Antibody Signatures Reflect Different Disease Pathologies in Patients With Schistosomiasis Due to Schistosoma japonicum

Infection with Schistosoma japonicum causes high levels of pathology that is predominantly determined by the cellular and humoral response of the host. However, the specific antibody response that arises during the development of disease is largely undescribed in Asian schistosomiasis-endemic populations. A schistosome protein microarray was used to compare the antibody profiles of subjects with acute infection, with early or advanced disease associated with severe pathology, with chronic infection, and subjects exposed but stool negative for S. japonicum eggs to the antibody profiles of nonexposed controls. Twenty-five immunodominant antigens were identified, including vaccine candidates, tetraspanin-related proteins, transporter molecules, and unannotated proteins. Additionally, individuals with severe pathology had a limited specific antibody response, suggesting that individuals with mild disease may use a broad and strong antibody response, particularly against surface-exposed proteins, to control pathology and/or infection. Our study has identified specific antigens that can discriminate between S. japonicum-exposed groups with different pathologies and may also allow the host to control disease pathology and provide resistance to parasite infection.

Proteomic analysis of coronary sinus serum reveals leucine-rich α2-glycoprotein as a novel biomarker of ventricular dysfunction and heart failure

BACKGROUND: Heart failure (HF) prevention strategies require biomarkers that identify disease manifestation. Increases in B-type natriuretic peptide (BNP) correlate with increased risk of cardiovascular events and HF development. We hypothesize that coronary sinus serum from a high BNP hypertensive population reflects an active pathological process and can be used for biomarker exploration. Our aim was to discover differentially expressed disease-associated proteins that identify patients with ventricular dysfunction and HF.

METHODS AND RESULTS: Coronary sinus serum from 11 asymptomatic, hypertensive patients underwent quantitative differential protein expression analysis by 2-dimensional difference gel electrophoresis. Proteins were identified using mass spectrometry and then studied by enzyme-linked immunosorbent assay in sera from 40 asymptomatic, hypertensive patients and 105 patients across the spectrum of ventricular dysfunction (32 asymptomatic left ventricular diastolic dysfunction, 26 diastolic HF, and 47 systolic HF patients). Leucine-rich α2-glycoprotein (LRG) was consistently overexpressed in high BNP serum. LRG levels correlate significantly with BNP in hypertensive, asymptomatic left ventricular diastolic dysfunction, diastolic HF, and systolic HF patient groups (P≤0.05). LRG levels were able to identify HF independent of BNP. LRG correlates with coronary sinus serum levels of tumor necrosis factor-α (P=0.009) and interleukin-6 (P=0.021). LRG is expressed in myocardial tissue and correlates with transforming growth factor-βR1 (P<0.001) and α-smooth muscle actin (P=0.025) expression.

CONCLUSIONS: LRG was identified as a serum biomarker that accurately identifies patients with HF. Multivariable modeling confirmed that LRG is a stronger identifier of HF than BNP and this is independent of age, sex, creatinine, ischemia, β-blocker therapy, and BNP.

STPA-SafeSec: Safety and Security Analysis for Cyber-Physical Systems

Cyber-physical systems tightly integrate physical processes and information and communication technologies. As today’s critical infrastructures, e.g., the power grid or water distribution networks, are complex cyber-physical systems, ensuring their safety and security becomes of paramount importance. Traditional safety analysis methods, such as HAZOP, are ill-suited to assess these systems. Furthermore, cybersecurity vulnerabilities are often not considered critical, because their effects on the physical processes are not fully understood. In this work, we present STPA-SafeSec, a novel analysis methodology for both safety and security. Its results show the dependencies between cybersecurity vulnerabilities and system safety. Using this information, the most effective mitigation strategies to ensure safety and security of the system can be readily identified. We apply STPA-SafeSec to a use case in the power grid domain, and highlight its benefits.

