“Forward-Thinking” in U.S. Biobanking

Aims: Do biobanks enact policies and plans that allow them to anticipate and respond to potential challenges? If a biobank has one such policy or plan, is it likely to have more? Using survey data from 456 U.S. biobanks, we assess four possible indicators of such “forward-thinking.

End-of-life experiences of mothers with advanced cancer: perspectives of widowed fathers

Despite the importance of parenting-related responsibilities for adult patients with terminal illnesses who have dependent children, little is known about the psychological concerns of dying parents and their families at the end of life (EOL). The aim of this study was to elicit widowed fathers’ perspectives on how parental status may have influenced the EOL experiences of mothers with advanced cancer

Biobanks containing clinical specimens: Defining characteristics, policies, and practices

Biobanks – collections of human biological specimens stored for future research use – are crucial for biomedical advancement. One of the most common ways that biobanks acquire specimens is to obtain residual or “leftover” samples originally collected for clinical care from hospitals, clinical laboratories and pathology departments. Little is known about the characteristics of biobanks that store specimens from clinical sources, or their policies and practices.In this paper, we present data from the subset of 261 biobanks in our 2012 national survey that stores specimens from clinical sources, focusing on a number of ethical issues that have been raised in the literature.Most biobanks are part of larger organizations, mainly academic medical centers, and most report standardized systems for managing acquisition, storage, and release to researchers. Yet, there is considerable diversity in policies and practices regarding informed consent, return of research results, ownership of specimens and technology developed, utilization, and disposition of remaining specimens after researchers have acquired, them. We document tremendous heterogeneity in the composition of these collections, the number and type of specimens stored, and number of requests for specimens per year.Responding to this variation presents significant challenges for those who manage the collections, demanding careful consideration and planning to maintain high quality practices in acquisition, storage, and release of specimens all the while striving to protect the rights of subjects

Quantitative chemical mapping of InGaN quantum wells from calibrated high-angle annular dark field micrographs

We present a simple and robust method to acquire quantitative maps of compositional fluctuations in nanostructures from low magnification high-angle annular dark field (HAADF) micrographs calibrated by energy-dispersive X-ray (EDX) spectroscopy in scanning transmission electron microscopy (STEM) mode. We show that a nonuniform background in HAADF-STEM micrographs can be eliminated, to a first approximation, by use of a suitable analytic function. The uncertainty in probe position when collecting an EDX spectrum renders the calibration of HAADF-STEM micrographs indirect, and a statistical approach has been developed to determine the position with confidence. Our analysis procedure, presented in a flowchart to facilitate the successful implementation of the method by users, was applied to discontinuous InGaN/GaN quantum wells in order to obtain quantitative determinations of compositional fluctuations on the nanoscale

Suboptimal Surveillance for and Knowledge of Hepatocellular Carcinoma Among Primary Care Providers

A large proportion of patients with cirrhosis are seen only by their primary care provider (PCP). Surveillance for hepatocellular carcinoma (HCC) therefore depends on PCPs in these cases. We aimed to assess PCP knowledge and practice of HCC surveillance

Stewardship Practices of U.S. Biobanks

Biobanks require new governance models that address their ethical and regulatory challenges. One model relies on stewardship of specimens throughout their life course. Here, we discuss findings from our survey of 456 U.S. biobank managers that addressed whether and how biobanks steward their specimens. The findings reveal that most bio-banks do not create ongoing relationships with contributors but do practice stewardship over storing and sharing of specimens. Biobanks now need guidance to fully articulate stewardship practices that ensure respect for contributors while facilitating research

Phytoplankton dynamics in relation to seasonal variability and upwelling and relaxation patterns at the mouth of Ria de Aveiro (West Iberian Margin) over a four-year period

From June 2004 to December 2007, samples were weekly collected at a fixed station located at the mouth of Ria de Aveiro (West Iberian Margin). We examined the seasonal and inter-annual fluctuations in composition and community structure of the phytoplankton in relation to the main environmental drivers and assessed the influence of the oceano-graphic regime, namely changes in frequency and intensity of upwelling events, over the dynamics of the phytoplankton assemblage. The samples were consistently handled and a final subset of 136 OTUs (taxa with relative abundance > 0.01%) was subsequently submitted to various multivariate analyses. The phytoplankton assemblage showed significant changes at all temporal scales but with an overriding importance of seasonality over longer-(inter-annual) or shorter-term fluctuations (upwelling-related). Sea-surface temperature, salinity and maximum upwelling index were retrieved as the main driver of seasonal change. Seasonal signal was most evident in the fluctuations of chlorophyll a concentration and in the high turnover from the winter to spring phytoplankton assemblage. The seasonal cycle of production and succession was disturbed by upwelling events known to disrupt thermal stratification and induce changes in the phytoplankton assemblage. Our results indicate that both the frequency and intensity of physical forcing were important drivers of such variability, but the outcome in terms of species composition was highly dependent on the available local pool of species and the timing of those events in relation to the seasonal cycle. We conclude that duration, frequency and intensity of upwelling events, which vary seasonally and inter-annually, are paramount for maintaining long-term phytoplankton diversity likely by allowing unstable coexistence and incorporating species turnover at different scales. Our results contribute to the understanding of the complex mechanisms of coastal phytoplankton dynamics in relation to changing physical forcing which is fundamental to improve predictability of future prospects under climate change.Portuguese Foundation for Science and Technology (FCT, Portugal) [SFRH/BPD/ 94562/2013]; FEDER funds; national funds; CESAM [UID/AMB/50017]; FCT/MEC through national funds; FEDERinfo:eu-repo/semantics/publishedVersio

