PhosFox: a bioinformatics tool for peptide-level processing of LC-MS/MS-based phosphoproteomic data

Background: It is possible to identify thousands of phosphopeptides and -proteins in a single experiment with mass spectrometry-based phosphoproteomics. However, a current bottleneck is the downstream data analysis which is often laborious and requires a number of manual steps.Results: Toward automating the analysis steps, we have developed and implemented a software, PhosFox, which enables peptide-level processing of phosphoproteomic data generated by multiple protein identification search algorithms, including Mascot, Sequest, and Paragon, as well as cross-comparison of their identification results. The software supports both qualitative and quantitative phosphoproteomics studies, as well as multiple between-group comparisons. Importantly, PhosFox detects uniquely phosphorylated peptides and proteins in one sample compared to another. It also distinguishes differences in phosphorylation sites between phosphorylated proteins in different samples. Using two case study examples, a qualitative phosphoproteome dataset from human keratinocytes and a quantitative phosphoproteome dataset from rat kidney inner medulla, we demonstrate here how PhosFox facilitates an efficient and in-depth phosphoproteome data analysis. PhosFox was implemented in the Perl programming language and it can be run on most common operating systems. Due to its flexible interface and open source distribution, the users can easily incorporate the program into their MS data analysis workflows and extend the program with new features. PhosFox source code, implementation and user instructions are freely available from https://bitbucket.org/phintsan/phosfox.Conclusions: PhosFox facilitates efficient and more in-depth comparisons between phosphoproteins in case-control settings. The open source implementation is easily extendable to accommodate additional features for widespread application use cases

A Radar-Based Hail Climatology of Australia

In Australia, hailstorms present considerable public safety and economic risks, where they are considered the most damaging natural hazard in terms of annual insured losses. Despite these impacts, the current climatological distribution of hailfall across the continent is still comparatively poorly understood. This study aims to supplement previous national hail climatologies, such as those based on environmental proxies or satellite radiometer data, with more direct radar-based hail observations. The heterogeneous and incomplete nature of the Australian radar network complicates this task and prompts the introduction of some novel methodological elements. We introduce an empirical correction technique to account for hail reflectivity biases at C-band, derived by comparing overlapping C- and S-band observations. Furthermore, we demonstrate how object-based hail swath analysis may be used to produce resolution-invariant hail frequencies, and describe an interpolation method used to create a spatially continuous hail climatology. The Maximum Estimated Size of Hail (MESH) parameter is then applied to a mixture of over fifty operational radars in the Australian radar archive, resulting in the first nationwide, radar-based hail climatology. The spatiotemporal distribution of hailstorms is examined, including their physical characteristics, seasonal and diurnal frequency, and regional variations of such properties across the continent.Comment: Revision 1 of manuscript submitted to Monthly Weather Revie

The Effects of Spatial Interpolation on a Novel, Dual-Doppler 3D Wind Retrieval Technique

Three-dimensional wind retrievals from ground-based Doppler radars have played an important role in meteorological research and nowcasting over the past four decades. However, in recent years, the proliferation of open-source software and increased demands from applications such as convective parameterizations in numerical weather prediction models has led to a renewed interest in these analyses. In this study, we analyze how a major, yet often-overlooked, error source effects the quality of retrieved 3D wind fields. Namely, we investigate the effects of spatial interpolation, and show how the common practice of pre-gridding radial velocity data can degrade the accuracy of the results. Alternatively, we show that assimilating radar data directly at their observation locations improves the retrieval of important dynamic features such as the rear flank downdraft and mesocyclone within a simulated supercell, while also reducing errors in vertical vorticity, horizontal divergence, and all three velocity components.Comment: Revised version submitted to JTECH. Includes new section with a real data cas

Temperature-dependent spin gap and singlet ground state in BaCuSi2O6

Bulk magnetic measurements and inelastic neutron scattering were used to investigate the spin-singlet ground state and magnetic gap excitations in BaCuSi2O6, a quasi-2-dimensional antiferromagnet with a bilayer structure. The results are well described by a model based on weakly interacting antiferromagnetic dimers. A strongly temperature-dependent dispersion in the gap modes was found. We suggest that the observed excitations are analogous to magneto-excitons in light rare-earth compounds, but are an intrinsic property of a simple Heisenberg Hamiltonian for the S=1/2 magnetic bilayer.Comment: 10 pages, 4 figures, REVTeX and PS for text, PS for figures direct download: http://papillon.phy.bnl.gov/preprints/bacusio.htm

