Display omitted
•The USDA’s CRP retires cropland to provide ecosystem services.•CRP uses a competitive auction to select offers.•An environmental benefits index, with cost an additive factor, ranks ...offers.•All offers are subject to a parcel specific bid cap.•Alternative auction mechanisms (quota and reference price) are considered.
The United States Department of Agriculture’s Conservation Reserve Program (CRP) has evolved from near open enrollment, to competitive enrollment, and now to a mixture of competitive and targeted enrollment. This paper reviews the history of the CRP and the evolution of its enrollment mechanism. I discuss the use of bid caps and the Environmental Benefits Index bid ranking mechanism in the “general” CRP; and the use of highly targeted, but non-competitive, “continuous” CRP. Possible challenges of these designs are discussed, and alternative auction mechanisms are considered that could be more cost effective.
The weighted ensemble (WE) methodology orchestrates quasi-independent parallel simulations run with intermittent communication that can enhance sampling of rare events such as protein conformational ...changes, folding, and binding. The WE strategy can achieve superlinear scaling-the unbiased estimation of key observables such as rate constants and equilibrium state populations to greater precision than would be possible with ordinary parallel simulation. WE software can be used to control any dynamics engine, such as standard molecular dynamics and cell-modeling packages. This article reviews the theoretical basis of WE and goes on to describe successful applications to a number of complex biological processes-protein conformational transitions, (un)binding, and assembly processes, as well as cell-scale processes in systems biology. We furthermore discuss the challenges that need to be overcome in the next phase of WE methodological development. Overall, the combined advances in WE methodology and software have enabled the simulation of long-timescale processes that would otherwise not be practical on typical computing resources using standard simulation.
Abstract Background Neuroinflammation and white matter pathology have each been independently associated with schizophrenia, and experimental studies have revealed mechanisms by which the two can ...interact in vitro, but whether these abnormalities simultaneously co-occur in people with schizophrenia remains unclear. Method We searched MEDLINE, EMBASE, PsycINFO and Web of Science from inception through 12 January 2014 for studies reporting human data on the relationship between microglial or astroglial activation, or cytokines and white matter pathology in schizophrenia. Results Fifteen studies totaling 792 subjects (350 with schizophrenia, 346 controls, 49 with bipolar disorder, 37 with major depressive disorder and 10 with Alzheimer's disease) met all eligibility criteria. Five neuropathological and two neuroimaging studies collectively yielded consistent evidence of an association between schizophrenia and microglial activation, particularly in white rather than gray matter regions. Ultrastructural analysis revealed activated microglia near dystrophic and apoptotic oligodendroglia, demyelinating and dysmyelinating axons and swollen and vacuolated astroglia in subjects with schizophrenia but not controls. Two neuroimaging studies found an association between carrier status for a functional single nucleotide polymorphism in the interleukin-1β gene and abnormal white as well as gray matter volumes in schizophrenia but not controls. A neuropathological study found that orbitofrontal white matter neuronal density was increased in schizophrenia cases exhibiting high transcription levels of pro-inflammatory cytokines relative to those exhibiting low transcription levels and to controls. Schizophrenia was associated with decreased astroglial density specifically in subgenual cingulate white matter and anterior corpus callosum, but not other gray or white matter areas. Astrogliosis was consistently absent. Data on astroglial gene expression, mRNA expression and protein concentration were inconsistent. Conclusion Neuroinflammation is associated with white matter pathology in people with schizophrenia, and may contribute to structural and functional disconnectivity, even at the first episode of psychosis.
The production of elements by rapid neutron capture (r-process) in neutron-star mergers is expected theoretically and is supported by multimessenger observations
of gravitational-wave event GW170817: ...this production route is in principle sufficient to account for most of the r-process elements in the Universe
. Analysis of the kilonova that accompanied GW170817 identified
delayed outflows from a remnant accretion disk formed around the newly born black hole
as the dominant source of heavy r-process material from that event
. Similar accretion disks are expected to form in collapsars (the supernova-triggering collapse of rapidly rotating massive stars), which have previously been speculated to produce r-process elements
. Recent observations of stars rich in such elements in the dwarf galaxy Reticulum II
, as well as the Galactic chemical enrichment of europium relative to iron over longer timescales
, are more consistent with rare supernovae acting at low stellar metallicities than with neutron-star mergers. Here we report simulations that show that collapsar accretion disks yield sufficient r-process elements to explain observed abundances in the Universe. Although these supernovae are rarer than neutron-star mergers, the larger amount of material ejected per event compensates for the lower rate of occurrence. We calculate that collapsars may supply more than 80 per cent of the r-process content of the Universe.
