Waterborne GPR survey for estimating bottom-sediment variability: A survey on the Po River, Turin, Italy

We conducted an integrated geophysical survey on a stretch of the river Po in order to check the GPR ability to discriminate the variability of riverbed sediments through an analysis of the bottom reflection amplitudes. We conducted continuous profiles with a 200-MHzGPR system and a handheld broadband EM sensor.Aconductivity meter and a TDR provided punctual measurements of water conductivity, permittivity, and temperature. The processing and interpretation of the GEM-2 and GPR data were enhanced by reciprocal results and by integration with the punctual measurements of the EM properties of the water. We used a processing flow that improved the radargram images and preserved the amplitude ratios among the different profiles and the frequency content at the bottom reflection signal.We derived the water attenuation coefficient both from the punctual measurements using the Maxwell formulas and from the interpretation of the GPR data, finding an optimal matching between the two values. The GPR measurements provided maps of the bathymetry and of the bottom reflection amplitude. The high reflectivity of the riverbed, derived from the GPR interpretation, agreed with the results of the direct sampling campaign that followed the geophysical survey. The variability of the bottom-reflection-amplitudes map, which was not confirmed by the direct sampling, could also have been caused by scattering phenomena due to the riverbed clasts which are dimensionally comparable to the wavelength of the radar pulse

The indirect costs of agency nurses in South Africa: a case study in two public sector hospitals

PKBackground: Globally, flexible work arrangements - through the use of temporary nursing staff - are an important strategy for dealing with nursing shortages in hospitals. Objective: The objective of the study was to determine the direct and indirect costs of agency nurses, as well as the advantages and the problems associated with agency nurse utilisation in two public sector hospitals in South Africa. Methods: Following ethical approval, two South African public sector hospitals were selected purposively. Direct costs were determined through an analysis of hospital expenditure information for a 5-year period from 2005 until 2010, obtained from the national transversal Basic Accounting System database. At each hospital, semi-structured interviews were conducted with the chief executive officer, executive nursing services manager, the maternity or critical care unit nursing manager, the human resource manager, and the finance manager. Indirect costs measured were the time spent on pre-employment checks, and nurse recruitment, orientation, and supervision. All expenditure is expressed in South African Rands (R: 1 USD R7, 2010 prices). Results: In the 2009/10 financial year, Hospital 1 spent R38.86 million (US$5.55 million) on nursing agencies, whereas Hospital 2 spent R10.40 million (US$1.49 million). The total estimated time spent per week on indirect cost activities at Hospital 1 was 51.5 hours, and 60 hours at Hospital 2. The estimated monetary value of this time at Hospital 1 was R962,267 (US$137,467) and at Hospital 2 the value was R300,121 (US$42,874), thus exceeding the weekly direct costs of nursing agencies. Agency nurses assisted the selected hospitals in dealing with problems of nurse recruitment, absenteeism, shortages, and skills gaps in specialised clinical areas. The problems experienced with agency nurses included their perceived lack of commitment, unreliability, and providing sub-optimal quality of patient care. Conclusion: Hospital managers and policy-makers need to address the effective utilisation of agency nurses and quality of patient care in tandem

Concordance of copy number abnormality detection using SNP arrays and Multiplex Ligation-dependent Probe Amplification (MLPA) in acute lymphoblastic leukaemia

In acute lymphoblastic leukaemia, MLPA has been used in research studies to identify clinically relevant copy number abnormality (CNA) profiles. However, in diagnostic settings other techniques are often employed. We assess whether equivalent CNA profiles are called using SNP arrays, ensuring platform independence. We demonstrate concordance between SNP6.0 and MLPA CNA calling on 143 leukaemia samples from two UK trials; comparing 1,287 calls within eight genes and a region. The techniques are 99% concordant using manually augmented calling, and 98% concordant using an automated pipeline. We classify these discordant calls and examine reasons for discordance. In nine cases the circular binary segmentation (CBS) algorithm failed to detect focal abnormalities or those flanking gaps in IKZF1 probe coverage. Eight cases were discordant due to probe design differences, with focal abnormalities detectable using one technique not observable by the other. Risk classification using manually augmented array calling resulted in four out of 143 patients being assigned to a different CNA risk group and eight patients using the automated pipeline. We conclude that MLPA defined CNA profiles can be accurately mirrored by SNP6.0 or similar array platforms. Automated calling using the CBS algorithm proved successful, except for IKZF1 which should be manually inspected

An unbiased proteomics approach to identify human cytomegalovirus RNA-associated proteins

AbstractPost-transcriptional events regulate herpesvirus gene expression, yet few herpesvirus RNA-binding proteins have been identified. We used an unbiased approach coupling oligo(dT) affinity capture with proteomics to identify viral RNA-associated proteins during infection. Using this approach, we identified and confirmed changes in the abundance or activity of two host RNA-associated proteins, DHX9 and DDX3, in cells infected with human cytomegalovirus (HCMV). We also identified and confirmed previously unreported activities for the HCMV US22 and pp71 proteins as RNA-associated viral proteins and confirmed that a known viral RNA-binding protein, pTRS1, associates with RNA in infected cells. Further, we found that HCMV pp71 co-sedimented with polysomes, associated with host and viral RNAs, and stimulated the overall rate of protein synthesis. These results demonstrate that oligo(dT) affinity capture coupled with proteomics provides a rapid and straightforward means to identify RNA-associated viral proteins during infection that may participate in the post-transcriptional control of gene expression

Human Cytomegalovirus pTRS1 and pIRS1 Antagonize Protein Kinase R To Facilitate Virus Replication

