P- and S- wave velocities of consolidated sediments from a seafloor seismic survey in the North Celtic Sea Basin, offshore Ireland

A geophysical survey was conducted over a hydrocarbon prospect in the North Celtic Sea Basin using a small array of ocean-bottom seismographs (OBSs). The purpose of this study was to determine the ratio of (P) compressional- to (S) shear-wave velocity of consolidated sedimentary rocks in order to constrain possible subsurface variations in pore-fluid content. The ratio of VP and VS- is known to be particularly sensitive to lithology, porosity and pore-fluid content, making it a useful parameter for evaluating hydrocarbon prospects. OBSs offer a relatively cheap and time-effective means of acquiring multi-component data compared with ocean-bottom cables. In this contribution, we demonstrate the ability of an OBS survey comprising three pairs of two OBSs spaced at 1.6 km to recover lateral variations in the VP/VS ratio. A key requirement of this type of study is that S-waves will be generated by mode conversions in the subsurface, since they cannot be generated in nor travel through fluids. In this survey, the contrast in physical properties of the hard seabed of the North Celtic Sea Basin provided a means of generating converted S-waves. Two-dimensional ray-tracing and forward modeling was used to create both VP and VS models along a profile crossing the Blackrock prospect in the North Celtic Sea Basin. These models comprise four layers and extend to a maximum depth of 1.1 km. The observed northward decrease in the VP/VS ratio at depths of 500-1000 m below the seafloor in the study area is interpreted to represent lateral variation in the amount of gas present in the pore space of Upper Cretaceous chalks and shales overlying the prospective reservoir

A combined low-radio frequency/X-ray study of galaxy groups I. Giant Metrewave Radio Telescope observations at 235 MHz and 610 MHz

We present new Giant Metrewave Radio Telescope observations at 235 MHz and 610 MHz of 18 X-ray bright galaxy groups. These observations are part of an extended project, presented here and in future papers, which combines low-frequency radio and X-ray data to investigate the interaction between central active galactic nuclei (AGN) and the intra-group medium (IGM). The radio images show a very diverse population of group-central radio sources, varying widely in size, power, morphology and spectral index. Comparison of the radio images with Chandra and XMM-Newton X-ray images shows that groups with significant substructure in the X-ray band and marginal radio emission at >= 1 GHz host low-frequency radio structures that correlate with substructures in IGM. Radio-filled X-ray cavities, the most evident form of AGN/IGM interaction in our sample, are found in half of the systems, and are typically associated with small, low- or mid-power double radio sources. Two systems, NGC5044 and NGC4636, possess multiple cavities, which are isotropically distributed around the group center, possibly due to group weather. In other systems the radio/X-ray correlations are less evident. However, the AGN/IGM interaction can manifest itself through the effects of the high-pressure medium on the morphology, spectral properties and evolution of the radio-emitting plasma. In particular, the IGM can confine fading radio lobes in old/dying radio galaxies and prevent them from dissipating quickly. Evidence for radio emission produced by former outbursts that coexist with current activity is found in six groups of the sample.Comment: Accepted for publication in the Astrophysical Journal Supplement Series, 26 pages, 18 figures. A version with high-quality figures is http://www.astro.umd.edu/~simona/giacintucci_hr.pd

Understanding the factors controlling the photo-oxidation of natural DNA by enantiomerically pure intercalating ruthenium polypyridyl complexes through TA/TRIR studies with polydeoxynucleotides and mixed sequence oligodeoxynucleotides

Ruthenium polypyridyl complexes which can sensitise the photo-oxidation of nucleic acids and other biological molecules show potential for photo-therapeutic applications. In this article a combination of transient visible absorption (TrA) and time-resolved infra-red (TRIR) spectroscopy are used to compare the photo-oxidation of guanine by the enantiomers of [Ru(TAP)2(dppz)]2+ in both polymeric {poly(dG-dC), poly(dA-dT) and natural DNA} and small mixed-sequence duplex-forming oligodeoxynucleotides. The products of electron transfer are readily monitored by the appearance of a characteristic TRIR band centred at ca. 1700 cm?1 for the guanine radical cation and a band centered at ca. 515 nm in the TrA for the reduced ruthenium complex. It is found that efficient electron transfer requires that the complex be intercalated at a G-C base-pair containing site. Significantly, changes in the nucleobase vibrations of the TRIR spectra induced by the bound excited state before electron transfer takes place are used to identify preferred intercalation sites in mixed-sequence oligodeoxynucleotides and natural DNA. Interestingly, with natural DNA, while it is found that quenching is inefficient in the picosecond range, a slower electron transfer process occurs, which is not found with the mixed-sequence duplex-forming oligodeoxynucleotides studied

Inter- and Intra-Observer Agreement of PD-L1 SP142 Scoring in Breast Carcinoma:A Large Multi-Institutional International Study

