Generating Peptide Mass Spectrometry Ground Truth Data

Very few quantitative evaluations exist for precursor mass spectrometry data due to the lack of tools for enabling the manual feature finding necessary to generate this data. Other lacks the ability to capture, edit, save, and view precursor mass spectrometry data. We present JS-MS 2.0, a software suite that provides a dependency-free, browser-based, one click, cross-platform solution for creating precursor ground truth. The software retains the first version’s capacity for loading, viewing, and navigating MS1 data in 2- and 3-D, and adds tools for capturing, editing, saving and viewing isotopic envelope and extracted isotopic chromatogram features. The software can also be used to view and explore the results of feature finding algorithms. JS-MS 2.0 enables faster creation and inspection of precursor mass spectrometry ground truth data. It is publicly available with a GPL 2.0 license at github.com/optimusmoose/jsms

Energy Storage Roadmap for Northern Appalachia 2022

The Northern Appalachian counties (Western PA, Eastern OH and West Virginia) have legacy energy industry engineering, workforce and research advantages that have made the region a prime location for the development of energy storage manufacturing and deployment. Already over 200 private companies are engaged in the energy storage business regionally. Further assets include the many research universities and laboratories in the region, together with a low cost of living compared to other energy storage clusters. The study identifies the energy storage industry assets and explores strategies for cluster development in Northern Appalachia

Evidence for conservation in antigen gene sequences combined with extensive polymorphism at VNTR loci

Theileria parva is a tick‐transmitted apicomplexan protozoan parasite that infects lymphocytes of cattle and African Cape buffalo (Syncerus caffer), causing a frequently fatal disease of cattle in eastern, central and southern Africa. A live vaccination procedure, known as infection and treatment method (ITM), the most frequently used version of which comprises the Muguga, Serengeti‐transformed and Kiambu 5 stocks of T. parva, delivered as a trivalent cocktail, is generally effective. However, it does not always induce 100% protection against heterologous parasite challenge. Knowledge of the genetic diversity of T. parva in target cattle populations is therefore important prior to extensive vaccine deployment. This study investigated the extent of genetic diversity within T. parva field isolates derived from Ankole (Bos taurus) cattle in south‐western Uganda using 14 variable number tandem repeat (VNTR) satellite loci and the sequences of two antigen‐encoding genes that are targets of CD8+T‐cell responses induced by ITM, designated Tp1 and Tp2. The findings revealed a T. parva prevalence of 51% confirming endemicity of the parasite in south‐western Uganda. Cattle‐derived T. parva VNTR genotypes revealed a high degree of polymorphism. However, all of the T. parva Tp1 and Tp2 alleles identified in this study have been reported previously, indicating that they are widespread geographically in East Africa and highly conserved

Simultaneous amplicon sequencing to explore co- occurrence patterns of bacterial, archaeal and eukaryotic microorganisms in rumen microbial communities

Ruminants rely on a complex rumen microbial community to convert dietary plant material to energy-yielding products. Here we developed a method to simultaneously analyze the community's bacterial and archaeal 16S rRNA genes, ciliate 18S rRNA genes and anaerobic fungal internal transcribed spacer 1 genes using 12 DNA samples derived from 11 different rumen samples from three host species (Ovis aries, Bos taurus, Cervus elephas) and multiplex 454 Titanium pyrosequencing. We show that the mixing ratio of the group-specific DNA templates before emulsion PCR is crucial to compensate for differences in amplicon length. This method, in contrast to using a non-specific universal primer pair, avoids sequencing non-targeted DNA, such as plant- or endophyte-derived rRNA genes, and allows increased or decreased levels of community structure resolution for each microbial group as needed. Communities analyzed with different primers always grouped by sample origin rather than by the primers used. However, primer choice had a greater impact on apparent archaeal community structure than on bacterial community structure, and biases for certain methanogen groups were detected. Co-occurrence analysis of microbial taxa from all three domains of life suggested strong within- and between-domain correlations between different groups of microorganisms within the rumen. The approach used to simultaneously characterize bacterial, archaeal and eukaryotic components of a microbiota should be applicable to other communities occupying diverse habitats

The Realm and Frontiers of Mycosis Fungoides

Objectives Chronic renal failure (CRF) is associated with altered systemic arterial tone and hypertension. Myogenic constriction and endothelium-derived hyperpolarizing factor (EDHF)-dependent relaxation represent major vasoregulatory mechanisms in small systemic arteries. Elevated myogenic response and impaired EDHF might participate in the development of essential hypertension; however, their role in CRF-related hypertension is unknown. We investigated whether myogenic response and EDHF are altered in subtotally nephrectornized (sNX) rats and whether these changes are modifiable by chronic treatment with angiotensin-converting enzyme (ACE) inhibitor. Methods In a pressure arteriograph, myogenic constriction and EDHF-mediated relaxation were evaluated in small mesenteric arteries isolated from male Wistar rats 15 weeks after either sham operation (n = 7) (SHAM), sNX (n = 12) or sNX followed by 9 weeks of treatment with lisinopril (sNX + LIS, 2.5 mg/kg, n = 13). Results Surprisingly, myogenic response was reduced in hypertensive CRF rats (maximal myogenic tone: 37 +/- 2 and 18 +/- 4%, P <0.01; peak myogenic index: -0.80 +/- 0.08 and -0.40 +/- 0.12%/mmHg, P <0.05 in SHAM and sNX respectively). At the same time EDHF-mediated relaxation was also impaired (maximal response: 92 +/- 2 and 77 +/- 5%, P <0.01; pD(2): 6.5 +/- 0.1 and 5.9 +/- 0.1, P <0.05). Both myogenic response and EDHF were inversely related to the severity of renal failure and restored by treatment with lisinopril to levels found in SHAM animals. Conclusion Major constrictive (myogenic) and dilatory (EDHF) mechanisms of small systemic arteries are impaired in hypertensive CRF rats. These alterations do not seem to participate in the development of hypertension, being rather directly related to the severity of renal impairment. Both systemic vascular changes might be restored by renoprotective treatment with ACE inhibitor