ABSTRACT Human cytomegalovirus (HCMV) counteracts host defenses that otherwise act to limit viral protein synthesis. One such defense is the antiviral kinase protein kinase R (PKR), which inactivates the eukaryotic initiation factor 2 (eIF2) translation initiation factor upon binding to viral double-stranded RNAs. Previously, the viral TRS1 and IRS1 proteins were found to antagonize the antiviral kinase PKR outside the context of HCMV infection, and the expression of either pTRS1 or pIRS1 was shown to be necessary for HCMV replication. In this study, we found that expression of either pTRS1 or pIRS1 is necessary to prevent PKR activation during HCMV infection and that antagonism of PKR is critical for efficient viral replication. Consistent with a previous study, we observed decreased overall levels of protein synthesis, reduced viral protein expression, and diminished virus replication in the absence of both pTRS1 and pIRS1. In addition, both PKR and eIF2α were phosphorylated during infection when pTRS1 and pIRS1 were absent. We also found that expression of pTRS1 was both necessary and sufficient to prevent stress granule formation in response to eIF2α phosphorylation. Depletion of PKR prevented eIF2α phosphorylation, rescued HCMV replication and protein synthesis, and reversed the accumulation of stress granules in infected cells. Infection with an HCMV mutant lacking the pTRS1 PKR binding domain resulted in PKR activation, suggesting that pTRS1 inhibits PKR through a direct interaction. Together our results show that antagonism of PKR by HCMV pTRS1 and pIRS1 is critical for viral protein expression and efficient HCMV replication. IMPORTANCE To successfully replicate, viruses must counteract host defenses that limit viral protein synthesis. We have identified inhibition of the antiviral kinase PKR by the viral proteins TRS1 and IRS1 and shown that this is a critical step in HCMV replication. Our results suggest that inhibiting pTRS1 and pIRS1 function or restoring PKR activity during infection may be a successful strategy to limit HCMV disease

The Lunar Orbiter Photographic System

Lunar orbiter photographic syste

Stribild: A Review of Component Characteristics and Combination Drug Efficacy

BACKGROUND: Numerous methods have been devised to combat human immunodeficiency virus (HIV) replication and disease progression. Composed of an integrase strand transfer inhibitor, a pharmacoenhancer, and two reverse transcriptase inhibitors, Stribild is a relatively new combination HIV drug formulated for once-a-day dosing. METHODS: Relevant information, original research articles and reviews, were gathered primarily through the use of the PubMed database. The search was conducted without date restrictions in order to collect both historical and recent information concerning HIV, individual drugs, and combinations for a thorough overview. RESULTS: Stribild, when taken with food, provides therapeutic drug concentrations as seen through comparison with the respective individual or boosted individual drugs. Stribild non-inferiority has been shown when compared to other HIV drug combinations, ritonavir-boosted atazanavir or efavirenz each with a tenofovir disoproxil fumarate (TDF) and emtricitabine (FTC) backbone. The co-formulation also retained high viral suppression in patients switching from other regimens, such as efavirenz/TDF/FTC, raltegravir/TDF/FTC, or various ritonavir-boosted protease inhibitors with TDF/FTC. The elvitegravir and cobicistat combination was unaffected by moderate hepatic impairment; however, hepatic and renal function along with changes in bone mineral density should be monitored closely. Stribild presented with relatively few side effect occurrences, but drug interactions may pose a larger problem for continuous therapy. CONCLUSIONS: Stribild provides viral suppression, comparable to other combination HIV drugs through review of non-inferiority and regimen simplification studies, with minimal adverse effects. Although the breadth of Stribild effectiveness has begun to unfold, studies are lacking in older patients as well as adolescents

Mechanism of Protein Kinase R Inhibition by Human Cytomegalovirus pTRS1

ABSTRACT Double-stranded RNAs (dsRNA) produced during human cytomegalovirus (HCMV) infection activate the antiviral kinase protein kinase R (PKR), which potently inhibits virus replication. The HCMV pTRS1 and pIRS1 proteins antagonize PKR to promote HCMV protein synthesis and replication; however, the mechanism by which pTRS1 inhibits PKR is unclear. PKR activation occurs in a three-step cascade. First, binding to dsRNA triggers PKR homodimerizaton. PKR dimers then autophosphorylate, leading to a conformational shift that exposes the binding site for the PKR substrate eIF2α. Consistent with previous in vitro studies, we found that pTRS1 bound and inhibited PKR. pTRS1 binding to PKR was not mediated by an RNA intermediate, and mutations in the pTRS1 RNA binding domain did not affect PKR binding or inhibition. Rather, mutations that disrupted the pTRS1 interaction with PKR ablated the ability of pTRS1 to antagonize PKR activation by dsRNA. pTRS1 did not block PKR dimerization and could bind and inhibit a constitutively dimerized PKR kinase domain. In addition, pTRS1 binding to PKR inhibited PKR kinase activity. Single amino acid point mutations in the conserved eIF2α binding domain of PKR disrupted pTRS1 binding and rendered PKR resistant to inhibition by pTRS1. Consistent with a critical role for the conserved eIF2α contact site in PKR binding, pTRS1 bound an additional eIF2α kinase, heme-regulated inhibitor (HRI), and inhibited eIF2α phosphorylation in response to an HRI agonist. Together our data suggest that pTRS1 inhibits PKR by binding to conserved amino acids in the PKR eIF2α binding site and blocking PKR kinase activity. IMPORTANCE The antiviral kinase PKR plays a critical role in controlling HCMV replication. This study furthered our understanding of how HCMV evades inhibition by PKR and identified new strategies for how PKR activity might be restored during infection to limit HCMV disease