SIG-DB: leveraging homomorphic encryption to Securely Interrogate privately held Genomic DataBases

Genomic data are becoming increasingly valuable as we develop methods to utilize the information at scale and gain a greater understanding of how genetic information relates to biological function. Advances in synthetic biology and the decreased cost of sequencing are increasing the amount of privately held genomic data. As the quantity and value of private genomic data grows, so does the incentive to acquire and protect such data, which creates a need to store and process these data securely. We present an algorithm for the Secure Interrogation of Genomic DataBases (SIG-DB). The SIG-DB algorithm enables databases of genomic sequences to be searched with an encrypted query sequence without revealing the query sequence to the Database Owner or any of the database sequences to the Querier. SIG-DB is the first application of its kind to take advantage of locality-sensitive hashing and homomorphic encryption to allow generalized sequence-to-sequence comparisons of genomic data.Comment: 38 pages, 3 figures, 4 tables, 1 supplemental table, 7 supplemental figure

Prevalence Rates of Arthritis Among US Older Adults with Varying Degrees of Depression: Findings from the 2011 to 2014 National Health and Nutrition Examination Survey

Arthritis and depressive symptoms often interact and negatively influence one another to worsen mental and physical health outcomes. Better characterization of arthritis rates among older adults with different levels of depressive symptoms is an important step toward informing mental health professionals of the need to detect and respond to arthritis and related mental health complications. The primary objective is to determine arthritis rates among US older adults with varying degrees of depression. Using National Health and Nutrition Examination Survey 2011 to 2014 data (N = 4792), we first identified participants aged ≥50 years. Measures screened for depressive symptoms and self‐reported doctor‐diagnosed arthritis. Weighted logistic regression models were conducted. Prevalence of arthritis was 55.0%, 62.9%, and 67.8% in participants with minor, moderate, and severe depression, respectively. In both unadjusted and adjusted regression models, a significant association between moderate depression and arthritis persisted. There were also significant associations between minor and severe depression with arthritis. Arthritis is commonly reported in participants with varying degrees of depression. This study highlights the importance of screening for and treating arthritis‐related pain in older adults with depressive symptoms and the need for future geriatric psychiatry research on developing integrated biopsychosocial interventions for these common conditions

Prevalence Rates of Arthritis Among US Older Adults with Varying Degrees of Depression: Findings from the 2011 to 2014 National Health and Nutrition Examination Survey

Arthritis and depressive symptoms often interact and negatively influence one another to worsen mental and physical health outcomes. Better characterization of arthritis rates among older adults with different levels of depressive symptoms is an important step toward informing mental health professionals of the need to detect and respond to arthritis and related mental health complications. The primary objective is to determine arthritis rates among US older adults with varying degrees of depression. Using National Health and Nutrition Examination Survey 2011 to 2014 data (N = 4792), we first identified participants aged ≥50 years. Measures screened for depressive symptoms and self‐reported doctor‐diagnosed arthritis. Weighted logistic regression models were conducted. Prevalence of arthritis was 55.0%, 62.9%, and 67.8% in participants with minor, moderate, and severe depression, respectively. In both unadjusted and adjusted regression models, a significant association between moderate depression and arthritis persisted. There were also significant associations between minor and severe depression with arthritis. Arthritis is commonly reported in participants with varying degrees of depression. This study highlights the importance of screening for and treating arthritis‐related pain in older adults with depressive symptoms and the need for future geriatric psychiatry research on developing integrated biopsychosocial interventions for these common conditions

Enrichment of CpG island shore region hypermethylation in epigenetic breast field cancerization

While changes in DNA methylation are known to occur early in breast carcinogenesis and the landscape of breast tumour DNA methylation is profoundly altered compared with normal tissue, there have been limited efforts to identify DNA methylation field cancerization effects in histologically normal breast tissue adjacent to tumour. Matched tumour, histologically normal tissue of the ipsilateral breast (ipsilateral-normal), and histologically normal tissue of the contralateral breast (contralateral-normal) were obtained from nine women undergoing bilateral mastectomy. Laser capture microdissection was used to select epithelial cells from normal tissue, and neoplastic cells from tumour for genome-scale measures of DNA methylation with the Illumina HumanMethylationEPIC array. We identified substantially more CpG loci that were differentially methylated between contralateral-normal and tumour (63,271 CpG loci q \u3c 0.01), than between ipsilateral-normal and tumour (38,346 CpG loci q \u3c 0.01). We identified differential methylation in ipsilateral-normal relative to contralateral-normal tissue (9,562 CpG loci p \u3c 0.01). In this comparison, hypomethylated loci were significantly enriched for breast cancer-relevant transcription factor binding sites including those for ESR1, FoxA1, and GATA3 and hypermethylated loci were significantly enriched for CpG island shore regions. In addition, progression of shore hypermethylation was observed in tumours compared to matched ipsilateral normal tissue, and these alterations tracked to several well-established tumour suppressor genes. Our results indicate an epigenetic field effect in surrounding histologically normal tissue. This work offers an opportunity to focus investigations of early DNA methylation alterations in breast carcinogenesis and potentially develop epigenetic biomarkers of disease risk

