Hyperspectral unmixing with material variability using social sparsity

International audienceWe apply social-norms for the first time to the problem of hyperspectral unmixing while modeling spectral variability. These norms are built with inter-group penalties which are combined in a global intra-group penalization that can enforce selection of entire endmember bundles; this results in the selection of a few representative materials even in the presence of large endmembers bundles capturing each material's variability. We demonstrate improvements quantitatively on synthetic data and qualitatively on real data for three cases of social norms: group, elitist, and a fractional social norm, respectively. We find that the greatest improvements arise from using either the group or fractional flavor

The impact of cow size on cow-calf and postweaning progeny performance in the Nebraska Sandhills

Optimizing beef production system efficiency requires an understanding of genetic potential suitable for a given production environment. Therefore, the objective of this retrospective analysis was to determine the influence of cow body weight (BW) adjusted to a common body condition score (BCS) of 5 at weaning-influenced cow-calf performance and postweaning steer and heifer progeny performance. Data were collected at the Gudmundsen Sandhills Laboratory, Whitman, NE, on crossbred, mature cows (n = 1,607) from 2005 to 2017. Cow BCS at calving, prebreeding, and weaning were positively associated (P \u3c 0.01) with greater cow BW. Increasing cow BW was positively associated (P \u3c 0.01) with the percentage of cows that conceived during a 45-d breeding season. For every additional 100-kg increase in cow BW, calf BW increased (P \u3c 0.01) at birth by 2.70 kg and adjusted 205-d weaning BW by 14.76 kg. Calf preweaning average daily gain (ADG) increased (P \u3c 0.01) 0.06 kg/d for every additional 100-kg increase in cow BW. Heifer progeny BW increased (P \u3c 0.01) postweaning with every additional 100-kg increase in dam BW. Dam BW did not influence (P ≥ 0.11) heifer puberty status prior to breeding, overall pregnancy rates, or the percentage of heifers calving in the first 21 d of the calving season. Steer initial feedlot BW increased by 7.20 kg, reimplant BW increased by 10.47 kg, and final BW increased by 10.29 kg (P ≤ 0.01) for every additional 100-kg increase in dam BW. However, steer feedlot ADG was not influenced (P \u3e 0.67) by dam BW. Hot carcass weights of steers were increased (P = 0.01) by 6.48 kg with every additional 100-kg increase in cow BW. In a hypothetical model using the regression coefficients from this study, regardless of pricing method, cow-calf producers maximize the highest amount of profit by selecting smaller cows. Overall, larger-sized cows within this herd and production system of the current study had increased reproductive performance and offspring BW; however, total production output and economic returns would be potentially greater when utilizing smaller-sized cows

Effects of red clover isoflavones on tall fescue seed fermentation and microbial populations \u3ci\u3ein vitro\u3c/i\u3e

Negative impacts of endophyte-infected Lolium arundinaceum (Darbyshire) (tall fescue) are responsible for over $2 billion in losses to livestock producers annually. While the influence of endophyte-infected tall fescue has been studied for decades, mitigation methods have not been clearly elucidated. Isoflavones found in Trifolium pratense (red clover) have been the subject of recent research regarding tall fescue toxicosis mitigation. Therefore, the aim of this study was to determine the effect of ergovaline and red clover isoflavones on rumen microbial populations, fiber degradation, and volatile fatty acids (VFA) in an in vitro system. Using a dose of 1.10 mg × L-1, endophyte-infected or endophyte-free tall fescue seed was added to ANKOM fiber bags with or without 2.19 mg of isoflavones in the form of a control, powder, or pulverized tablet, resulting in a 2 × 3 factorial arrangements of treatments. Measurements of pH, VFA, bacterial taxa, as well as the disappearance of neutral detergent fiber (aNDF), acid detergent fiber (ADF), and crude protein (CP) were taken after 48 h of incubation. aNDF disappearance values were significantly altered by seed type (P = 0.003) and isoflavone treatment (P = 0.005), and ADF disappearance values were significantly different in a seed × isoflavone treatment interaction (P ≤ 0.05). A seed × isoflavone treatment interaction was also observed with respect to CP disappearance (P ≤ 0.05). Eighteen bacterial taxa were significantly altered by seed × isoflavone treatment interaction groups (P ≤ 0.05), eight bacterial taxa were increased by isoflavones (P ≤ 0.05), and ten bacterial taxa were altered by seed type (P ≤ 0.05). Due to the beneficial effect of isoflavones on tall fescue seed fiber degradation, these compounds may be viable options for mitigating fescue toxicosis. Further research should be conducted to determine physiological implications as well as microbiological changes in vivo

