Annotation Studio: multimedia text annotation for students

Annotation Studio will be a web-based application that actively engages students in interpreting literary texts and other humanities documents. While strengthening students' new media literacies, this open source web application will develop traditional humanistic skills including close reading, textual analysis, persuasive writing, and critical thinking. Initial features will include: 1) easy-to-use annotation tools that facilitate linking and comparing primary texts with multi-media source, variation, and adaptation documents; 2) sharable collections of multimedia materials prepared by faculty and student users; 3) multiple filtering and display mechanisms for texts, written annotations, and multimedia annotations; 4) collaboration functionality; and 5) multimedia composition tools. Products of the start-up phase will include a working prototype, feedback from students and instructors, and a white paper summarizing lessons learned

Genetic fine mapping and genomic annotation defines causal mechanisms at type 2 diabetes susceptibility loci.

We performed fine mapping of 39 established type 2 diabetes (T2D) loci in 27,206 cases and 57,574 controls of European ancestry. We identified 49 distinct association signals at these loci, including five mapping in or near KCNQ1. 'Credible sets' of the variants most likely to drive each distinct signal mapped predominantly to noncoding sequence, implying that association with T2D is mediated through gene regulation. Credible set variants were enriched for overlap with FOXA2 chromatin immunoprecipitation binding sites in human islet and liver cells, including at MTNR1B, where fine mapping implicated rs10830963 as driving T2D association. We confirmed that the T2D risk allele for this SNP increases FOXA2-bound enhancer activity in islet- and liver-derived cells. We observed allele-specific differences in NEUROD1 binding in islet-derived cells, consistent with evidence that the T2D risk allele increases islet MTNR1B expression. Our study demonstrates how integration of genetic and genomic information can define molecular mechanisms through which variants underlying association signals exert their effects on disease

New genetic loci link adipose and insulin biology to body fat distribution.

Body fat distribution is a heritable trait and a well-established predictor of adverse metabolic outcomes, independent of overall adiposity. To increase our understanding of the genetic basis of body fat distribution and its molecular links to cardiometabolic traits, here we conduct genome-wide association meta-analyses of traits related to waist and hip circumferences in up to 224,459 individuals. We identify 49 loci (33 new) associated with waist-to-hip ratio adjusted for body mass index (BMI), and an additional 19 loci newly associated with related waist and hip circumference measures (P < 5 × 10(-8)). In total, 20 of the 49 waist-to-hip ratio adjusted for BMI loci show significant sexual dimorphism, 19 of which display a stronger effect in women. The identified loci were enriched for genes expressed in adipose tissue and for putative regulatory elements in adipocytes. Pathway analyses implicated adipogenesis, angiogenesis, transcriptional regulation and insulin resistance as processes affecting fat distribution, providing insight into potential pathophysiological mechanisms

An Expanded Genome-Wide Association Study of Type 2 Diabetes in Europeans.

To characterize type 2 diabetes (T2D)-associated variation across the allele frequency spectrum, we conducted a meta-analysis of genome-wide association data from 26,676 T2D case and 132,532 control subjects of European ancestry after imputation using the 1000 Genomes multiethnic reference panel. Promising association signals were followed up in additional data sets (of 14,545 or 7,397 T2D case and 38,994 or 71,604 control subjects). We identified 13 novel T2D-associated loci (P < 5 × 10(-8)), including variants near the GLP2R, GIP, and HLA-DQA1 genes. Our analysis brought the total number of independent T2D associations to 128 distinct signals at 113 loci. Despite substantially increased sample size and more complete coverage of low-frequency variation, all novel associations were driven by common single nucleotide variants. Credible sets of potentially causal variants were generally larger than those based on imputation with earlier reference panels, consistent with resolution of causal signals to common risk haplotypes. Stratification of T2D-associated loci based on T2D-related quantitative trait associations revealed tissue-specific enrichment of regulatory annotations in pancreatic islet enhancers for loci influencing insulin secretion and in adipocytes, monocytes, and hepatocytes for insulin action-associated loci. These findings highlight the predominant role played by common variants of modest effect and the diversity of biological mechanisms influencing T2D pathophysiology.Please refer to the manuscript or visit the publisher's website for funding infomation

