212 research outputs found

    Obscured phylogeny and possible recombinational dormancy in Escherichia coli

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    <p>Abstract</p> <p>Background</p> <p><it>Escherichia coli </it>is one of the best studied organisms in all of biology, but its phylogenetic structure has been difficult to resolve with current data and analytical techniques. We analyzed single nucleotide polymorphisms in chromosomes of representative strains to reconstruct the topology of its emergence.</p> <p>Results</p> <p>The phylogeny of <it>E. coli </it>varies according to the segment of chromosome analyzed. Recombination between extant <it>E. coli </it>groups is largely limited to only three intergroup pairings.</p> <p>Conclusions</p> <p>Segment-dependent phylogenies most likely are legacies of a complex recombination history. However, <it>E. coli </it>are now in an epoch in which they no longer broadly share DNA. Using the definition of species as organisms that freely exchange genetic material, this recombinational dormancy could reflect either the end of <it>E. coli </it>as a species, or herald the coalescence of <it>E. coli </it>groups into new species.</p

    Reasoning Under Uncertainty: Towards Collaborative Interactive Machine Learning

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    In this paper, we present the current state-of-the-art of decision making (DM) and machine learning (ML) and bridge the two research domains to create an integrated approach of complex problem solving based on human and computational agents. We present a novel classification of ML, emphasizing the human-in-the-loop in interactive ML (iML) and more specific on collaborative interactive ML (ciML), which we understand as a deep integrated version of iML, where humans and algorithms work hand in hand to solve complex problems. Both humans and computers have specific strengths and weaknesses and integrating humans into machine learning processes might be a very efficient way for tackling problems. This approach bears immense research potential for various domains, e.g., in health informatics or in industrial applications. We outline open questions and name future challenges that have to be addressed by the research community to enable the use of collaborative interactive machine learning for problem solving in a large scale

    Estimating the Impact of the Recent Economic Crisis on Work Time in Turkey

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    This paper provides estimates of the impact of the recent economic crisis on paid and unpaid work time in Turkey. The data used in this study come from the first and only time-use survey available at the national level. Infrequency of collection of time-use data in Turkey does not allow us to make a direct comparison of pre-versus postcrisis time-use patterns. We introduce a tractable way for estimating these possible effects by measuring the impact of an increase in unemployment risk on time-use patterns of women and men living in couple households. The method developed here can be applied to other developing-country cases where there is a lack of longitudinal data availability. Our findings support the argument that economic crises reinforce the preexisting gender inequalities in work time

    The genome sequence of E. coli W (ATCC 9637): comparative genome analysis and an improved genome-scale reconstruction of E. coli

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    Background: Escherichia coli is a model prokaryote, an important pathogen, and a key organism for industrial biotechnology. E. coli W (ATCC 9637), one of four strains designated as safe for laboratory purposes, has not been sequenced. E. coli W is a fast-growing strain and is the only safe strain that can utilize sucrose as a carbon source. Lifecycle analysis has demonstrated that sucrose from sugarcane is a preferred carbon source for industrial bioprocesses

    Social Movements in Urban Society: The City as A Space of Politicization

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    Recent anti-systemic social movements have illustrated the central role of cities in social movement mobilization. We not only highlight the characteristics of urban social relations that make cities fertile ground for mobilization, but also point to the disjunctures between the geographies and spatialities of social relations in the city, and the geographies and spatialities of many systemic processes. Struggles for a more just society must consider the broad geographies and spatialities of oppression, which we illustrate with a brief analysis of the Occupy movement. Finally, we introduce the next five articles in this special issue, all illustrating the importance of the geographies and spatialities of urban social struggle

    A 680,000-person megastudy of nudges to encourage vaccination in pharmacies

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    Encouraging vaccination is a pressing policy problem. To assess whether text-based reminders can encourage pharmacy vaccination and what kinds of messages work best, we conducted a megastudy. We randomly assigned 689,693 Walmart pharmacy patients to receive one of 22 different text reminders using a variety of different behavioral science principles to nudge flu vaccination or to a business-as-usual control condition that received no messages. We found that the reminder texts that we tested increased pharmacy vaccination rates by an average of 2.0 percentage points, or 6.8%, over a 3-mo follow-up period. The most-effective messages reminded patients that a flu shot was waiting for them and delivered reminders on multiple days. The top-performing intervention included two texts delivered 3 d apart and communicated to patients that a vaccine was “waiting for you.” Neither experts nor lay people anticipated that this would be the best-performing treatment, underscoring the value of simultaneously testing many different nudges in a highly powered megastudy.https://www.pnas.org/content/pnas/119/6/e2115126119.full.pd

    A study of genetic polymorphisms of milk β-lactoglobulin, α S1 -casein, β-casein, and κ-casein in five dairy breeds

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    Gene frequencies of the milk β-lactoglobulin, α S1 -casein, β-casein, and κ-casein loci have been estimated from 1663 cows of five dairy breeds. Departure from Hardy-Weinberg equilibrium was found only in the κ-casein system in Jerseys. However, chance alone could have accounted for this single significant finding. Results of pairwise comparisons among the five breeds of allele frequencies at these milk protein loci indicate that of the 40 possible tests, only six comparisons are not significant at the 5% probability level. It would appear that these breeds are characterizable in terms of the gene frequencies of these milk protein loci. Nonindependent assortment of genotypes among these milk protein loci was also studied. The closely linked casein loci were not independent in almost all the breeds where tests could be carried out. The only exception was between the α S1 -casein and κ-casein loci in Holsteins. β-Lactoglobulin was independent of the casein loci in all breeds except Brown Swiss, where it was found to be significantly associated with κ-casein. Close linkage is proposed as an important factor for maintaining the observed milk protein polymorphisms.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/44176/1/10528_2004_Article_BF00485960.pd

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    It is a standard practice to test for the signature of homologous recombination in studies examining the genetic diversity of bacterial populations. Although it has emerged that homologous recombination rates can vary widely between species, comparing the results from different studies is made difficult by the diversity of estimation methods used. Here, Multi Locus Sequence Typing (MLST) datasets from a wide variety of bacteria and archaea are analyzed using the ClonalFrame method. This enables a direct comparison between species and allows for a first exploration of the question whether phylogeny or ecology is the primary determinant of homologous recombination rate
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