Optical Spectra of SNR Candidates in NGC 300

We present moderate-resolution (<5A) long-slit optical spectra of 51 nebular objects in the nearby Sculptor Group galaxy NGC 300 obtained with the 2.3 meter Advanced Technology Telescope at Siding Spring Observatory, Australia. Adopting the criterion of [SII]/Ha>=0.4 to confirm supernova remnants (SNRs) from optical spectra, we find that of 28 objects previously proposed as SNRs from optical observations, 22 meet this criterion with six showing [SII]/Ha of less than 0.4. Of 27 objects suggested as SNRs from radio data, four are associated with the 28 previously proposed SNRs. Of these four, three (included in the 22 above) meet the criterion. In all, 22 of the 51 nebular objects meet the [SII]/Ha criterion as SNRs while the nature of the remaining 29 objects remains undetermined by these observations.Comment: Accepted for publication in Astrophysics & Space Scienc

Targeted Cattle Grazing to Enhance Sage-Grouse Brood-Rearing Habitat

Often, greater sage-grouse (Centrocercus urophasianus) brood-rearing habitats dominated by dense mountain big sagebrush (Artemisia tridentata vaseyana; &gt;10-25% canopy cover) limit important forbs and arthropods sage-grouse rely on during summer. We investigated whether protein supplementation could concentrate cattle during fall to reduce sagebrush canopy cover and increase the diversity and abundance of forbs and arthropods. We applied targeted cattle grazing within three large, contiguous pastures in the Beaverhead Mountains of southwestern Montana. In each pasture, we selected one 4-ha macroplot of dense sagebrush (&gt;30%). Within each macroplot, we placed low-moisture block protein supplement in four microsites (78.5-m2) and compared cattle response to four untreated control microsites. The following summer we measured herbaceous canopy cover and composition, shrub canopy cover, ground cover, forb and arthropod diversity, and arthropod density for each treated and untreated microsites. Mountain big sagebrush canopy cover was 71% less in treated vs. untreated microsites (11% vs. 38% canopy cover, respectively; P &lt;0.001). Bite count observations indicated that sagebrush cover was reduced by cattle trampling rather than browsing, as sagebrush comprised &lt;1% of cattle diets. Forb diversity was 13% greater in treated microsites (P = 0.094), forb species richness was 16% greater in treated microsites (P = 0.044), and forb composition trended higher in treated microsites (45% of herbaceous composition in treated microsites vs. 32% in untreated microsites; P = 0.106). Lepidoptera density trended 18% greater in treated microsites (P = .133). Our results indicate that protein supplementation during late fall can concentrate cattle to enhance sage-grouse brood-rearing habitat

Drought effects on composition and yield for corn stover, mixed grasses, and \u3ci\u3eMiscanthus\u3c/i\u3e as bioenergy feedstocks

Drought conditions in 2012 were some of the most severe in recent history. The purpose of this study is to examine the impact of drought on quality, quantity, and theoretical ethanol yield (TEY) of three bioenergy feedstocks, corn stover, mixed grasses from Conservation Reserve Program lands, and Miscanthus × giganteus. To assess drought effects on these feedstocks, samples from 2010 (minimal to no drought) and 2012 (severe drought) were compared from multiple locations in the US. In all feedstocks, drought significantly increased extractives and reduced structural sugars and lignin; subsequently, TEYs were reduced 10–15%. Biomass yields were significantly reduced for M. × giganteus and mixed grasses. When reduction in quality and quantity were combined, TEYs decreased 26–59%. Drought negatively affected biomass quality and quantity that resulted in significant TEY reductions. Such fluctuations in biomass quality and yield may have significant consequences for developing lignocellulosic biorefineries

Drought effects on composition and yield for corn stover, mixed grasses, and \u3ci\u3eMiscanthus\u3c/i\u3e as bioenergy feedstocks

Drought conditions in 2012 were some of the most severe in recent history. The purpose of this study is to examine the impact of drought on quality, quantity, and theoretical ethanol yield (TEY) of three bioenergy feedstocks, corn stover, mixed grasses from Conservation Reserve Program lands, and Miscanthus × giganteus. To assess drought effects on these feedstocks, samples from 2010 (minimal to no drought) and 2012 (severe drought) were compared from multiple locations in the US. In all feedstocks, drought significantly increased extractives and reduced structural sugars and lignin; subsequently, TEYs were reduced 10–15%. Biomass yields were significantly reduced for M. × giganteus and mixed grasses. When reduction in quality and quantity were combined, TEYs decreased 26–59%. Drought negatively affected biomass quality and quantity that resulted in significant TEY reductions. Such fluctuations in biomass quality and yield may have significant consequences for developing lignocellulosic biorefineries

Memory for Semantically Related and Unrelated Declarative Information: The Benefit of Sleep, the Cost of Wake

