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Annals of the New York Academy of Sciences

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https://www.readbyqxmd.com/read/28072904/resistance-diagnosis-and-the-changing-economics-of-antibiotic-discovery
#1
David McAdams
Point-of-care diagnostics that can determine an infection's antibiotic sensitivity increase the profitability of new antibiotics that enjoy patent protection, even when such diagnostics reduce the quantity of antibiotics sold. Advances in the science and technology underpinning rapid resistance diagnostics can therefore be expected to spur efforts to discover and develop new antibiotics, especially those with a narrow spectrum of activity that would otherwise fail to find a market.
January 10, 2017: Annals of the New York Academy of Sciences
https://www.readbyqxmd.com/read/28036113/evolutionary-ecology-of-virus-emergence
#2
John J Dennehy
The cross-species transmission of viruses into new host populations, termed virus emergence, is a significant issue in public health, agriculture, wildlife management, and related fields. Virus emergence requires overlap between host populations, alterations in virus genetics to permit infection of new hosts, and adaptation to novel hosts such that between-host transmission is sustainable, all of which are the purview of the fields of ecology and evolution. A firm understanding of the ecology of viruses and how they evolve is required for understanding how and why viruses emerge...
December 30, 2016: Annals of the New York Academy of Sciences
https://www.readbyqxmd.com/read/28009055/life-history-evolution-reproduction-and-the-origins-of-sex-dependent-aging-and-longevity
#3
Robert C Brooks, Michael G Garratt
Males and females in many species differ in how they age and how long they live. These differences have motivated much research, concerning both their evolution and the underlying mechanisms that cause them. We review how differences in male and female life histories have evolved to shape patterns of aging and some of the mechanisms and pathways involved. We pay particular attention to three areas where considerable potential for synergy between mechanistic and evolutionary research exists: (1) the role of estrogens, androgens, the growth hormone/insulin-like growth factor 1 pathway, and the mechanistic target of rapamycin signaling pathway in sex-dependent growth and reproduction; (2) sexual conflict over mating rate and fertility, and how mate presence or mating can become an avenue for males and females to directly affect each other's life span; and (3) the link between dietary restriction and aging, and the emerging understanding that only the restriction of certain nutrients is involved and that this is linked to reproduction...
December 23, 2016: Annals of the New York Academy of Sciences
https://www.readbyqxmd.com/read/28009051/a-brief-primer-on-genomic-epidemiology-lessons-learned-from-mycobacterium-tuberculosis
#4
Jennifer L Guthrie, Jennifer L Gardy
Genomics is now firmly established as a technique for the investigation and reconstruction of communicable disease outbreaks, with many genomic epidemiology studies focusing on revealing transmission routes of Mycobacterium tuberculosis. In this primer, we introduce the basic techniques underlying transmission inference from genomic data, using illustrative examples from M. tuberculosis and other pathogens routinely sequenced by public health agencies. We describe the laboratory and epidemiological scenarios under which genomics may or may not be used, provide an introduction to sequencing technologies and bioinformatics approaches to identifying transmission-informative variation and resistance-associated mutations, and discuss how variation must be considered in the light of available clinical and epidemiological information to infer transmission...
December 23, 2016: Annals of the New York Academy of Sciences
https://www.readbyqxmd.com/read/28009050/factors-influencing-micronutrient-bioavailability-in-biofortified-crops
#5
Aurélie Bechoff, Claudie Dhuique-Mayer
Dietary and human factors have been found to be the major factors influencing the bioavailability of micronutrients, such as provitamin A carotenoid (pVAC), iron, and zinc, in biofortified crops. Dietary factors are related to food matrix structure and composition. Processing can improve pVAC bioavailability by disrupting the food matrix but can also result in carotenoid losses. By degrading antinutrients, such as phytate, processing can also enhance mineral bioavailability. In in vivo interventions, biofortified crops have been shown to be overall efficacious in reducing micronutrient deficiency, with bioconversion factors varying between 2...