The assessment of PD-L1 expression in TNBC is a prerequisite for selecting patients for immunotherapy. The accurate assessment of PD-L1 is pivotal, but the data suggest poor reproducibility. A total of 100 core biopsies were stained using the VENTANA Roche SP142 assay, scanned and scored by 12 pathologists. Absolute agreement, consensus scoring, Cohen's Kappa and intraclass correlation coefficient (ICC) were assessed. A second scoring round after a washout period to assess intra-observer agreement was carried out. Absolute agreement occurred in 52% and 60% of cases in the first and second round, respectively. Overall agreement was substantial (Kappa 0.654-0.655) and higher for expert pathologists, particularly on scoring TNBC (6.00 vs. 0.568 in the second round). The intra-observer agreement was substantial to almost perfect (Kappa: 0.667-0.956), regardless of PD-L1 scoring experience. The expert scorers were more concordant in evaluating staining percentage compared with the non-experienced scorers (R2 = 0.920 vs. 0.890). Discordance predominantly occurred in low-expressing cases around the 1% value. Some technical reasons contributed to the discordance. The study shows reassuringly strong inter- and intra-observer concordance among pathologists in PD-L1 scoring. A proportion of low-expressors remain challenging to assess, and these would benefit from addressing the technical issues, testing a different sample and/or referring for expert opinions

Controlled dehydration of a ruthenium complex-DNA crystal induces reversible DNA kinking

Hydration-dependent DNA deformation has been known since Rosalind Franklin recognised that the relative humidity of the sample had to be maintained to observe a single conformation in DNA fibre diffraction. We now report for the first time the crystal structure, at the atomic level, of a dehydrated form of a DNA duplex and demonstrate the reversible interconversion to the hydrated form at room temperature. This system, containing d(TCGGCGCCGA) in the presence of Λ-[Ru(TAP)2(dppz)]2+ (TAP = 1,4,5,8-tetraazaphenanthrene, dppz = dipyridophenazine), undergoes a partial transition from an A/B hybrid to the A-DNA conformation, at 84-79% relative humidity. This is accompanied by an increase in kink at the central step from 22° to 51°, with a large movement of the terminal bases forming the intercalation site. This transition is reversible on rehydration. Seven datasets, collected from one crystal at room temperature, show the consequences of dehydration at near-atomic resolution. This result highlights that crystals, traditionally thought of as static systems, are still dynamic and therefore can be the subject of further experimentation

FAS-dependent cell death in α-synuclein transgenic oligodendrocyte models of multiple system atrophy

Multiple system atrophy is a parkinsonian neurodegenerative disorder. It is cytopathologically characterized by accumulation of the protein p25α in cell bodies of oligodendrocytes followed by accumulation of aggregated α-synuclein in so-called glial cytoplasmic inclusions. p25α is a stimulator of α-synuclein aggregation, and coexpression of α-synuclein and p25α in the oligodendroglial OLN-t40-AS cell line causes α-synuclein aggregate-dependent toxicity. In this study, we investigated whether the FAS system is involved in α-synuclein aggregate dependent degeneration in oligodendrocytes and may play a role in multiple system atrophy. Using rat oligodendroglial OLN-t40-AS cells we demonstrate that the cytotoxicity caused by coexpressing α-synuclein and p25α relies on stimulation of the death domain receptor FAS and caspase-8 activation. Using primary oligodendrocytes derived from PLP-α-synuclein transgenic mice we demonstrate that they exist in a sensitized state expressing pro-apoptotic FAS receptor, which makes them sensitive to FAS ligand-mediated apoptosis. Immunoblot analysis shows an increase in FAS in brain extracts from multiple system atrophy cases. Immunohistochemical analysis demonstrated enhanced FAS expression in multiple system atrophy brains notably in oligodendrocytes harboring the earliest stages of glial cytoplasmic inclusion formation. Oligodendroglial FAS expression is an early hallmark of oligodendroglial pathology in multiple system atrophy that mechanistically may be coupled to α-synuclein dependent degeneration and thus represent a potential target for protective intervention

Upregulation of pirin expression by chronic cigarette smoking is associated with bronchial epithelial cell apoptosis

BACKGROUND: Cigarette smoke disrupts the protective barrier established by the airway epithelium through direct damage to the epithelial cells, leading to cell death. Since the morphology of the airway epithelium of smokers does not typically demonstrate necrosis, the most likely mechanism for epithelial cell death in response to cigarette smoke is apoptosis. We hypothesized that cigarette smoke directly up-regulates expression of apoptotic genes, which could play a role in airway epithelial apoptosis. METHODS: Microarray analysis of airway epithelium obtained by bronchoscopy on matched cohorts of 13 phenotypically normal smokers and 9 non-smokers was used to identify specific genes modulated by smoking that were associated with apoptosis. Among the up-regulated apoptotic genes was pirin (3.1-fold, p < 0.002), an iron-binding nuclear protein and transcription cofactor. In vitro studies using human bronchial cells exposed to cigarette smoke extract (CSE) and an adenovirus vector encoding the pirin cDNA (AdPirin) were performed to test the direct effect of cigarette smoke on pirin expression and the effect of pirin expression on apoptosis. RESULTS: Quantitative TaqMan RT-PCR confirmed a 2-fold increase in pirin expression in the airway epithelium of smokers compared to non-smokers (p < 0.02). CSE applied to primary human bronchial epithelial cell cultures demonstrated that pirin mRNA levels increase in a time-and concentration-dependent manner (p < 0.03, all conditions compared to controls). Overexpression of pirin, using the vector AdPirin, in human bronchial epithelial cells was associated with an increase in the number of apoptotic cells assessed by both TUNEL assay (5-fold, p < 0.01) and ELISA for cytoplasmic nucleosomes (19.3-fold, p < 0.01) compared to control adenovirus vector. CONCLUSION: These observations suggest that up-regulation of pirin may represent one mechanism by which cigarette smoke induces apoptosis in the airway epithelium, an observation that has implications for the pathogenesis of cigarette smoke-induced diseases