nodes and 2591 edges and comprises from four clusters. Enrichment of these clusters separately lead to carbohydrate metabolism, long chain fatty acid and regulation of JAK-STAT and IL-17 signaling pathways, respectively. Also seven genes selected as hub-bottleneck include: IL6, AKT1, TP53, TNF, JUN, VEGFA and PPARG. Enrichment of these proteins and their first neighbors in network by OMIM database lead to diabetes and obesity as ancestors of NAFLD and AD. Systems biology methods, specifically PPI networks, can be useful for analyzing complicated related diseases. Finding Hub and bottleneck proteins should be the goal of drug designing and introducing disease markers.

Juvenile bottlenecks and salinity shape grey mullet assemblages in Mediterranean estuaries

NASA Astrophysics Data System (ADS)

Cardona, Luis; Hereu, Bernat; Torras, Xavier

2008-05-01

Previous research has suggested that competitive bottlenecks may exist for the Mediterranean grey mullets (Osteichthyes, Mugilidae) at the fry stage with the exotic Cyprinus carpio (Osteichthyes, Cyprinidae) playing a central role. As a consequence, the structure of grey mullet assemblages at later stages is thought to reflect previous competition as well as differences in osmoregulatory skills. This paper tests that hypothesis by examining four predictions about the relative abundance of five grey mullet species in 42 Western Mediterranean estuary sites from three areas (Aiguamolls de l'Empordà, Ebro Delta and Minorca) differing in the salinity level and occurrence of C. carpio. Field data confirmed the predictions as: (1) Liza aurata and Mugil cephalus were scarce everywhere and never dominated the assemblage; (2) Liza saliens dominated the assemblage where the salinity level was higher than 13; (3) Liza ramado always dominated the assemblage where the salinity level was lower than 13 and C. carpio was present; and (4) Chelon labrosus dominated the assemblage only where the salinity level was lower than 13 and C. carpio was absent. The catch per unit effort of C. labrosus of any size was smaller in the presence of C. carpio than where it had not been introduced, which is in agreement with the juvenile competitive bottleneck hypothesis. Discriminant analysis confirmed that the assemblage structure was linked to the salinity level and the occurrence of C. carpio for both early juveniles and late juveniles as well as adults. The data reported here reveal that the structure of grey mullet assemblages inhabiting Mediterranean estuaries is determined by salinity and competitive interactions at the fry stage.

Analysis of viral (zucchini yellow mosaic virus) genetic diversity during systemic movement through a Cucurbita pepo vine

PubMed Central

Holmes, E.C.; Stephenson, A.G.

2014-01-01

Determining the extent and structure of intra-host genetic diversity and the magnitude and impact of population bottlenecks is central to understanding the mechanisms of viral evolution. To determine the nature of viral evolution following systemic movement through a plant, we performed deep sequencing of 23 leaves that grew sequentially along a single Cucurbita pepo vine that was infected with zucchini yellow mosaic virus (ZYMV), and on a leaf that grew in on a side branch. Strikingly, of 112 genetic (i.e. sub-consensus) variants observed in the data set as a whole, only 22 were found in multiple leaves. Similarly, only three of the 13 variants present in the inoculating population were found in the subsequent leaves on the vine. Hence, it appears that systemic movement is characterized by sequential population bottlenecks, although not sufficient to reduce the population to a single virion as multiple variants were consistently transmitted between leaves. In addition, the number of variants within a leaf increases as a function of distance from the inoculated (source) leaf, suggesting that the circulating sap may serve as a continual source of virus. Notably, multiple mutational variants were observed in the cylindrical Inclusion (CI) protein (known to be involved in both cell-to-cell and systemic movement of the virus) that were present in multiple (19/24) leaf samples. These mutations resulted in a conformational change, suggesting that they might confer a selective advantage in systemic movement within the vine. Overall, these data reveal that bottlenecks occur during systemic movement, that variants circulate in the phloem sap throughout the infection process, and that important conformational changes in CI protein may arise during individual infections. PMID:25107623

Who has the D? How clear decision roles enhance organizational performance.

PubMed

Rogers, Paul; Blenko, Marcia

2006-01-01

Decisions are the coin of the realm in business. But even in highly respected companies, decisions can get stuck inside the organization like loose change. As a result, the entire decision-making process can stall, usually at one of four bottlenecks: global versus local, center versus business unit, function versus function, and inside versus outside partners. Decision-making bottlenecks can occur whenever there is ambiguity or tension over who gets to decide what. For example, do marketers or product developers get to decide the features of a new product? Should a major capital investment depend on the approval of the business unit that will own it, or should headquarters make the final call? Which decisions can be delegated to an outsourcing partner, and which must be made internally? Bain consultants Paul Rogers and Marcia Blenko use an approach called RAPID (recommend, agree, perform, input, and decide) to help companies unclog their decision-making bottlenecks by explicitly defining roles and responsibilities. For example, British American Tobacco struck a new balance between global and local decision making to take advantage of the company's scale while maintaining its agility in local markets. At Wyeth Pharmaceuticals, a growth opportunity revealed the need to push more decisions down to the business units. And at the UK department-store chain John Lewis, buyers and sales staff clarified their decision roles in order to implement a new strategy for selling its salt and pepper mills. When revamping its decision-making process, a company must take some practical steps: Align decision roles with the most important sources of value, make sure that decisions are made by the right people at the right levels of the organization, and let the people who will live with the new process help design it.

Narrow Bottlenecks Affect Pea Seedborne Mosaic Virus Populations during Vertical Seed Transmission but not during Leaf Colonization

PubMed Central

Johansen, Elisabeth Ida; Simon, Vincent; Jacquemond, Mireille; Senoussi, Rachid

2014-01-01

The effective size of populations (Ne) determines whether selection or genetic drift is the predominant force shaping their genetic structure and evolution. Populations having high Ne adapt faster, as selection acts more intensely, than populations having low Ne, where random effects of genetic drift dominate. Estimating Ne for various steps of plant virus life cycle has been the focus of several studies in the last decade, but no estimates are available for the vertical transmission of plant viruses, although virus seed transmission is economically significant in at least 18% of plant viruses in at least one plant species. Here we study the co-dynamics of two variants of Pea seedborne mosaic virus (PSbMV) colonizing leaves of pea plants (Pisum sativum L.) during the whole flowering period, and their subsequent transmission to plant progeny through seeds. Whereas classical estimators of Ne could be used for leaf infection at the systemic level, as virus variants were equally competitive, dedicated stochastic models were needed to estimate Ne during vertical transmission. Very little genetic drift was observed during the infection of apical leaves, with Ne values ranging from 59 to 216. In contrast, a very drastic genetic drift was observed during vertical transmission, with an average number of infectious virus particles contributing to the infection of a seedling from an infected mother plant close to one. A simple model of vertical transmission, assuming a cumulative action of virus infectious particles and a virus density threshold required for vertical transmission to occur fitted the experimental data very satisfactorily. This study reveals that vertically-transmitted viruses endure bottlenecks as narrow as those imposed by horizontal transmission. These bottlenecks are likely to slow down virus adaptation and could decrease virus fitness and virulence. PMID:24415934

The impact of selection, gene flow and demographic history on heterogeneous genomic divergence: three-spine sticklebacks in divergent environments.

PubMed

Ferchaud, Anne-Laure; Hansen, Michael M

2016-01-01

Heterogeneous genomic divergence between populations may reflect selection, but should also be seen in conjunction with gene flow and drift, particularly population bottlenecks. Marine and freshwater three-spine stickleback (Gasterosteus aculeatus) populations often exhibit different lateral armour plate morphs. Moreover, strikingly parallel genomic footprints across different marine-freshwater population pairs are interpreted as parallel evolution and gene reuse. Nevertheless, in some geographic regions like the North Sea and Baltic Sea, different patterns are observed. Freshwater populations in coastal regions are often dominated by marine morphs, suggesting that gene flow overwhelms selection, and genomic parallelism may also be less pronounced. We used RAD sequencing for analysing 28 888 SNPs in two marine and seven freshwater populations in Denmark, Europe. Freshwater populations represented a variety of environments: river populations accessible to gene flow from marine sticklebacks and large and small isolated lakes with and without fish predators. Sticklebacks in an accessible river environment showed minimal morphological and genomewide divergence from marine populations, supporting the hypothesis of gene flow overriding selection. Allele frequency spectra suggested bottlenecks in all freshwater populations, and particularly two small lake populations. However, genomic footprints ascribed to selection could nevertheless be identified. No genomic regions were consistent freshwater-marine outliers, and parallelism was much lower than in other comparable studies. Two genomic regions previously described to be under divergent selection in freshwater and marine populations were outliers between different freshwater populations. We ascribe these patterns to stronger environmental heterogeneity among freshwater populations in our study as compared to most other studies, although the demographic history involving bottlenecks should also be considered in the interpretation of results. © 2015 John Wiley & Sons Ltd.

Diversity at the Locus Associated with Transcription of a Variable Surface Antigen of Pneumocystis carinii as an Index of Population Structure and Dynamics in Infected Rats

PubMed Central

Keely, Scott P.; Cushion, Melanie T.; Stringer, James R.

2003-01-01

Pneumocystis carinii expresses a surface glycoprotein called MSG. Different isoforms of MSG are encoded by a gene family spread over at least 15 telomeric sites. Only one locus, called UCS, supports the production of MSG mRNA. Previous studies showed that P. carinii populations from individual rats exhibited high degrees of diversity with respect to the MSG genes attached to the UCS locus. This diversity could have been generated primarily in the rats studied. Alternatively, the rats may have been infected by P. carinii organisms that were already different at the UCS locus. To investigate this issue, we examined the UCS locus in P. carinii from rats that had been exposed to few of the microbes at a specified time, which produced a bottleneck in the microbial population. Some of the rats with bottlenecks produced P. carinii populations in which a single MSG sequence resided at the UCS locus in 80 to 90% of the organisms, showing that P. carinii can proliferate within a rat without generating the very high levels of UCS diversity previously seen. From the degree of diversity observed in the bottlenecked populations, the maximum rate of switching appeared to be 0.01 event per generation. These data also suggest that the infectious dose is as low as one organism, that rats that share a cage readily infect each other, and that the doubling time of P. carinii in vivo is ∼3 days. In addition, we found that inoculation with 107 P. carinii organisms from a population highly heterogeneous at the UCS locus reproduced this heterogeneity. By contrast, shifts in population structure occurred in rats given 104 P. carinii organisms, suggesting that a small fraction of these proliferated. PMID:12496148

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

Allelic Differences within and among Sister Spores of the Arbuscular Mycorrhizal Fungus Glomus etunicatum Suggest Segregation at Sporulation

PubMed Central

St-Arnaud, Marc; Hijri, Mohamed

2013-01-01

Arbuscular mycorrhizal fungi (AMF) are root-inhabiting fungi that form mutualistic symbioses with their host plants. AMF are made up of coenocytic networks of hyphae through which nuclei and organelles can freely migrate. In this study, we investigated the possibility of a genetic bottleneck and segregation of allelic variation at sporulation for a low-copy Polymerase1-like gene, PLS. Specifically, our objectives were (1) to estimate what allelic diversity is passed on to a single spore (2) to determine whether this diversity is less than the total amount of variation found in all spores (3) to investigate whether there is any differential segregation of allelic variation. We inoculated three tomato plants with a single spore of Glomus etunicatum each and after six months sampled between two and three daughter spores per tomato plant. Pyrosequencing PLS amplicons in eight spores revealed high levels of allelic diversity; between 43 and 152 alleles per spore. We corroborated the spore pyrosequencing results with Sanger- and pyrosequenced allele distributions from the original parent isolate. Both sequencing methods retrieved the most abundant alleles from the offspring spore allele distributions. Our results indicate that individual spores contain only a subset of the total allelic variation from the pooled spores and parent isolate. Patterns of allele diversity between spores suggest the possibility for segregation of PLS alleles among spores. We conclude that a genetic bottleneck could potentially occur during sporulation in AMF, with resulting differences in genetic variation among sister spores. We suggest that the effects of this bottleneck may be countered by anastomosis (hyphal fusion) between related hyphae. PMID:24386173

Mariposa port of entry bottleneck study : facilitating efficient, secure and economical cross-border transportation movements.

DOT National Transportation Integrated Search

2008-10-01

The Arizona-Sonora border has become increasingly important to both states economy : due to increased trade between the regions following the 1994 passage of the North American : Free Trade Agreement (NAFTA) and the establishment of maquiladora in...

Hybridization affects life-history traits and host specificity in Diorhabda spp

USDA-ARS?s Scientific Manuscript database

Hybridization is an influential evolutionary process that has been viewed alternatively as an evolutionary dead-end or as an important creative evolutionary force. In colonizing species, such as introduced biological control agents, hybridization can negate the effects of bottlenecks and genetic dri...

GiNA, an efficient and high-throughput software for horticultural phenotyping

USDA-ARS?s Scientific Manuscript database

Traditional methods for trait phenotyping have been a bottleneck for research in many crop species due to their intensive labor, high cost, complex implementation, lack of reproducibility and propensity to subjective bias. Recently, multiple high-throughput phenotyping platforms have been developed,...

Uncovering Ways of Thinking, Practicing, and Being through Decoding across Disciplines

ERIC Educational Resources Information Center

Miller-Young, Janice; Boman, Jennifer

2017-01-01

This chapter presents the bottlenecks identified by seven faculty members from diverse disciplines and an inductive content analysis of their Decoding interviews. Representative quotations illustrate themes in the interviews and we consider the implications for both faculty development and pedagogical research.

Experimental evolution of an alternating uni- and multicellular life cycle in Chlamydomonas reinhardtii

PubMed Central

Ratcliff, William C.; Herron, Matthew D.; Howell, Kathryn; Pentz, Jennifer T.; Rosenzweig, Frank; Travisano, Michael

2013-01-01

The transition to multicellularity enabled the evolution of large, complex organisms, but early steps in this transition remain poorly understood. Here we show that multicellular complexity, including development from a single cell, can evolve rapidly in a unicellular organism that has never had a multicellular ancestor. We subject the alga Chlamydomonas reinhardtii to conditions that favour multicellularity, resulting in the evolution of a multicellular life cycle in which clusters reproduce via motile unicellular propagules. While a single-cell genetic bottleneck during ontogeny is widely regarded as an adaptation to limit among-cell conflict, its appearance very early in this transition suggests that it did not evolve for this purpose. Instead, we find that unicellular propagules are adaptive even in the absence of intercellular conflict, maximizing cluster-level fecundity. These results demonstrate that the unicellular bottleneck, a trait essential for evolving multicellular complexity, can arise rapidly via co-option of the ancestral unicellular form. PMID:24193369

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

NASA Technical Reports Server (NTRS)

Sadeh, Norman M.