December 23, 2016: Annals of the New York Academy of Sciences
https://www.readbyqxmd.com/read/27997700/evolution-of-bird-genomes-a-transposon-s-eye-view
#6
Aurélie Kapusta, Alexander Suh
Birds, the most species-rich monophyletic group of land vertebrates, have been subject to some of the most intense sequencing efforts to date, making them an ideal case study for recent developments in genomics research. Here, we review how our understanding of bird genomes has changed with the recent sequencing of more than 75 species from all major avian taxa. We illuminate avian genome evolution from a previously neglected perspective: their repetitive genomic parasites, transposable elements (TEs) and endogenous viral elements (EVEs)...
December 20, 2016: Annals of the New York Academy of Sciences
https://www.readbyqxmd.com/read/27997690/application-of-genomic-technologies-to-measure-and-monitor-antibiotic-resistance-in-animals
#7
Jian-Qiang Su, Li Cui, Qing-Lin Chen, Xin-Li An, Yong-Guan Zhu
One of the richest reservoirs of antibiotic-resistant bacteria and genes, animal intestinal microbiota contributes to the spread of antibiotic resistance in the environment and, potentially, to human pathogens. Both culture-based genomic technology and culture-independent metagenomics have been developed to investigate the abundance and diversity of antibiotic resistance genes. The characteristics, strengths, limitations, and challenges of these genomic approaches are discussed in this review in the context of antibiotic resistance in animals...
December 20, 2016: Annals of the New York Academy of Sciences
https://www.readbyqxmd.com/read/27936291/pleiotropy-constraint-and-modularity-in-the-evolution-of-life-histories-insights-from-genomic-analyses
#8
Kimberly A Hughes, Jeff Leips
Multicellular organisms display an enormous range of life history (LH) strategies and present an evolutionary conundrum; despite strong natural selection, LH traits are characterized by high levels of genetic variation. To understand the evolution of life histories and maintenance of this variation, the specific phenotypic effects of segregating alleles and the genetic networks in which they act need to be elucidated. In particular, the extent to which LH evolution is constrained by the pleiotropy of alleles contributing to LH variation is generally unknown...
December 9, 2016: Annals of the New York Academy of Sciences
https://www.readbyqxmd.com/read/27936288/staple-crops-biofortified-with-increased-vitamins-and-minerals-considerations-for-a-public-health-strategy
#9
Maria Nieves Garcia-Casal, Juan Pablo Peña-Rosas, Boitshepo Giyose
Biofortification of staple crops has been proposed as a strategy to address micronutrient malnutrition, particularly with respect to insufficient intake of vitamin A, iron, zinc, and folate. The World Health Organization, in collaboration with the Food and Agriculture Organization of the United Nations and the Sackler Institute for Nutrition Science at the New York Academy of Sciences, convened a technical consultation entitled "Staple Crops Biofortified with Vitamins and Minerals: Considerations for a Public Health Strategy" in April 2016...
December 9, 2016: Annals of the New York Academy of Sciences
https://www.readbyqxmd.com/read/27936284/utility-of-preclinical-drug-versus-food-choice-procedures-to-evaluate-candidate-medications-for-methamphetamine-use-disorder
#10
Matthew L Banks
Substance use disorders are diagnosed as a manifestation of inappropriate behavioral allocation toward abused drugs and away from other behaviors maintained by more adaptive nondrug reinforcers (e.g., money and social relationships). Substance use disorder treatment goals include not only decreasing drug-maintained behavior but also promoting behavioral reallocation toward these socially adaptive alternative reinforcers. Preclinical drug self-administration procedures that offer concurrent access to both drug and nondrug reinforcers provide a translationally relevant dependent measure of behavioral allocation that may be useful for candidate medication evaluation...
