105 research outputs found
Meeting report : Ocean âomics science, technology and cyberinfrastructure : current challenges and future requirements (August 20-23, 2013)
© The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Standards in Genomic Sciences 9 (2014): 1251-1258, doi:10.4056/sigs.5749944.The National Science Foundationâs EarthCube End User Workshop was held at USCâs Wrigley Marine Science Center on Catalina Island, California in August 2013. The workshop was designed to explore and characterise the needs and tools available to the community focusing on microbial and physical oceanography research with a particular focus on âomic research. The assembled researchers outlined the existing concerns regarding the vast data resources that are being generated, and how we will deal with these resources as their volume and diversity increases. Particular attention was focused on the tools for handling and analysing the existing data, and on the need for the construction and curation of diverse federated databases, as well as development of shared interoperable, âbig-data capableâ analytical tools. The key outputs from this workshop include (i) critical scientific challenges and cyberinfrastructure constraints, (ii) the current and future ocean âomics science grand challenges and questions, and (iii) data management, analytical and associated and cyber-infrastructure capabilities required to meet critical current and future scientific challenges. The main thrust of the meeting and the outcome of this report is a definition of the âomics tools, technologies and infrastructures that facilitate continued advance in ocean science biology, marine biogeochemistry, and biological oceanography.We gratefully acknowledge support for the Ocean âOmics EarthCube end-user workshop by the Geo-sciences Division of the U.S. National Science Foundation
Financing U.S. Graduate Medical Education: A Policy Position Paper of the Alliance for Academic Internal Medicine and the American College of Physicians
In this position paper, the Alliance for Academic Internal Medicine and the American College of Physicians examine the state of graduate medical education (GME) financing in the United States and recent proposals to reform GME funding. They make a series of recommendations to reform the current funding system to better align GME with the needs of the nation's health care workforce. These recommendations include using Medicare GME funds to meet policy goals and to ensure an adequate supply of physicians, a proper specialty mix, and appropriate training sites; spreading the costs of financing GME across the health care system; evaluating the true cost of training a resident and establishing a single per-resident amount; increasing transparency and innovation; and ensuring that primary care residents receive training in well-functioning ambulatory settings that are financially supported for their training roles
Does technology and Innovation Management improve Market Position? Empirical Evidence from Innovating Firms in South Africa
There is a growing recognition of the central role of technology and knowledge management for market success of organizations. Little is empirically know, however, about this relationship. Drawing on the South African Innovation Survey, a unique dataset on innovative behavior of South African firms in manufacturing and services, this paper investigates the question to what extent and in which ways do technology and innovation management activities affect firmsâ market position. Findings show that conducting technology strategy activities pays out. Moreover, especially a combination of internal and external technology audits seems to be beneficial for organizational performance
A meta-analysis of CAG (cytarabine, aclarubicin, G-CSF) regimen for the treatment of 1029 patients with acute myeloid leukemia and myelodysplastic syndrome
The regimen of cytarabine, aclarubicin and G-CSF (CAG) has been widely used in China and Japan for treatment of acute myeloid leukemia (AML) and myelodysplastic syndrome (MDS). We searched literature on CAG between 1995 and 2010 and performed a meta-analysis to determine its overall efficacy using a random-effects or fixed-effects model. Thirty five trials with a total of 1029 AML (n = 814) and MDS (n = 215) patients were included for analysis. The CR rate of AML (57.9%) was significantly higher than that of MDS (45.7%) (p < 0.01). No difference in CR was noted between the new (56.7%) and relapsed/refractory AML (60.1%) (p > 0.05). The CR rate was also significantly higher in patients with favorable (64.5%) and intermediate (69.6%) karyotypes than those with unfavorable one (29.5%) (p < 0.05). Remarkably, the CR rate of CAG was significantly higher than those of non-CAG regimens (odds ratio 2.43). CAG regimen was well tolerated, with cardiotoxicity in 2.3% and early death in 5.2% of the cases. In conclusion, CAG regimen was an effective and safe regimen for the treatment of AML, and may be more effective than non-CAG regimens. Randomized controlled trials are strongly recommended to evaluate its efficacy and safety in comparison with the current standard treatment
Distinct Genetic Architectures for Male and Female Inflorescence Traits of Maize