1992-01-01

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. Current research efforts include: adaptation of MICRO-BOSS to deal with sequence-dependent setups and development of micro-opportunistic reactive scheduling techniques that will enable the system to patch the schedule in the presence of contingencies such as machine breakdowns, raw materials arriving late, job cancellations, etc.

GrigoraSNPs: Optimized Analysis of SNPs for DNA Forensics.

PubMed

Ricke, Darrell O; Shcherbina, Anna; Michaleas, Adam; Fremont-Smith, Philip

2018-04-16

High-throughput sequencing (HTS) of single nucleotide polymorphisms (SNPs) enables additional DNA forensic capabilities not attainable using traditional STR panels. However, the inclusion of sets of loci selected for mixture analysis, extended kinship, phenotype, biogeographic ancestry prediction, etc., can result in large panel sizes that are difficult to analyze in a rapid fashion. GrigoraSNP was developed to address the allele-calling bottleneck that was encountered when analyzing SNP panels with more than 5000 loci using HTS. GrigoraSNPs uses a MapReduce parallel data processing on multiple computational threads plus a novel locus-identification hashing strategy leveraging target sequence tags. This tool optimizes the SNP calling module of the DNA analysis pipeline with runtimes that scale linearly with the number of HTS reads. Results are compared with SNP analysis pipelines implemented with SAMtools and GATK. GrigoraSNPs removes a computational bottleneck for processing forensic samples with large HTS SNP panels. Published 2018. This article is a U.S. Government work and is in the public domain in the USA.

Improved cyberinfrastructure for integrated hydrometeorological predictions within the fully-coupled WRF-Hydro modeling system

NASA Astrophysics Data System (ADS)

gochis, David; hooper, Rick; parodi, Antonio; Jha, Shantenu; Yu, Wei; Zaslavsky, Ilya; Ganapati, Dinesh

2014-05-01

The community WRF-Hydro system is currently being used in a variety of flood prediction and regional hydroclimate impacts assessment applications around the world. Despite its increasingly wide use certain cyberinfrastructure bottlenecks exist in the setup, execution and post-processing of WRF-Hydro model runs. These bottlenecks result in wasted time, labor, data transfer bandwidth and computational resource use. Appropriate development and use of cyberinfrastructure to setup and manage WRF-Hydro modeling applications will streamline the entire workflow of hydrologic model predictions. This talk will present recent advances in the development and use of new open-source cyberinfrastructure tools for the WRF-Hydro architecture. These tools include new web-accessible pre-processing applications, supercomputer job management applications and automated verification and visualization applications. The tools will be described successively and then demonstrated in a set of flash flood use cases for recent destructive flood events in the U.S. and in Europe. Throughout, an emphasis on the implementation and use of community data standards for data exchange is made.

Phonon bottleneck identification in disordered nanoporous materials

NASA Astrophysics Data System (ADS)

Romano, Giuseppe; Grossman, Jeffrey C.

2017-09-01

Nanoporous materials are a promising platform for thermoelectrics in that they offer high thermal conductivity tunability while preserving good electrical properties, a crucial requirement for high-efficiency thermal energy conversion. Understanding the impact of the pore arrangement on thermal transport is pivotal to engineering realistic materials, where pore disorder is unavoidable. Although there has been considerable progress in modeling thermal size effects in nanostructures, it has remained a challenge to screen such materials over a large phase space due to the slow simulation time required for accurate results. We use density functional theory in connection with the Boltzmann transport equation to perform calculations of thermal conductivity in disordered porous materials. By leveraging graph theory and regressive analysis, we identify the set of pores representing the phonon bottleneck and obtain a descriptor for thermal transport, based on the sum of the pore-pore distances between such pores. This approach provide a simple tool to estimate phonon suppression in realistic porous materials for thermoelectric applications and enhance our understanding of heat transport in disordered materials.

Slow cooling and highly efficient extraction of hot carriers in colloidal perovskite nanocrystals.

PubMed

Li, Mingjie; Bhaumik, Saikat; Goh, Teck Wee; Kumar, Muduli Subas; Yantara, Natalia; Grätzel, Michael; Mhaisalkar, Subodh; Mathews, Nripan; Sum, Tze Chien

2017-02-08

Hot-carrier solar cells can overcome the Schottky-Queisser limit by harvesting excess energy from hot carriers. Inorganic semiconductor nanocrystals are considered prime candidates. However, hot-carrier harvesting is compromised by competitive relaxation pathways (for example, intraband Auger process and defects) that overwhelm their phonon bottlenecks. Here we show colloidal halide perovskite nanocrystals transcend these limitations and exhibit around two orders slower hot-carrier cooling times and around four times larger hot-carrier temperatures than their bulk-film counterparts. Under low pump excitation, hot-carrier cooling mediated by a phonon bottleneck is surprisingly slower in smaller nanocrystals (contrasting with conventional nanocrystals). At high pump fluence, Auger heating dominates hot-carrier cooling, which is slower in larger nanocrystals (hitherto unobserved in conventional nanocrystals). Importantly, we demonstrate efficient room temperature hot-electrons extraction (up to ∼83%) by an energy-selective electron acceptor layer within 1 ps from surface-treated perovskite NCs thin films. These insights enable fresh approaches for extremely thin absorber and concentrator-type hot-carrier solar cells.

Ultracompliant Heterogeneous Copper-Tin Nanowire Arrays Making a Supersolder.

PubMed

Gong, Wei; Li, Pengfei; Zhang, Yunheng; Feng, Xuhui; Major, Joshua; DeVoto, Douglas; Paret, Paul; King, Charles; Narumanchi, Sreekant; Shen, Sheng

2018-06-13

Due to the substantial increase in power density, thermal interface resistance that can constitute more than 50% of the total thermal resistance has generally become a bottleneck for thermal management in electronics. However, conventional thermal interface materials (TIMs) such as solder, epoxy, gel, and grease cannot fulfill the requirements of electronics for high-power and long-term operation. Here, we demonstrate a high-performance TIM consisting of a heterogeneous copper-tin nanowire array, which we term "supersolder" to emulate the role of conventional solders in bonding various surfaces. The supersolder is ultracompliant with a shear modulus 2-3 orders of magnitude lower than traditional solders and can reduce the thermal resistance by two times as compared with the state-of-the-art TIMs. This supersolder also exhibits excellent long-term reliability with >1200 thermal cycles over a wide temperature range. By resolving this critical thermal bottleneck, the supersolder enables electronic systems, ranging from microelectronics and portable electronics to massive data centers, to operate at lower temperatures with higher power density and reliability.

Engineering oilseeds for sustainable production of industrial and nutritional feedstocks: solving bottlenecks in fatty acid flux.

PubMed

Cahoon, Edgar B; Shockey, Jay M; Dietrich, Charles R; Gidda, Satinder K; Mullen, Robert T; Dyer, John M

2007-06-01

Oilseeds provide a unique platform for the production of high-value fatty acids that can replace non-sustainable petroleum and oceanic sources of specialty chemicals and aquaculture feed. However, recent efforts to engineer the seeds of crop and model plant species to produce new types of fatty acids, including hydroxy and conjugated fatty acids for industrial uses and long-chain omega-3 polyunsaturated fatty acids for farmed fish feed, have met with only modest success. The collective results from these studies point to metabolic 'bottlenecks' in the engineered plant seeds that substantially limit the efficient or selective flux of unusual fatty acids between different substrate pools and ultimately into storage triacylglycerol. Evidence is emerging that diacylglycerol acyltransferase 2, which catalyzes the final step in triacylglycerol assembly, is an important contributor to the synthesis of unusual fatty acid-containing oils, and is likely to be a key target for future oilseed metabolic engineering efforts.

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

PubMed

Teli, Mohammad Nayeem; Anderson, Charles

2009-01-01

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

Interfacing a high performance disk array file server to a Gigabit LAN

NASA Technical Reports Server (NTRS)

Seshan, Srinivasan; Katz, Randy H.

1993-01-01

Our previous prototype, RAID-1, identified several bottlenecks in typical file server architectures. The most important bottleneck was the lack of a high-bandwidth path between disk, memory, and the network. Workstation servers, such as the Sun-4/280, have very slow access to peripherals on busses far from the CPU. For the RAID-2 system, we addressed this problem by designing a crossbar interconnect, Xbus board, that provides a 40MB/s path between disk, memory, and the network interfaces. However, this interconnect does not provide the system CPU with low latency access to control the various interfaces. To provide a high data rate to clients on the network, we were forced to carefully and efficiently design the network software. A block diagram of the system hardware architecture is given. In the following subsections, we describe pieces of the RAID-2 file server hardware that had a significant impact on the design of the network interface.

Research on the key technologies of 3D spatial data organization and management for virtual building environments

NASA Astrophysics Data System (ADS)

Gong, Jun; Zhu, Qing

2006-10-01

As the special case of VGE in the fields of AEC (architecture, engineering and construction), Virtual Building Environment (VBE) has been broadly concerned. Highly complex, large-scale 3d spatial data is main bottleneck of VBE applications, so 3d spatial data organization and management certainly becomes the core technology for VBE. This paper puts forward 3d spatial data model for VBE, and the performance to implement it is very high. Inherent storage method of CAD data makes data redundant, and doesn't concern efficient visualization, which is a practical bottleneck to integrate CAD model, so An Efficient Method to Integrate CAD Model Data is put forward. Moreover, Since the 3d spatial indices based on R-tree are usually limited by their weakness of low efficiency due to the severe overlap of sibling nodes and the uneven size of nodes, a new node-choosing algorithm of R-tree are proposed.

Retrospective analyses of the bottleneck in purification of eukaryotic proteins from Escherichia coli as affected by molecular weight, cysteine content and isoelectric point

PubMed Central

Jeon, Won Bae

2015-01-01

Experimental bioinformatics data obtained from an E. coli cell-based eukaryotic protein purification experiment were analyzed in order to identify any bottleneck as well as the factors affecting the target purification. All targets were expressed as His-tagged maltose-binding protein (MBP) fusion constructs and were initially purified by immobilized metal affinity chromatography (IMAC). The targets were subsequently separated from the His-tagged MBP through TEV protease cleavage followed by a second IMAC isolation. Of the 743 total purification trials, 342 yielded more than 3 mg of target proteins for structural studies. The major reason for failure of target purification was poor TEV proteolysis. The overall success rate for target purification decreased linearly as cysteine content or isoelectric point (pI) of the target increased. This pattern of pI versus overall success rate strongly suggests that pI should be incorporated into target scoring criteria with a threshold value. PMID:20510014

Transmission bottlenecks and RNAi collectively influence tick-borne flavivirus evolution.

PubMed

Grubaugh, Nathan D; Rückert, Claudia; Armstrong, Philip M; Bransfield, Angela; Anderson, John F; Ebel, Gregory D; Brackney, Doug E

2016-07-01

Arthropod-borne RNA viruses exist within hosts as heterogeneous populations of viral variants and, as a result, possess great genetic plasticity. Understanding the micro-evolutionary forces shaping these viruses can provide insights into how they emerge, adapt, and persist in new and changing ecological niches. While considerable attention has been directed toward studying the population dynamics of mosquito-borne viruses, little is known about tick-borne virus populations. Therefore, using a mouse and Ixodes scapularis tick transmission model, we examined Powassan virus (POWV; Flaviviridae, Flavivirus ) populations in and between both the vertebrate host and arthropod vector. We found that genetic bottlenecks, RNAi-mediated diversification, and selective constraints collectively influence POWV evolution. Together, our data provide a mechanistic explanation for the slow, long-term evolutionary trends of POWV, and suggest that all arthropod-borne viruses encounter similar selective pressures at the molecular level (i.e. RNAi), yet evolve much differently due to their unique rates and modes of transmission.

A population genetic analysis of the midget faded rattlesnake in Wyoming

USGS Publications Warehouse

Oyler-McCance, Sara J.; Parker, J.M.

2010-01-01

Little is known about the population biology of midget faded rattlesnakes, a sensitive subspecies of the Western Rattlesnake, despite conservation efforts to protect them. We conducted a molecular genetic study of midget faded rattlesnakes in southwestern Wyoming to investigate population genetic structure in this area, particularly with reference to Flaming Gorge Reservoir and its associated human activities, and to document levels of genetic diversity. We genotyped 229 snakes from 11 sampling sites using 9 microsatellite loci. We found significant levels of genetic structure among sites that were better explained by geographic region and isolation by distance than by position relative to waterways. Sites on either side of the reservoir at its widest point were not significantly different. Six of the sites showed signatures of a population bottleneck using an alpha value of 0.05. Three of these bottlenecked sites (the three most northern) were the most genetically distinct and occur in areas of greatest impact from human activity.

Algorithm and Architecture Independent Benchmarking with SEAK

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

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

2016-05-23

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

Selection on hemagglutinin imposes a bottleneck during mammalian transmission of reassortant H5N1 influenza viruses

PubMed Central

Wilker, Peter R.; Dinis, Jorge M.; Starrett, Gabriel; Imai, Masaki; Hatta, Masato; Nelson, Chase W.; O’Connor, David H.; Hughes, Austin L.; Neumann, Gabriele; Kawaoka, Yoshihiro; Friedrich, Thomas C.

2013-01-01

The emergence of human-transmissible H5N1 avian influenza viruses poses a major pandemic threat. H5N1 viruses are thought to be highly genetically diverse both among and within hosts, but the effects of this diversity on viral replication and transmission are poorly understood. Here we use deep sequencing to investigate the impact of within-host viral variation on adaptation and transmission of H5N1 viruses in ferrets. We show that although within-host genetic diversity in hemagglutinin (HA) increases during replication in inoculated ferrets, HA diversity is dramatically reduced upon respiratory droplet transmission, where infection is established by only 1–2 distinct HA segments from a diverse source virus population in transmitting animals. Moreover, minor HA variants present in as little as 5.9% of viruses within the source animal become dominant in ferrets infected via respiratory droplets. These findings demonstrate that selective pressures acting during influenza virus transmission among mammals impose a significant bottleneck. PMID:24149915

Cultural Hitchhiking in the Matrilineal Whales.

PubMed

Whitehead, Hal; Vachon, Felicia; Frasier, Timothy R

2017-05-01

Five species of whale with matrilineal social systems (daughters remain with mothers) have remarkably low levels of mitochondrial DNA diversity. Non-heritable matriline-level demography could reduce genetic diversity but the required conditions are not consistent with the natural histories of the matrilineal whales. The diversity of nuclear microsatellites is little reduced in the matrilineal whales arguing against bottlenecks. Selective sweeps of the mitochondrial genome are feasible causes but it is not clear why these only occurred in the matrilineal species. Cultural hitchhiking (cultural selection reducing diversity at neutral genetic loci transmitted in parallel to the culture) is supported in sperm whales which possess suitable matrilineal socio-cultural groups (coda clans). Killer whales are delineated into ecotypes which likely originated culturally. Culture, bottlenecks and selection, as well as their interactions, operating between- or within-ecotypes, may have reduced their mitochondrial diversity. The societies, cultures and genetics of false killer and two pilot whale species are insufficiently known to assess drivers of low mitochondrial diversity.

