871 research outputs found
Soft topographic map for clustering and classification of bacteria
In this work a new method for clustering and building a
topographic representation of a bacteria taxonomy is presented. The method is based on the analysis of stable parts of the genome, the so-called “housekeeping genes”. The proposed method generates topographic maps of the bacteria taxonomy, where relations among different
type strains can be visually inspected and verified. Two well known DNA alignement algorithms are applied to the genomic sequences. Topographic maps are optimized to represent the similarity among the sequences according to their evolutionary distances. The experimental analysis is carried out on 147 type strains of the Gammaprotebacteria
class by means of the 16S rRNA housekeeping gene. Complete sequences of the gene have been retrieved from the NCBI public database. In the experimental tests the maps show clusters of homologous type strains and present some singular cases potentially due to incorrect classification
or erroneous annotations in the database
A Critical Review of Anti‐Bullying Programs in North American Elementary Schools
BACKGROUNDBullying behavior is a concern among school‐aged youth and anti‐bullying programs have been implemented in schools throughout North America. Most anti‐bullying programs are delivered to adolescent youth because antisocial‐aggressive behaviors are typically associated with this developmental stage. This paper is a review of empirically evaluated school‐based bullying prevention and intervention programs in North American elementary schools.METHODSWe conducted a systematic, critical review of bullying prevention programming. Data were analyzed to determine the study method, intervention components, measurement of bullying, aggression, or peer victimization, outcomes measured, and results.RESULTSOur review resulted in the identification of 10 interventions aimed at youth in grades K‐6 enrolled in North American elementary schools. Effective intervention strategies targeted a variety of bullying behaviors using diverse mechanisms and included a school—and community‐wide approach. Direct outcomes of the reviewed evaluations were centered on bullying, aggression, and victimization. Indirect outcomes of review evaluations included strategies for bystanders, school achievement, perceived school safety, and knowledge or attitudes about bullying.CONCLUSIONSRecommendations for promising practices in effective bullying intervention programming are offered. The review concludes with suggestions for supporting school health staff and in‐service teachers drawn from the body of research, and offers direction for future study.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/151360/1/josh12814_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/151360/2/josh12814.pd
Chapter: Landcare on the Poverty-Protection Interface in an Asian Watershed
Serious methodological and policy hurdles constrain effective natural resource
management that alleviates poverty while protecting environmental services in tropical
watersheds. We review the development of an approach to integrate biodiversity
conservation and agroforestry development through the active involvement of
communities and their local governments near the Kitanglad Range Natural Park in the
Manupali watershed, central Mindanao, the Philippines. Agroforestry innovations were
developed to suit the biophysical and socioeconomic conditions of the buffer zone.
These included practices for tree farming, and conservation farming for annual cropping
on slopes. Institutional innovations improved resource management, resulting in an
effective social contract to protect the natural biodiversity o f the park. Fruit and timber
tree production dramatically increased, re-establishing tree cover in the buffer zone.
Natural vegetative contour strips were installed on several hundred sloping farms. Soil
erosion and runoff declined, while the buffer strips increased maize yields by an average
of 0.5 t/ha on hill-slope farms. The scientific knowledge base guided the development
and implementation of a natural resource management plan for the municipality of
Lantapan. A dynamic grassroots movement o f farmer-led Landcare groups evolved in the villages near the park boundary, which had significant impact on conservation in both the
natural and managed ecosystems. Encroachment in the natural park was reduced 95% in three
years. The local Landcare groups also restored stream corridor vegetation. This integrated
approach has been recognized as a national model for local natural resource and watershed
management in the Philippines. Currently, the collaborating institutions are evolving a negotiation
support system to resolve the interactions between the three management domains: the park,
the ancestral domain claim, and the municipalities. This integrated systems approach operated
effectively with highly constrained funding, suggesting that commitment and impact may best
be stimulated by a “drip-feed” approach rather than by large, externally funded efforts
Overview of mathematical approaches used to model bacterial chemotaxis I: the single cell
Mathematical modeling of bacterial chemotaxis systems has been influential and insightful in helping to understand experimental observations. We provide here a comprehensive overview of the range of mathematical approaches used for modeling, within a single bacterium, chemotactic processes caused by changes to external gradients in its environment. Specific areas of the bacterial system which have been studied and modeled are discussed in detail, including the modeling of adaptation in response to attractant gradients, the intracellular phosphorylation cascade, membrane receptor clustering, and spatial modeling of intracellular protein signal transduction. The importance of producing robust models that address adaptation, gain, and sensitivity are also discussed. This review highlights that while mathematical modeling has aided in understanding bacterial chemotaxis on the individual cell scale and guiding experimental design, no single model succeeds in robustly describing all of the basic elements of the cell. We conclude by discussing the importance of this and the future of modeling in this area