We compared the genetic architecture of thirteen maize morphological traits in a large population of recombinant inbred lines. Four traits from the male inflorescence (tassel) and three traits from the female inflorescence (ear) were measured and studied using linkage and genome-wide association analyses and compared to three flowering and three leaf traits previously studied in the same population. Inflorescence loci have larger effects than flowering and leaf loci, and ear effects are larger than tassel effects. Ear trait models also have lower predictive ability than tassel, flowering, or leaf trait models. Pleiotropic loci were identified that control elongation of ear and tassel, consistent with their common developmental origin. For these pleiotropic loci, the ear effects are larger than tassel effects even though the same causal polymorphisms are likely involved. This implies that the observed differences in genetic architecture are not due to distinct features of the underlying polymorphisms. Our results support the hypothesis that genetic architecture is a function of trait stability over evolutionary time, since the traits that changed most during the relatively recent domestication of maize have the largest effects
Genomic and epigenetic evidence for oxytocin receptor deficiency in autism
<p>Abstract</p> <p>Background</p> <p>Autism comprises a spectrum of behavioral and cognitive disturbances of childhood development and is known to be highly heritable. Although numerous approaches have been used to identify genes implicated in the development of autism, less than 10% of autism cases have been attributed to single gene disorders.</p> <p>Methods</p> <p>We describe the use of high-resolution genome-wide tilepath microarrays and comparative genomic hybridization to identify copy number variants within 119 probands from multiplex autism families. We next carried out DNA methylation analysis by bisulfite sequencing in a proband and his family, expanding this analysis to methylation analysis of peripheral blood and temporal cortex DNA of autism cases and matched controls from independent datasets. We also assessed oxytocin receptor (OXTR) gene expression within the temporal cortex tissue by quantitative real-time polymerase chain reaction (PCR).</p> <p>Results</p> <p>Our analysis revealed a genomic deletion containing the oxytocin receptor gene, <it>OXTR </it>(MIM accession no.: 167055), previously implicated in autism, was present in an autism proband and his mother who exhibits symptoms of obsessive-compulsive disorder. The proband's affected sibling did not harbor this deletion but instead may exhibit epigenetic misregulation of this gene through aberrant gene silencing by DNA methylation. Further DNA methylation analysis of the CpG island known to regulate <it>OXTR </it>expression identified several CpG dinucleotides that show independent statistically significant increases in the DNA methylation status in the peripheral blood cells and temporal cortex in independent datasets of individuals with autism as compared to control samples. Associated with the increase in methylation of these CpG dinucleotides is our finding that <it>OXTR </it>mRNA showed decreased expression in the temporal cortex tissue of autism cases matched for age and sex compared to controls.</p> <p>Conclusion</p> <p>Together, these data provide further evidence for the role of OXTR and the oxytocin signaling pathway in the etiology of autism and, for the first time, implicate the epigenetic regulation of <it>OXTR </it>in the development of the disorder.</p> <p>See the related commentary by Gurrieri and Neri: <url>http://www.biomedcentral.com/1741-7015/7/63</url></p
Size Doesn't Matter: Towards a More Inclusive Philosophy of Biology
notes: As the primary author, OâMalley drafted the paper, and gathered and analysed data (scientific papers and talks). Conceptual analysis was conducted by both authors.publication-status: Publishedtypes: ArticlePhilosophers of biology, along with everyone else, generally perceive life to fall into two broad categories, the microbes and macrobes, and then pay most of their attention to the latter. âMacrobeâ is the word we propose for larger life forms, and we use it as part of an argument for microbial equality. We suggest that taking more notice of microbes â the dominant life form on the planet, both now and throughout evolutionary history â will transform some of the philosophy of biologyâs standard ideas on ontology, evolution, taxonomy and biodiversity. We set out a number of recent developments in microbiology â including biofilm formation, chemotaxis, quorum sensing and gene transfer â that highlight microbial capacities for cooperation and communication and break down conventional thinking that microbes are solely or primarily single-celled organisms. These insights also bring new perspectives to the levels of selection debate, as well as to discussions of the evolution and nature of multicellularity, and to neo-Darwinian understandings of evolutionary mechanisms. We show how these revisions lead to further complications for microbial classification and the philosophies of systematics and biodiversity. Incorporating microbial insights into the philosophy of biology will challenge many of its assumptions, but also give greater scope and depth to its investigations
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State of the California Current 2013-14: El Niño Looming
In 2013, the California current was dominated by
strong coastal upwelling and high productivity. Indices
of total cumulative upwelling for particular coastal
locations reached some of the highest values on record.