Avaliação agronômica de uma coleção de germoplasma de cafeeiros no Estado do Paraná

During the period from 1977 to 1982 a trial was carried out in Jacarezinho, PR, Brazil, with 18 introductions of coffee (Coffea arabica L.) to assess the yield potential, plant architectural features, fruit maturity, bean characteristics and reaction to leaf rust and leaf miner. Results were compared with those of cultivar Catuaí-Amarelo which is extensively planted in Brazil and lcatu. Differences in yield and other traits among plants were significant. Nine introductions showed similar yield when compared with Catuaí-Amarelo (4,629 kg/ha). Four have shown dwarf habit, and fourteen presented early fruit maturing characteristic. All introductions were susceptible to coffee rust, produced high percentage of flat beans and low percentage to shell-beans. The introduction T-974 was lesser attacked by leaf miner.Durante o período de 1977 a 1982 conduziu-se um experimento em Jacarezinho, Paraná, com 18 introduções de café (Coffea arabica L.), com o objetivo de avaliar o rendimento de produção, arquitetura das plantas, maturação, características da semente, e o comportamento das plantas quanto à reação à ferrugem-alaranjada e ao bicho-mineiro. Os resultados foram comparados com o da cultivar Catuaí-Amarelo que é extensivamente cultivada no Brasil e Icatu. Houve diferenças significativas em produção e em outras variáveis, entre as plantas. Após quatro colheitas consecutivas, nove introduções produziram café beneficiado similar ao da cultivar Catuaí-Amarelo (4.629 kg/ha). Quatro caracterizam-se pelo porte baixo, e quatorze, pela maturação precoce dos frutos. Todas as introduções foram suscetíveis à ferrugem e apresentaram altas percentagens de semente tipo chato e baixa percentagem de semente tipo concha. A introdução T-974 foi menos atacada pelo bicho-mineiro

Hole depletion and localization due to disorder in insulating PrBa2Cu3O7-d: a Compton scattering study

The (mostly) insulating behaviour of PrBa2Cu3O7-d is still unexplained and even more interesting since the occasional appearance of superconductivity in this material. Since YBa2Cu3O7-d is nominally iso-structural and always superconducting, we have measured the electron momentum density in these materials. We find that they differ in a striking way, the wavefunction coherence length in PrBa2Cu3O7-d being strongly suppressed. We conclude that Pr on Ba-site substitution disorder is responsible for the metal-insulator transition. Preliminary efforts at growth with a method to prevent disorder yield 90K superconducting PrBa2Cu3O7-d crystallites.Comment: 4 pages, 3 figures, revised version submitted to PR

Segmentation of polarimetric radar imagery using statistical texture

Weather radars are increasingly being used to study the interaction between wildfires and the atmosphere, owing to the enhanced spatio-temporal resolution of radar data compared to conventional measurements, such as satellite imagery and in situ sensing. An important requirement for the continued proliferation of radar data for this application is the automatic identification of fire-generated particle returns (pyrometeors) from a scene containing a diverse range of echo sources, including clear air, ground and sea clutter, and precipitation. The classification of such particles is a challenging problem for common image segmentation approaches (e.g. fuzzy logic or unsupervised machine learning) due to the strong overlap in radar variable distributions between each echo type. Here, we propose the following two-step method to address these challenges: (1) the introduction of secondary, texture-based fields, calculated using statistical properties of gray-level co-occurrence matrices (GLCMs), and (2) a Gaussian mixture model (GMM), used to classify echo sources by combining radar variables with texture-based fields from (1). Importantly, we retain all information from the original measurements by performing calculations in the radar's native spherical coordinate system and introduce a range-varying-window methodology for our GLCM calculations to avoid range-dependent biases. We show that our method can accurately classify pyrometeors' plumes, clear air, sea clutter, and precipitation using radar data from recent wildfire events in Australia and find that the contrast of the radar correlation coefficient is the most skilful variable for the classification. The technique we propose enables the automated detection of pyrometeors' plumes from operational weather radar networks, which may be used by fire agencies for emergency management purposes or by scientists for case study analyses or historical-event identification.</p

The Mouse Gastrointestinal Bacteria Catalogue enables translation between the mouse and human gut microbiotas via functional mapping.