Large-scale association analysis provides insights into the genetic architecture and pathophysiology of type 2 diabetes

To extend understanding of the genetic architecture and molecular basis of type 2 diabetes (T2D), we conducted a meta-analysis of genetic variants on the Metabochip involving 34,840 cases and 114,981 controls, overwhelmingly of European descent. We identified ten previously unreported T2D susceptibility loci, including two demonstrating sex-differentiated association. Genome-wide analyses of these data are consistent with a long tail of further common variant loci explaining much of the variation in susceptibility to T2D. Exploration of the enlarged set of susceptibility loci implicates several processes, including CREBBP-related transcription, adipocytokine signalling and cell cycle regulation, in diabetes pathogenesis

Publisher Correction: Sex-dimorphic genetic effects and novel loci for fasting glucose and insulin variability.

A Correction to this paper has been published: https://doi.org/10.1038/s41467-021-21276-3</jats:p

Flavour Chemicals in a Sample of Non-Cigarette Tobacco Products Without Explicit Flavour Names Sold in New York City in 2015

Background Youth who experiment with tobacco often start with flavoured products. In New York City (NYC), local law restricts sales of all tobacco products with ‘characterising flavours’ except for ‘tobacco, menthol, mint and wintergreen’. Enforcement is based on packaging: explicit use of a flavour name (eg, ‘strawberry’) or image depicting a flavour (eg, a fruit) is presumptive evidence that a product is flavoured and therefore prohibited. However, a tobacco product may contain significant levels of added flavour chemicals even when the label does not explicitly use a flavour name. Methods Sixteen tobacco products were purchased within NYC in 2015 that did not have explicit flavour names, along with three with flavour names. These were analysed for 92 known flavour chemicals plus triacetin by gas chromatography/mass spectrometry. Results 14 of the 16 products had total determined flavour chemical levels that were higher (\u3e0.3 mg/g) than in previously studied flavour-labelled products and of a chemical profile indicating added flavour chemicals. Conclusions The results suggest that the tobacco industry has responded to sales restrictions by renaming flavoured products to avoid explicitly identifying them as flavoured. While chemical analysis is the most precise means of identifying flavours in tobacco products, federal tobacco laws pre-empt localities from basing regulations on that approach, limiting enforcement options. If the Food and Drug Administration would mandate that all tobacco products must indicate when flavourings are present above a specific level, local jurisdictions could enforce their sales restrictions. A level of 0.1 mg/g for total added flavour chemicals is suggested here as a relevant reference value for regulating added flavour chemicals in tobacco products

Conformational state and charge determine the interfacial film formation and film stability of β-lactoglobulin

The mechanical stability of protein-stabilized emulsions depends on physiochemical interactions within the interfacial protein film. However, intermolecular interactions vary with the protein's conformational state and charge and may in turn affect the mechanical stability through modifications in the three-staged interfacial stabilization; migration, adsorption and film formation at the oil/water-interface. Therefore, the aim of our study was to investigate the different protein conformations within the interfacial stabilization process by applying bulk water conditions and to determine the protein film stability against mechanical stress. For this purpose, we analyzed the structure and interactions of β-lactoglobulin in water and at the oil/water-interface at pH 7, pH 7NaCl (containing 100 mM NaCl) and pH 9 with membrane-osmometry, Fourier-transform-infrared-spectroscopy, extrinsic fluorescence and ζ-potential. Moreover, we characterized the conformational state and charge in context with the molecule density and interfacial film properties via Langmuir trough analysis, interfacial shear and dilatational rheology. Distinct unfolding of monomers and dimers at pH 9 resulted in the lowest interfacial molecule density but at the same time the highest film stability due to pronounced structural flexibility. In comparison, β-lactoglobulin at pH 7 was monomeric, unfolding was less pronounced, and interfacial molecule density was higher. Electrostatic shielding of β-lactoglobulin dimers at pH 7NaCl resulted in the highest density but least stable protein film that approached low molecular weight surfactant behavior due to few and weak intermolecular interactions. Our research contributes to the control of the emulsion stability against mechanical stress by varying intermolecular interactions within the interfacial protein film