The impact of cross-kingdom molecular forensics on genetic privacy

Recent advances in metagenomic technology and computational prediction may inadvertently weaken an individual’s reasonable expectation of privacy. Through cross-kingdom genetic and metagenomic forensics, we can already predict at least a dozen human phenotypes with varying degrees of accuracy. There is also growing potential to detect a “molecular echo” of an individual’s microbiome from cells deposited on public surfaces. At present, host genetic data from somatic or germ cells provide more reliable information than microbiome samples. However, the emerging ability to infer personal details from different microscopic biological materials left behind on surfaces requires in-depth ethical and legal scrutiny. There is potential to identify and track individuals, along with new, surreptitious means of genetic discrimination. This commentary underscores the need to update legal and policy frameworks for genetic privacy with additional considerations for the information that could be acquired from microbiome-derived data. The article also aims to stimulate ubiquitous discourse to ensure the protection of genetic rights and liberties in the post-genomic era

Dielectronic Recombination in He+ Ions

This research was sponsored by the National Science Foundation Grant NSF PHY-931478

Fluctuating Nematic Elastomer Membranes: a New Universality Class

We study the flat phase of nematic elastomer membranes with rotational symmetry spontaneously broken by in-plane nematic order. Such state is characterized by a vanishing elastic modulus for simple shear and soft transverse phonons. At harmonic level, in-plane orientational (nematic) order is stable to thermal fluctuations, that lead to short-range in-plane translational (phonon) correlations. To treat thermal fluctuations and relevant elastic nonlinearities, we introduce two generalizations of two-dimensional membranes in a three dimensional space to arbitrary D-dimensional membranes embedded in a d-dimensional space, and analyze their anomalous elasticities in an expansion about D=4. We find a new stable fixed point, that controls long-scale properties of nematic elastomer membranes. It is characterized by singular in-plane elastic moduli that vanish as a power-law eta_lambda=4-D of a relevant inverse length scale (e.g., wavevector) and a finite bending rigidity. Our predictions are asymptotically exact near 4 dimensions.Comment: 18 pages, 4 eps figures. submitted to PR

Minimum Wages and Poverty with Income-Sharing

Textbook analysis tells us that in a competitive labor market, the introduction of a minimum wage in terms of poverty rather than in terms of unemployment. This paper makes three contributions to the basic theory of the minimum wage. First, we analyze the effects of a higher minimum wage in terms of poverty rather than in terms of unemployment. Second, we extend the standard textbook model to allow for income-sharing between employed and unemployed persons in society. Third, we extend the basic model to deal with income sharing within families. We find that there are situations in which a higher minimum wage raises poverty, others where it reduces poverty, and yet others in which poverty is unchanged. We characterize precisely how the poverty effect depends on four parameters: the degree of poverty aversion, the elasticity of labor demand, the ratio of the minimum wage to the poverty line, and the extent of income-sharing. Thus, shifting the perspective from unemployment to poverty leads to a considerable enrichment of the theory of the minimum wage

Changes in the ceIl membrane of Lactobacillus bulgaricus during storage following freeze-drying

The mechanism of inactivation of freeze-dried Lactobacillus bulgaricus during storage in maltodextrin under controlled humidity was investigated. Evidence is presented supporting the hypothesis that membrane damage occurs during storage. A study on the lipid composition of the cells by gas chromatography showed a decrease in the unsaturated and saturated fatty acid content of the cell. Further evidence indicating membrane damage includes a decrease in membrane bound proton-translocating ATPase activity

Loans, logins and lasting the course: Academic library use and student retention

Activities and services that improve student engagement and retention in the higher education sector are important not only to individual student’s success but also to university planning and funding. This paper reports on a quantitative study that was carried out to explore whether use of the library by new university students is associated with continued enrolment. Students’ socioeconomic background and age were also examined in relation to library use. Limited to commencing students in March 2010 at Curtin University, the study drew on demographic data from the University’s enrolment system and instances of library use from the Library’s management system. Results of the statistical analyses indicate that library use is associated with retention, and importantly, library use in the early weeks of a student’s first semester is associated with retention. ‘Mature aged’ (21 years and over) students displayed different library use patterns than their younger colleagues and there was some variation in library use between students from different socioeconomic backgrounds. Findings from this study suggest that academic libraries can contribute to the retention of students and that carefully targeted programs and services may improve library use by some groups of students

Haplotype reference consortium panel: Practical implications of imputations with large reference panels

Recently, the Haplotype Reference Consortium (HRC) released a large imputation panel that allows more accurate imputation of genetic variants. In this study, we compared a set of directly assayed common and rare variants from an exome array to imputed genotypes, that is, 1000 genomes project (1000GP) and HRC. We showed that imputation using the HRC panel improved the concordance between assayed and imputed genotypes at common, and especially, low-frequency variants. Furthermore, we performed a genome-wide association meta-analysis of vertical cup-disc ratio, a highly heritable endophenotype of glaucoma, in four cohorts using 1000GP and HRC imputations. We compared the results of the meta-analysis using 1000GP to the meta-analysis results using HRC. Overall, we found that using HRC imputation significantly improved P values (P = 3.07 × 10-61), particularly for suggestive variants. Both meta-analyses were performed in the same sample size, yet we found eight genome-wide significant loci in the HRC-based meta-analysis versus seven genome-wide significant loci in the 1000GP-based meta-analysis. This study provides supporting evidence of the new avenues for gene discovery and fine mapping that the HRC imputation panel offers

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types

Locating Photography

The specter of global dissemination haunted photography from its very beginning. This chapter explains two aspects of photography's “globalization”: its use as a “western” technique to document an increasingly colonized world and its dissemination around the world and its adoption by local practitioners. In rural and small‐town central India, the studio retains a central place in most people's encounters with photography. Martín Chambi would retain a lifelong adherence to the purity of the photographic image but other indigenista photographers, such as Juan Manuel Figueroa Aznar, would increasingly use paint alongside photography. A World System Photography, seen in networks that fold locally articulated practices into trajectories that fuse technics, history, and culture, can help people think in new ways about the “location” of photography. Locations have to be re‐imagined as “Terra Infirma”, unstable and complex positions which may have more of the quality of linking sections of a network than of territories

Extensive microbial diversity within the chicken gut microbiome revealed by metagenomics and culture

Background The chicken is the most abundant food animal in the world. However, despite its importance, the chicken gut microbiome remains largely undefined. Here, we exploit culture-independent and culture-dependent approaches to reveal extensive taxonomic diversity within this complex microbial community. Results We performed metagenomic sequencing of fifty chicken faecal samples from two breeds and analysed these, alongside all (n = 582) relevant publicly available chicken metagenomes, to cluster over 20 million non-redundant genes and to construct over 5,500 metagenome-assembled bacterial genomes. In addition, we recovered nearly 600 bacteriophage genomes. This represents the most comprehensive view of taxonomic diversity within the chicken gut microbiome to date, encompassing hundreds of novel candidate bacterial genera and species. To provide a stable, clear and memorable nomenclature for novel species, we devised a scalable combinatorial system for the creation of hundreds of well-formed Latin binomials. We cultured and genome-sequenced bacterial isolates from chicken faeces, documenting over forty novel species, together with three species from the genus Escherichia, including the newly named species Escherichia whittamii. Conclusions Our metagenomic and culture-based analyses provide new insights into the bacterial, archaeal and bacteriophage components of the chicken gut microbiome. The resulting datasets expand the known diversity of the chicken gut microbiome and provide a key resource for future high-resolution taxonomic and functional studies on the chicken gut microbiome