Numerous studies have examined sleep's influence on a range of hippocampus-dependent declarative memory tasks, from text learning to spatial navigation. In this study, we examined the impact of sleep, wake, and time-of-day influences on the processing of declarative information with strong semantic links (semantically related word pairs) and information requiring the formation of novel associations (unrelated word pairs). Participants encoded a set of related or unrelated word pairs at either 9am or 9pm, and were then tested after an interval of 30 min, 12 hr, or 24 hr. The time of day at which subjects were trained had no effect on training performance or initial memory of either word pair type. At 12 hr retest, memory overall was superior following a night of sleep compared to a day of wakefulness. However, this performance difference was a result of a pronounced deterioration in memory for unrelated word pairs across wake; there was no sleep-wake difference for related word pairs. At 24 hr retest, with all subjects having received both a full night of sleep and a full day of wakefulness, we found that memory was superior when sleep occurred shortly after learning rather than following a full day of wakefulness. Lastly, we present evidence that the rate of deterioration across wakefulness was significantly diminished when a night of sleep preceded the wake period compared to when no sleep preceded wake, suggesting that sleep served to stabilize the memories against the deleterious effects of subsequent wakefulness. Overall, our results demonstrate that 1) the impact of 12 hr of waking interference on memory retention is strongly determined by word-pair type, 2) sleep is most beneficial to memory 24 hr later if it occurs shortly after learning, and 3) sleep does in fact stabilize declarative memories, diminishing the negative impact of subsequent wakefulness

Chandra and Very Large Array Observations of the Nearby Sd Galaxy NGC 45

We present an analysis of high angular resolution observations made in the X-ray and the radio with the Chandra X-ray Observatory and the Karl Jansky Very Large Array (VLA), respectively, of the nearby spiral galaxy NGC 45. This galaxy is the third that we have considered in a study of the supernova remnant (SNR) populations of nearby spiral galaxies and the present work represents the first detailed analysis of the discrete X-ray and radio source populations of this galaxy. We analyzed data sets from the three pointed observations made of this galaxy with Chandra along with a merged data set obtained from combining these data sets: the total effective exposure time of the merged data set is 63515 s. A total of 25 discrete X-ray sources are found in the entire field of view of the ACIS-S3 chip, with 16 sources found within the visual extent of the galaxy. We estimate that as many as half of the sources detected in the entire field of view of the ACIS-S3 chip and seven of the sources detected in the optical extent of NGC 45 may be background sources. We analyzed the spectral properties of the discrete X-ray sources within the galaxy and conclude that the majority of these sources are X-ray binaries. We have searched for counterparts at different wavelengths to the discrete X-ray sources and we find two associations: one with a star cluster and the other with a background galaxy. We have found one source that is clearly variable within one observation and seven that are seen to vary from one observation to another. We also conduct a photometric analysis to determine the near-infrared fluxes of the discrete X-ray sources in Spitzer Infrared Array Camera channels. We constructed a cumulative luminosity function of the discrete X-ray sources seen toward NGC 45: taking into account simultaneously the luminosity function of background sources, the fitted slope of the cumulative luminosity function Γ = –1.3_(-1.6)^(+0.7) (all error bounds correspond to 90% confidence intervals). The VLA observations reveal seven discrete radio sources: we find no overlaps between these sources and the X-ray detected sources. Based on their measured spectral indices and their locations with respect to the visible extent of NGC 45, we classify one source as a candidate radio SNR associated with the galaxy and the others as likely background galaxies seen in projection toward NGC 45. Finally, we discuss the properties of a background cluster of galaxies (denoted as CXOU J001354.2–231254.7) seen in projection toward NGC 45 and detected by the Chandra observations. The fit parameters to the extracted Chandra spectra of this cluster are a column density N_H = 0.07(<0.14) × 10^(22) cm^(−2), a temperature kT = 4.22_(-1.42)^(+2.08) keV, an abundance Z = 0.30(<0.75) relative to solar and a redshift z = 0.28 ± 0.14. From the fit parameters we derive an electron number density n_e = 4(±1) × 10^(−3) cm^(−3), an unabsorbed X-ray luminosity L_(0.5-7.0keV) ~ 8.77(±0.96) × 10^(43) erg s^(−1) for the cluster and an X-ray emitting mass M = 2.32(±1.75) × 10^(12)M_☉

Cacao seeds are a "Super Fruit": A comparative analysis of various fruit powders and products

<p>Abstract</p> <p>Background</p> <p>Numerous popular media sources have developed lists of "Super Foods" and, more recently, "Super Fruits". Such distinctions often are based on the antioxidant capacity and content of naturally occurring compounds such as polyphenols within those whole fruits or juices of the fruit which may be linked to potential health benefits. Cocoa powder and chocolate are made from an extract of the seeds of the fruit of <it>the Theobroma cacao </it>tree. In this study, we compared cocoa powder and cocoa products to powders and juices derived from fruits commonly considered "Super Fruits".</p> <p>Results</p> <p>Various fruit powders and retail fruit products were obtained and analyzed for antioxidant capacity (ORAC (μM TE/g)), total polyphenol content (TP (mg/g)), and total flavanol content (TF (mg/g)). Among the various powders that were tested, cocoa powder was the most concentrated source of ORAC and TF. Similarly, dark chocolate was a significantly more concentrated source of ORAC and TF than the fruit juices.</p> <p>Conclusions</p> <p>Cocoa powder and dark chocolate had equivalent or significantly greater ORAC, TP, and TF values compared to the other fruit powders and juices tested, respectively. Cacao seeds thus provide nutritive value beyond that derived from their macronutrient composition and appear to meet the popular media's definition of a "Super Fruit".</p