Spectroscopic and Mechanistic Studies of Heterodimetallic Forms of Metallo-β-lactamase NDM-1
In an effort to characterize the roles of each metal ion in metallo-β-lactamase NDM-1, heterodimetallic analogues (CoCo-, ZnCo-, and CoCd-) of the enzyme were generated and characterized. UV–vis, 1H NMR, EPR, and EXAFS spectroscopies were used to confirm the fidelity of the metal substitutions, including the presence of a homogeneous, heterodimetallic cluster, with a single-atom bridge. This marks the first preparation of a metallo-β-lactamase selectively substituted with a paramagnetic metal ion, Co(II), either in the Zn1 (CoCd-NDM-1) or in the Zn2 site (ZnCo-NDM-1), as well as both (CoCo-NDM-1). We then used these metal-substituted forms of the enzyme to probe the reaction mechanism, using steady-state and stopped-flow kinetics, stopped-flow fluorescence, and rapid-freeze-quench EPR. Both metal sites show significant effects on the kinetic constants, and both paramagnetic variants (CoCd- and ZnCo-NDM-1) showed significant structural changes on reaction with substrate. These changes are discussed in terms of a minimal kinetic mechanism that incorporates all of the data
Big-Data-Driven Materials Science and its FAIR Data Infrastructure
This chapter addresses the forth paradigm of materials research -- big-data
driven materials science. Its concepts and state-of-the-art are described, and
its challenges and chances are discussed. For furthering the field, Open Data
and an all-embracing sharing, an efficient data infrastructure, and the rich
ecosystem of computer codes used in the community are of critical importance.
For shaping this forth paradigm and contributing to the development or
discovery of improved and novel materials, data must be what is now called FAIR
-- Findable, Accessible, Interoperable and Re-purposable/Re-usable. This sets
the stage for advances of methods from artificial intelligence that operate on
large data sets to find trends and patterns that cannot be obtained from
individual calculations and not even directly from high-throughput studies.
Recent progress is reviewed and demonstrated, and the chapter is concluded by a
forward-looking perspective, addressing important not yet solved challenges.Comment: submitted to the Handbook of Materials Modeling (eds. S. Yip and W.
Andreoni), Springer 2018/201
The Role of Genomics in the Identification, Prediction, and Prevention of Biological Threats
In all likelihood, it is only a matter of time before our public health system will face a major biological threat, whether intentionally dispersed or originating from a known or newly emerging infectious disease. It is necessary not only to increase our reactive “biodefense,” but also to be proactive and increase our preparedness. To achieve this goal, it is essential that the scientific and public health communities fully embrace the genomic revolution, and that novel bioinformatic and computing tools necessary to make great strides in our understanding of these novel and emerging threats be developed. Genomics has graduated from a specialized field of science to a research tool that soon will be routine in research laboratories and clinical settings. Because the technology is becoming more affordable, genomics can and should be used proactively to build our preparedness and responsiveness to biological threats. All pieces, including major continued funding, advances in next-generation sequencing technologies, bioinformatics infrastructures, and open access to data and metadata, are being set in place for genomics to play a central role in our public health system
Emergent complex neural dynamics
A large repertoire of spatiotemporal activity patterns in the brain is the
basis for adaptive behaviour. Understanding the mechanism by which the brain's
hundred billion neurons and hundred trillion synapses manage to produce such a
range of cortical configurations in a flexible manner remains a fundamental
problem in neuroscience. One plausible solution is the involvement of universal
mechanisms of emergent complex phenomena evident in dynamical systems poised
near a critical point of a second-order phase transition. We review recent
theoretical and empirical results supporting the notion that the brain is
naturally poised near criticality, as well as its implications for better
understanding of the brain
Does owning a pet protect older people against loneliness?
This article has been made available through the Brunel Open Access Publishing Fund.Pet ownership is thought to make a positive contribution to health, health behaviours and the general well-being of older people. More specifically pet ownership is often proposed as a solution to the problem of loneliness in later life and specific 'pet based' interventions have been developed to combat loneliness. However the evidence to support this relationship is slim and it is assumed that pet ownership is a protection against loneliness rather than a response to loneliness. The aim of this paper is to examine the association between pet ownership and loneliness by exploring if pet ownership is a response to, or protection against, loneliness using Waves 0-5 from the English Longitudinal Study of Ageing (ELSA)
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