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McCluskeyUSCultureCollection.pdf
No full textThe U.S. Culture Collection Network was formed in 2012 by a group of culture collection scientists and stakeholders in order to continue the progress established previously through efforts of an ad hoc group. The network is supported by a Research Coordination Network grant from the U.S. National Science Foundation (NSF) and has the goals of promoting interaction among collections, encouraging the adoption of best practices, and protecting endangered or orphaned collections. After prior meetings to discuss best practices, shared data, and synergy with genome programs, the network held a meeting at the U.S. Department of Agriculture (USDA)-Agricultural Research Service (ARS) National Center for Genetic Resources Preservation (NCGRP) in Fort Collins, Colorado in October 2015 specifically to discuss collections that are vulnerable because of changes in funding programs, or are at risk of loss because of retirement or lack of funding. The meeting allowed collection curators who had already backed up their resources at the USDA NCGRP to visit the site, and brought collection owners, managers, and stakeholders together. Eight formal collections have established off-site backups with the USDA-ARS, ensuring that key material will be preserved for future research. All of the collections with backup at the NCGRP are public distributing collections including U.S. NSF-supported genetic stock centers, USDA-ARS collections, and university-supported collections. Facing the retirement of several pioneering researchers, the community discussed the value of preserving personal research collections and agreed that a mechanism to preserve these valuable collections was essential to any future national culture collection system. Additional input from curators of plant and animal collections emphasized that collections of every kind face similar challenges in developing long-range plans for sustainability
Production of Ceratonova shasta Myxospores from Salmon Carcasses: Carcass Removal Is Not a Viable Management Option
Get PDFSevere infection by the endemic myxozoan parasite, Ceratonova (synonym, Ceratomyxa) shasta, has been associated with declines in and impaired recovery efforts of populations of fall-run Chinook Salmon Oncorhynchus tshawytscha in the Klamath River, California. The parasite has a complex life cycle involving a polychaete worm host as well as a salmon host. Myxospore transmission of this parasite, from salmon to polychaete, is a life cycle step during which there is a potential for applied disease management. A 3-year data set on prevalence, intensity, and spore characteristics of C. shasta myxospores was obtained from adult Chinook Salmon carcasses surveyed in the main stem of the Klamath River and three of its tributaries, Bogus Creek and the Shasta and Trinity rivers. Annual prevalence of myxospore detection in salmon intestines ranged from 22% to 52%, and spore concentration values per intestinal scraping ranged from 3.94 × 10² to 1.47 × 10⁷ spores. A prevalence of 7.3% of all carcasses examined produced >5.0 × 10⁵ spores, and these carcasses with “high” spore counts accounted for 76–95% of the total spores in a given spawning season. Molecular analysis of visually negative carcasses showed that 45–87% of these samples had parasite DNA, indicating they contained either low spore numbers or presporogonic stages of the parasite. Myxospores were rarely found in carcasses of freshly spawned adults but were common in decomposed carcasses of both sexes. The date of collection or age (based indirectly on FL) did not influence detection. The longer prespawn residence time for spring-run Chinook Salmon compared with that for fall-run Chinook Salmon in the Trinity River was associated with higher spore loads. The dye exclusion method for assessing spore viability in fresh smears indicated an inverse relationship in spore integrity and initial spore concentration. A carcass-removal pilot project in Bogus Creek for 6 weeks in the fall of 2008 (907 carcasses removed) and 2009 (1,799 carcasses removed) failed to measurably influence the DNA quantity of C. shasta in targeted waters. Combined with the high numbers of carcasses that contributed myxospores, we therefore deemed that this labor-intensive approach is not a viable management option to reduce the infectivity of C. shasta in Chinook Salmon in the Klamath River
Digital excess loop delay compensation technique with embedded truncator for continuous-time delta–sigma modulators