December 9, 2016: Annals of the New York Academy of Sciences
https://www.readbyqxmd.com/read/27918838/quality-of-governance-and-effectiveness-of-protected-areas-crucial-concepts-for-conservation-planning
#11
Johanna Eklund, Mar Cabeza
Protected areas (PAs) are a key tool for biodiversity conservation and play a central role in the Convention on Biological Diversity. Recently, the effectiveness of PAs has been questioned, and assessing how effective they are in enabling the future persistence of biodiversity is not trivial. Here, we focus on terrestrial PAs and clarify the terminology related to PA effectiveness, distinguishing between management and ecological aspects. We suggest that the quality of governance affects both aspects of effectiveness but recognize a lack of synthetic understanding of the topic...
December 5, 2016: Annals of the New York Academy of Sciences
https://www.readbyqxmd.com/read/27918837/global-pulses-scenario-status-and-outlook
#12
P K Joshi, P Parthasarathy Rao
Although pulse production grew significantly by 1.3% between 1980 and 2013, its per capita availability remained stagnant at around 6.5 kg/capita/year. In 1961, its availability was 9.3 kg/capita/year. One consequence of slower growth in its production is rising pulse prices, which are twice that of cereals. The declining availability of pulses also triggered a boom in its trade, with 19% of the global pulse production traded in 2011 compared with 7% in 1980. In absolute terms, there has been a more than fourfold increase in pulse trade, compared with an only 1...
December 5, 2016: Annals of the New York Academy of Sciences
https://www.readbyqxmd.com/read/27918836/evolvix-best-names-for-semantic-reproducibility-across-code2brain-interfaces
#13
Laurence Loewe, Katherine S Scheuer, Seth A Keel, Vaibhav Vyas, Ben Liblit, Bret Hanlon, Michael C Ferris, John Yin, Inês Dutra, Anthony Pietsch, Christine G Javid, Cecilia L Moog, Jocelyn Meyer, Jerdon Dresel, Brian McLoone, Sonya Loberger, Arezoo Movaghar, Morgaine Gilchrist-Scott, Yazeed Sabri, Dave Sescleifer, Ivan Pereda-Zorrilla, Andrew Zietlow, Rodrigo Smith, Samantha Pietenpol, Jacob Goldfinger, Sarah L Atzen, Erika Freiberg, Noah P Waters, Claire Nusbaum, Erik Nolan, Alyssa Hotz, Richard M Kliman, Ayalew Mentewab, Nathan Fregien, Martha Loewe
Names in programming are vital for understanding the meaning of code and big data. We define code2brain (C2B) interfaces as maps in compilers and brains between meaning and naming syntax, which help to understand executable code. While working toward an Evolvix syntax for general-purpose programming that makes accurate modeling easy for biologists, we observed how names affect C2B quality. To protect learning and coding investments, C2B interfaces require long-term backward compatibility and semantic reproducibility (accurate reproduction of computational meaning from coder-brains to reader-brains by code alone)...
December 5, 2016: Annals of the New York Academy of Sciences
https://www.readbyqxmd.com/read/27918835/the-ubiquitous-self-what-the-properties-of-self-bias-tell-us-about-the-self
#14
Jie Sui, Glyn W Humphreys
People show systematic biases in perception, memory, and attention to favor information related to themselves over information related to other people. Researchers have examined these biases in order to throw light on the nature of the self. We review this evidence in memory, face recognition, and simple perceptual matching tasks through objective measures of self-biases. We argue that the self serves as a stable anchor across different forms of judgment and that referring a stimulus to ourselves enhances the binding of stimulus features at different stages of processing (e...
December 5, 2016: Annals of the New York Academy of Sciences
https://www.readbyqxmd.com/read/27875856/antimicrobial-resistance-surveillance-in-the-genomic-age
#15
Andrew G McArthur, Kara K Tsang
The loss of effective antimicrobials is reducing our ability to protect the global population from infectious disease. However, the field of antibiotic drug discovery and the public health monitoring of antimicrobial resistance (AMR) is beginning to exploit the power of genome and metagenome sequencing. The creation of novel AMR bioinformatics tools and databases and their continued development will advance our understanding of the molecular mechanisms and threat severity of antibiotic resistance, while simultaneously improving our ability to accurately predict and screen for antibiotic resistance genes within environmental, agricultural, and clinical settings...