Precision and linearity targets for validation of an IFNγ ELISPOT, cytokine flow cytometry, and tetramer assay using CMV peptides

<p>Abstract</p> <p>Background</p> <p>Single-cell assays of immune function are increasingly used to monitor T cell responses in immunotherapy clinical trials. Standardization and validation of such assays are therefore important to interpretation of the clinical trial data. Here we assess the levels of intra-assay, inter-assay, and inter-operator precision, as well as linearity, of CD8+ T cell IFNγ-based ELISPOT and cytokine flow cytometry (CFC), as well as tetramer assays.</p> <p>Results</p> <p>Precision was measured in cryopreserved PBMC with a low, medium, or high response level to a CMV pp65 peptide or peptide mixture. Intra-assay precision was assessed using 6 replicates per assay; inter-assay precision was assessed by performing 8 assays on different days; and inter-operator precision was assessed using 3 different operators working on the same day. Percent CV values ranged from 4% to 133% depending upon the assay and response level. Linearity was measured by diluting PBMC from a high responder into PBMC from a non-responder, and yielded R²values from 0.85 to 0.99 depending upon the assay and antigen.</p> <p>Conclusion</p> <p>These data provide target values for precision and linearity of single-cell assays for those wishing to validate these assays in their own laboratories. They also allow for comparison of the precision and linearity of ELISPOT, CFC, and tetramer across a range of response levels. There was a trend toward tetramer assays showing the highest precision, followed closely by CFC, and then ELISPOT; while all three assays had similar linearity. These findings are contingent upon the use of optimized protocols for each assay.</p

VESPA: software to facilitate genomic annotation of prokaryotic organisms through integration of proteomic and transcriptomic data

<p>Abstract</p> <p>Background</p> <p>The procedural aspects of genome sequencing and assembly have become relatively inexpensive, yet the full, accurate structural annotation of these genomes remains a challenge. Next-generation sequencing transcriptomics (RNA-Seq), global microarrays, and tandem mass spectrometry (MS/MS)-based proteomics have demonstrated immense value to genome curators as individual sources of information, however, integrating these data types to validate and improve structural annotation remains a major challenge. Current visual and statistical analytic tools are focused on a single data type, or existing software tools are retrofitted to analyze new data forms. We present Visual Exploration and Statistics to Promote Annotation (VESPA) is a new interactive visual analysis software tool focused on assisting scientists with the annotation of prokaryotic genomes though the integration of proteomics and transcriptomics data with current genome location coordinates.</p> <p>Results</p> <p>VESPA is a desktop Java™ application that integrates high-throughput proteomics data (peptide-centric) and transcriptomics (probe or RNA-Seq) data into a genomic context, all of which can be visualized at three levels of genomic resolution. Data is interrogated via searches linked to the genome visualizations to find regions with high likelihood of mis-annotation. Search results are linked to exports for further validation outside of VESPA or potential coding-regions can be analyzed concurrently with the software through interaction with BLAST. VESPA is demonstrated on two use cases (<it>Yersinia pestis </it>Pestoides F and <it>Synechococcus </it>sp. PCC 7002) to demonstrate the rapid manner in which mis-annotations can be found and explored in VESPA using either proteomics data alone, or in combination with transcriptomic data.</p> <p>Conclusions</p> <p>VESPA is an interactive visual analytics tool that integrates high-throughput data into a genomic context to facilitate the discovery of structural mis-annotations in prokaryotic genomes. Data is evaluated via visual analysis across multiple levels of genomic resolution, linked searches and interaction with existing bioinformatics tools. We highlight the novel functionality of VESPA and core programming requirements for visualization of these large heterogeneous datasets for a client-side application. The software is freely available at <url>https://www.biopilot.org/docs/Software/Vespa.php</url>.</p

Unimodality Problems in Ehrhart Theory

Ehrhart theory is the study of sequences recording the number of integer points in non-negative integral dilates of rational polytopes. For a given lattice polytope, this sequence is encoded in a finite vector called the Ehrhart $h^*$-vector. Ehrhart $h^*$-vectors have connections to many areas of mathematics, including commutative algebra and enumerative combinatorics. In this survey we discuss what is known about unimodality for Ehrhart $h^*$-vectors and highlight open questions and problems.Comment: Published in Recent Trends in Combinatorics, Beveridge, A., et al. (eds), Springer, 2016, pp 687-711, doi 10.1007/978-3-319-24298-9_27. This version updated October 2017 to correct an error in the original versio