We give two different and simple constructions for dimensionality reduction in
ℓ
2
via linear mappings that are sparse: only an
O
(
ε
)-fraction of entries in each column of our embedding matrices ...are non-zero to achieve distortion 1 +
ε
with high probability, while still achieving the asymptotically optimal number of rows. These are the first constructions to provide subconstant sparsity for all values of parameters, improving upon previous works of Achlioptas 2003 and Dasgupta et al. 2010. Such distributions can be used to speed up applications where
ℓ
2
dimensionality reduction is used.
IMPORTANCE: Limited evidence exists on salary differences between male and female academic physicians, largely owing to difficulty obtaining data on salary and factors influencing salary. Existing ...studies have been limited by reliance on survey-based approaches to measuring sex differences in earnings, lack of contemporary data, small sample sizes, or limited geographic representation. OBJECTIVE: To analyze sex differences in earnings among US academic physicians. DESIGN, SETTING, AND PARTICIPANTS: Freedom of Information laws mandate release of salary information of public university employees in several states. In 12 states with salary information published online, salary data were extracted on 10 241 academic physicians at 24 public medical schools. These data were linked to a unique physician database with detailed information on sex, age, years of experience, faculty rank, specialty, scientific authorship, National Institutes of Health funding, clinical trial participation, and Medicare reimbursements (proxy for clinical revenue). Sex differences in salary were estimated after adjusting for these factors. EXPOSURES: Physician sex. MAIN OUTCOMES AND MEASURES: Annual salary. RESULTS: Among 10 241 physicians, female physicians (n = 3549) had lower mean (SD) unadjusted salaries than male physicians ($206 641 $88 238 vs $257 957 $137 202; absolute difference, $51 315 95% CI, $46 330-$56 301). Sex differences persisted after multivariable adjustment ($227 783 95% CI, $224 117-$231 448 vs $247 661 95% CI, $245 065-$250 258 with an absolute difference of $19 878 95% CI, $15 261-$24 495). Sex differences in salary varied across specialties, institutions, and faculty ranks. For example, adjusted salaries of female full professors ($250 971 95% CI, $242 307-$259 635) were comparable to those of male associate professors ($247 212 95% CI, $241 850-$252 575). Among specialties, adjusted salaries were highest in orthopedic surgery ($358 093 95% CI, $344 354-$371 831), surgical subspecialties ($318 760 95% CI, $311 030-$326 491), and general surgery ($302 666 95% CI, $294 060-$311 272) and lowest in infectious disease, family medicine, and neurology (mean income, <$200 000). Years of experience, total publications, clinical trial participation, and Medicare payments were positively associated with salary. CONCLUSIONS AND RELEVANCE: Among physicians with faculty appointments at 24 US public medical schools, significant sex differences in salary exist even after accounting for age, experience, specialty, faculty rank, and measures of research productivity and clinical revenue.
Adsorption-based phenomena are important in gas separations, such as the treatment of greenhouse-gas and toxic-gas pollutants, and in water-adsorption-based heat pumps for solar cooling systems. The ...ability to tune the pore size, shape and functionality of crystalline porous coordination polymers--or metal-organic frameworks (MOFs)--has made them attractive materials for such adsorption-based applications. The flexibility and guest-molecule-dependent response of MOFs give rise to unexpected and often desirable adsorption phenomena. Common to all isothermal gas adsorption phenomena, however, is increased gas uptake with increased pressure. Here we report adsorption transitions in the isotherms of a MOF (DUT-49) that exhibits a negative gas adsorption; that is, spontaneous desorption of gas (methane and n-butane) occurs during pressure increase in a defined temperature and pressure range. A combination of in situ powder X-ray diffraction, gas adsorption experiments and simulations shows that this adsorption behaviour is controlled by a sudden hysteretic structural deformation and pore contraction of the MOF, which releases guest molecules. These findings may enable technologies using frameworks capable of negative gas adsorption for pressure amplification in micro- and macroscopic system engineering. Negative gas adsorption extends the series of counterintuitive phenomena such as negative thermal expansion and negative refractive indices and may be interpreted as an adsorptive analogue of force-amplifying negative compressibility transitions proposed for metamaterials.
