Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Coffee Consumption among Adults in the United States by Demographic Variables and Purchase Location: Analyses of NHANES 2011–2016 Data

Coffee, obtained from various sources, is consumed by most United States adults. The present analyses of one and two 24-h dietary recalls for 14,865 persons aged ≥20 years in the 2011–2016 National Health and Nutrition Examination Survey (NHANES 2011–2016) aimed to identify socio-demographic predictors of coffee consumption and to examine whether coffee purchase locations differed by population sub-group. Given the emphasis on food and beverage consumption patterns, the relation between coffee consumption and compliance with the Dietary Guidelines of Americans was also examined. Coffee was consumed by 59% of the sample (n = 8551). Survey-adjusted mean intake among consumers was 544.7 g/day. Percent consumers and mean amounts consumed were highest among adults aged 51–70 years (p < 0.001), higher income groups (p < 0.001), and non-Hispanic Whites (p < 0.001). About 74% of coffee consumers obtained their coffee from stores, 9.8% from fast food restaurants, 4.3% from convenience stores, and 4.2% from someone else. Coffee source locations also varied by age, education, income, and race/ethnicity. Coffee consumers had significantly higher Healthy Eating Index (HEI-2015) and higher Nutrient-Rich Foods (NRF9.3) scores in energy-adjusted models and significantly higher HEI 2015 scores in multivariable models. In multivariable models, coffee consumers had diets with less added sugar (p < 0.001) but slightly more fat (of all types, including monounsaturated (MUFA), polyunsaturated (PUFA), saturated and solid fats), cholesterol, and alcohol. Their diets had more potassium and magnesium (p < 0.001) but less vitamin C (p < 0.001). Mean caffeine consumption was 233 mg/day for consumers and 72.3 mg/day for non-consumers. Coffee consumption patterns in the US vary across socio-demographic groups

Eggs modulate the inflammatory response to carbohydrate restricted diets in overweight men

<p>Abstract</p> <p>Background</p> <p>Carbohydrate restricted diets (CRD) consistently lower glucose and insulin levels and improve atherogenic dyslipidemia [decreasing triglycerides and increasing HDL cholesterol (HDL-C)]. We have previously shown that male subjects following a CRD experienced significant increases in HDL-C only if they were consuming a higher intake of cholesterol provided by eggs compared to those individuals who were taking lower concentrations of dietary cholesterol. Here, as a follow up of our previous study, we examined the effects of eggs (a source of both dietary cholesterol and lutein) on adiponectin, a marker of insulin sensitivity, and on inflammatory markers in the context of a CRD.</p> <p>Methods</p> <p>Twenty eight overweight men [body mass index (BMI) 26–37 kg/m²] aged 40–70 y consumed an ad libitum CRD (% energy from CHO:fat:protein = 17:57:26) for 12 wk. Subjects were matched by age and BMI and randomly assigned to consume eggs (EGG, n = 15) (640 mg additional cholesterol/day provided by eggs) or placebo (SUB, n = 13) (no additional dietary cholesterol). Fasting blood samples were drawn before and after the intervention to assess plasma lipids, insulin, adiponectin and markers of inflammation including C-reactive protein (CRP), tumor necrosis factor-alpha (TNF-α), interleukin-8 (IL-8), monocyte chemoattractant protein-1 (MCP-1), intercellular adhesion molecule-1 (ICAM-1), and vascular cell adhesion molecule-1(VCAM-1).</p> <p>Results</p> <p>Body weight, percent total body fat and trunk fat were reduced for all subjects after 12 wk (P < 0.0001). Increases in adiponectin were also observed (P < 0.01). Subjects in the EGG group had a 21% increase in this adipokine compared to a 7% increase in the SUB group (P < 0.05). Plasma CRP was significantly decreased only in the EGG group (P < 0.05). MCP-1 levels were decreased for the SUB group (P < 0.001), but unchanged in the EGG group. VCAM-1, ICAM-1, TNF-α, and IL-8 were not modified by CRD or eggs.</p> <p>Conclusion</p> <p>A CRD with daily intake of eggs decreased plasma CRP and increased plasma adiponectin compared to a CRD without eggs. These findings indicate that eggs make a significant contribution to the anti-inflammatory effects of CRD, possibly due to the presence of cholesterol, which increases HDL-C and to the antioxidant lutein which modulates certain inflammatory responses.</p

The challenge to understand the zoo of particle transport regimes during resonant wave-particle interactions for given survey-mode wave spectra

Quasilinear theories have been shown to well describe a range of transport phenomena in magnetospheric, space, astrophysical and laboratory plasma “weak turbulence” scenarios. It is well known that the resonant diffusion quasilinear theory for the case of a uniform background field may formally describe particle dynamics when the electromagnetic wave amplitude and growth rates are sufficiently “small”, and the bandwidth is sufficiently “large”. However, it is important to note that for a given wave spectrum that would be expected to give rise to quasilinear transport, the quasilinear theory may indeed apply for given range of resonant pitch-angles and energies, but may not apply for some smaller, or larger, values of resonant pitch-angle and energy. That is to say that the applicability of the quasilinear theory can be pitch-angle dependent, even in the case of a uniform background magnetic field. If indeed the quasilinear theory does apply, the motion of particles with different pitch-angles are still characterised by different timescales. Using a high-performance test-particle code, we present a detailed analysis of the applicability of quasilinear theory to a range of different wave spectra that would otherwise “appear quasilinear” if presented by e.g., satellite survey-mode data. We present these analyses as a function of wave amplitude, wave coherence and resonant particle velocities (energies and pitch-angles), and contextualise the results using theory of resonant overlap and small amplitude criteria. In doing so, we identify and classify five different transport regimes that are a function of particle pitch-angle. The results in our paper demonstrate that there can be a significant variety of particle responses (as a function of pitch-angle) for very similar looking survey-mode electromagnetic wave products, even if they appear to satisfy all appropriate quasilinear criteria. In recent years there have been a sequence of very interesting and important results in this domain, and we argue in favour of continuing efforts on: (i) the development of new transport theories to understand the importance of these, and other, diverse electron responses; (ii) which are informed by statistical analyses of the relationship between burst- and survey-mode spacecraft data