Sustainable forest biomass: a review of current residue harvesting guidelines

http://blogs.biomedcentral.com/on-physicalsciences/2021/04/15/forest-bioenergy-sustainable/Forest biomass harvesting guidelines help ensure the ecological sustainability of forest residue harvesting for bioenergy and bioproducts, and hence contribute to social license for a growing bioeconomy. Guidelines, typically voluntary, provide a means to achieve outcomes often required by legislation, and must address needs related to local or regional context, jurisdictional compatibility with regulations, issues of temporal and spatial scale, and incorporation of appropriate scientific information. Given this complexity, comprehensive reviews of existing guidelines can aid in development of new guidelines or revision of existing ones. We reviewed 32 guidelines covering 43 jurisdictions in the USA, Canada, Europe and East Asia to expand upon information evaluated and recommendations provided in previous guideline reviews, and compiled a searchable spreadsheet of direct quotations from documents as a foundation for our review. Guidelines were considered in the context of sustainable forest management (SFM), focusing on guideline scope and objectives, environmental sustainability concerns (soils, site productivity, biodiversity, water and carbon) and social concerns (visual aesthetics, recreation, and preservation of cultural, historical and archaeological sites). We discuss the role of guidelines within the context of other governance mechanisms such as SFM policies, trade regulations and non-state market-driven (NSMD) standards, including certification systems. The review provides a comprehensive resource for those developing guidelines, or defining sustainability standards for market access or compliance with public regulations, and/or concerned about the sustainability of forest biomass harvesting. We recommend that those developing or updating guidelines consider (i) the importance of well-defined and understood terminology, consistent where possible with guidelines in other jurisdictions or regions; (ii) guidance based on locally relevant research, and periodically updated to incorporate current knowledge and operational experience; (iii) use of indicators of sensitive soils, sites, and stands which are relevant to ecological processes and can be applied operationally; and (iv) incorporation of climate impacts, long-term soil carbon storage, and general carbon balance considerations when defining sustainable forest biomass availability. Successful implementation of guidelines depends both on the relevance of the information and on the process used to develop and communicate it; hence, appropriate stakeholders should be involved early in guideline development.Peer reviewe

Deficiency of Leishmania phosphoglycans influences the magnitude but does not affect the quality of secondary (memory) anti-Leishmania immunity

Despite inducing very low IFN-γ response and highly attenuated in vivo, infection of mice with phosphoglycan (PG) deficient Leishmania major (lpg2-) induces protection against virulent L. major challenge. Here, we show that mice infected with lpg2- L. major generate Leishmania-specific memory T cells. However, in vitro and in vivo proliferation, IL-10 and IFN-γ production by lpg2- induced memory cells were impaired in comparison to those induced by wild type (WT) parasites. Interestingly, TNF recall response was comparable to WT infected mice. Despite the impaired proliferation and IFN-γ response, lpg2- infected mice were protected against virulent L. major challenge and their T cells mediated efficient infection-induced immunity. In vivo depletion and neutralization studies with mAbs demonstrated that lpg2- L. major-induced resistance was strongly dependent on IFN-γ, but independent of TNF and CD8(+) T cells. Collectively, these data show that the effectiveness of secondary anti-Leishmania immunity depends on the quality (and not the magnitude) of IFN-γ response. These observations provide further support for consideration of lpg2- L. major as a live-attenuated candidate for leishmanization in humans since it protects strongly against virulent challenge, without inducing pathology in infected animals

Thin film versus paper-like reduced graphene oxide: Comparative study of structural, electrical, and thermoelectrical properties

We report fabrication of reduced graphene oxide (rGO) films using chemical reduction by hydrazine hydrate and rGO paper-like samples using low temperature treatment reduction. Structural analysis confirms the formation of the rGO structure for both samples. Current-voltage (I-V) measurements of the rGO film reveal semiconductor behavior with the maximum current value of similar to 3 x 10(-4) A. The current for the rGO paper sample is found to be, at least, one order of magnitude higher. Moreover, bipolar resistance switching, corresponding to memristive behavior of type II, is observed in the I-V data of the rGO paper. Although precise values of the rGO film conductivity and the Seebeck coefficient could not be measured, rGO paper shows an electrical conductivity of 6.7 x 10(2)S/m and Seebeck coefficient of -6 mu V/degrees C. Thus, we demonstrate a simplified way for the fabrication of rGO paper that possesses better and easier measurable macroscopic electrical properties than that of rGO thin film. Published by AIP Publishing

Science and technology requirements to explore caves in our Solar System

Research on planetary caves requires cross-planetary-body investigations spanning multiple disciplines, including geology, climatology, astrobiology, robotics, human exploration and operations. The community determined that a roadmap was needed to establish a common framework for planetary cave research. This white paper is our initial conception

Potentiating Effects of MPL on DSPC Bearing Cationic Liposomes Promote Recombinant GP63 Vaccine Efficacy: High Immunogenicity and Protection

Visceral leishmaniasis (VL), a vector-transmitted disease caused by Leishmania donovani, is potentially fatal if left untreated. Vaccination against VL has received limited attention compared with cutaneous leishmaniasis, although the need for an effective vaccine is pressing for the control of the disease. Earlier, we observed protective efficacy using leishmanial antigen (Ag) in the presence of either cationic liposomes or monophosphoryl lipid A-trehalose dicorynomycolate (MPL-TDM) against experimental VL through the intraperitoneal (i.p.) route of administration in the mouse model. However, this route of immunization is not adequate for human use. For this work, we developed vaccine formulations combining cationic liposomes with MPL-TDM using recombinant GP63 (rGP63) as protein Ag through the clinically relevant subcutaneous (s.c.) route. Two s.c. injections with rGP63 in association with cationic liposomes and MPL-TDM showed enhanced immune responses that further resulted in high protective levels against VL in the mouse model. This validates the combined use of MPL-TDM as an immunopotentiator and liposomes as a suitable vaccine delivery system

In vivo PET imaging of the neuroinflammatory response in rat spinal cord injury using the TSPO tracer [F-18]GE-180 and effect of docosahexaenoic acid

Centre for Trauma Sciences, funded by the Barts & The London Charity, GE Healthcare Ltd, the Experimental Medicine Awards from the Blizard Institute and the Imaging Centre at the Barts Cancer Institute