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

PubMed Central

Bijelic, Aleksandar; Rompel, Annette

2015-01-01

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

Time-Lapse Analysis of Human Embryonic Stem Cells Reveals Multiple Bottlenecks Restricting Colony Formation and Their Relief upon Culture Adaptation

PubMed Central

Barbaric, Ivana; Biga, Veronica; Gokhale, Paul J.; Jones, Mark; Stavish, Dylan; Glen, Adam; Coca, Daniel; Andrews, Peter W.

2014-01-01

Summary Using time-lapse imaging, we have identified a series of bottlenecks that restrict growth of early-passage human embryonic stem cells (hESCs) and that are relieved by karyotypically abnormal variants that are selected by prolonged culture. Only a minority of karyotypically normal cells divided after plating, and these were mainly cells in the later stages of cell cycle at the time of plating. Furthermore, the daughter cells showed a continued pattern of cell death after division, so that few formed long-term proliferating colonies. These colony-forming cells showed distinct patterns of cell movement. Increasing cell density enhanced cell movement facilitating cell:cell contact, which resulted in increased proportion of dividing cells and improved survival postplating of normal hESCs. In contrast, most of the karyotypically abnormal cells reentered the cell cycle on plating and gave rise to healthy progeny, without the need for cell:cell contacts and independent of their motility patterns. PMID:25068128

A Real-time Breakdown Prediction Method for Urban Expressway On-ramp Bottlenecks

NASA Astrophysics Data System (ADS)

Ye, Yingjun; Qin, Guoyang; Sun, Jian; Liu, Qiyuan

2018-01-01

Breakdown occurrence on expressway is considered to relate with various factors. Therefore, to investigate the association between breakdowns and these factors, a Bayesian network (BN) model is adopted in this paper. Based on the breakdown events identified at 10 urban expressways on-ramp in Shanghai, China, 23 parameters before breakdowns are extracted, including dynamic environment conditions aggregated with 5-minutes and static geometry features. Different time periods data are used to predict breakdown. Results indicate that the models using 5-10 min data prior to breakdown performs the best prediction, with the prediction accuracies higher than 73%. Moreover, one unified model for all bottlenecks is also built and shows reasonably good prediction performance with the classification accuracy of breakdowns about 75%, at best. Additionally, to simplify the model parameter input, the random forests (RF) model is adopted to identify the key variables. Modeling with the selected 7 parameters, the refined BN model can predict breakdown with adequate accuracy.

Assessment of multimodal freight bottlenecks and alleviation strategies for upper Midwest region.

DOT National Transportation Integrated Search

2010-05-01

The freight that passes through the Mississippi Valley Region is high volume and has a substantial impact on the economy of the : region. According to the BTS-sponsored Commodity Flow Survey, trucks carried almost 2.5 billion tons of freight across t...

Physiology and Assessment as Low-Hanging Fruit for Education Overhaul

ERIC Educational Resources Information Center

Ribeiro, Sidarta; Mota, Natália Bezerra; da Rocha Fernandes, Valter; Deslandes, Andrea Camaz; Brockington, Guilherme; Copelli, Mauro

2016-01-01

Physiology and assessment constitute major bottlenecks of school learning among students with low socioeconomic status. The limited resources and household overcrowding typical of poverty produce deficits in nutrition, sleep, and exercise that strongly hinder physiology and hence learning. Likewise, overcrowded classrooms hamper the assessment of…

Bottlenecks

ERIC Educational Resources Information Center

Grinstead, Robert R.

1972-01-01

Solid wastes that go at low cost into municipal landfills contain valuable raw materials which technology is not equipped to handle on a large scale. Identifying the key stumbling blocks may help divert the flow of wastes to useful purposes rather than into permanent burial sites. First of a two-part article. (BL)

Genetic diversity, linkage disequilibrium, and association mapping analyses of gossypium barbadense l. germplasm and cultivars

USDA-ARS?s Scientific Manuscript database

Limited polymorphism and narrow genetic base, due to genetic bottleneck through historic domestication, highlight a need for comprehensive characterization and utilization of existing genetic diversity in cotton germplasm collections. In this study, 288 worldwide Gossypium barbadense L. cotton germ...

Evidence for a population bottleneck in an Apicomplexan parasite of caribou and reindeer, Besnoitia tarandi

USDA-ARS?s Scientific Manuscript database

The evolutionary history and epidemiology of parasites may be reflected in the extent and geographic distribution of their genetic variation. Among coccidian parasites, the population structure of only Toxoplasma gondii has been extensively examined. Intraspecific variation in other coccidia, for ...

Identifying pathways for improving household food self-sufficiency outcomes in the hills of Nepal

USDA-ARS?s Scientific Manuscript database

Maintaining and improving food security in mountain regions is an ongoing challenge. There are many facets to the problem, including comparatively high levels of system diversity and crop-livestock integration, challenging terrain and transportation bottlenecks, declining labor availability due to o...

Attentional Limits in Memory Retrieval--Revisited

ERIC Educational Resources Information Center

Green, Collin; Johnston, James C.; Ruthruff, Eric

2011-01-01

Carrier and Pashler (1995) concluded--based on locus-of-slack dual-task methodology--that memory retrieval was subject to a central bottleneck. However, this conclusion conflicts with evidence from other lines of research suggesting that memory retrieval proceeds autonomously, in parallel with many other mental processes. In the present…

New additions to the cancer precision medicine toolkit.

PubMed

Mardis, Elaine R

2018-04-13

New computational and database-driven tools are emerging to aid in the interpretation of cancer genomic data as its use becomes more common in clinical evidence-based cancer medicine. Two such open source tools, published recently in Genome Medicine, provide important advances to address the clinical cancer genomics data interpretation bottleneck.

Applying high resolution mass spectrometry and network analysis to assess exposure to a novel androgen, spironolactone, on metabolic pathways in fish

EPA Science Inventory

Although metabolomics can successfully detect effects from overall contaminant exposure, its ability to elucidate specific metabolic pathways impacted by those exposures can be hindered by bottlenecks in metabolite identification. However, improved analytical approaches that com...

GENOME WIDE ASSOCIATION STUDY DISSECTING GENETIC ARCHITECTURE OF GRAIN PHYSICOCHEMICAL TRAITS IN RICE

USDA-ARS?s Scientific Manuscript database

Given the rapid advances in genomic technologies, phenotyping has become the bottleneck for revealing gene-trait relationships. Therefore, developing a means to rapidly and accurately phenotype thousands of genotypes can allow us to more fully utilize the genomic data that is currently available. A ...

Lights, camera, action: high-throughput plant phenotyping is ready for a close-up

USDA-ARS?s Scientific Manuscript database

Modern techniques for crop improvement rely on both DNA sequencing and accurate quantification of plant traits to identify genes and germplasm of interest. With rapid advances in DNA sequencing technologies, plant phenotyping is now a bottleneck in advancing crop yields [1,2]. Furthermore, the envir...

Problems and Trends Regarding Vocational Teachers in China

ERIC Educational Resources Information Center

Kuang, Ying

2014-01-01

At present, China's vocational education system is undergoing a transition process from growing in size to improving in quality. Teacher and teaching force issues are a bottleneck and critical factor that will determine whether the transformation will be successful. The real-world problems of the number, deployment, capacity, and training systems…

The Many Ways Data Must Flow.

ERIC Educational Resources Information Center

La Brecque, Mort

1984-01-01

To break the bottleneck inherent in today's linear computer architectures, parallel schemes (which allow computers to perform multiple tasks at one time) are being devised. Several of these schemes are described. Dataflow devices, parallel number-crunchers, programing languages, and a device based on a neurological model are among the areas…

Malus sieversii, a valuable genetic resource for disease resistance in apple

USDA-ARS?s Scientific Manuscript database

Domesticated crop cultivars inevitably represent a subset of the genetic variation found in their wild ancestors (progenitors) due to genetic bottlenecks that result during the process of crop domestication. Malus sieversii, a wild apple species native to Central Asia, is one of the ancestral proge...

Evidence of bottleneck and isolation by distance in an endangered species from the Tropical Andean hotspot

USDA-ARS?s Scientific Manuscript database

The Tropical Andes is the most diverse of the recognized plant conservation hotspots. In contrast, there exists scant knowledge about patterns of genetic variation within its constituent species. Understanding genetic variation is essential to develop successful conservation plans. Phaedranassa tun...

Expertise Increases the Functional Overlap between Face and Object Perception

ERIC Educational Resources Information Center

McKeeff, Thomas J.; McGugin, Rankin W.; Tong, Frank; Gauthier, Isabel

2010-01-01

Recent studies indicate that expertise with objects can interfere with face processing. Although competition occurs between faces and objects of expertise, it remains unclear whether this reflects an expertise-specific bottleneck or the fact that objects of expertise grab attention and thereby consume more central resources. We investigated the…

A dynamic flux balance model and bottleneck identification of glucose, xylose, xylulose co-fermentation in Saccharomyces cerevisiae

USDA-ARS?s Scientific Manuscript database

Economically viable production of lignocellulosic ethanol requires efficient conversion of feedstock sugars to ethanol. Saccharomyces cerevisiae cannot ferment xylose, the main five-carbon sugars in biomass, but can ferment xylulose, an enzymatically derived isomer. Xylulose fermentation is slow rel...

Using Cloud Storage for NMR Data Distribution

ERIC Educational Resources Information Center

Soulsby, David

2012-01-01

An approach using Google Groups as method for distributing student-acquired NMR data has been implemented. We describe how to configure NMR spectrometer software so that data is uploaded to a laboratory section specific Google Group, thereby removing bottlenecks associated with printing and processing at the spectrometer workstation. Outside of…

Can Mentoring Assist in the School-to-Work Transition?

ERIC Educational Resources Information Center

Lang, Martin

2010-01-01

Purpose: Due to recent bottlenecks in the apprenticeship market the transition from general schooling into the German employment system has become more and more problematic for many pupils over the past years. In particular, young persons with migrant backgrounds, low academic achievement or missing school graduations need special help from…

Task-Set Reconfiguration and Perceptual Processing: Behavioral and Electrophysiological Evidence

ERIC Educational Resources Information Center

Mackenzie, Ian G.; Leuthold, Hartmut

2011-01-01

Oriet and Jolicoeur (2003) proposed that an endogenous task-set reconfiguration process acts as a hard bottleneck during which even early perceptual processing is impossible. We examined this assumption using a psychophysiological approach. Participants were required to switch between magnitude and parity judgment tasks within a predictable task…

Web-based bioinformatics workflows for end-to-end RNA-seq data computation and analysis in agricultural animal species

USDA-ARS?s Scientific Manuscript database

Remarkable advances in next-generation sequencing (NGS) technologies, bioinformatics algorithms, and computational technologies have significantly accelerated genomic research. However, complicated NGS data analysis still remains as a major bottleneck. RNA-seq, as one of the major area in the NGS fi...

Analyzing the genomes of wild and cultivated beets

USDA-ARS?s Scientific Manuscript database

Sugar beet is an important crop plant that accounts for roughly 25% of the world's sugar production per year. We have previously shown that sugar beet has a quite narrow genetic base, presumably due to a domestication bottleneck. To increase the crop ´s stress tolerance, the introduction of desirabl...

High-throughput profiling and analysis of plant responses over time to abiotic stress

USDA-ARS?s Scientific Manuscript database

Energy sorghum (Sorghum bicolor (L.) Moench) is a rapidly growing, high-biomass, annual crop prized for abiotic stress tolerance. Measuring genotype-by-environment (G x E) interactions remains a progress bottleneck. High throughput phenotyping within controlled environments has been proposed as a po...

Gene Flow Among Different Teosinte Taxa and Into the Domesticated Maize Gene Pool

USDA-ARS?s Scientific Manuscript database

Maize (Zea mays ssp. mays) was domesticated from one wild species ancestor, the Balsas teosinte (Zea mays ssp. parviglumis) about 9000 years ago. Higher levels of gene diversity are found in teosinte taxa compared to maize following domestication and selection bottlenecks. Diversity in maize can b...

76 FR 78967 - Second Tier Environmental Impact Statement: Jackson County, MO

Federal Register 2010, 2011, 2012, 2013, 2014

2011-12-20

... determine an improvement strategy for the corridor to address the following needs: Improve safety, reduce.... Various concepts were combined to develop 15 initial strategies that were screened down to four first tier strategies. These four strategies included the No-Build Strategy, Improve Key Bottlenecks Strategy, Add...

Bottle-Neck Feature Extraction Structures for Multilingual Training and Porting (Pub Version, Open Access)

DTIC Science & Technology

2016-05-03

24 Mel-scaled filters applied on squared FFT magnitudes (critical band energies, CRBE) and 10 F0-related coefficients. The filter- bank spans...Acknowledgements This work was supported by the Intelligence Advanced Research Projects Activity (IARPA) via Department of Defense US Army Research Laboratory

One Bottleneck at a Time

ERIC Educational Resources Information Center

Bonner, J. Jose; Lotter, Christine; Harwood, William

2004-01-01

Teachers can easily identify what subjects their students have trouble with, whether it is transcription and translation, glycolysis and fermentation, balancing chemical equations, or vector analysis of forces acting on an object. Yet, no matter how teachers try to make these complex issues more accessible to students, or how new editions of…

Talking About Trials: Overcoming Bottlenecks in Clinical Communication

Cancer.gov

Participation in clinical trials by adult patients is dismally low. No one knows how many patients are offered the opportunity to enroll in trials. NCI researchers are studying how patients hear about trials, whether they discuss enrollment with their providers, and the roles they play in deciding to participate in a trial.

BC4GO: a full-text corpus for the BioCreative IV GO Task

USDA-ARS?s Scientific Manuscript database

Gene function curation via Gene Ontology (GO) annotation is a common task among Model Organism Database (MOD) groups. Due to its manual nature, this task is time-consuming and labor-intensive, and thus considered one of the bottlenecks in literature curation. There have been many previous attempts a...