Get PDFA novel implementation is proposed to relax the specifications of the internal feedback path for a continuous-time delta-sigma modulator. A truncator is embedded into the digital excess loop delay (ELD) compensation path. Thermometer-coded truncation is achieved by re-ordering the reference voltages of the internal quantiser. This requires only a small amount of extra digital circuitry compared to the conventional digital ELD compensation. The digital encoder controlling the digital-to-analogue converter is simple, and it only introduces a small ELD.Keywords: continuous-time delta-sigma modulators, reference voltages, digital excess loop delay compensation, digital circuits, embedded truncator, extra digital circuitry, reference circuits, internal feedback path, digital-to-analogue converter, thermometer-coded truncation, thermometers, delta-sigma modulation, internal quantiser, digital encode
MedlockJanVetMedAmeliorationReproduction-Associated_SupportingInformation.zip
No full textImpact of reproductive processes upon female health has yielded conflicting results; particularly in relation to the role of
reproduction-associated stress. We used the viviparous tsetse fly to determine if lactation, birth and involution lead to
damage from oxidative stress (OS) that impairs subsequent reproductive cycles. Tsetse females carry an intrauterine larva to
full term at each pregnancy cycle, and lactate to nourish them with milk secretions produced by the accessory gland ( = milk
gland) organ. Unlike most K-strategists, tsetse females lack an apparent period of reproductive senescence allowing the
production of 8–10 progeny over their entire life span. In a lactating female, over 47% of the maternal transcriptome is
associated with the generation of milk proteins. The resulting single larval offspring weighs as much as the mother at birth.
In studying this process we noted an increase in specific antioxidant enzyme (AOE) transcripts and enzymatic activity at
critical times during lactation, birth and involution in the milk gland/fat body organ and the uterus. Suppression of
superoxide dismutase (sod) decreased fecundity in subsequent reproductive cycles in young mothers and nearly abolished
fecundity in geriatric females. Loss of fecundity was in part due to the inability of the mother to produce adequate milk to
support larval growth. Longevity was also impaired after sod knockdown. Generation of OS in virgin females through
exogenous treatment with hydrogen peroxide at times corresponding to pregnancy intervals reduced survival, which was
exacerbated by sod knockdown. AOE expression may prevent oxidative damage associated with the generation of nutrients
by the milk gland, parturition and milk gland breakdown. Our results indicate that prevention of OS is essential for females
to meet the growing nutritional demands of juveniles during pregnancy and to repair the damage that occurs at birth. This
process is particularly important for females to remain fecund during the latter portion of their lifetime
Toward a digital resilience
Get PDFAs we contend with human impacts on the biosphere, there is rightfully a great emphasis now on community adaptation and resilience to climate change. Recent innovations in information technologies and analyses are helping communities to become more resilient. However, not often discussed in this vein is a path toward digital resilience. If mapping and information tools are to help communities, it stands to reason that they must be resilient themselves, as well as the data that they are based on. In other words, digital tools can help make communities resilient by providing data, evidence-based advice on community decisions, etc., but the resilience of the tools themselves can also be an issue. Digital resilience means that to the greatest extent possible, data and tools should be freely accessible, interchangeable, operational, of high quality, and up-to-date so that they can help give rise to the resilience of communities or other entities using them. Given the speed at which humans are altering the biosphere, the usefulness and effectiveness of these technologies must keep pace. This article reviews and recommends three fundamental digital practices, particularly from the standpoint of geospatial data and for community resilience and policy-making. These are: (1) create and implement a culture that consistently shares not only data, but workflows and use cases with the data, especially within maps and geographic information systems or GIS; (2) use maps and other visuals to tell compelling stories that many different kinds of audiences will understand and remember; and (3) be more open to different kinds of partnerships to reduce project costs, yield better results, and foster public awareness and behavioral change
Reporting Discrepancies between the ClinicalTrials.gov Results Database and Peer Reviewed Publications
Get PDFBACKGROUND: Result summaries are now required to be reported in ClinicalTrials.gov for many 1 trials of drugs and
devices.
PURPOSE: To evaluate the consistency of reporting in trials that are both registered in the ClinicalTrials.gov results
database and published in the literature.
DATA SOURCES: ClinicalTrials.gov results database, matched publications identified through both ClinicalTrials.gov
and a manual search of two electronic databases.