The role of endogenous H2S formation in reversible remodeling of lung tissue during hibernation in the Syrian hamster

During hibernation, small mammals alternate between periods of metabolic suppression and low body temperature ('torpor') and periods of full metabolic recovery with euthermic temperatures ('arousal'). Previously, we demonstrated marked structural remodeling of the lung during torpor, which is rapidly reversed during arousal. We also found that cooling of hamster cells increased endogenous production of H2S through the enzyme cystathionine-beta-synthase (CBS). H2S suppresses the immune response and increases deposition of collagen. Therefore, we examined inflammatory markers and matrix metalloproteinase (MMP) activity in relation to CBS expression and H2S levels in lungs of euthermic and hibernating Syrian hamsters. Lung remodeling during torpor was confirmed by a strong increase in both collagenous and non-collagenous hydroxyproline content. The number of leukocytes in lung was unchanged in any phase of hibernation, while adhesion molecules VCAM-1 and ICAM-1, and the inflammatory marker NF-kappa B (P65) were modestly upregulated in torpor. Gelatinase activity was decreased in lungs from torpid animals, indicating inhibition of the Zn2+-dependent MMP-2 and MMP-9. Moreover, expression of CBS and tissue levels of H2S were increased in torpor. All changes normalized during arousal. Inhibition of gelatinase activity in torpor is likely caused by quenching of Zn2+ by the sulphide ion of H2S. In accord, inhibition of CBS normalized gelatinase activity in torpid animals. Conversely, NaHS decreased the gelatinase activity of euthermic animals, which was attenuated by excess Zn2+. Similar results were obtained on the activity of the Zn2+-dependent angiotensin converting enzyme. Our data indicate that increased production of H2S through CBS in hamster lungs during torpor contributes to remodeling by inhibition of gelatinase activity and possibly by suppression of the inflammatory response. Although administration of H2S is known to induce metabolic suppression in nonhibernating mammals ('suspended animation'), this is the first report implying endogenous H2S production in natural hibernation

Discovery of Extremely Embedded X-ray Sources in the R Coronae Australis Star Forming Core

With the XMM-Newton and Chandra observatories, we detected two extremely embedded X-ray sources in the R Corona Australis (R CrA) star forming core, near IRS 7. These sources, designated as XB and XA, have X-ray absorption columns of ~3e23 cm-2 equivalent to AV ~180 mag. They are associated with the VLA centimeter radio sources 10E and 10W, respectively. XA is the counterpart of the near-infrared source IRS 7, whereas XB has no K-band counterpart above 19.4 mag. This indicates that XB is younger than typical Class I protostars, probably a Class 0 protostar or in an intermediate phase between Class 0 and Class I. The X-ray luminosity of XB varied between 29<log LX <31.2 ergs s-1 on timescales of 3-30 months. XB also showed a monotonic increase in X-ray brightness by a factor of two in 30 ksec during an XMM-Newton observation. The XMM-Newton spectra indicate emission from a hot plasma with kT ~3-4 keV and also show fluorescent emission from cold iron. Though the X-ray spectrum from XB is similar to flare spectra from Class I protostars in luminosity and temperature, the light curve does not resemble the lightcurves of magnetically generated X-ray flares because the variability timescale of XB is too long and because variations in X-ray count rate were not accompanied by variations in spectral hardness. The short-term variation of XB may be caused by the partial blocking of the X-ray plasma, while the month-long flux enhancement may be driven by mass accretion.Comment: 26 pages, 8 figures, To be published in ApJ in April 200

Apocenter pile-up and arcs: a narrow dust ring around HD 129590

Observations of debris disks have significantly improved over the past decades, both in terms of sensitivity and spatial resolution. At near-infrared wavelengths, new observing strategies and post-processing algorithms allow us to drastically improve the final images, revealing faint structures in the disks. These structures inform us about the properties and spatial distribution of the small dust particles. We present new $H$-band observations of the disk around HD 129590, which display an intriguing arc-like structure in total intensity but not in polarimetry, and propose an explanation for the origin of this arc. Assuming geometric parameters for the birth ring of planetesimals, our model provides the positions of millions of particles of different sizes to compute scattered light images. We demonstrate that if the grain size distribution is truncated or strongly peaks at a size larger than the radiation pressure blow-out size we are able to produce an arc quite similar to the observed one. If the birth ring is radially narrow, given that particles of a given size have similar eccentricities, they will have their apocenters at the same distance from the star. Since this is where the particles will spend most of their time, this results in a "apocenter pile-up" that can look like a ring. Due to more efficient forward scattering this arc only appears in total intensity observations and remains undetected in polarimetric data. This scenario requires sharp variations either in the grain size distribution or for the scattering efficiencies $Q_\mathrm{sca}$. Alternative possibilities such as a wavy size distribution and a size-dependent phase function are interesting candidates to strengthen the apocenter pile-up. We also discuss why such arcs are not commonly detected in other systems, which can mainly be explained by the fact that most parent belts are usually broad.Comment: Accepted for publication in A&A, abstract shortene