Chlorophyll a levels were high throughout spring and
summer. Catches of upwelling-related fish species were
also high. After a moderate drop in upwelling during fall
2013, the California current system underwent a major
change in phase. Three major basin-scale indicators, the
PDO, the NPGO, and the ENSO-MEI, all changed
phase at some point during the winter of 2013/14. The
PDO changed to positive values, indicative of warmer
waters in the North Pacific; the NPGO to negative values,
indicative of lower productivity along the coast; and
the MEI to positive values, indicative of an oncoming
El Niño. Whereas the majority of the California Current
system appears to have transitioned to an El Niño
state by August 2014, based on decreases in upwelling
and chlorophyll a concentration, and increases in SST,
there still remained pockets of moderate upwelling,
cold water, and high chlorophyll a biomass at various central
coast locations, unlike patterns seen during the
more major El Niños (e.g., the 97â98 event). Catches of
rockfish, market squid, euphausiids, and juvenile sanddab
remained high along the central coast, whereas catches
of sardine and anchovy were low throughout the CCS.
2014 appears to be heading towards a moderate El Niño
state, with some remaining patchy regions of upwelling-driven
productivity along the coast. Superimposed on
this pattern, three major regions have experienced possibly
non-El Niño-related warming since winter: the
Bering Sea, the Gulf of Alaska, and offshore of southern
California. It is unclear how this warming may interact
with the predicted El Niño, but the result will likely be
reduced growth or reproduction for many key fisheries
species
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State of the California Current 2012â13: No Such Thing as an "Average" Year
This report reviews the state of the California Current System (CCS) between winter 2012 and spring 2013, and includes observations from Washington State to Baja California. During 2012, large-scale climate modes indicated the CCS remained in a cool, productive phase present since 2007. The upwelling season was delayed north of 42ËN, but regions to the south, especially 33Ë to 36ËN, experienced average to above average upwelling that persisted throughout the summer. Contrary to the indication of high production suggested by the climate indices, chlorophyll observed from surveys
and remote sensing was below average along much of
the coast. As well, some members of the forage assemblages
along the coast experienced low abundances in
2012 surveys. Specifically, the concentrations of all lifestages
observed directly or from egg densities of Pacific
sardine, Sardinops sagax, and northern anchovy, Engraulis
mordax, were less than previous yearsâ survey estimates.
However, 2013 surveys and observations indicate an
increase in abundance of northern anchovy. During winter
2011/2012, the increased presence of northern copepod
species off northern California was consistent with
stronger southward transport. Krill and small-fraction
zooplankton abundances, where examined, were generally
above average. North of 42ËN, salps returned to
typical abundances in 2012 after greater observed concentrations
in 2010 and 2011. In contrast, salp abundance
off central and southern California increased after a
period of southward transport during winter 2011/2012.
Reproductive success of piscivorous Brandtâs cormorant,
Phalacrocorax penicillatus, was reduced while planktivorous
Cassinâs auklet, Ptychoramphus aleuticus was elevated.
Differences between the productivity of these two seabirds
may be related to the available forage assemblage observed in the surveys. California sea lion pups from
San Miguel Island were undernourished resulting in a
pup mortality event perhaps in response to changes in
forage availability. Limited biological data were available
for spring 2013, but strong winter upwelling coastwide
indicated an early spring transition, with the strong
upwelling persisting into early summer
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