STUDY SELECTION: 10% random sample of Phase III or IV trials with results in the ClinicalTrials.gov results
database, completed before January 1, 2009, with two or more arms.
DATA EXTRACTION: One reviewer extracted data from ClinicalTrials.gov results database and matching publications.
A subsample was independently verified. Basic design features and results were compared between reporting
sources and discrepancies were summarized.
DATA SYNTHESIS: Of 110 reviewed trials with results, most were industry-sponsored, parallel design, drug studies.
The most common inconsistency was the number of secondary outcome measures reported (80%). There were 16
trials (15%) that reported the primary outcome description inconsistently and 22 (20%) in which the primary
outcome value was reported inconsistently. A total of 38 trials inconsistently reported the number of individuals
with a serious adverse event (SAE), of which 33 (87%) reported more SAEs in ClinicalTrials.gov. Among the 84
trials that reported SAEs in ClinicalTrials.gov, 11 publications did not mention SAEs, 5 reported SAEs as zero or
not occurring, and 21 reported a different number of SAEs. In 29 trials that reported deaths in ClinicalTrials.gov,
28% differed with the matched publication.
LIMITATIONS: Small sample that includes earliest results posted to the database and therefore may reflect
inexperience with the submission process.
CONCLUSIONS: Reporting discrepancies between the ClinicalTrials.gov results database and matching publications
are common. It is unclear which reporting source contains the most accurate account of trial results.
ClinicalTrials.gov may provide a more comprehensive description of trial adverse events than the publication.This is an author's peer-reviewed final manuscript, as accepted by the publisher. The published article is copyrighted by the American College of Physicians and can be found at: http://annals.org/
MillerJessicaHMSCAssessingRelativeImportance_TablesS1-S3.pdf
No full textResearch on regulatory mechanisms in biological populations often focuses on environmental covariates. An integrated
approach that combines environmental indices with organismal-level information can provide additional insight on
regulatory mechanisms. Survival of spring/summer Snake River Chinook salmon (Oncorhynchus tshawytscha) is consistently
low whereas some adjacent populations with similar life histories experience greater survival. It is not known if populations
with differential survival respond similarly during early marine residence, a critical period in the life history. Ocean
collections, genetic stock identification, and otolith analyses were combined to evaluate the growth-mortality and match-mismatch
hypotheses during early marine residence of spring/summer Snake River Chinook salmon. Interannual variation in
juvenile attributes, including size at marine entry and marine growth rate, was compared with estimates of survival and
physical and biological metrics. Multiple linear regression and multi-model inference were used to evaluate the relative
importance of biological and physical metrics in explaining interannual variation in survival. There was relatively weak
support for the match-mismatch hypothesis and stronger evidence for the growth-mortality hypothesis. Marine growth and
size at capture were strongly, positively related to survival, a finding similar to spring Chinook salmon from the Mid-Upper
Columbia River. In hindcast models, basin-scale indices (Pacific Decadal Oscillation (PDO) and the North Pacific Gyre
Oscillation (NPGO)) and biological indices (juvenile salmon catch-per-unit-effort (CPUE) and a copepod community index
(CCI)) accounted for substantial and similar portions of variation in survival for juvenile emigration years 1998–2008 (R² > 0.70). However, in forecast models for emigration years 2009–2011, there was an increasing discrepancy between
predictions based on the PDO (50–448% of observed value) compared with those based on the NPGO (68–212%) or
biological indices (CPUE and CCI: 83–172%). Overall, the PDO index was remarkably informative in earlier years but other
basin-scale and biological indices provided more accurate indications of survival in recent years
Enhanced third harmonic generation by organic materials on high-Q plasmonic photonic crystals
