Describing a new food group classification system for UK biobank: analysis of food groups and sources of macro- and micronutrients in 208,200 participants.

PURPOSE: The UK Biobank study collected detailed dietary data using a web-based self-administered 24 h assessment tool, the Oxford WebQ. We aimed to describe a comprehensive food grouping system for this questionnaire and to report dietary intakes and key sources of selected nutrients by sex and education. METHODS: Participants with at least one valid 24-h questionnaire were included (n = 208,200). Dietary data were grouped based on the presence of nutrients as well as culinary use, processing, and plant/animal origin. For each food group, we calculated the contribution to energy intake, key macronutrients, and micronutrients. We also identified the top contributors to energy intake, free sugars and saturated fat by sex and education. RESULTS: From the 93 food groups, the top five contributors to energy intake (in descending order) were: desserts/cakes/pastries; white bread; white pasta/rice; bananas/other fruit; semi-skimmed milk. Wine, beer, and fruit juices were the top beverage contributors to overall energy intake. Biscuits, and desserts/cakes/pastries were the highest contributors to free sugars, total fat, and saturated fat intakes, but also contributed to the calcium and iron intakes. Top contributors to energy, saturated fat, and free sugars were broadly similar by sex and education category, with small differences in average nutrient intakes across the population. CONCLUSION: This new food classification system will support the growing interest in the associations between food groups and health outcomes and the development of food-based dietary guidelines. Food group variables will be available to all users of the UK Biobank WebQ questionnaire

A Transdisciplinary Approach to Determining the Provenience of a Distorted, Pre-Columbian Skull Recovered in Rural Idaho

Transdisciplinary research involves cooperation, exchange of information, sharing of resources and integration of disciplines to achieve a common scientific goal. In this study, collaborators utilized tools and knowledge of materials science, anthropology, archaeology, geosciences and biology in an attempt to determine the provenience of skeletal remains of unknown origin. The exchange of ideas and skills along with the crossing of disciplines in this study sucessfully allowed the incorporation of expertise from many team members. This transdisciplinary approach to research provided a more comprehensive and detailed analysis than any one field alone could provide. An archaeological assessment of a human skull recovered in rural Idaho recognized cranial deformation and post-mortem application of a red pigment. A combination of scanning electron microscopy (SEM), x-ray fluorescence (XRF) and energy-dispersive x-ray spectroscopy (EDS) identified the major and trace elements present in the red post-mortem pigment as cinnabar and rare earth metals. Analysis via carbon and oxygen stable isotopes from teeth and bone to provided insight into the diet and habitat for distinct segments of the individual’s life, indicating a regional separation in early life versus late adulthood. Radiocarbon dating determined the approximate age of the skull to be between 600-700 years old and a forensic mtDNA assessmentcategorized a mitochondrial haplogroup for the remains as originating from the East African or Arabian Peninsula

Association of Variants at 1q32 and STAT3 with Ankylosing Spondylitis Suggests Genetic Overlap with Crohn's Disease

Ankylosing spondylitis (AS) is a common inflammatory arthritic condition. Overt inflammatory bowel disease (IBD) occurs in about 10% of AS patients, and in addition 70% of AS cases may have subclinical terminal ileitis. Spondyloarthritis is also common in IBD patients. We therefore tested Crohn's disease susceptibility genes for association with AS, aiming to identify pleiotropic genetic associations with both diseases. Genotyping was carried out using Sequenom and Applied Biosystems TaqMan and OpenArray technologies on 53 markers selected from 30 Crohn's disease associated genomic regions. We tested genotypes in a population of unrelated individual cases (n = 2,773) and controls (n = 2,215) of white European ancestry for association with AS. Statistical analysis was carried out using a Cochran-Armitage test for trend in PLINK. Strong association was detected at chr1q32 near KIF21B (rs11584383, P = 1.6×10−10, odds ratio (OR) = 0.74, 95% CI:0.68–0.82). Association with disease was also detected for 2 variants within STAT3 (rs6503695, P = 4.6×10−4. OR = 0.86 (95% CI:0.79–0.93); rs744166, P = 2.6×10−5, OR = 0.84 (95% CI:0.77–0.91)). Association was confirmed for IL23R (rs11465804, P = 1.2×10−5, OR = 0.65 (95% CI:0.54–0.79)), and further associations were detected for IL12B (rs10045431, P = 5.2×10−5, OR = 0.83 (95% CI:0.76–0.91)), CDKAL1 (rs6908425, P = 1.1×10−4, OR = 0.82 (95% CI:0.74–0.91)), LRRK2/MUC19 (rs11175593, P = 9.9×10−5, OR = 1.92 (95% CI: 1.38–2.67)), and chr13q14 (rs3764147, P = 5.9×10−4, OR = 1.19 (95% CI: 1.08–1.31)). Excluding cases with clinical IBD did not significantly affect these findings. This study identifies chr1q32 and STAT3 as ankylosing spondylitis susceptibility loci. It also further confirms association for IL23R and detects suggestive association with another 4 loci. STAT3 is a key signaling molecule within the Th17 lymphocyte differentiation pathway and further enhances the case for a major role of this T-lymphocyte subset in ankylosing spondylitis. Finally these findings suggest common aetiopathogenic pathways for AS and Crohn's disease and further highlight the involvement of common risk variants across multiple diseases