A Study of Ninth-Grade Transition Practices across the Commonwealth of Virginia

ERIC Educational Resources Information Center

Childress, Toni Leigh Pardue

2013-01-01

Concerns over the academic success of first-time ninth-grade students transitioning into the high school setting continue to stimulate substantial interest in identifying the various factors that cause the ninth-grade bottleneck. Extensive research shows that when ninth-grade students transition into the high school setting, students have a…

Dependency graph for code analysis on emerging architectures

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

Shashkov, Mikhail Jurievich; Lipnikov, Konstantin

Direct acyclic dependency (DAG) graph is becoming the standard for modern multi-physics codes.The ideal DAG is the true block-scheme of a multi-physics code. Therefore, it is the convenient object for insitu analysis of the cost of computations and algorithmic bottlenecks related to statistical frequent data motion and dymanical machine state.

Floods, Bottlenecks and Backwaters: An Analysis of Expansion in Higher Education in Norway.

ERIC Educational Resources Information Center

Aamodt, Per O.

1995-01-01

Discussion of the pressures for expansion in Norwegian higher education looks at both long-term trends (need for a better-educated workforce and rising level in parents' education) and current demographic, individual, and political forces (a deteriorating labor market, younger students, competition for admission). Whether this situation is unique…

Policy Debate in Ethiopian Teacher Education: Retrospection and Future Direction

ERIC Educational Resources Information Center

Shishigu, Aweke; Gemechu, Eyasu; Michael, Kassa; Atnafu, Mulugeta; Ayalew, Yenealem

2017-01-01

Though, Ethiopia registered an extraordinary achievement in terms of increasing student enrolment, still quality of education remains a challenge and is becoming a bottleneck. One of the problems might be the structure and nature of teacher education itself. The purpose of this study therefore was to critically examine the existing literature and…

On the Application of Corpus of Contemporary American English in Vocabulary Instruction

ERIC Educational Resources Information Center

Yusu, Xu

2014-01-01

The development of corpus linguistics has laid theoretical foundation and provided technical support for breaking the bottleneck in traditional vocabulary instruction in China. Corpora allow access to authentic data and show frequency patterns of words and grammar construction. Such patterns can be used to improve language materials or to directly…

Analysis of large-scale gene expression data.

PubMed

Sherlock, G

2000-04-01

The advent of cDNA and oligonucleotide microarray technologies has led to a paradigm shift in biological investigation, such that the bottleneck in research is shifting from data generation to data analysis. Hierarchical clustering, divisive clustering, self-organizing maps and k-means clustering have all been recently used to make sense of this mass of data.

From Ability to Action: Designing Instruction for Critical Thinking Dispositions.

ERIC Educational Resources Information Center

Leader, Lars F.; Middleton, James A.

This paper explains the importance of disposition as an essential aspect of critical thinking and suggests how instruction can be designed to promote learners' development of the dispositional side of critical thinking. Topics addressed include: (1) the dispositional bottleneck between opportunity and action, i.e., sensitivity to occasion; (2)…

The Problem State: A Cognitive Bottleneck in Multitasking

ERIC Educational Resources Information Center

Borst, Jelmer P.; Taatgen, Niels A.; van Rijn, Hedderik

2010-01-01

The main challenge for theories of multitasking is to predict when and how tasks interfere. Here, we focus on interference related to the problem state, a directly accessible intermediate representation of the current state of a task. On the basis of Salvucci and Taatgen's (2008) threaded cognition theory, we predict interference if 2 or more…

Testing the Predictions of the Central Capacity Sharing Model

ERIC Educational Resources Information Center

Tombu, Michael; Jolicoeur, Pierre

2005-01-01

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

Voices from the Swamp: Identifying the Professional Development Needs of Principals.

ERIC Educational Resources Information Center

Goddard, J. Tim

During the mid- to late-1990s, economic downturns, outmigration of residents, and school closures in Nova Scotia contributed to a lack of movement among school administrators and thus a bottleneck of candidates seeking promotion to the principalship. This paper presents findings of a study that identified the professional-development needs of…

Improving Supervision for Students at a Distance: Videoconferencing for Group Meetings

ERIC Educational Resources Information Center

Könings, Karen D.; Popa, Daniela; Gerken, Maike; Giesbers, Bas; Rienties, Bart C.; van der Vleuten, Cees P. M.; van Merriënboer, Jeroen J. G.

2016-01-01

Every year, thousands of students go abroad for part of their study programme. Supervision from the home institution is then crucial for good study progress. Providing supervision and feedback at a distance is challenging. This project aims to identify bottlenecks for supervision and hypothesises that online supervisory group meetings with…

Collaborations Could Help Ease the Nursing Bottleneck

ERIC Educational Resources Information Center

Hoover, Eric

2009-01-01

Community colleges everywhere are searching for experienced nurses with advanced degrees who are willing to leave their jobs and return to the classroom, usually for significantly less pay. People who fit that description have long been difficult to find, but the need for them is growing. The dearth of instructors has contributed significantly to…

Decoding the Disciplines: An Approach to Scientific Thinking

ERIC Educational Resources Information Center

Pinnow, Eleni

2016-01-01

The Decoding the Disciplines methodology aims to teach students to think like experts in discipline-specific tasks. The central aspect of the methodology is to identify a bottleneck in the course content: a particular topic that a substantial number of students struggle to master. The current study compared the efficacy of standard lecture and…

Thailand--Secondary Education for Employment, Volume I: A Policy Note.

ERIC Educational Resources Information Center

Abelmann, Charles; Johanson, Richard; Kohtbantau, Achariya; Moock, Peter; Poshyananda, Tanaporn; Trivisvavet, Supamas

In Thailand, the need for skills in the labor force will become even greater in the next decade as the country's industrial and service companies seek to increase productivity through technological and organizational change. Historically, the limited provision of secondary education was a major bottleneck in skills development in Thailand. Major…

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.

CRISPR and personalized Treg therapy: new insights into the treatment of rheumatoid arthritis.

PubMed

Safari, Fatemeh; Farajnia, Safar; Arya, Maryam; Zarredar, Habib; Nasrolahi, Ava

2018-06-01

Rheumatoid arthritis (RA), as one of the most disabling autoimmune diseases, is a common health problem that progressively reduces the life quality of patients. Although various biologics have been introduced for RA, attempts to establish an efficient long-term therapies failed due to the heterogeneity of this disease. In the last decade, immunomodulatory approaches such as T cell adoptive therapy have been developed for controlling autoimmunity. Regulatory T cells (Tregs), the major self-tolerance mediator, are crucial for down-regulation of aberrant immune stimulations. Hence, recruiting ex vivo Tregs emerged as a promising therapy for a variety of autoimmune diseases. The major bottleneck of the Treg adoptive therapy is maintaining the in vivo stability and plasticity of these fascinating cells. Recent progress in genome editing technology clustered regularly interspaced short palindromic repeats (CRISPR) in combination with CRISPR-associated (Cas) 9 system provided a new solution for this bottleneck. The present paper discusses RA pathogenesis and the potential application of new developments in CRISPR-mediated Treg genome editing in personalized therapy of RA.

Performance measurements of the first RAID prototype

NASA Technical Reports Server (NTRS)

Chervenak, Ann L.

1990-01-01

The performance is examined of Redundant Arrays of Inexpensive Disks (RAID) the First, a prototype disk array. A hierarchy of bottlenecks was discovered in the system that limit overall performance. The most serious is the memory system contention on the Sun 4/280 host CPU, which limits array bandwidth to 2.3 MBytes/sec. The array performs more successfully on small random operations, achieving nearly 300 I/Os per second before the Sun 4/280 becomes CPU limited. Other bottlenecks in the system are the VME backplane, bandwidth on the disk controller, and overheads associated with the SCSI protocol. All are examined in detail. The main conclusion is that to achieve the potential bandwidth of arrays, more powerful CPU's alone will not suffice. Just as important are adequate host memory bandwidth and support for high bandwidth on disk controllers. Current disk controllers are more often designed to achieve large numbers of small random operations, rather than high bandwidth. Operating systems also need to change to support high bandwidth from disk arrays. In particular, they should transfer data in larger blocks, and should support asynchronous I/O to improve sequential write performance.

Killer whale nuclear genome and mtDNA reveal widespread population bottleneck during the last glacial maximum.

PubMed

Moura, Andre E; Janse van Rensburg, Charlene; Pilot, Malgorzata; Tehrani, Arman; Best, Peter B; Thornton, Meredith; Plön, Stephanie; de Bruyn, P J Nico; Worley, Kim C; Gibbs, Richard A; Dahlheim, Marilyn E; Hoelzel, Alan Rus

2014-05-01

Ecosystem function and resilience is determined by the interactions and independent contributions of individual species. Apex predators play a disproportionately determinant role through their influence and dependence on the dynamics of prey species. Their demographic fluctuations are thus likely to reflect changes in their respective ecological communities and habitat. Here, we investigate the historical population dynamics of the killer whale based on draft nuclear genome data for the Northern Hemisphere and mtDNA data worldwide. We infer a relatively stable population size throughout most of the Pleistocene, followed by an order of magnitude decline and bottleneck during the Weichselian glacial period. Global mtDNA data indicate that while most populations declined, at least one population retained diversity in a stable, productive ecosystem off southern Africa. We conclude that environmental changes during the last glacial period promoted the decline of a top ocean predator, that these events contributed to the pattern of diversity among extant populations, and that the relatively high diversity of a population currently in productive, stable habitat off South Africa suggests a role for ocean productivity in the widespread decline.

Slow cooling and highly efficient extraction of hot carriers in colloidal perovskite nanocrystals

PubMed Central

Li, Mingjie; Bhaumik, Saikat; Goh, Teck Wee; Kumar, Muduli Subas; Yantara, Natalia; Grätzel, Michael; Mhaisalkar, Subodh; Mathews, Nripan; Sum, Tze Chien

2017-01-01

Hot-carrier solar cells can overcome the Shockley-Queisser limit by harvesting excess energy from hot carriers. Inorganic semiconductor nanocrystals are considered prime candidates. However, hot-carrier harvesting is compromised by competitive relaxation pathways (for example, intraband Auger process and defects) that overwhelm their phonon bottlenecks. Here we show colloidal halide perovskite nanocrystals transcend these limitations and exhibit around two orders slower hot-carrier cooling times and around four times larger hot-carrier temperatures than their bulk-film counterparts. Under low pump excitation, hot-carrier cooling mediated by a phonon bottleneck is surprisingly slower in smaller nanocrystals (contrasting with conventional nanocrystals). At high pump fluence, Auger heating dominates hot-carrier cooling, which is slower in larger nanocrystals (hitherto unobserved in conventional nanocrystals). Importantly, we demonstrate efficient room temperature hot-electrons extraction (up to ∼83%) by an energy-selective electron acceptor layer within 1 ps from surface-treated perovskite NCs thin films. These insights enable fresh approaches for extremely thin absorber and concentrator-type hot-carrier solar cells. PMID:28176882

Automated Software Development Workstation (ASDW)

NASA Technical Reports Server (NTRS)

Fridge, Ernie

1990-01-01

Software development is a serious bottleneck in the construction of complex automated systems. An increase of the reuse of software designs and components has been viewed as a way to relieve this bottleneck. One approach to achieving software reusability is through the development and use of software parts composition systems. A software parts composition system is a software development environment comprised of a parts description language for modeling parts and their interfaces, a catalog of existing parts, a composition editor that aids a user in the specification of a new application from existing parts, and a code generator that takes a specification and generates an implementation of a new application in a target language. The Automated Software Development Workstation (ASDW) is an expert system shell that provides the capabilities required to develop and manipulate these software parts composition systems. The ASDW is now in Beta testing at the Johnson Space Center. Future work centers on responding to user feedback for capability and usability enhancement, expanding the scope of the software lifecycle that is covered, and in providing solutions to handling very large libraries of reusable components.

Genetic and life-history consequences of extreme climate events

PubMed Central

Mangel, Marc; Jesensek, Dusan; Garza, John Carlos; Crivelli, Alain J.

2017-01-01

Climate change is predicted to increase the frequency and intensity of extreme climate events. Tests on empirical data of theory-based predictions on the consequences of extreme climate events are thus necessary to understand the adaptive potential of species and the overarching risks associated with all aspects of climate change. We tested predictions on the genetic and life-history consequences of extreme climate events in two populations of marble trout Salmo marmoratus that have experienced severe demographic bottlenecks due to flash floods. We combined long-term field and genotyping data with pedigree reconstruction in a theory-based framework. Our results show that after flash floods, reproduction occurred at a younger age in one population. In both populations, we found the highest reproductive variance in the first cohort born after the floods due to a combination of fewer parents and higher early survival of offspring. A small number of parents allowed for demographic recovery after the floods, but the genetic bottleneck further reduced genetic diversity in both populations. Our results also elucidate some of the mechanisms responsible for a greater prevalence of faster life histories after the extreme event. PMID:28148745

Compact representation of continuous energy surfaces for more efficient protein design

PubMed Central

Hallen, Mark A.; Gainza, Pablo; Donald, Bruce R.

2015-01-01

In macromolecular design, conformational energies are sensitive to small changes in atom coordinates, so modeling the small, continuous motions of atoms around low-energy wells confers a substantial advantage in structural accuracy; however, modeling these motions comes at the cost of a very large number of energy function calls, which form the bottleneck in the design calculation. In this work, we remove this bottleneck by consolidating all conformational energy evaluations into the precomputation of a local polynomial expansion of the energy about the “ideal” conformation for each low-energy, “rotameric” state of each residue pair. This expansion is called Energy as Polynomials in Internal Coordinates (EPIC), where the internal coordinates can be sidechain dihedrals, backrub angles, and/or any other continuous degrees of freedom of a macromolecule, and any energy function can be used without adding any asymptotic complexity to the design. We demonstrate that EPIC efficiently represents the energy surface for both molecular-mechanics and quantum-mechanical energy functions, and apply it specifically to protein design to model both sidechain and backbone degrees of freedom. PMID:26089744

The habitat and nature of early life.

PubMed

Nisbet, E G; Sleep, N H

2001-02-22

Earth is over 4,500 million years old. Massive bombardment of the planet took place for the first 500-700 million years, and the largest impacts would have been capable of sterilizing the planet. Probably until 4,000 million years ago or later, occasional impacts might have heated the ocean over 100 degrees C. Life on Earth dates from before about 3,800 million years ago, and is likely to have gone through one or more hot-ocean 'bottlenecks'. Only hyperthermophiles (organisms optimally living in water at 80-110 degrees C) would have survived. It is possible that early life diversified near hydrothermal vents, but hypotheses that life first occupied other pre-bottleneck habitats are tenable (including transfer from Mars on ejecta from impacts there). Early hyperthermophile life, probably near hydrothermal systems, may have been non-photosynthetic, and many housekeeping proteins and biochemical processes may have an original hydrothermal heritage. The development of anoxygenic and then oxygenic photosynthesis would have allowed life to escape the hydrothermal setting. By about 3,500 million years ago, most of the principal biochemical pathways that sustain the modern biosphere had evolved, and were global in scope.