Get PDFThe enhanced optical nonlinearity enabled by localized plasmonic fields has been well studied for all-optical switching processing (AOSP) devices for future optical communication systems. In this work, plasmonic photonic crystals with a nonlinear polycarbonate/polymethine blend cladding layer are designed to enhance the third harmonic generation (THG) at the telecom wavelengths (~1550 nm). Due to the presence of he two-dimensional (2-D) gold nano-patch arrays with improved Q-factor and high local fields, more than 20 × of enhanced THG signals in the hybrid organic-plasmonic nanostructure are experimentally observed. The enhanced THG in the hybrid organic-plasmonic materials suggested that such extraordinary nonlinear effects can be used for AOSP devices and wavelength conversion.This is the publisher’s final pdf. The published article is copyrighted by the Optical Society of America and can be found at: http://www.opticsinfobase.org/oe/home.cfm
Landauer, Kubo, and microcanonical approaches to quantum transport and noise: A comparison and implications for cold-atom dynamics
Get PDFWe compare the Landauer, Kubo, and microcanonical [J. Phys.: Condens. Matter 16, 8025 (2005)] approaches
to quantum transport for the average current, the entanglement entropy, and the semiclassical full-counting
statistics (FCS). Our focus is on the applicability of these approaches to isolated quantum systems such as
ultracold atoms in engineered optical potentials. For two lattices connected by a junction, we find that the current
and particle number fluctuations from the microcanonical approach compare well with the values predicted by
the Landauer formalism and FCS assuming a binomial distribution. However, we demonstrate that well-defined
reservoirs (i.e., particles in Fermi-Dirac distributions) are not present for a substantial duration of the quasi-steady
state. Thus, on the one hand, the Landauer assumption of reservoirs and/or inelastic effects is not necessary for
establishing a quasi-steady state. Maintaining such a state indefinitely requires an infinite system, and in this limit
well-defined Fermi-Dirac distributions can occur. On the other hand, as we show, the existence of a finite speed
of particle propagation preserves the quasi-steady state irrespective of the existence of well-defined reservoirs.
This indicates that global observables in finite systems may be substantially different from those predicted by
an uncritical application of the Landauer formalism, with its underlying thermodynamic limit. Therefore, the
microcanonical formalism which is designed for closed, finite-size quantum systems seems more suitable for
studying particle dynamics in ultracold atoms. Our results highlight both the connection and differences with
more traditional approaches to calculating transport properties in condensed matter systems, and will help guide
the way to their simulations in cold-atom systems
Gatekeepers or Intermediaries? The Role of Clinicians in Commercial Genomic Testing
Get PDFBACKGROUND: Many commentators on ‘‘direct-to-consumer’’ genetic risk information have raised concerns that giving results to individuals with insufficient knowledge and training in genomics may harm consumers, the health care system, and society. In response, several commercial laboratories offering genomic risk profiling have shifted to more traditional ‘‘direct-to-provider’’ (DTP) marketing strategies, repositioning clinicians as the intended recipients of advertising of laboratory services and as gatekeepers to personal genomic information. Increasing popularity of next generation sequencing puts a premium on ensuring that those who are charged with interpreting, translating, communicating and managing commercial genomic risk information are appropriately equipped for the job. To shed light on their gatekeeping role, we conducted a study to assess how and why early clinical users of genomic risk assessment incorporate these tools in their clinical practices and how they interpret genomic information for their patients.
METHODS and FINDINGS: We conducted qualitative in-depth interviews with 18 clinicians providing genomic risk assessment services to their patients in partnership with DNA Direct and Navigenics. Our findings suggest that clinicians learned most of what they knew about genomics directly from the commercial laboratories. Clinicians rely on the expertise of the commercial laboratories without the ability to critically evaluate the knowledge or assess risks.
CONCLUSIONS: DTP service delivery model cannot guarantee that providers will have adequate expertise or sound clinical judgment. Even if clinicians want greater genomic knowledge, the current market structure is unlikely to build the independent substantive expertise of clinicians, but rather promote its continued outsourcing. Because commercial laboratories have the most ‘‘skin in the game’’ financially, genetics professionals and policymakers should scrutinize the scientific validity and clinical soundness of the process by which these laboratories interpret their findings to assess whether self-interested commercial sources are the most appropriate entities for gate-keeping genomic interpretation