The VLT-FLAMES Tarantula Survey XXI. Stellar spin rates of O-type spectroscopic binaries

Context: The initial distribution of spin rates of massive stars is a fingerprint of their elusive formation process. It also sets a key initial condition for stellar evolution and is thus an important ingredient in stellar population synthesis. So far, most studies have focused on single stars. Most O stars are, however, found in multiple systems. 

Aims: By establishing the spin-rate distribution of a sizeable sample of O-type spectroscopic binaries and by comparing the distributions of binary subpopulations with one another and with that of presumed-single stars in the same region, we aim to constrain the initial spin distribution of O stars in binaries, and to identify signatures of the physical mechanisms that affect the evolution of the spin rates of massive stars. 

Methods: We use ground-based optical spectroscopy obtained in the framework of the VLT-FLAMES Tarantula Survey (VFTS) to establish the projected equatorial rotational velocities (ν_esini) for components of 114 spectroscopic binaries in 30 Doradus. The ν_esini values are derived from the full width at half maximum (FWHM) of a set of spectral lines, using a FWHM vs. ν_esini calibration that we derive based on previous line analysis methods applied to single O-type stars in the VFTS sample. 

Results: The overall ν_esini distribution of the primary stars resembles that of single O-type stars in the VFTS, featuring a low-velocity peak (at ν_esini<200 kms^-1) and a shoulder at intermediate velocities (200 <ν_esini<300 kms^-1). The distributions of binaries and single stars, however, differ in two ways. First, the main peak at ν_esini ~ 100kms^-1 is broader and slightly shifted towards higher spin rates in the binary distribution than that of the presumed-single stars. This shift is mostly due to short-period binaries (P_orb~<10 d). Second, the ν_esini distribution of primaries lacks a significant population of stars spinning faster than 300 kms^-1, while such a population is clearly present in the single-star sample. The ν_esini distribution of binaries with amplitudes of radial velocity variation in the range of 20 to 200 kms^-1 (mostly binaries with P_orb ~ 10-1000 d and/or with q<0.5) is similar to that of single O stars below ν_esini_~<170kms^-1. 

Conclusions: Our results are compatible with the assumption that binary components formed with the same spin distribution as single stars, and that this distribution contains few or no fast-spinning stars. The higher average spin rate of stars in short-period binaries may either be explained by spin-up through tides in such tight binary systems, or by spin-down of a fraction of the presumed-single stars and long-period binaries through magnetic braking (or by a combination of both mechanisms). Most primaries and secondaries of SB2 systems with P_orb~<10 d appear to have similar rotational velocities. This is in agreement with tidal locking in close binaries where the components have similar radii. The lack of very rapidly spinning stars among binary systems supports the idea that most stars with ν_esini_~> 300kms^-1 in the single-star sample are actually spun-up post-binary interaction products. Finally, the overall similarities (low-velocity peak and intermediate-velocity shoulder) of the spin distribution of binary and single stars argue for a massive star formation process in which the initial spin is set independently of whether stars are formed as single stars or as components of a binary system.

A compendium of myeloma-associated chromosomal copy number abnormalities and their prognostic value.

To obtain a comprehensive genomic profile of presenting multiple myeloma cases we performed high-resolution single nucleotide polymorphism mapping array analysis in 114 samples alongside 258 samples analyzed by U133 Plus 2.0 expression array (Affymetrix). We examined DNA copy number alterations and loss of heterozygosity (LOH) to define the spectrum of minimally deleted regions in which relevant genes of interest can be found. The most frequent deletions are located at 1p (30%), 6q (33%), 8p (25%), 12p (15%), 13q (59%), 14q (39%), 16q (35%), 17p (7%), 20 (12%), and 22 (18%). In addition, copy number-neutral LOH, or uniparental disomy, was also prevalent on 1q (8%), 16q (9%), and X (20%), and was associated with regions of gain and loss. Based on fluorescence in situ hybridization and expression quartile analysis, genes of prognostic importance were found to be located at 1p (FAF1, CDKN2C), 1q (ANP32E), and 17p (TP53). In addition, we identified common homozygously deleted genes that have functions relevant to myeloma biology. Taken together, these analyses indicate that the crucial pathways in myeloma pathogenesis include the nuclear factor-κB pathway, apoptosis, cell-cycle regulation, Wnt signaling, and histone modifications. This study was registered at http://isrctn.org as ISRCTN68454111.