Does fish larval dispersal differ between high and low latitudes?

Author Posting. © The Author(s), 2013. This is the author's version of the work. It is posted here by permission of The Royal Society for personal use, not for redistribution. The definitive version was published in Proceedings of the Royal Society B Biological Sciences 280 (2013): 20130327, doi:10.1098/rspb.2013.0327.Several factors lead to expectations that the scale of larval dispersal and population connectivity of marine animals differs with latitude. We examine this expectation for demersal shorefishes, including relevant mechanisms, assumptions, and evidence. We explore latitudinal differences in: 1) biological (e.g., species composition, spawning mode, pelagic larval duration (PLD)), 2) physical (e.g., water movement, habitat fragmentation), and 3) biophysical factors (primarily temperature, which could strongly affect development, swimming ability, or feeding). Latitudinal differences exist in taxonomic composition, habitat fragmentation, temperature, and larval swimming, and each could influence larval dispersal. Nevertheless, clear evidence for latitudinal differences in larval dispersal at the level of broad faunas is lacking. For example, PLD is strongly influenced by taxon, habitat, and geographic region, but no independent latitudinal trend is present in published PLD values. Any trends in larval dispersal may be obscured by a lack of appropriate information, or use of ‘off the shelf’ information that is biased with regard to the species assemblages in areas of concern. Biases may also be introduced from latitudinal differences in taxa or spawning modes, as well as limited latitudinal sampling. We suggest research to make progress on the question of latitudinal trends in larval dispersal.TK was supported by the Norwegian Research Council through project MENUII #190286. JML was supported by ARC Discovery Grant DP110100695. JEC and RRW were supported by the Partnership for the Interdisciplinary Study of Coastal Oceans, funded by The David and Lucille Packard Foundation and the Gordon and Betty Moore Foundation.2014-03-2

Rare copy number variants: a point of rarity in genetic risk for bipolar disorder and schizophrenia

Context: Recent studies suggest that copy number variation in the human genome is extensive and may play an important role in susceptibility to disease, including neuropsychiatric disorders such as schizophrenia and autism. The possible involvement of copy number variants (CNVs) in bipolar disorder has received little attention to date. Objectives: To determine whether large (>100 000 base pairs) and rare (found in <1% of the population) CNVs are associated with susceptibility to bipolar disorder and to compare with findings in schizophrenia. Design: A genome-wide survey of large, rare CNVs in a case-control sample using a high-density microarray. Setting: The Wellcome Trust Case Control Consortium. Participants: There were 1697 cases of bipolar disorder and 2806 nonpsychiatric controls. All participants were white UK residents. Main Outcome Measures: Overall load of CNVs and presence of rare CNVs. Results: The burden of CNVs in bipolar disorder was not increased compared with controls and was significantly less than in schizophrenia cases. The CNVs previously implicated in the etiology of schizophrenia were not more common in cases with bipolar disorder. Conclusions: Schizophrenia and bipolar disorder differ with respect to CNV burden in general and association with specific CNVs in particular. Our data are consistent with the possibility that possession of large, rare deletions may modify the phenotype in those at risk of psychosis: those possessing such events are more likely to be diagnosed as having schizophrenia, and those without them are more likely to be diagnosed as having bipolar disorder

Introducing a new breed of wine yeast: interspecific hybridisation between a commercial Saccharomyces cerevisiae wine yeast and Saccharomyces mikatae

