141 research outputs found

    Partial bisulfite conversion for unique template sequencing

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    We introduce a new protocol, mutational sequencing or muSeq, which uses sodium bisulfite to randomly deaminate unmethylated cytosines at a fixed and tunable rate. The muSeq protocol marks each initial template molecule with a unique mutation signature that is present in every copy of the template, and in every fragmented copy of a copy. In the sequenced read data, this signature is observed as a unique pattern of C-to-T or G-to-A nucleotide conversions. Clustering reads with the same conversion pattern enables accurate count and long-range assembly of initial template molecules from short-read sequence data. We explore count and low-error sequencing by profiling 135 000 restriction fragments in a PstI representation, demonstrating that muSeq improves copy number inference and significantly reduces sporadic sequencer error. We explore long-range assembly in the context of cDNA, generating contiguous transcript clusters greater than 3,000 bp in length. The muSeq assemblies reveal transcriptional diversity not observable from short-read data alone

    High Avidity CD8+ T Cells Efficiently Eliminate Motile HIV-Infected Targets and Execute a Locally Focused Program of Anti-Viral Function

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    The dissemination of HIV from an initial site of infection is facilitated by motile HIV-infected CD4+ T-cells. However, the impact of infected target cell migration on antigen recognition by HIV-specific CD8+ T-cells is unclear. Using a 3D in vitro model of tissue, we visualized dynamic interactions between HIV-infected or peptide-pulsed CD4+ T-cells and HIV-specific CD8+ T-cells. CTLs engaged motile HIV-infected targets, but ∌50% of targets broke contact and escaped. In contrast, immobilized target cells were readily killed, indicating target motility directly inhibits CD8+ T-cell function. Strong calcium signals occurred in CTLs killing a motile target but calcium signaling was weak or absent in CTLs which permitted target escape. Neutralization of adhesion receptors LFA-1 and CD58 inhibited CD8+ T-cell function within the 3D matrix, demonstrating that efficient motile target lysis as dependent on adhesive engagement of targets. Antigen sensitivity (a convolution of antigen density, TCR avidity and CD8 coreceptor binding) is also critical for target recognition. We modulated this parameter (known as functional avidity but referred to here as “avidity” for the sake of simplicity) by exploiting common HIV escape mutations and measured their impact on CTL function at the single-cell level. Targets pulsed with low avidity mutant antigens frequently escaped while CTLs killed targets bearing high avidity antigen with near-perfect efficiency. CTLs engaged, arrested, and killed an initial target bearing high avidity antigen within minutes, but serial killing was surprisingly rare. CD8 cells remained committed to their initial dead target for hours, accumulating TCR signals that sustained secretion of soluble antiviral factors. These data indicate that high-avidity CD8+ T-cells execute an antiviral program in the precise location where antigen has been sensed: CTL effector functions are spatiotemporally coordinated with an early lytic phase followed by a sustained stationary secretory phase to control local viral infection

    Does shade improve light interception efficiency? A comparison among seedlings from shade-tolerant and -intolerant temperate deciduous tree species

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    ‱ Here, we tested two hypotheses: shading increases light interception efficiency (LIE) of broadleaved tree seedlings, and shade-tolerant species exhibit larger LIEs than do shade-intolerant ones. The impact of seedling size was taken into account to detect potential size-independent effects on LIE. LIE was defined as the ratio of mean light intercepted by leaves to light intercepted by a horizontal surface of equal area. ‱ Seedlings from five species differing in shade tolerance (Acer saccharum, Betula alleghaniensis, A. pseudoplatanus, B. pendula, Fagus sylvatica) were grown under neutral shading nets providing 36, 16 and 4% of external irradiance. Seedlings (1- and 2-year-old) were three-dimensionally digitized, allowing calculation of LIE. ‱ Shading induced dramatic reduction in total leaf area, which was lowest in shade-tolerant species in all irradiance regimes. Irradiance reduced LIE through increasing leaf overlap with increasing leaf area. There was very little evidence of significant size-independent plasticity of LIE. ‱ No relationship was found between the known shade tolerance of species and LIE at equivalent size and irradiance