Overcoming bottlenecks in the membrane protein structural biology pipeline.

PubMed

Hardy, David; Bill, Roslyn M; Jawhari, Anass; Rothnie, Alice J

2016-06-15

Membrane proteins account for a third of the eukaryotic proteome, but are greatly under-represented in the Protein Data Bank. Unfortunately, recent technological advances in X-ray crystallography and EM cannot account for the poor solubility and stability of membrane protein samples. A limitation of conventional detergent-based methods is that detergent molecules destabilize membrane proteins, leading to their aggregation. The use of orthologues, mutants and fusion tags has helped improve protein stability, but at the expense of not working with the sequence of interest. Novel detergents such as glucose neopentyl glycol (GNG), maltose neopentyl glycol (MNG) and calixarene-based detergents can improve protein stability without compromising their solubilizing properties. Styrene maleic acid lipid particles (SMALPs) focus on retaining the native lipid bilayer of a membrane protein during purification and biophysical analysis. Overcoming bottlenecks in the membrane protein structural biology pipeline, primarily by maintaining protein stability, will facilitate the elucidation of many more membrane protein structures in the near future. © 2016 The Author(s). published by Portland Press Limited on behalf of the Biochemical Society.

Research on three-phase traffic flow modeling based on interaction range

NASA Astrophysics Data System (ADS)

Zeng, Jun-Wei; Yang, Xu-Gang; Qian, Yong-Sheng; Wei, Xu-Ting

2017-12-01

On the basis of the multiple velocity difference effect (MVDE) model and under short-range interaction, a new three-phase traffic flow model (S-MVDE) is proposed through careful consideration of the influence of the relationship between the speeds of the two adjacent cars on the running state of the rear car. The random slowing rule in the MVDE model is modified in order to emphasize the influence of vehicle interaction between two vehicles on the probability of vehicles’ deceleration. A single-lane model which without bottleneck structure under periodic boundary conditions is simulated, and it is proved that the traffic flow simulated by S-MVDE model will generate the synchronous flow of three-phase traffic theory. Under the open boundary, the model is expanded by adding an on-ramp, the congestion pattern caused by the bottleneck is simulated at different main road flow rates and on-ramp flow rates, which is compared with the traffic congestion pattern observed by Kerner et al. and it is found that the results are consistent with the congestion characteristics in the three-phase traffic flow theory.

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

NASA Astrophysics Data System (ADS)

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

2016-12-01

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

Comparison of genetic diversity and population structure between two Schistosoma japonicum isolates--the field and the laboratory.

PubMed

Bian, Chao-Rong; Gao, Yu-Meng; Lamberton, Poppy H L; Lu, Da-Bing

2015-06-01

Schistosomiasis japonicum is one of the most important human parasitic diseases, and a number of studies have recently elucidated the difference in biological characteristics of S. japonicum among different parasite isolates, for example, between the field and the laboratory isolates. Therefore, the understanding of underlying genetic mechanism is of both theoretical and practical importance. In this study, we used six microsatellite markers to assess genetic diversity, population structure, and the bottleneck effect (a sharp reduction in population size) of two parasite populations, one field and one laboratory. A total of 136 S. japonicum cercariae from the field and 86 from the laboratory, which were genetically unique within single snails, were analyzed. The results showed bigger numbers of alleles and higher allelic richness in the field parasite population than in the laboratory indicating lower genetic diversity in the laboratory parasites. A bottleneck effect was detected in the laboratory population. When the field and laboratory isolates were combined, there was a clear distinction between two parasite populations using the software Structure. These genetic differences may partially explain the previously observed contrasted biological traits.

Ultracompliant Heterogeneous Copper-Tin Nanowire Arrays Making a Supersolder

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

Narumanchi, Sreekant V; Feng, Xuhui; Major, Joshua

Due to the substantial increase in power density, thermal interface resistance that can constitute more than 50% of the total thermal resistance has generally become a bottleneck for thermal management in electronics. However, conventional thermal interface materials (TIMs) such as solder, epoxy, gel, and grease cannot fulfill the requirements of electronics for high-power and long-term operation. Here, we demonstrate a high-performance TIM consisting of a heterogeneous copper-tin nanowire array, which we term 'supersolder' to emulate the role of conventional solders in bonding various surfaces. The supersolder is ultracompliant with a shear modulus 2-3 orders of magnitude lower than traditional soldersmore » and can reduce the thermal resistance by two times as compared with the state-of-the-art TIMs. This supersolder also exhibits excellent long-term reliability with >1200 thermal cycles over a wide temperature range. By resolving this critical thermal bottleneck, the supersolder enables electronic systems, ranging from microelectronics and portable electronics to massive data centers, to operate at lower temperatures with higher power density and reliability.« less

Temperature and pressure tuneable swollen bicontinuous cubic phases approaching nature's length scales.

PubMed

Barriga, H M G; Tyler, A I I; McCarthy, N L C; Parsons, E S; Ces, O; Law, R V; Seddon, J M; Brooks, N J

2015-01-21

Bicontinuous cubic structures offer enormous potential in applications ranging from protein crystallisation to drug delivery systems and have been observed in cellular membrane structures. One of the current bottlenecks in understanding and exploiting these structures is that cubic scaffolds produced in vitro are considerably smaller in size than those observed in biological systems, differing by almost an order of magnitude in some cases. We have addressed this technological bottleneck and developed a methodology capable of manufacturing highly swollen bicontinuous cubic membranes with length scales approaching those seen in vivo. Crucially, these cubic systems do not require the presence of proteins. We have generated highly swollen Im3m symmetry bicontinuous cubic phases with lattice parameters of up to 480 Å, composed of ternary mixtures of monoolein, cholesterol and negatively charged lipid (DOPS or DOPG) and we have been able to tune their lattice parameters. The swollen cubic phases are highly sensitive to both temperature and pressure; these structural changes are likely to be controlled by a fine balance between lipid headgroup repulsions and lateral pressure in the hydrocarbon chain region.

A Fluidic Hourglass

NASA Astrophysics Data System (ADS)

Marin, Alvaro; Lhuissier, Henri; Rossi, Massimiliano; Volk, Andreas; Kähler, Christian J.

2016-11-01

A group of objects passing through a constriction might get eventually stuck. It occurs no matter what type of object is considered: sand in an hourglass, particles in a fluid through a porous medium or people leaving a room in panic. The case of particles in a fluid affects porous mediums, filters and membranes, which become unusable when clogged. Certainly the adherence of the particles to the walls and to each other is an important parameter in such systems, but even without adherence the clogging probability is far from negligible. Focusing in these low-adherence regimes, we use microfluidic devices with a bottleneck of squared cross-section through which we force dilute polystyrene particle solutions with diameters comparable to the bottleneck size and down to one tenth its size. In such low friction conditions we show experimental evidence of a strong transition at a critical particle-to-neck ratio, just as it occurs in dry granular systems. We describe analytically such a transition by modeling the arch formation as a purely stochastic process, which yields a good agreement with the experimental data. Deutsche Forschungsgemeinschaft KA1808/22-1.

Health as a bridge to peace and trust in Myanmar: The 21st Century Panglong Conference.

PubMed

Tang, Kun; Zhao, Yingxi

2017-06-28

The twenty-first Century Panglong Conference, proposed by Aung San Suu Kyi and her National League for Democracy, has concluded with unsatisfactory results. This five-day conference attracted global attention and wide endorsements from the United Nations and many other key stakeholders. The broad framework of the peace dialogue included various social and economic issues. However, the implication of the conference on the health system strengthening efforts in ethnic areas was largely unknown. Although a "convergence model" was proposed by organizations in Thai-Myanmar borders as a roadmap for integrations of the national and ethnic health systems years ago, the genuine bottlenecks beneath have not been addressed. This commentary discussed the Panglong Conference and its implication for the health systems in ethnic regions, as well as the bottlenecks of a "peace process" in health sector. It outlined a few key steps to achieve health system convergence between national and ethnic health systems, the outcome of which will not only improve the health status of the ethnic regions, but also help strengthen mutual trust and understanding among peoples, as a powerful bridge for peace.

Fluctuating bottleneck model studies on kinetics of DNA escape from α-hemolysin nanopores

NASA Astrophysics Data System (ADS)

Bian, Yukun; Wang, Zilin; Chen, Anpu; Zhao, Nanrong

2015-11-01

We have proposed a fluctuation bottleneck (FB) model to investigate the non-exponential kinetics of DNA escape from nanometer-scale pores. The basic idea is that the escape rate is proportional to the fluctuating cross-sectional area of DNA escape channel, the radius r of which undergoes a subdiffusion dynamics subjected to fractional Gaussian noise with power-law memory kernel. Such a FB model facilitates us to obtain the analytical result of the averaged survival probability as a function of time, which can be directly compared to experimental results. Particularly, we have applied our theory to address the escape kinetics of DNA through α-hemolysin nanopores. We find that our theoretical framework can reproduce the experimental results very well in the whole time range with quite reasonable estimation for the intrinsic parameters of the kinetics processes. We believe that FB model has caught some key features regarding the long time kinetics of DNA escape through a nanopore and it might provide a sound starting point to study much wider problems involving anomalous dynamics in confined fluctuating channels.

Impact of introducing the pneumococcal and rotavirus vaccines into the routine immunization program in Niger.

PubMed

Lee, Bruce Y; Assi, Tina-Marie; Rajgopal, Jayant; Norman, Bryan A; Chen, Sheng-I; Brown, Shawn T; Slayton, Rachel B; Kone, Souleymane; Kenea, Hailu; Welling, Joel S; Connor, Diana L; Wateska, Angela R; Jana, Anirban; Wiringa, Ann E; Van Panhuis, Willem G; Burke, Donald S

2012-02-01

We investigated whether introducing the rotavirus and pneumococcal vaccines, which are greatly needed in West Africa, would overwhelm existing supply chains (i.e., the series of steps required to get a vaccine from the manufacturers to the target population) in Niger. As part of the Bill and Melinda Gates Foundation-funded Vaccine Modeling Initiative, we developed a computational model to determine the impact of introducing these new vaccines to Niger's Expanded Program on Immunization vaccine supply chain. Introducing either the rotavirus vaccine or the 7-valent pneumococcal conjugate vaccine could overwhelm available storage and transport refrigerator space, creating bottlenecks that would prevent the flow of vaccines down to the clinics. As a result, the availability of all World Health Organization Expanded Program on Immunization vaccines to patients might decrease from an average of 69% to 28.2% (range = 10%-51%). Addition of refrigerator and transport capacity could alleviate this bottleneck. Our results suggest that the effects on the vaccine supply chain should be considered when introducing a new vaccine and that computational models can help assess evolving needs and prevent problems with vaccine delivery.

Embedded system of image storage based on fiber channel

NASA Astrophysics Data System (ADS)

Chen, Xiaodong; Su, Wanxin; Xing, Zhongbao; Wang, Hualong

2008-03-01

In domains of aerospace, aviation, aiming, and optic measure etc., the embedded system of imaging, processing and recording is absolutely necessary, which has small volume, high processing speed and high resolution. But the embedded storage technology becomes system bottleneck because of developing slowly. It is used to use RAID to promote storage speed, but it is unsuitable for the embedded system because of its big volume. Fiber channel (FC) technology offers a new method to develop the high-speed, portable storage system. In order to make storage subsystem meet the needs of high storage rate, make use of powerful Virtex-4 FPGA and high speed fiber channel, advance a project of embedded system of digital image storage based on Xilinx Fiber Channel Arbitrated Loop LogiCORE. This project utilizes Virtex- 4 RocketIO MGT transceivers to transmit the data serially, and connects many Fiber Channel hard drivers by using of Arbitrated Loop optionally. It can achieve 400MBps storage rate, breaks through the bottleneck of PCI interface, and has excellences of high-speed, real-time, portable and massive capacity.

Low Dose X-Ray Speckle Visibility Spectroscopy Reveals Nanoscale Dynamics in Radiation Sensitive Ionic Liquids

NASA Astrophysics Data System (ADS)

Verwohlt, Jan; Reiser, Mario; Randolph, Lisa; Matic, Aleksandar; Medina, Luis Aguilera; Madsen, Anders; Sprung, Michael; Zozulya, Alexey; Gutt, Christian

2018-04-01

X-ray radiation damage provides a serious bottleneck for investigating microsecond to second dynamics on nanometer length scales employing x-ray photon correlation spectroscopy. This limitation hinders the investigation of real time dynamics in most soft matter and biological materials which can tolerate only x-ray doses of kGy and below. Here, we show that this bottleneck can be overcome by low dose x-ray speckle visibility spectroscopy. Employing x-ray doses of 22-438 kGy and analyzing the sparse speckle pattern of count rates as low as 6.7 ×10-3 per pixel, we follow the slow nanoscale dynamics of an ionic liquid (IL) at the glass transition. At the prepeak of nanoscale order in the IL, we observe complex dynamics upon approaching the glass transition temperature TG with a freezing in of the alpha relaxation and a multitude of millisecond local relaxations existing well below TG . We identify this fast relaxation as being responsible for the increasing development of nanoscale order observed in ILs at temperatures below TG .

File-access characteristics of parallel scientific workloads

NASA Technical Reports Server (NTRS)

Nieuwejaar, Nils; Kotz, David; Purakayastha, Apratim; Best, Michael; Ellis, Carla Schlatter

1995-01-01

Phenomenal improvements in the computational performance of multiprocessors have not been matched by comparable gains in I/O system performance. This imbalance has resulted in I/O becoming a significant bottleneck for many scientific applications. One key to overcoming this bottleneck is improving the performance of parallel file systems. The design of a high-performance parallel file system requires a comprehensive understanding of the expected workload. Unfortunately, until recently, no general workload studies of parallel file systems have been conducted. The goal of the CHARISMA project was to remedy this problem by characterizing the behavior of several production workloads, on different machines, at the level of individual reads and writes. The first set of results from the CHARISMA project describe the workloads observed on an Intel iPSC/860 and a Thinking Machines CM-5. This paper is intended to compare and contrast these two workloads for an understanding of their essential similarities and differences, isolating common trends and platform-dependent variances. Using this comparison, we are able to gain more insight into the general principles that should guide parallel file-system design.

Comparing the visual spans for faces and letters

PubMed Central

He, Yingchen; Scholz, Jennifer M.; Gage, Rachel; Kallie, Christopher S.; Liu, Tingting; Legge, Gordon E.