Phenomenological Equations of State for the Quark-Gluon Plasma

Two phenomenological models describing an SU(N) quark-gluon plasma are presented. The first is obtained from high temperature expansions of the free energy of a massive gluon, while the second is derived by demanding color neutrality over a certain length scale. Each model has a single free parameter, exhibits behavior similar to lattice simulations over the range T_d - 5T_d, and has the correct blackbody behavior for large temperatures. The N = 2 deconfinement transition is second order in both models, while N = 3,4, and 5 are first order. Both models appear to have a smooth large-N limit. For N >= 4, it is shown that the trace of the Polyakov loop is insufficient to characterize the phase structure; the free energy is best described using the eigenvalues of the Polyakov loop. In both models, the confined phase is characterized by a mutual repulsion of Polyakov loop eigenvalues that makes the Polyakov loop expectation value zero. In the deconfined phase, the rotation of the eigenvalues in the complex plane towards 1 is responsible for the approach to the blackbody limit over the range T_d - 5T_d. The addition of massless quarks in SU(3) breaks Z(3) symmetry weakly and eliminates the deconfining phase transition. In contrast, a first-order phase transition persists with sufficiently heavy quarks.Comment: 22 pages, RevTeX, 9 eps file

A Platform-Independent Method for Detecting Errors in Metagenomic Sequencing Data: DRISEE

We provide a novel method, DRISEE (duplicate read inferred sequencing error estimation), to assess sequencing quality (alternatively referred to as “noise” or “error”) within and/or between sequencing samples. DRISEE provides positional error estimates that can be used to inform read trimming within a sample. It also provides global (whole sample) error estimates that can be used to identify samples with high or varying levels of sequencing error that may confound downstream analyses, particularly in the case of studies that utilize data from multiple sequencing samples. For shotgun metagenomic data, we believe that DRISEE provides estimates of sequencing error that are more accurate and less constrained by technical limitations than existing methods that rely on reference genomes or the use of scores (e.g. Phred). Here, DRISEE is applied to (non amplicon) data sets from both the 454 and Illumina platforms. The DRISEE error estimate is obtained by analyzing sets of artifactual duplicate reads (ADRs), a known by-product of both sequencing platforms. We present DRISEE as an open-source, platform-independent method to assess sequencing error in shotgun metagenomic data, and utilize it to discover previously uncharacterized error in de novo sequence data from the 454 and Illumina sequencing platforms

Improved GaN-based HEMT performance by nanocrystalline diamond capping

As a wide-bandgap semiconductor, gallium nitride (GaN) is an attractive material for next-generation power devices. To date, the capabilities of GaN-based high electron mobility transistors (HEMTs) have been limited by self-heating effects (drain current decreases due to phonon scattering-induced carrier velocity reductions at high drain fields). Despite awareness of this, attempts to mitigate thermal impairment have been limited due to the difficulties involved with placing high thermal conductivity materials close to heat sources in the device. Heat spreading schemes have involved growth of AIGaN/GaN on single crystal or CVD diamond, or capping of fullyprocessed HEMTs using nanocrystalline diamond (NCD). All approaches have suffered from reduced HEMT performance or limited substrate size. Recently, a "gate after diamond" approach has been successfully demonstrated to improve the thermal budget of the process by depositing NCD before the thermally sensitive Schottky gate and also to enable large-area diamond implementation

Prediction of survival among patients receiving transarterial chemoembolization for hepatocellular carcinoma: A response-based approach

Background and aims: The heterogeneity of intermediate-stage hepatocellular carcinoma (HCC) and the widespread use of transarterial chemoembolization (TACE) outside recommended guidelines have encouraged the development of scoring systems that predict patient survival. The aim of this study was to build and validate statistical models that offer individualized patient survival prediction using response to TACE as a variable. Approach and results: Clinically relevant baseline parameters were collected for 4,621 patients with HCC treated with TACE at 19 centers in 11 countries. In some of the centers, radiological responses (as assessed by modified Response Evaluation Criteria in Solid Tumors [mRECIST]) were also accrued. The data set was divided into a training set, an internal validation set, and two external validation sets. A pre-TACE model ("Pre-TACE-Predict") and a post-TACE model ("Post-TACE-Predict") that included response were built. The performance of the models in predicting overall survival (OS) was compared with existing ones. The median OS was 19.9 months. The factors influencing survival were tumor number and size, alpha-fetoprotein, albumin, bilirubin, vascular invasion, cause, and response as assessed by mRECIST. The proposed models showed superior predictive accuracy compared with existing models (the hepatoma arterial embolization prognostic score and its various modifications) and allowed for patient stratification into four distinct risk categories whose median OS ranged from 7 months to more than 4 years. Conclusions: A TACE-specific and extensively validated model based on routinely available clinical features and response after first TACE permitted patient-level prognosticatio

The UK national breast cancer screening programme for survivors of Hodgkin lymphoma detects breast cancer at an early stage