Specific JAK2 mutation (JAK2R683) and multiple gene deletions in Down syndrome acute lymphoblastic leukemia

Children with Down syndrome (DS) have a greatly increased risk of acute megakaryoblastic leukemia (AMKL) and acute lymphoblastic leukemia (ALL). Both DS-AMKL and the related transient myeloproliferative disorder (TMD) have GATA1 mutations as obligatory, early events. To identify mutations contributing to leukemogenesis in DS-ALL, we undertook sequencing of candidate genes, including FLT3, RAS, PTPN11, BRAF, and JAK2. Sequencing of the JAK2 pseudokinase domain identified a specific, acquired mutation, JAK2R683, in 12 (28%) of 42 DS-ALL cases. Functional studies of the common JAK2R683G mutation in murine Ba/F3 cells showed growth factor independence and constitutive activation of the JAK/STAT signaling pathway. High-resolution SNP array analysis of 9 DS-ALL cases identified additional submicroscopic deletions in key genes, including ETV6, CDKN2A, and PAX5. These results infer a complex molecular pathogenesis for DS-ALL leukemogenesis, with trisomy 21 as an initiating or first hit and with chromosome aneuploidy, gene deletions, and activating JAK2 mutations as complementary genetic events. (Blood. 2009; 113: 646-648)

TRIPPy: Trailed Image Photometry in Python

Photometry of moving sources typically suffers from a reduced signal-to-noise ratio (S/N) or flux measurements biased to incorrect low values through the use of circular apertures. To address this issue, we present the software package, TRIPPy: TRailed Image Photometry in Python. TRIPPy introduces the pill aperture, which is the natural extension of the circular aperture appropriate for linearly trailed sources. The pill shape is a rectangle with two semicircular end-caps and is described by three parameters, the trail length and angle, and the radius. The TRIPPy software package also includes a new technique to generate accurate model point-spread functions (PSFs) and trailed PSFs (TSFs) from stationary background sources in sidereally tracked images. The TSF is merely the convolution of the model PSF, which consists of a moffat profile, and super-sampled lookup table. From the TSF, accurate pill aperture corrections can be estimated as a function of pill radius with an accuracy of 10 mmag for highly trailed sources. Analogous to the use of small circular apertures and associated aperture corrections, small radius pill apertures can be used to preserve S/Ns of low flux sources, with appropriate aperture correction applied to provide an accurate, unbiased flux measurement at all S/Ns.

Characterising the TP53-deleted subgroup of chronic lymphocytic leukemia: an analysis of additional cytogenetic abnormalities detected by interphase fluorescence in situ hybridisation and array-based comparative genomic hybridisation.

Deletion of the TP53 gene on chromosome 17p13.1 is the prognostic factor associated with the shortest survival in CLL. We used array-based comparative genomic hybridisation (arrayCGH) to identify additional DNA copy number changes in peripheral blood samples from 74 LRF CLL4 trial patients, 37 with >or=5% and 37 without TP53-deleted cells. ArrayCGH reliably detected deletions on 17p, including the TP53 locus, in cases with >or=50%TP53-deleted cells detected by fluorescence in situ hybridisation, plus seven additional cases with deleted regions on 17p excluding TP53. Losses on chromosomal regions 18p and/or 20p were found exclusively in cases with >or=5%TP53-deleted cells (por=5%TP53-deleted cases (p=0.02). In particular, amplification of 2p and deletion of 6q were both more frequent. Cases with >20%TP53-deleted cells had the worst prognosis in the LRF CLL4 trial.