Interspecific hybrids are commonplace in agriculture and horticulture; bread wheat and grapefruit are but two examples. The benefits derived from interspecific hybridisation include the potential of generating advantageous transgressive phenotypes. This paper describes the generation of a new breed of wine yeast by interspecific hybridisation between a commercial Saccharomyces cerevisiae wine yeast strain and Saccharomyces mikatae, a species hitherto not associated with industrial fermentation environs. While commercially available wine yeast strains provide consistent and reliable fermentations, wines produced using single inocula are thought to lack the sensory complexity and rounded palate structure obtained from spontaneous fermentations. In contrast, interspecific yeast hybrids have the potential to deliver increased complexity to wine sensory properties and alternative wine styles through the formation of novel, and wider ranging, yeast volatile fermentation metabolite profiles, whilst maintaining the robustness of the wine yeast parent. Screening of newly generated hybrids from a cross between a S. cerevisiae wine yeast and S. mikatae (closely-related but ecologically distant members of the Saccharomyces sensu stricto clade), has identified progeny with robust fermentation properties and winemaking potential. Chemical analysis showed that, relative to the S. cerevisiae wine yeast parent, hybrids produced wines with different concentrations of volatile metabolites that are known to contribute to wine flavour and aroma, including flavour compounds associated with non-Saccharomyces species. The new S. cerevisiae x S. mikatae hybrids have the potential to produce complex wines akin to products of spontaneous fermentation while giving winemakers the safeguard of an inoculated ferment.Jennifer R. Bellon, Frank Schmid, Dimitra L. Capone, Barbara L. Dunn, Paul J. Chamber

The Carbon-Sulfur Link in the Remineralization of Organic Carbon in Surface Sediments

Here we present the carbon isotopic composition of dissolved inorganic carbon (DIC) and the sulfur isotopic composition of sulfate, along with changes in sulfate concentrations, of the pore fluid collected from a series of sediment cores located along a depth transect on the Iberian Margin. We use these data to explore the coupling of microbial sulfate reduction (MSR) to organic carbon oxidation in the uppermost (up to nine meters) sediment. We argue that the combined use of the carbon and sulfur isotopic composition, of DIC and sulfate respectively, in sedimentary pore fluids, viewed through a δ13CDIC vs. δ34SSO4 cross plot, reveals significant insight into the nature of carbon-sulfur coupling in marine sedimentary pore fluids on continental margins. Our data show systemic changes in the carbon and sulfur isotopic composition of DIC and sulfate (respectively) where, at all sites, the carbon isotopic composition of the DIC decreases before the sulfur isotopic composition of sulfate increases. We compare our results to global data and show that this behavior persists over a range of sediment types, locations and water depths. We use a reactive-transport model to show how changes in the amount of DIC in seawater, the carbon isotopic composition of organic matter, the amount of organic carbon oxidation by early diagenetic reactions, and the presence and source of methane influence the carbon and sulfur isotopic composition of sedimentary pore fluids and the shape of the δ13CDIC vs. δ34SSO4 cross plot. The δ13C of the DIC released during sulfate reduction and sulfate-driven anaerobic oxidation of methane is a major control on the minimum δ13CDIC value in the δ13CDIC vs. δ34SSO4 cross plot, with the δ13C of the organic carbon being important during both MSR and combined sulfate reduction, sulfate-driven AOM and methanogenesis

Comparison of estimated 20-Hz pulse fin whale source levels from the tropical Pacific and Eastern North Atlantic Oceans to other recorded populations

D.H. was funded by the Office of Naval Research (Award: N00014-16-1-2364). J.M.O. was funded under Award: N00014-16-1-2860 also from the Office of Naval Research.Passive acoustic monitoring, mitigation, animal density estimation, and comprehensive understanding of the impact of sound on marine animals all require accurate information on vocalization source level to be most effective. This study focused on examining the uncertainty related to passive sonar equation terms that ultimately contribute to the variability observed in estimated source levels of fin whale calls. Differences in hardware configuration, signal detection methods, sample size, location, and time were considered in interpreting the variability of estimated fin whale source levels. Data from Wake Island in the Pacific Ocean and off Portugal in the Atlantic Ocean provided the opportunity to generate large datasets of estimated source levels to better understand sources of uncertainty leading to the observed variability with and across years. Average seasonal source levels from the Wake Island dataset ranged from 175 to 188 dB re 1 μPa m, while the 2007–2008 seasonal average detected off Portugal was 189 dB re 1 μPa m. Owing to the large inherent variability within and across this and other studies that potentially masks true differences between populations, there is no evidence to conclude that the source level of 20-Hz fin whale calls are regionally or population specific.Publisher PDFPeer reviewe

Association of Circulating Tumor DNA Testing Before Tissue Diagnosis With Time to Treatment Among Patients With Suspected Advanced Lung Cancer: The ACCELERATE Nonrandomized Clinical Trial.