BACKGROUND: Supradiaphragmatic radiotherapy (SRT) to treat Hodgkin's lymphoma (HL) at a young age increases the risk of breast cancer (BC). A national notification risk assessment and screening programme (NRASP) for women who were treated with SRT before the age of 36 years was instituted in the United Kingdom in 2003. In this study, we report the implementation and screening results from the largest English Cancer Network. METHODS: A total of 417 eligible women were identified through cancer registry/hospital databases and from follow-up (FU) clinics. Screening results were collated retrospectively, and registry searches were used to capture BC cases. RESULTS: Of the 417 women invited for clinical review, 243 (58%) attended. Of these 417 women, 23 (5.5%) have been diagnosed with BC, a standardised incidence ratio of 2.9 compared with the age-matched general population. Of five invasive BCs diagnosed within the NRASP, none involved axillary lymph nodes compared with 7 of 13 (54%) diagnosed outside the programme (P<0.10). The mean latency for BC cases was 19.5±8.35 years and the mean FU duration for those unaffected by BC was 14.6±9.11 years (P<0.01), suggesting that those unaffected by BC remain at high risk. Recall and negative biopsy rates were acceptable (10.5 and 0.8%, respectively). CONCLUSIONS: The NRASP appears to detect BC at an early stage with acceptable biopsy rates, although numbers are small. Determination of NRASP results on a national basis is required for the accurate evaluation of screening efficacy in women previously treated with SRT

Changes in weight loss, body composition and cardiovascular disease risk after altering macronutrient distributions during a regular exercise program in obese women

<p>Abstract</p> <p>Background</p> <p>This study's purpose investigated the impact of different macronutrient distributions and varying caloric intakes along with regular exercise for metabolic and physiological changes related to weight loss.</p> <p>Methods</p> <p>One hundred forty-one sedentary, obese women (38.7 ± 8.0 yrs, 163.3 ± 6.9 cm, 93.2 ± 16.5 kg, 35.0 ± 6.2 kg•m^-2, 44.8 ± 4.2% fat) were randomized to either no diet + no exercise control group (CON) a no diet + exercise control (ND), or one of four diet + exercise groups (high-energy diet [HED], very low carbohydrate, high protein diet [VLCHP], low carbohydrate, moderate protein diet [LCMP] and high carbohydrate, low protein [HCLP]) in addition to beginning a 3x•week^-1supervised resistance training program. After 0, 1, 10 and 14 weeks, all participants completed testing sessions which included anthropometric, body composition, energy expenditure, fasting blood samples, aerobic and muscular fitness assessments. Data were analyzed using repeated measures ANOVA with an alpha of 0.05 with LSD post-hoc analysis when appropriate.</p> <p>Results</p> <p>All dieting groups exhibited adequate compliance to their prescribed diet regimen as energy and macronutrient amounts and distributions were close to prescribed amounts. Those groups that followed a diet and exercise program reported significantly greater anthropometric (waist circumference and body mass) and body composition via DXA (fat mass and % fat) changes. Caloric restriction initially reduced energy expenditure, but successfully returned to baseline values after 10 weeks of dieting and exercising. Significant fitness improvements (aerobic capacity and maximal strength) occurred in all exercising groups. No significant changes occurred in lipid panel constituents, but serum insulin and HOMA-IR values decreased in the VLCHP group. Significant reductions in serum leptin occurred in all caloric restriction + exercise groups after 14 weeks, which were unchanged in other non-diet/non-exercise groups.</p> <p>Conclusions</p> <p>Overall and over the entire test period, all diet groups which restricted their caloric intake and exercised experienced similar responses to each other. Regular exercise and modest caloric restriction successfully promoted anthropometric and body composition improvements along with various markers of muscular fitness. Significant increases in relative energy expenditure and reductions in circulating leptin were found in response to all exercise and diet groups. Macronutrient distribution may impact circulating levels of insulin and overall ability to improve strength levels in obese women who follow regular exercise.</p

Impact of Selection and Demography on the Diffusion of Lactase Persistence

BACKGROUND: The lactase enzyme allows lactose digestion in fresh milk. Its activity strongly decreases after the weaning phase in most humans, but persists at a high frequency in Europe and some nomadic populations. Two hypotheses are usually proposed to explain the particular distribution of the lactase persistence phenotype. The gene-culture coevolution hypothesis supposes a nutritional advantage of lactose digestion in pastoral populations. The calcium assimilation hypothesis suggests that carriers of the lactase persistence allele(s) (LCT*P) are favoured in high-latitude regions, where sunshine is insufficient to allow accurate vitamin-D synthesis. In this work, we test the validity of these two hypotheses on a large worldwide dataset of lactase persistence frequencies by using several complementary approaches. METHODOLOGY: We first analyse the distribution of lactase persistence in various continents in relation to geographic variation, pastoralism levels, and the genetic patterns observed for other independent polymorphisms. Then we use computer simulations and a large database of archaeological dates for the introduction of domestication to explore the evolution of these frequencies in Europe according to different demographic scenarios and selection intensities. CONCLUSIONS: Our results show that gene-culture coevolution is a likely hypothesis in Africa as high LCT*P frequencies are preferentially found in pastoral populations. In Europe, we show that population history played an important role in the diffusion of lactase persistence over the continent. Moreover, selection pressure on lactase persistence has been very high in the North-western part of the continent, by contrast to the South-eastern part where genetic drift alone can explain the observed frequencies. This selection pressure increasing with latitude is highly compatible with the calcium assimilation hypothesis while the gene-culture coevolution hypothesis cannot be ruled out if a positively selected lactase gene was carried at the front of the expansion wave during the Neolithic transition in Europe