Funder: Royal SocietyHuman health and disease have increasingly been shown to be impacted by the gut microbiota, and mouse models are essential for investigating these effects. However, the compositions of human and mouse gut microbiotas are distinct, limiting translation of microbiota research between these hosts. To address this, we constructed the Mouse Gastrointestinal Bacteria Catalogue (MGBC), a repository of 26,640 high-quality mouse microbiota-derived bacterial genomes. This catalog enables species-level analyses for mapping functions of interest and identifying functionally equivalent taxa between the microbiotas of humans and mice. We have complemented this with a publicly deposited collection of 223 bacterial isolates, including 62 previously uncultured species, to facilitate experimental investigation of individual commensal bacteria functions in vitro and in vivo. Together, these resources provide the ability to identify and test functionally equivalent members of the host-specific gut microbiotas of humans and mice and support the informed use of mouse models in human microbiota research.Sir Henry Dale Fellowship jointly funded by Wellcome Trust and Royal Society [206245/Z/17/Z]. Rosetrees Trust [A2194]. Wellcome Trust [098051]

Tumor Necrosis Factor-α and Muc2 Mucin Play Major Roles in Disease Onset and Progression in Dextran Sodium Sulphate-Induced Colitis

The sequential events and the inflammatory mediators that characterize disease onset and progression of ulcerative colitis (UC) are not well known. In this study, we evaluated the early pathologic events in the pathogenesis of colonic ulcers in rats treated with dextran sodium sulfate (DSS). Following a lag phase, day 5 of DSS treatment was found clinically most critical as disease activity index (DAI) exhibited an exponential rise with severe weight loss and rectal bleeding. Surprisingly, on days 1-2, colonic TNF-α expression (70-80-fold) and tissue protein (50-fold) were increased, whereas IL-1β only increased on days 7-9 (60-90-fold). Days 3-6 of DSS treatment were characterized by a prominent down regulation in the expression of regulatory cytokines (40-fold for IL-10 and TGFβ) and mucin genes (15-18 fold for Muc2 and Muc3) concomitant with depletion of goblet cell and adherent mucin. Remarkably, treatment with TNF-α neutralizing antibody markedly altered DSS injury with reduced DAI, restoration of the adherent and goblet cell mucin and IL-1β and mucin gene expression. We conclude that early onset colitis is dependent on TNF-α that preceded depletion of adherent and goblet cell mucin prior to epithelial cell damage and these biomarkers can be used as therapeutic targets for UC

Patterns of mandibular invasion in oral squamous cell carcinoma of the mandibular region

BACKGROUND: Mandibular resections are routinely carried out for achieving a R0 resection for oral cancers. However, the need of mandibular resection to achieve this has always been questioned. The present study was carried out to define the pattern of mandibular involvement in carcinoma of the mandibular region. PATIENTS AND METHODS: A total of 25 consecutive patients who had undergone mandibular resection and were found to have mandibular invasion were studied in a prospective open fashion. After decalcification the specimens were serially sectioned at 1 cm interval to identify invasion of mandibular bone. Type of invasion, route of spread and host cell reactions were also recorded. RESULTS: The mandibular involvement was infiltrative in 14(56%) and erosive in 11(44%). It was cortical in 5(20%), marrow involvement was seen in 15(60%) while 5(20%) had spread through the inferior alveolar canal. Of the 25, 24(96%) lesions were located with in 1 cm of the mandible. CONCLUSION: The possibility of mandibular involvement is higher in patients where tumours are located with in 1 cm of the mandible. Involvement of mandible through the canal of inferior alveolar nerve in the present study was relatively high (20%). Therefore it is recommended that before a decision is taken to preserve the mandible it should be thoroughly screened for possible involvement