November 22, 2016: Annals of the New York Academy of Sciences
https://www.readbyqxmd.com/read/27862006/developmental-sexual-dimorphism-and-the-evolution-of-mechanisms-for-adjustment-of-sex-ratios-in-mammals
#16
Elissa Z Cameron, Amy M Edwards, Laura M Parsley
Sex allocation theory predicts biased offspring sex ratios in relation to local conditions if they would maximize parental lifetime reproductive return. In mammals, the extent of the birth sex bias is often unpredictable and inconsistent, leading some to question its evolutionary significance. For facultative adjustment of sex ratios to occur, males and females would need to be detectably different from an early developmental stage, but classic sexual dimorphism arises from hormonal influences after gonadal development...
November 18, 2016: Annals of the New York Academy of Sciences
https://www.readbyqxmd.com/read/27862002/distributed-data-networks-a-blueprint-for-big-data-sharing-and-healthcare-analytics
#17
Jennifer R Popovic
This paper defines the attributes of distributed data networks and outlines the data and analytic infrastructure needed to build and maintain a successful network. We use examples from one successful implementation of a large-scale, multisite, healthcare-related distributed data network, the U.S. Food and Drug Administration-sponsored Sentinel Initiative. Analytic infrastructure-development concepts are discussed from the perspective of promoting six pillars of analytic infrastructure: consistency, reusability, flexibility, scalability, transparency, and reproducibility...
November 18, 2016: Annals of the New York Academy of Sciences
https://www.readbyqxmd.com/read/27862010/extension-of-research-data-repository-system-to-support-direct-compute-access-to-biomedical-datasets-enhancing-dataverse-to-support-large-datasets
#18
Bill McKinney, Peter A Meyer, Mercè Crosas, Piotr Sliz
Access to experimental X-ray diffraction image data is important for validation and reproduction of macromolecular models and indispensable for the development of structural biology processing methods. In response to the evolving needs of the structural biology community, we recently established a diffraction data publication system, the Structural Biology Data Grid (SBDG, data.sbgrid.org), to preserve primary experimental datasets supporting scientific publications. All datasets published through the SBDG are freely available to the research community under a public domain dedication license, with metadata compliant with the DataCite Schema (schema...
November 10, 2016: Annals of the New York Academy of Sciences
https://www.readbyqxmd.com/read/27861983/genomic-and-metagenomic-technologies-to-explore-the-antibiotic-resistance-mobilome
#19
José L Martínez, Teresa M Coque, Val F Lanza, Fernando de la Cruz, Fernando Baquero
Antibiotic resistance is a relevant problem for human health that requires global approaches to establish a deep understanding of the processes of acquisition, stabilization, and spread of resistance among human bacterial pathogens. Since natural (nonclinical) ecosystems are reservoirs of resistance genes, a health-integrated study of the epidemiology of antibiotic resistance requires the exploration of such ecosystems with the aim of determining the role they may play in the selection, evolution, and spread of antibiotic resistance genes, involving the so-called resistance mobilome...
November 10, 2016: Annals of the New York Academy of Sciences
https://www.readbyqxmd.com/read/27859384/new-views-on-the-selection-acting-on-genetic-polymorphism-in-central-metabolic-genes
#20
Walter F Eanes
Studies of the polymorphism of central metabolic genes as a source of fitness variation in natural populations date back to the discovery of allozymes in the 1960s. The unique features of these genes and their enzymes and our knowledge base greatly facilitates the systems-level study of this group. The expectation that pathway flux control is central to understanding the molecular evolution of genes is discussed, as well as studies that attempt to place gene-specific molecular evolution and polymorphism into a context of pathway and network architecture...
November 10, 2016: Annals of the New York Academy of Sciences
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