The central region of the msp gene of Treponema denticola has sequence heterogeneity among clinical samples, obtained from patients with periodontitis

<p>Abstract</p> <p>Background</p> <p><it>Treponema denticola </it>is an oral spirochete involved in the pathogenesis and progression of periodontal disease. Of its virulence factors, the major surface protein (MSP) plays a role in the interaction between the treponeme and host. To understand the possible evolution of this protein, we analyzed the sequence of the <it>msp </it>gene in 17 <it>T. denticola </it>positive clinical samples.</p> <p>Methods</p> <p>Nucleotide and amino acid sequence of MSP have been determined by PCR amplification and sequencing in seventeen <it>T. denticola </it>clinical specimens to evaluate the genetic variability and the philogenetic relationship of the <it>T. denticola msp </it>gene among the different amplified sequence of positive samples. In silico antigenic analysis was performed on each MSP sequences to determined possible antigenic variation.</p> <p>Results</p> <p>The <it>msp </it>sequences showed two highly conserved 5' and 3' ends and a central region that varies substantially. Phylogenetic analysis categorized the 17 specimens into 2 principal groups, suggesting a low rate of evolutionary variability and an elevated degree of conservation of <it>msp </it>in clinically derived genetic material. Analysis of the predicted antigenic variability between isolates, demonstrated that the major differences lay between amino acids 200 and 300.</p> <p>Conclusion</p> <p>These findings showed for the first time, the nucleotide and amino acids variation of the <it>msp </it>gene in infecting <it>T. denticola</it>, <it>in vivo</it>. This data suggested that the antigenic variability found in to the MSP molecule, may be an important factor involved in immune evasion by <it>T. denticola</it>.</p

Mycobacterium tuberculosis Induces an Atypical Cell Death Mode to Escape from Infected Macrophages

BACKGROUND: Macrophage cell death following infection with Mycobacterium tuberculosis plays a central role in tuberculosis disease pathogenesis. Certain attenuated strains induce extrinsic apoptosis of infected macrophages but virulent strains of M. tuberculosis suppress this host response. We previously reported that virulent M. tuberculosis induces cell death when bacillary load exceeds approximately 20 per macrophage but the precise nature of this demise has not been defined. METHODOLOGY/PRINCIPAL FINDINGS: We analyzed the characteristics of cell death in primary murine macrophages challenged with virulent or attenuated M. tuberculosis complex strains. We report that high intracellular bacillary burden causes rapid and primarily necrotic death via lysosomal permeabilization, releasing hydrolases that promote Bax/Bak-independent mitochondrial damage and necrosis. Cell death was independent of cathepsins B or L and notable for ultrastructural evidence of damage to lipid bilayers throughout host cells with depletion of several host phospholipid species. These events require viable bacteria that can respond to intracellular cues via the PhoPR sensor kinase system but are independent of the ESX1 system. CONCLUSIONS/SIGNIFICANCE: Cell death caused by virulent M. tuberculosis is distinct from classical apoptosis, pyroptosis or pyronecrosis. Mycobacterial genes essential for cytotoxicity are regulated by the PhoPR two-component system. This atypical death mode provides a mechanism for viable bacilli to exit host macrophages for spreading infection and the eventual transition to extracellular persistence that characterizes advanced pulmonary tuberculosis

Effects of antiplatelet therapy on stroke risk by brain imaging features of intracerebral haemorrhage and cerebral small vessel diseases: subgroup analyses of the RESTART randomised, open-label trial

Background Findings from the RESTART trial suggest that starting antiplatelet therapy might reduce the risk of recurrent symptomatic intracerebral haemorrhage compared with avoiding antiplatelet therapy. Brain imaging features of intracerebral haemorrhage and cerebral small vessel diseases (such as cerebral microbleeds) are associated with greater risks of recurrent intracerebral haemorrhage. We did subgroup analyses of the RESTART trial to explore whether these brain imaging features modify the effects of antiplatelet therapy