IMPORTANCE Liquid biopsy has emerged as a complement to tumor tissue profiling for advanced non-small cell lung cancer (NSCLC). The optimal way to integrate liquid biopsy into the diagnostic algorithm for patients with newly diagnosed advanced NSCLC remains unclear. OBJECTIVE To evaluate the use of circulating tumor DNA (ctDNA) genotyping before tissue diagnosis among patients with suspected advanced NSCLC and its association with time to treatment. DESIGN, SETTING, AND PARTICIPANTS This single-group nonrandomized clinical trial was conducted among 150 patients at the Princess Margaret Cancer Centre-University Health Network (Toronto, Ontario, Canada) between July 1, 2021, and November 30, 2022. Patients referred for investigation and diagnosis of lung cancer were eligible if they had radiologic evidence of advanced lung cancer prior to a tissue diagnosis. INTERVENTIONS Patients underwent plasma ctDNA testing with a next-generation sequencing (NGS) assay before lung cancer diagnosis. Diagnostic biopsy and tissue NGS were performed per standard of care. MAIN OUTCOME AND MEASURES The primary end point was time from referral to treatment initiation among patients with advanced nonsquamous NSCLC using ctDNA testing before diagnosis (ACCELERATE [Accelerating Lung Cancer Diagnosis Through Liquid Biopsy] cohort). This cohort was compared with a reference cohort using standard tissue genotyping after tissue diagnosis. RESULTS Of the 150 patients (median age at diagnosis, 68 years [range, 33-91 years]; 80 men [53%]) enrolled, 90 (60%) had advanced nonsquamous NSCLC. The median time to treatment was 39 days (IQR, 27-52 days) for the ACCELERATE cohort vs 62 days (IQR, 44-82 days) for the reference cohort (P < .001). Among the ACCELERATE cohort, the median turnaround time from sample collection to genotyping results was 7 days (IQR, 6-9 days) for plasma and 23 days (IQR, 18-28 days) for tissue NGS (P < .001). Of the 90 patients with advanced nonsquamous NSCLC, 21 (23%) started targeted therapy before tissue NGS results were available, and 11 (12%) had actionable alterations identified only through plasma testing. CONCLUSIONS AND RELEVANCE This nonrandomized clinical trial found that the use of plasma ctDNA genotyping before tissue diagnosis among patients with suspected advanced NSCLC was associated with accelerated time to treatment compared with a reference cohort undergoing standard tissue testing. TRIAL REGISTRATION ClinicalTrials.gov Identifier: NCT04863924

A Pilot study of the Sharing Risk Information Tool (ShaRIT) for Families with Hereditary Breast and Ovarian Cancer Syndrome

<p>Abstract</p> <p>Background</p> <p>Individuals who carry deleterious BRCA mutations face significantly elevated risks of breast, ovarian, and other cancers. These individuals are also responsible for informing relatives of their increased risk for carrying the family BRCA mutation. Few interventions have been developed to facilitate this family communication process.</p> <p>Methods</p> <p>We developed the Sharing Risk Information Tool (ShaRIT), a personalized educational intervention, to support BRCA carriers as they discuss BRCA positive results and their implications with relatives. We conducted a pilot study of 19 BRCA carriers identified through the University of California San Francisco Cancer Risk Program. Our study had two aims: 1) to assess the feasibility and acceptability of ShaRIT, and 2) describe characteristics associated with increased family communication and BRCA testing. Participants in our study were divided into two groups: those who had not received ShaRIT as part of their genetic counseling protocol (control group, n = 10) and those who received ShaRIT (n = 9).</p> <p>Results</p> <p>All 9 women who received ShaRIT reported that it was a useful resource. Characteristics associated with increased sharing and testing included: female gender, degree of relationship, and frequency of communication. Increased pedigree knowledge showed a trend toward higher rates of sharing.</p> <p>Conclusions</p> <p>Both participants and genetic counselors considered ShaRIT a well-received, comprehensive tool for disseminating individual risk information and clinical care guidelines to Hereditary Breast and Ovarian Cancer Syndrome families. Because of this, ShaRIT has been incorporated as standard of care at our institution. In the future we hope to evaluate the effects of ShaRIT on family communication and family testing in larger populations of BRCA positive families.</p