2015-01-01

The visual span—the number of adjacent text letters that can be reliably recognized on one fixation—has been proposed as a sensory bottleneck that limits reading speed (Legge, Mansfield, & Chung, 2001). Like reading, searching for a face is an important daily task that involves pattern recognition. Is there a similar limitation on the number of faces that can be recognized in a single fixation? Here we report on a study in which we measured and compared the visual-span profiles for letter and face recognition. A serial two-stage model for pattern recognition was developed to interpret the data. The first stage is characterized by factors limiting recognition of isolated letters or faces, and the second stage represents the interfering effect of nearby stimuli on recognition. Our findings show that the visual span for faces is smaller than that for letters. Surprisingly, however, when differences in first-stage processing for letters and faces are accounted for, the two visual spans become nearly identical. These results suggest that the concept of visual span may describe a common sensory bottleneck that underlies different types of pattern recognition. PMID:26129858

Reduced Mtdna Diversity in the Ngobe Amerinds of Panama

PubMed Central

Kolman, C. J.; Bermingham, E.; Cooke, R.; Ward, R. H.; Arias, T. D.; Guionneau-Sinclair, F.

1995-01-01

Mitochondrial DNA (mtDNA) haplotype diversity was determined for 46 Ngobe Amerinds sampled widely across their geographic range in western Panama. The Ngobe data were compared with mtDNA control region I sequences from two additional Amerind groups located at the northern and southern extremes of Amerind distribution, the Nuu-Chah-Nulth of the Pacific Northwest and the Chilean Mapuche and from one Na-Dene group, the Haida of the Pacific Northwest. The Ngobe exhibit the lowest mtDNA control region sequence diversity yet reported for an Amerind group. Moreover, they carry only two of the four Amerind founding lineages first described by Wallace and coworkers. We posit that the Ngobe passed through a population bottleneck caused by ethnogenesis from a small founding population and/or European conquest and colonization. Dating of the Ngobe population expansion using the HARPENDING et al. approach to the analysis of pairwise genetic differences indicates a Ngobe expansion at roughly 6800 years before present (range: 1850-14,000 years before present), a date more consistent with a bottleneck at Chibcha ethnogenesis than a conquest-based event. PMID:7635293

A synergetic combination of small and large neighborhood schemes in developing an effective procedure for solving the job shop scheduling problem.

PubMed

Amirghasemi, Mehrdad; Zamani, Reza

2014-01-01

This paper presents an effective procedure for solving the job shop problem. Synergistically combining small and large neighborhood schemes, the procedure consists of four components, namely (i) a construction method for generating semi-active schedules by a forward-backward mechanism, (ii) a local search for manipulating a small neighborhood structure guided by a tabu list, (iii) a feedback-based mechanism for perturbing the solutions generated, and (iv) a very large-neighborhood local search guided by a forward-backward shifting bottleneck method. The combination of shifting bottleneck mechanism and tabu list is used as a means of the manipulation of neighborhood structures, and the perturbation mechanism employed diversifies the search. A feedback mechanism, called repeat-check, detects consequent repeats and ignites a perturbation when the total number of consecutive repeats for two identical makespan values reaches a given threshold. The results of extensive computational experiments on the benchmark instances indicate that the combination of these four components is synergetic, in the sense that they collectively make the procedure fast and robust.

Chimeric cellulase matrix for investigating intramolecular synergism between non-hydrolytic disruptive functions of carbohydrate-binding modules and catalytic hydrolysis.

PubMed

Wang, Yuguo; Tang, Rentao; Tao, Jin; Wang, Xiaonan; Zheng, Baisong; Feng, Yan

2012-08-24

The conversion of renewable cellulosic biomass is of considerable interest for the production of biofuels and materials. The bottleneck in the efficient conversion is the compactness and resistance of crystalline cellulose. Carbohydrate-binding modules (CBMs), which disrupt crystalline cellulose via non-hydrolytic mechanisms, are expected to overcome this bottleneck. However, the lack of convenient methods for quantitative analysis of the disruptive functions of CBMs have hindered systematic studies and molecular modifications. Here we established a practical and systematic platform for quantifying and comparing the non-hydrolytic disruptive activities of CBMs via the synergism of CBMs and a catalytic module within designed chimeric cellulase molecules. Bioinformatics and computational biology were also used to provide a deeper understanding. A convenient vector was constructed to serve as a cellulase matrix into which heterologous CBM sequences can be easily inserted. The resulting chimeric cellulases were suitable for studying disruptive functions, and their activities quantitatively reflected the disruptive functions of CBMs on crystalline cellulose. In addition, this cellulase matrix can be used to construct novel chimeric cellulases with high hydrolytic activities toward crystalline cellulose.

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

Loss of Mhc and Neutral Variation in Peary Caribou: Genetic Drift Is Not Mitigated by Balancing Selection or Exacerbated by Mhc Allele Distributions

PubMed Central

Taylor, Sabrina S.; Jenkins, Deborah A.; Arcese, Peter

2012-01-01

Theory and empirical results suggest that the rate of loss of variation at Mhc and neutral microsatellite loci may differ because selection influences Mhc genes, and because a high proportion of rare alleles at Mhc loci may result in high rates of loss via drift. Most published studies compare Mhc and microsatellite variation in various contemporary populations to infer the effects of population size on genetic variation, even though different populations are likely to have different demographic histories that may also affect contemporary genetic variation. We directly compared loss of variation at Mhc and microsatellite loci in Peary caribou by comparing historical and contemporary samples. We observed that similar proportions of genetic variation were lost over time at each type of marker despite strong evidence for selection at Mhc genes. These results suggest that microsatellites can be used to estimate genome-wide levels of variation, but also that adaptive potential is likely to be lost following population bottlenecks. However, gene conversion and recombination at Mhc loci may act to increase variation following bottlenecks. PMID:22655029

Queueing-Based Synchronization and Entrainment for Synthetic Gene Oscillators

NASA Astrophysics Data System (ADS)

Mather, William; Butzin, Nicholas; Hochendoner, Philip; Ogle, Curtis

Synthetic gene oscillators have been a major focus of synthetic biology research since the beginning of the field 15 years ago. They have proven to be useful both for biotechnological applications as well as a testing ground to significantly develop our understanding of the design principles behind synthetic and native gene oscillators. In particular, the principles governing synchronization and entrainment of biological oscillators have been explored using a synthetic biology approach. Our work combines experimental and theoretical approaches to specifically investigate how a bottleneck for protein degradation, which is present in most if not all existing synthetic oscillators, can be leveraged to robustly synchronize and entrain biological oscillators. We use both the terminology and mathematical tools of queueing theory to intuitively explain the role of this bottleneck in both synchronization and entrainment, which extends prior work demonstrating the usefulness of queueing theory in synthetic and native gene circuits. We conclude with an investigation of how synchronization and entrainment may be sensitive to the presence of multiple proteolytic pathways in a cell that couple weakly through crosstalk. This work was supported by NSF Grant #1330180.

Inferring the Mode of Selection from the Transient Response to Demographic Perturbations

NASA Astrophysics Data System (ADS)

Balick, Daniel; Do, Ron; Reich, David; Sunyaev, Shamil

2014-03-01

Despite substantial recent progress in theoretical population genetics, most models work under the assumption of a constant population size. Deviations from fixed population sizes are ubiquitous in natural populations, many of which experience population bottlenecks and re-expansions. The non-equilibrium dynamics introduced by a large perturbation in population size are generally viewed as a confounding factor. In the present work, we take advantage of the transient response to a population bottleneck to infer features of the mode of selection and the distribution of selective effects. We develop an analytic framework and a corresponding statistical test that qualitatively differentiates between alleles under additive and those under recessive or more general epistatic selection. This statistic can be used to bound the joint distribution of selective effects and dominance effects in any diploid sexual organism. We apply this technique to human population genetic data, and severely restrict the space of allowed selective coefficients in humans. Additionally, one can test a set of functionally or medically relevant alleles for the primary mode of selection, or determine the local regional variation in dominance coefficients along the genome.

Mammalian adaptation of influenza A(H7N9) virus is limited by a narrow genetic bottleneck

PubMed Central

Zaraket, Hassan; Baranovich, Tatiana; Kaplan, Bryan S.; Carter, Robert; Song, Min-Suk; Paulson, James C.; Rehg, Jerold E.; Bahl, Justin; Crumpton, Jeri C.; Seiler, Jon; Edmonson, Michael; Wu, Gang; Karlsson, Erik; Fabrizio, Thomas; Zhu, Huachen; Guan, Yi; Husain, Matloob; Schultz-Cherry, Stacey; Krauss, Scott; McBride, Ryan; Webster, Robert G.; Govorkova, Elena A.; Zhang, Jinghui; Russell, Charles J.; Webby, Richard J.

2015-01-01

Human infection with avian influenza A(H7N9) virus is associated mainly with the exposure to infected poultry. The factors that allow interspecies transmission but limit human-to-human transmission are unknown. Here we show that A/Anhui/1/2013(H7N9) influenza virus infection of chickens (natural hosts) is asymptomatic and that it generates a high genetic diversity. In contrast, diversity is tightly restricted in infected ferrets, limiting further adaptation to a fully transmissible form. Airborne transmission in ferrets is accompanied by the mutations in PB1, NP and NA genes that reduce viral polymerase and neuraminidase activity. Therefore, while A(H7N9) virus can infect mammals, further adaptation appears to incur a fitness cost. Our results reveal that a tight genetic bottleneck during avian-to-mammalian transmission is a limiting factor in A(H7N9) influenza virus adaptation to mammals. This previously unrecognized biological mechanism limiting species jumps provides a measure of adaptive potential and may serve as a risk assessment tool for pandemic preparedness. PMID:25850788

Inferring Demographic History Using Two-Locus Statistics.

PubMed

Ragsdale, Aaron P; Gutenkunst, Ryan N

2017-06-01

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

Optical Access Networks

NASA Astrophysics Data System (ADS)

Zheng, Jun; Ansari, Nirwan

2005-02-01

Call for Papers: Optical Access Networks With the wide deployment of fiber-optic technology over the past two decades, we have witnessed a tremendous growth of bandwidth capacity in the backbone networks of today's telecommunications infrastructure. However, access networks, which cover the "last-mile" areas and serve numerous residential and small business users, have not been scaled up commensurately. The local subscriber lines for telephone and cable television are still using twisted pairs and coaxial cables. Most residential connections to the Internet are still through dial-up modems operating at a low speed on twisted pairs. As the demand for access bandwidth increases with emerging high-bandwidth applications, such as distance learning, high-definition television (HDTV), and video on demand (VoD), the last-mile access networks have become a bandwidth bottleneck in today's telecommunications infrastructure. To ease this bottleneck, it is imperative to provide sufficient bandwidth capacity in the access networks to open the bottleneck and thus present more opportunities for the provisioning of multiservices. Optical access solutions promise huge bandwidth to service providers and low-cost high-bandwidth services to end users and are therefore widely considered the technology of choice for next-generation access networks. To realize the vision of optical access networks, however, many key issues still need to be addressed, such as network architectures, signaling protocols, and implementation standards. The major challenges lie in the fact that an optical solution must be not only robust, scalable, and flexible, but also implemented at a low cost comparable to that of existing access solutions in order to increase the economic viability of many potential high-bandwidth applications. In recent years, optical access networks have been receiving tremendous attention from both academia and industry. A large number of research activities have been carried out or are now underway this hot area. The purpose of this feature issue is to expose the networking community to the latest research breakthroughs and progresses in the area of optical access networks.

Energetic payoff of tool use for capuchin monkeys in the caatinga: variation by season and habitat type.

PubMed

Emidio, Ricardo Almeida; Ferreira, Renata Gonçalves

2012-04-01

In this paper, we analyze predictions from the energetic bottleneck and opportunity models to explain the use of stones to crack open encased fruit by capuchins in dry environments. The energetic bottleneck model argues that tool use derives from the need to crack open hard-encased fruits which are key resources during periods of food scarcity. The opportunity model argues that tool use by capuchins derives from simultaneous access to stones and encased fruits. The study was conducted in the Caatinga biome, northeastern Brazil, at two areas where capuchin monkeys (Sapajus libidinosus and Sapajus spp.) regularly use stones to crack open encased fruit of Syagrus cearensis and Manihot dichotoma. Energetic gains were inferred based on the number of tool-use sites used and the mass of encased fruit consumed per month, and compared across seasons and areas occupied by the two groups. For the drier habitat, a significant increase in frequency of tool use (N(dry) = 329 vs. N(wet) = 59) and in the mean monthly mass of fruits consumed in the dry season (mean(dry) = 193g vs. mean(wet) = 13.5 g) offered support for the energetic bottleneck model. However, our inference of low energetic payoffs for tool using individuals (in the drier caatinga habitat from 13 to 193 cal·ind(-1) ·month(-1) and in the wetter caatinga habitat from 805 to 1150 cal·ind(-1) ·month(-1) ) offer support for the opportunity model. Finally, our analyses indicate that consumption of six S. cearensis fruits would equal the daily requirements of capuchins for β-carotene, and the consumption of 1.22 g·day(-1) of M. dichotoma encased fruit or 1.0 g·day(-1) of S. cearensis can supply capuchin's daily requirement of vitamin C. So, specific nutritional requirements may play a role in explaining the continuous consumption of encased fruit and customary use of stones to crack open encased fruit. © 2011 Wiley Periodicals, Inc.