    Designing a fashion driving forces website as an educational resource

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    Electronic educational resources support search activities and manipulate information effectively in learning environments, thus enhancing education. This paper discusses the development of an electronic timeline database that classifies design and fashion details; technological developments; socio-economical influences; availability and popularity within fashion trends; marketing and distribution; and influential people including designers, in a manner that facilitates ease of cross referencing events at the same point in time for a rich analysis of fashion. The study focuses on the driving forces of fashion during the 1920s as a starting point for a much larger database. The data is presented in the form of a website allowing students to better understand fashion trends with macro-environmental and marketing strategies. The electronic resource is a useful tool for fashion, textile and marketing students as an educational interface providing design, production and marketing data for fashion-related products particularly useful for the analysis of fashion trends

    Graduates of Lebanese medical schools in the United States: an observational study of international migration of physicians

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    BACKGROUND: As healthcare systems around the world are facing increasing physician shortages, more physicians are migrating from low to high income countries. As an illustrative case of international migration of physicians, we evaluated the current number and historical trends of Lebanese medical graduates (LMG) in the US, and compared their characteristics to those of US medical graduates (USMG) and other international medical graduates (IMG). METHODS: We evaluated the number of LMG using the 2004 the American Medical Association Physicians' Professional Data (AMA-PPD) and then compared it to the number of graduates of other countries. We evaluated the historical trends using the 1978–2004 historical files of the AMA-PPD. We analyzed the characteristics of all LMG and compared them to a random sample of 1000 USMG and a random sample of 1000 IMG using the 2004 AMA-PPD. RESULTS: In 2004, there were 2,796 LMG in the US, constituting 1.3% of all IMG. Compared to other foreign countries contributing to the US physician workforce, Lebanon ranked 2nd after adjusting for country population size (about 4 million) and 21st overall. About 40% of those who graduated from Lebanese medical schools in the last 25 years are currently active physicians in the US. Since 1978, the number of LMG in the US showed a consistent upward trend at a rate of approximately 71 additional graduates per year. Compared with USMG and IMG, LMG were more likely to work in medical research (OR = 2.31; 95% Confidence Interval (CI) = 1.21; 4.43 and OR = 2.63; 95% CI = 1.34; 5.01, respectively) and to be board certified (OR = 1.43; 95% CI = 1.14; 1.78 and OR = 2.04; 95% CI = 1.65;2.53, respectively) and less likely to be in family practice (OR = 0.14; 95% CI = 0.10; 0.19 and OR = 0.18; 95% CI = 0.12; 0.26, respectively). CONCLUSION: Given the magnitude and historical trends of migration of LMG to the US, further exploration of its causes and impact is warranted. High income countries should consider the consequences of their human resources policies on both low income countries' and their own healthcare systems

    Physicians' migration in Europe: an overview of the current situation

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    <p>Abstract</p> <p>Background</p> <p>The migration of medical professionals as a result of the expansion of the European Union is cause for concern. But there is a significant lack of information available about this phenomenon.</p> <p>Methods</p> <p>Search of secondary databases about the presence of european doctors working abroad, through two search engines in the Internet (Google and Pubmed) and a survey of professional organisations and regulators in countries of the European Union.</p> <p>Results</p> <p>The United Kingdom has more foreign doctors than all other European countries for which figures are available (Ireland, France, Germany, Norway, Portugal, Italy, Austria and Poland). Some 74,031 foreign doctors are registered in the UK, 30.94% of the total. European countries with the highest percentage of doctors working abroad are Ireland (47.5%, or 10,065 doctors) and Malta (23.1%, 376 doctors). The data obtained from Norway, France and Germany do not indicate an increase in the migration of professionals from countries recently incorporated into the EU.</p> <p>Conclusion</p> <p>There is significant mobility and heterogeneous distribution of doctors within the EEA and it should be cause for concern among health care authorities. However, there is no evidence about a possible increase in this phenomenon after the recent expansion of the EU.</p

    Cancer immunotherapy by immunosuppression

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    We have previously suggested that the stimulatory effect of a weak immune reaction on tumor growth may be necessary for the growth of incipient tumors. In the present paper, we enlarge upon and extend that idea by collecting evidence in the literature bearing upon this new hypothesis that a growing cancer, whether in man or mouse, is throughout its lifespan, probably growing and progressing because of continued immune stimulation by a weak immune reaction. We also suggest that prolonged immunosuppression might interfere with progression and thus be an aid to therapy. While most of the considerable evidence that supports the hypothesis comes from observations of experimental mouse tumors, there is suggestive evidence that human tumors may behave in much the same way, and as far as we can ascertain, there is no present evidence that necessarily refutes the hypothesis
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