We present a calibration of the tip of the red giant branch (TRGB) in the Large Magellanic Cloud (LMC) on the Hubble Space Telescope (HST)/ACS F814W system. We use archival HST observations to derive ...blending corrections and photometric transformations for two ground-based wide-area imaging surveys of the Magellanic Clouds. We show that these surveys are biased bright by up to ∼0.1 mag in the optical due to blending, and that the bias is a function of local stellar density. We correct the LMC TRGB magnitudes from Jang & Lee and use the geometric distance from Pietrzy ski et al. to obtain an absolute TRGB magnitude of . Applying this calibration to the TRGB magnitudes from Freedman et al. in SN Ia hosts yields a value for the Hubble constant of H0 = 72.4 2.0 km s−1 Mpc−1 for their TRGB+SNe Ia distance ladder. The difference in the TRGB calibration and the value of H0 derived here and by Freedman et al. primarily results from their overestimate of the LMC extinction, caused by inconsistencies in their different sources of TRGB photometry for the Magellanic Clouds. Using the same source of photometry (OGLE) for both Clouds and applying the aforementioned corrections yields a value for the LMC I-band TRGB extinction that is lower by 0.06 mag, consistent with independent OGLE reddening maps used by us and by Jang & Lee to calibrate TRGB and determine H0.
Abstract
RNA-Seq is a widely used method for studying the behavior of genes under different biological conditions. An essential step in an RNA-Seq study is normalization, in which raw data are ...adjusted to account for factors that prevent direct comparison of expression measures. Errors in normalization can have a significant impact on downstream analysis, such as inflated false positives in differential expression analysis. An underemphasized feature of normalization is the assumptions on which the methods rely and how the validity of these assumptions can have a substantial impact on the performance of the methods. In this article, we explain how assumptions provide the link between raw RNA-Seq read counts and meaningful measures of gene expression. We examine normalization methods from the perspective of their assumptions, as an understanding of methodological assumptions is necessary for choosing methods appropriate for the data at hand. Furthermore, we discuss why normalization methods perform poorly when their assumptions are violated and how this causes problems in subsequent analysis. To analyze a biological experiment, researchers must select a normalization method with assumptions that are met and that produces a meaningful measure of expression for the given experiment.
Abstract
Aims
This observational study characterized cardiovascular disease (CVD) mortality risk for multiple cancer sites, with respect to the following: (i) continuous calendar year, (ii) age at ...diagnosis, and (iii) follow-up time after diagnosis.
Methods and results
The Surveillance, Epidemiology, and End Results program was used to compare the US general population to 3 234 256 US cancer survivors (1973–2012). Standardized mortality ratios (SMRs) were calculated using coded cause of death from CVDs (heart disease, hypertension, cerebrovascular disease, atherosclerosis, and aortic aneurysm/dissection). Analyses were adjusted by age, race, and sex. Among 28 cancer types, 1 228 328 patients (38.0%) died from cancer and 365 689 patients (11.3%) died from CVDs. Among CVDs, 76.3% of deaths were due to heart disease. In eight cancer sites, CVD mortality risk surpassed index-cancer mortality risk in at least one calendar year. Cardiovascular disease mortality risk was highest in survivors diagnosed at <35 years of age. Further, CVD mortality risk is highest (SMR 3.93, 95% confidence interval 3.89–3.97) within the first year after cancer diagnosis, and CVD mortality risk remains elevated throughout follow-up compared to the general population.
Conclusion
The majority of deaths from CVD occur in patients diagnosed with breast, prostate, or bladder cancer. We observed that from the point of cancer diagnosis forward into survivorship cancer patients (all sites) are at elevated risk of dying from CVDs compared to the general US population. In endometrial cancer, the first year after diagnosis poses a very high risk of dying from CVDs, supporting early involvement of cardiologists in such patients.
PDF