Genetic variation in the invasive avian parasite, Philornis downsi (Diptera, Muscidae) on the Galápagos archipelago

PubMed Central

Dudaniec, Rachael Y; Gardner, Michael G; Donnellan, Steve; Kleindorfer, Sonia

2008-01-01

Background Understanding the dispersal and genetic structure of invasive insects across islands is important for designing management plans that are appropriate at spatial and temporal scales. For invasive parasites, population dynamics are largely determined by the distribution and density of their host species. The introduced parasitic fly, Philornis downsi, parasitises nestlings of endemic birds on all major islands of the Galápagos archipelago. The fly's high mortality and fitness impacts are of conservation concern for vulnerable and declining species of Darwin's finches. Using microsatellite data in Bayesian clustering and landscape genetic analyses, we examine gene flow and dispersal in P. downsi between three islands and across habitats (highlands, lowlands) and examine for the presence of population bottlenecks. We also examine variation at the mitochondrial gene CO1 across islands to establish if cryptic species were present. Results Both the mitochondrial and microsatellite data were consistent with there being a single species across islands. We found low genetic differentiation between islands and strong evidence for inter-island gene flow, or shared recent ancestry among individuals. Landscape genetic analysis identified two genetic clusters: one encompassing Santa Cruz and Isabela, and one on Floreana Island. There was no evidence of genetic differentiation between habitats and molecular variance was mainly attributable to within individuals. The combined P. downsi population was found to have undergone a population bottleneck. Conclusion Philornis downsi populations have high connectivity within and between islands, with low levels of genetic differentiation between Floreana and the other two islands examined. The genetic bottleneck found across islands suggests there was a small founding population or few introduction events of P. downsi. The high dispersal capacity and wide habitat use of P. downsi highlights the significant threat that this parasite poses to the Galápagos avifauna. Our findings are relevant for assessing the viability of methods to control P. downsi on Galápagos, such as the sterile insect technique. PMID:18671861

Genetic Signatures of Demographic Changes in an Avian Top Predator during the Last Century: Bottlenecks and Expansions of the Eurasian Eagle Owl in the Iberian Peninsula

PubMed Central

Graciá, Eva; Ortego, Joaquín; Godoy, José Antonio; Pérez-García, Juan Manuel; Blanco, Guillermo; del Mar Delgado, María; Penteriani, Vincenzo; Almodóvar, Irene; Botella, Francisco; Sánchez-Zapata, José Antonio

2015-01-01

The study of the demographic history of species can help to understand the negative impact of recent population declines in organisms of conservation concern. Here, we use neutral molecular markers to explore the genetic consequences of the recent population decline and posterior recovery of the Eurasian eagle owl (Bubo bubo) in the Iberian Peninsula. During the last century, the species was the object of extermination programs, suffering direct persecution by hunters until the 70’s. Moreover, during the last decades the eagle owl was severely impacted by increased mortality due to electrocution and the decline of its main prey species, the European rabbit (Oryctolagus cuniculus). In recent times, the decrease of direct persecution and the implementation of some conservation schemes have allowed the species’ demographic recovery. Yet, it remains unknown to which extent the past population decline and the later expansion have influenced the current species’ pattern of genetic diversity. We used eight microsatellite markers to genotype 235 eagle owls from ten Spanish subpopulations and analyse the presence of genetic signatures attributable to the recent population fluctuations experienced by the species. We found moderate levels of differentiation among the studied subpopulations and Bayesian analyses revealed the existence of three genetic clusters that grouped subpopulations from central, south-western and south-eastern Spain. The observed genetic structure could have resulted from recent human-induced population fragmentation, a patchy distribution of prey populations and/or the philopatric behaviour and habitat selection of the species. We detected an old population bottleneck, which occurred approximately 10,000 years ago, and significant signatures of recent demographic expansions. However, we did not find genetic signatures for a recent bottleneck, which may indicate that population declines were not severe enough to leave detectable signals on the species genetic makeup or that such signals have been eroded by the rapid demographic recovery experienced by the species in recent years. PMID:26230922

Subdecadal phytolith and charcoal records from Lake Malawi, East Africa imply minimal effects on human evolution from the ∼74 ka Toba supereruption.

PubMed

Yost, Chad L; Jackson, Lily J; Stone, Jeffery R; Cohen, Andrew S

2018-03-01

The temporal proximity of the ∼74 ka Toba supereruption to a putative 100-50 ka human population bottleneck is the basis for the volcanic winter/weak Garden of Eden hypothesis, which states that the eruption caused a 6-year-long global volcanic winter and reduced the effective population of anatomically modern humans (AMH) to fewer than 10,000 individuals. To test this hypothesis, we sampled two cores collected from Lake Malawi with cryptotephra previously fingerprinted to the Toba supereruption. Phytolith and charcoal samples were continuously collected at ∼3-4 mm (∼8-9 yr) intervals above and below the Toba cryptotephra position, with no stratigraphic breaks. For samples synchronous or proximal to the Toba interval, we found no change in low elevation tree cover, or in cool climate C 3 and warm season C 4 xerophytic and mesophytic grass abundance that is outside of normal variability. A spike in locally derived charcoal and xerophytic C 4 grasses immediately after the Toba eruption indicates reduced precipitation and die-off of at least some afromontane vegetation, but does not signal volcanic winter conditions. A review of Toba tuff petrological and melt inclusion studies suggest a Tambora-like 50 to 100 Mt SO 2 atmospheric injection. However, most Toba climate models use SO 2 values that are one to two orders of magnitude higher, thereby significantly overestimating the amount of cooling. A review of recent genetic studies finds no support for a genetic bottleneck at or near ∼74 ka. Based on these previous studies and our new paleoenvironmental data, we find no support for the Toba catastrophe hypothesis and conclude that the Toba supereruption did not 1) produce a 6-year-long volcanic winter in eastern Africa, 2) cause a genetic bottleneck among African AMH populations, or 3) bring humanity to the brink of extinction. Copyright © 2017 Elsevier Ltd. All rights reserved.

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

PubMed

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

2012-01-01

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

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

PubMed Central

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

2012-01-01

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

Reproductive Resilience to Food Shortage in a Small Heterothermic Primate

PubMed Central

Perret, Martine; Henry, Pierre-Yves

2012-01-01

The massive energetic costs entailed by reproduction in most mammalian females may increase the vulnerability of reproductive success to food shortage. Unexpected events of unfavorable climatic conditions are expected to rise in frequency and intensity as climate changes. The extent to which physiological flexibility allows organisms to maintain reproductive output constant despite energetic bottlenecks has been poorly investigated. In mammals, reproductive resilience is predicted to be maximal during early stages of reproduction, due to the moderate energetic costs of ovulation and gestation relative to lactation. We experimentally tested the consequences of chronic-moderate and short-acute food shortages on the reproductive output of a small seasonally breeding primate, the grey mouse lemur (Microcebus murinus) under thermo-neutral conditions. These two food treatments were respectively designed to simulate the energetic constraints imposed by a lean year (40% caloric restriction over eight months) or by a sudden, severe climatic event occurring shortly before reproduction (80% caloric restriction over a month). Grey mouse lemurs evolved under the harsh, unpredictable climate of the dry forest of Madagascar and should thus display great potential for physiological adjustments to energetic bottlenecks. We assessed the resilience of the early stages of reproduction (mating success, fertility, and gestation) to these contrasted food treatments, and on the later stages (lactation and offspring growth) in response to the chronic food shortage only. Food deprived mouse lemurs managed to maintain constant most reproductive parameters, including oestrus timing, estrogenization level at oestrus, mating success, litter size, and litter mass as well as their overall number of surviving offspring at weaning. However, offspring growth was delayed in food restricted mothers. These results suggest that heterothermic, fattening-prone mammals display important reproductive resilience to energetic bottlenecks. More generally, species living in variable and unpredictable habitats may have evolved a flexible reproductive physiology that helps buffer environmental fluctuations. PMID:22848507

Reproductive resilience to food shortage in a small heterothermic primate.

PubMed

Canale, Cindy I; Huchard, Elise; Perret, Martine; Henry, Pierre-Yves

2012-01-01

The massive energetic costs entailed by reproduction in most mammalian females may increase the vulnerability of reproductive success to food shortage. Unexpected events of unfavorable climatic conditions are expected to rise in frequency and intensity as climate changes. The extent to which physiological flexibility allows organisms to maintain reproductive output constant despite energetic bottlenecks has been poorly investigated. In mammals, reproductive resilience is predicted to be maximal during early stages of reproduction, due to the moderate energetic costs of ovulation and gestation relative to lactation. We experimentally tested the consequences of chronic-moderate and short-acute food shortages on the reproductive output of a small seasonally breeding primate, the grey mouse lemur (Microcebus murinus) under thermo-neutral conditions. These two food treatments were respectively designed to simulate the energetic constraints imposed by a lean year (40% caloric restriction over eight months) or by a sudden, severe climatic event occurring shortly before reproduction (80% caloric restriction over a month). Grey mouse lemurs evolved under the harsh, unpredictable climate of the dry forest of Madagascar and should thus display great potential for physiological adjustments to energetic bottlenecks. We assessed the resilience of the early stages of reproduction (mating success, fertility, and gestation) to these contrasted food treatments, and on the later stages (lactation and offspring growth) in response to the chronic food shortage only. Food deprived mouse lemurs managed to maintain constant most reproductive parameters, including oestrus timing, estrogenization level at oestrus, mating success, litter size, and litter mass as well as their overall number of surviving offspring at weaning. However, offspring growth was delayed in food restricted mothers. These results suggest that heterothermic, fattening-prone mammals display important reproductive resilience to energetic bottlenecks. More generally, species living in variable and unpredictable habitats may have evolved a flexible reproductive physiology that helps buffer environmental fluctuations.

Genetic variation in the invasive avian parasite, Philornis downsi (Diptera, Muscidae) on the Galápagos archipelago.

PubMed

Dudaniec, Rachael Y; Gardner, Michael G; Donnellan, Steve; Kleindorfer, Sonia

2008-07-31

Understanding the dispersal and genetic structure of invasive insects across islands is important for designing management plans that are appropriate at spatial and temporal scales. For invasive parasites, population dynamics are largely determined by the distribution and density of their host species. The introduced parasitic fly, Philornis downsi, parasitises nestlings of endemic birds on all major islands of the Galápagos archipelago. The fly's high mortality and fitness impacts are of conservation concern for vulnerable and declining species of Darwin's finches. Using microsatellite data in Bayesian clustering and landscape genetic analyses, we examine gene flow and dispersal in P. downsi between three islands and across habitats (highlands, lowlands) and examine for the presence of population bottlenecks. We also examine variation at the mitochondrial gene CO1 across islands to establish if cryptic species were present. Both the mitochondrial and microsatellite data were consistent with there being a single species across islands. We found low genetic differentiation between islands and strong evidence for inter-island gene flow, or shared recent ancestry among individuals. Landscape genetic analysis identified two genetic clusters: one encompassing Santa Cruz and Isabela, and one on Floreana Island. There was no evidence of genetic differentiation between habitats and molecular variance was mainly attributable to within individuals. The combined P. downsi population was found to have undergone a population bottleneck. Philornis downsi populations have high connectivity within and between islands, with low levels of genetic differentiation between Floreana and the other two islands examined. The genetic bottleneck found across islands suggests there was a small founding population or few introduction events of P. downsi. The high dispersal capacity and wide habitat use of P. downsi highlights the significant threat that this parasite poses to the Galápagos avifauna. Our findings are relevant for assessing the viability of methods to control P. downsi on Galápagos, such as the sterile insect technique.

Toll-like receptor variation in the bottlenecked population of the Seychelles warbler: computer simulations see the 'ghost of selection past' and quantify the 'drift debt'.

PubMed

Gilroy, D L; Phillips, K P; Richardson, D S; van Oosterhout, C

2017-07-01

Balancing selection can maintain immunogenetic variation within host populations, but detecting its signal in a postbottlenecked population is challenging due to the potentially overriding effects of drift. Toll-like receptor genes (TLRs) play a fundamental role in vertebrate immune defence and are predicted to be under balancing selection. We previously characterized variation at TLR loci in the Seychelles warbler (Acrocephalus sechellensis), an endemic passerine that has undergone a historical bottleneck. Five of seven TLR loci were polymorphic, which is in sharp contrast to the low genomewide variation observed. However, standard population genetic statistical methods failed to detect a contemporary signature of selection at any TLR locus. We examined whether the observed TLR polymorphism could be explained by neutral evolution, simulating the population's demography in the software DIYABC. This showed that the posterior distributions of mutation rates had to be unrealistically high to explain the observed genetic variation. We then conducted simulations with an agent-based model using typical values for the mutation rate, which indicated that weak balancing selection has acted on the three TLR genes. The model was able to detect evidence of past selection elevating TLR polymorphism in the prebottleneck populations, but was unable to discern any effects of balancing selection in the contemporary population. Our results show drift is the overriding evolutionary force that has shaped TLR variation in the contemporary Seychelles warbler population, and the observed TLR polymorphisms might be merely the 'ghost of selection past'. Forecast models predict immunogenetic variation in this species will continue to be eroded in the absence of contemporary balancing selection. Such 'drift debt' occurs when a gene pool has not yet reached its new equilibrium level of polymorphism, and this loss could be an important threat to many recently bottlenecked populations. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

Data simulation for the Lightning Imaging Sensor (LIS)

NASA Technical Reports Server (NTRS)

Boeck, William L.

1991-01-01

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

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

PubMed Central

Nagy, Christopher

2014-01-01

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

Evidence for recent populations bottlenecks in northern spotted owls (Strix occidentalis Caurina)

Treesearch

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

2009-01-01

The northern spotted owl (Strix occidentalis caurina) is one of the most controversial threatened subspecies ever listed under the US Endangered Species Act. Despite protection of its remaining forest habitat, recent field studies show continued declines of northern spotted owls. One potential threat to northern spotted owls which has not yet been...

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

ERIC Educational Resources Information Center

Firat, Mehmet

2013-01-01

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

The Effects of Simultaneous Developmental Processes: Factors Relating to the Career Development of Lesbian, Gay, and Bisexual Youth

ERIC Educational Resources Information Center

Schmidt, Christa K.; Nilsson, Johanna E.

2006-01-01

C. Hetherington (1991) hypothesized that lesbian, gay, and bisexual (LGB) adolescents may experience a "bottleneck effect" in career development because of internal psychological energy focusing on issues surrounding sexual identity. This assertion has not yet been tested, however, in the career development literature. The authors examined the…

Microbiome Data Science: Understanding Our Microbial Planet.

PubMed

Kyrpides, Nikos C; Eloe-Fadrosh, Emiley A; Ivanova, Natalia N

2016-06-01

Microbiology is experiencing a revolution brought on by recent developments in sequencing technology. The unprecedented volume of microbiome data being generated poses significant challenges that are currently hindering progress in the field. Here, we outline the major bottlenecks and propose a vision to advance microbiome research as a data-driven science. Copyright © 2016 Elsevier Ltd. All rights reserved.

Improvement of High-throughput Genotype Analysis After Implementation of a Dual-curve Sybr Green I-based Quantification and Normalization Procedure

USDA-ARS?s Scientific Manuscript database

The ability to rapidly screen a large number of individuals is the key to any successful plant breeding program. One of the primary bottlenecks in high throughput screening is the preparation of DNA samples, particularly the quantification and normalization of samples for downstream processing. A ...

nStudy: A System for Researching Information Problem Solving

ERIC Educational Resources Information Center

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

2017-01-01

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

Theory of Constraints: What Can We Learn to Support the Nursing Workforce?

PubMed

Pawlak, Roberta

2016-11-01

Demand for nurses is influenced by many factors. Labor statistics and health services literature reveal current and predicted supply gaps in meeting this demand. One strategy in response can be drawn from manufacturing industries. This column suggests the application of the Theory of Constraints in efforts to relieve bottlenecks in producing and retaining nurse labor.

Backward Response-Level Crosstalk in the Psychological Refractory Period Paradigm

ERIC Educational Resources Information Center

Miller, Jeff; Alderton, Mark

2006-01-01

Bottleneck models of psychological refractory period (PRP) tasks suggest that a Task 1 response should be unaffected by the Task 2 response in the same trial, because selection of the former finishes before selection of the latter begins. Contrary to this conception, the authors found backward response-level crosstalk effects in which Task 2…

Effects of increasing docosahexaenoic acid and arachidonic acid in brood diets of monodactylus sebae on fecundity, egg and larval quality, and egg fatty acid composition

USDA-ARS?s Scientific Manuscript database

Monodactylus sebae is a popular euryhaline ornamental fish species with limited aquaculture production. One of the bottlenecks to their commercial production has been knowledge of broodstock nutritional requirements. Therefore, three brood diets were formulated and fed to M. sebae brood to determine...

Combining field observations and genetic data to reconstruct the invasion of Phytophthora ramorum in California

Treesearch

Peter J.P. Croucher; Silvia Mascheretti; Matteo Garbelotto

2013-01-01

Although it has been convincingly shown that forest populations of the pathogen Phytophthora ramorum have undergone a significant bottleneck and reproduce exclusively asexually (Ivors et al. 2004, 2006; Mascheretti et al. 2008), objective results showing that nurseries were the original source of the introduction remain elusive (Mascheretti et al....

76 FR 38203 - Endangered and Threatened Wildlife and Plants; Amendment to the Draft Recovery Plan for the...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-06-29

..., habituation to captive conditions, and genetic bottlenecks. The prospects for long-term viability of the...] Endangered and Threatened Wildlife and Plants; Amendment to the Draft Recovery Plan for the Columbia Basin...), announce the availability of an amendment to the Draft Recovery Plan for the Columbia Basin Distinct...

Deep Thinking Increases Task-Set Shielding and Reduces Shifting Flexibility in Dual-Task Performance

ERIC Educational Resources Information Center

Fischer, Rico; Hommel, Bernhard

2012-01-01

Performing two tasks concurrently is difficult, which has been taken to imply the existence of a structural processing bottleneck. Here we sought to assess whether and to what degree one's multitasking abilities depend on the cognitive-control style one engages in. Participants were primed with creativity tasks that either called for divergent…

The interaction between propagule pressure, habitat suitablility and density-dependent reproduction in species invasion

Treesearch

Robert J. II Warren; Bahn Volker; Mark A. Bradford

2011-01-01

Seedling recruitment limitations create a demographic bottleneck that largely determines the viability and structure of plant populations and communities, and pose a core restriction on the colonization of novel habitat. We use a shade tolerant, invasive grass, Microstegium vimineum, to examine the interplay between seed and establishment limitations – phenomena that...

A Case Study of a Program for University STEM Faculty to Redesign Courses Using Technology

ERIC Educational Resources Information Center

Bernal, Elaine V.

2016-01-01

The purpose of this case study was to evaluate a multi-campus university program designed to support STEM faculty in redesigning bottleneck courses, with integration of technology as one strategy. Despite the positive student learning outcomes in course redesign programs with an aim to support faculty in technology integration, there remains a…

Teacher Diversity in Canada: Leaky Pipelines, Bottlenecks, and Glass Ceilings

ERIC Educational Resources Information Center

Ryan, James; Pollock, Katina; Antonelli, Fab

2009-01-01

This article examines the racial diversity of the teacher population in Canada. In particular, we compare the number of teachers of colour in Canadian elementary and secondary schools from the 2001 and 2006 Census data with the diversity of the student and general populations. We also explore ways to understand the gap between the proportion of…

Leveraging Technology to Alleviate Student Bottlenecks: The Self-Paced Online Tutorial--Writing (SPOT)

ERIC Educational Resources Information Center

Moore, Scott D.; Sanchez, Rudolph J.; Inoue, Asao B.; Statham, Russel D.; Zelezny, Lynnette; Covino, William A.

2014-01-01

The Self-Paced Online Tutorial (SPOT) represents the best kind of innovation because it uses digital technologies wisely and because it is based on well-established theory, research, and practice. Extended education plays a pivotal role in the attainment of the California State University's (CSU) vision of providing a high-quality, affordable, and…

Development of a Workbench to Address the Educational Data Mining Bottleneck

ERIC Educational Resources Information Center

Rodrigo, Ma. Mercedes T.; Baker, Ryan S. J. d.; McLaren, Bruce M.; Jayme, Alejandra; Dy, Thomas T.

2012-01-01

In recent years, machine-learning software packages have made it easier for educational data mining researchers to create real-time detectors of cognitive skill as well as of metacognitive and motivational behavior that can be used to improve student learning. However, there remain challenges to overcome for these methods to become available to…

Examinations and Educational Opportunity in China: Mobility and Bottlenecks for the Rural Poor

ERIC Educational Resources Information Center

Hannum, Emily; An, Xuehui; Cherng, Hua-Yu Sebastian

2011-01-01

Despite the important role played by examinations in educational stratification and mobility in China, to our knowledge there is no literature in English that investigates the impact of exams on educational attainment with empirical data. We address this gap with an investigation of how examinations shape opportunities for children of the rural…

Language processing is not a race against time.

PubMed

Baggio, Giosuè; Vicario, Carmelo M

2016-01-01

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

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

Jiang, Yunshan; DeVore, Peter T. S.; Jalali, Bahram

Optical computing accelerators help alleviate bandwidth and power consumption bottlenecks in electronics. In this paper, we show an approach to implementing logarithmic-type analog co-processors in silicon photonics and use it to perform the exponentiation operation and the recovery of a signal in the presence of multiplicative distortion. Finally, the function is realized by exploiting nonlinear-absorption-enhanced Raman amplification saturation in a silicon waveguide.

AtPDS over-expression in tomato: exposing unique patterns of carotenoid self-regulation and an alternative strategy for the enhancement of fruit carotenoid content

USDA-ARS?s Scientific Manuscript database

The regulation of plant carotenogenesis is an active research area for both biological discovery and practical implementation. In tomato, we demonstrate additional bottlenecks exist in the poly-cis-transformation of phytoene to lycopene in the context of ripening-induced PSY1 expression and activity...

Response Activation in Overlapping Tasks and the Response-Selection Bottleneck

ERIC Educational Resources Information Center

Schubert, Torsten; Fischer, Rico; Stelzel, Christine

2008-01-01

The authors investigated the impact of response activation on dual-task performance by presenting a subliminal prime before the stimulus in Task 2 (S2) of a psychological refractory period (PRP) task. Congruence between prime and S2 modulated the reaction times in Task 2 at short stimulus onset asynchrony despite a PRP effect. This Task 2…

An innovative computer design for modeling forest landscape change in very large spatial extents with fine resolutions

Treesearch

Jian Yang; Hong S. He; Stephen R. Shifley; Frank R. Thompson; Yangjian Zhang

2011-01-01

Although forest landscape models (FLMs) have benefited greatly from ongoing advances of computer technology and software engineering, computing capacity remains a bottleneck in the design and development of FLMs. Computer memory overhead and run time efficiency are primary limiting factors when applying forest landscape models to simulate large landscapes with fine...

The Chosen Tokens: Exploring the Work Experiences and Career Aspirations of Latina Midlevel Student Affairs Administrators in Higher Education

ERIC Educational Resources Information Center

Pertuz, Sofia Bautista

2017-01-01

Student Affairs serves as a viable career option for professionals working in higher education, including Latinas, who have increasingly entered as undergraduate students and found careers in student affairs. Latinas seem to be bottlenecked at midlevel, with few advancing to senior level leadership positions. According to the literature, negative…

A Candidate for the Attentional Bottleneck: Set-Size Specific Modulation of the Right TPJ during Attentive Enumeration

ERIC Educational Resources Information Center

Vetter, Petra; Butterworth, Brian; Bahrami, Bahador

2011-01-01

Several recent behavioral studies have shown that the enumeration of a small number of items (a process termed "subitizing") depends on the availability of attentional resources and is not a preattentive process as previously thought. Here we studied the neural correlates of visual enumeration under different attentional loads in a dual-task…

Evidence for an extreme bottleneck in a rare Mexican pinyon: genetic diversity, disequilibrium, and the mating system in Pinus maxamartinezii

Treesearch

F. Thomas Ledig; M. Thompson Conkle; Basilio Bermejo-Velázquez; Teobaldo Eguiluz-Piedra; Paul D. Hodgskiss; David R. Johnson; William S. Dvorak

1999-01-01

Maxipinon (Pinus maximartinezii Rzedowski), which is confined to a single population of approximately 2000 to 2500 mature trees, covers about 400 ha in southern Zacatecas, Mexico. Genetic diversity measured by expected heterozygosity was 0.122, which is moderate for pines. However, percentage polymorphic loci was low, 30.3%. The fixation index (

Aging Professors Create a Faculty Bottleneck

ERIC Educational Resources Information Center

June, Audrey Williams

2012-01-01

A growing proportion of the nation's professors are at the same point in their career: still working, but with the end of their careers in sight. Their tendency to remain on the job as long as their work is enjoyable--or, during economic downturns, long enough to make sure they have enough money to live on in retirement--has led the professoriate…

How to Construct Curricula for Finance Professional under Credit System in China

ERIC Educational Resources Information Center

Ma, Yuanyuan

2014-01-01

As a kind of teaching system, the credit system is constructed according to the elective system. It is benefit for improving teaching in implementing credit system. There are still some constraints during the transition from the academic year system to the credit one. In this paper, we shall first briefly introduce the bottleneck of credit system.…

Calculation and visualization of free energy barriers for several VOCs and TNT in HKUST-1.

PubMed

Sarkisov, Lev

2012-11-28

A simple protocol based on a lattice representation of the porous space is proposed to locate and characterize the free energy bottle-necks in rigid metal organic frameworks. As an illustration we apply this method to HKUST-1 to demonstrate that there are impassable free energy barriers for molecules of trinitrotoluene in this structure.

Hands-on resonance-enhanced photoacoustic detection

NASA Astrophysics Data System (ADS)

Euler, Manfred

2001-10-01

The design of an improved photoacoustic converter cell using kitchen equipment is described. It operates by changing manually the Helmholtz resonance frequency of bottles by adjusting the distance between the bottleneck and the outer ear. The experiment helps to gain insights in ear performance, in photoacoustic detection methods, in resonance phenomena and their role for detecting small periodic signals in the presence of noise.

Teacher as a Key Role Player to Induce Quality Education: Challenges and Prospects of Primary Schools in Addis Ababa

ERIC Educational Resources Information Center

Shishigu, Aweke

2016-01-01

There is no question that Ethiopia registered an extraordinary achievement in terms of increasing student enrolment, but quality education still remains a challenge and is becoming a bottleneck for the country. The efforts made to improve quality through Education Sector Development Plan (ESDP) are promising. But those changes are worse doing if…

Back of the Envelope Reasoning for Robust Quantitative Problem Solving

DTIC Science & Technology

2007-12-31

limited numeric vocabulary, for example, the Pirahã tribe in Amazonia [Gordon, 2004] and Munduruku [Pica et al., 2004], an Amazonian language... investigation of category structure: 1. Level of categorization: Rosch [1978] identifies three levels of categorization: subordinate, basic-level...Using Common Sense Knowledge to Overcome Brittleness and Knowledge Acquisition Bottlenecks. AI Magazine . Lenhart K. Schubert and Matthew Tong

Unstructured Grid Adaptation: Status, Potential Impacts, and Recommended Investments Toward CFD Vision 2030

NASA Technical Reports Server (NTRS)

Park, Michael A.; Krakos, Joshua A.; Michal, Todd; Loseille, Adrien; Alonso, Juan J.

2016-01-01

Unstructured grid adaptation is a powerful tool to control discretization error for Computational Fluid Dynamics (CFD). It has enabled key increases in the accuracy, automation, and capacity of some fluid simulation applications. Slotnick et al. provides a number of case studies in the CFD Vision 2030 Study: A Path to Revolutionary Computational Aerosciences to illustrate the current state of CFD capability and capacity. The authors forecast the potential impact of emerging High Performance Computing (HPC) environments forecast in the year 2030 and identify that mesh generation and adaptivity continue to be significant bottlenecks in the CFD work flow. These bottlenecks may persist because very little government investment has been targeted in these areas. To motivate investment, the impacts of improved grid adaptation technologies are identified. The CFD Vision 2030 Study roadmap and anticipated capabilities in complementary disciplines are quoted to provide context for the progress made in grid adaptation in the past fifteen years, current status, and a forecast for the next fifteen years with recommended investments. These investments are specific to mesh adaptation and impact other aspects of the CFD process. Finally, a strategy is identified to diffuse grid adaptation technology into production CFD work flows.

Development and bottlenecks of renewable electricity generation in China: a critical review.

PubMed

Hu, Yuanan; Cheng, Hefa

2013-04-02

This review provides an overview on the development and status of electricity generation from renewable energy sources, namely hydropower, wind power, solar power, biomass energy, and geothermal energy, and discusses the technology, policy, and finance bottlenecks limiting growth of the renewable energy industry in China. Renewable energy, dominated by hydropower, currently accounts for more than 25% of the total electricity generation capacity. China is the world's largest generator of both hydropower and wind power, and also the largest manufacturer and exporter of photovoltaic cells. Electricity production from solar and biomass energy is at the early stages of development in China, while geothermal power generation has received little attention recently. The spatial mismatch in renewable energy supply and electricity demand requires construction of long-distance transmission networks, while the intermittence of renewable energy poses significant technical problems for feeding the generated electricity into the power grid. Besides greater investment in research and technology development, effective policies and financial measures should also be developed and improved to better support the healthy and sustained growth of renewable electricity generation. Meanwhile, attention should be paid to the potential impacts on the local environment from renewable energy development, despite the wider benefits for climate change.

Real-Time Lunar Prospector Data Visualization Using Web-Based Java

NASA Technical Reports Server (NTRS)

Deardorff, D. Glenn; Green, Bryan D.; Gerald-Yamasaki, Michael (Technical Monitor)

1998-01-01

The Lunar Prospector was co-developed by NASA Ames Research Center and Lockheed Martin, and was launched on January 6th, 1998. Its mission is to search for water ice and various elements in the Moon's surface, map its magnetic and gravity fields, and detect volcanic activity. For the first time, the World Wide Web is being used to graphically display near-real-time data from a planetary exploration mission to the global public. Science data from the craft's instruments, as well as engineering data for the spacecraft subsystems, are continuously displayed in time-varying XY plots. The craft's current location is displayed relative to the whole Moon, and as an off-craft observer would see in the reference frame of the craft, with the lunar terrain scrolling underneath. These features are implemented as Java applets. Analyzed data (element and mass distribution) is presented as 3D lunar maps using VRML and Javascript. During the development phase, implementations of the Java Virtual Machine were just beginning to mature enough to adequately accommodate our target featureset; incomplete and varying implementations were the biggest bottleneck to our ideal of ubiquitous browser access. Bottlenecks notwithstanding, the reaction from the Internet community was overwhelmingly enthusiastic.