Development of data representation standards by the human proteome organization proteomics standards initiative.

OBJECTIVE: To describe the goals of the Proteomics Standards Initiative (PSI) of the Human Proteome Organization, the methods that the PSI has employed to create data standards, the resulting output of the PSI, lessons learned from the PSI's evolution, and future directions and synergies for the group. MATERIALS AND METHODS: The PSI has 5 categories of deliverables that have guided the group. These are minimum information guidelines, data formats, controlled vocabularies, resources and software tools, and dissemination activities. These deliverables are produced via the leadership and working group organization of the initiative, driven by frequent workshops and ongoing communication within the working groups. Official standards are subjected to a rigorous document process that includes several levels of peer review prior to release. RESULTS: We have produced and published minimum information guidelines describing what information should be provided when making data public, either via public repositories or other means. The PSI has produced a series of standard formats covering mass spectrometer input, mass spectrometer output, results of informatics analysis (both qualitative and quantitative analyses), reports of molecular interaction data, and gel electrophoresis analyses. We have produced controlled vocabularies that ensure that concepts are uniformly annotated in the formats and engaged in extensive software development and dissemination efforts so that the standards can efficiently be used by the community.Conclusion In its first dozen years of operation, the PSI has produced many standards that have accelerated the field of proteomics by facilitating data exchange and deposition to data repositories. We look to the future to continue developing standards for new proteomics technologies and workflows and mechanisms for integration with other omics data types. Our products facilitate the translation of genomics and proteomics findings to clinical and biological phenotypes. The PSI website can be accessed at http://www.psidev.info

A first attempt to model region-wide glacier surface mass balances in the Karakoram: findings and future challenges

In contrast to the central and eastern part of High Mountain Asia (HMA), no extensive glacier mass loss has been observed in the Karakoram during previous decades. However, the potential meteorological and glaciological causes of the so-called Karakoram Anomaly are diverse and still under debate. This paper introduces and presents a novel glacier Surface Mass Balance Model (glacierSMBM) to test whether the characteristic regional mass balance pattern can be reproduced using recent field, remote-sensing and reanalysis data as input. A major advantage of the model setup is the implementation of the non-linear effect of supra-glacial debris on the sub-surface ice melt. In addition to a first assessment of the annual surface mass balance from 1st August 2010 until 31st July 2011, a sensitivity analysis was performed to investigate the response of Karakoram glaciers to recent climate change. The mean modelled glacier mass balance for the Karakoram during the observation period is -0.92 m water equivalent (w.e.) a-1 and corresponds to an annual melt water contribution of ~12.66 km3. Data inaccuracies and the neglected process of snow redistribution from adjacent slopes are probably responsible for the bias in the model output. Despite the general offset between mass gain and mass loss, the model captures the characteristic features of the anomaly and indicates that positive glacier mass balances are mainly restricted to the central and northeastern part of the mountain range. From the evaluation of the sensitivity analysis, it can be concluded that the complex glacier response in the Karakoram is not the result of a single driver, but related to a variety of regional peculiarities such as the favourable meteorological conditions, the extensive supra-glacial debris and the timing of the main precipitation season

Topological mirror symmetry with fluxes

Motivated by SU(3) structure compactifications, we show explicitly how to construct half--flat topological mirrors to Calabi--Yau manifolds with NS fluxes. Units of flux are exchanged with torsion factors in the cohomology of the mirror; this is the topological complement of previous differential--geometric mirror rules. The construction modifies explicit SYZ fibrations for compact Calabi--Yaus. The results are of independent interest for SU(3) compactifications. For example one can exhibit explicitly which massive forms should be used for Kaluza--Klein reduction, proving previous conjectures. Formality shows that these forms carry no topological information; this is also confirmed by infrared limits and old classification theorems.Comment: 35 pages, 5 figure

Characterizing the weight-glycemia phenotypes of type 1 diabetes in youth and young adulthood

Introduction Individuals with type 1 diabetes (T1D) present with diverse body weight status and degrees of glycemic control, which may warrant different treatment approaches. We sought to identify subgroups sharing phenotypes based on both weight and glycemia and compare characteristics across subgroups. Research design and methods Participants: with T1D in the SEARCH study cohort (n=1817, 6.0-30.4 years) were seen at a follow-up visit >5 years after diagnosis. Hierarchical agglomerative clustering was used to group participants based on five measures summarizing the joint distribution of body mass index z-score (BMIz) and hemoglobin A1c (HbA1c) which were estimated by reinforcement learning tree predictions from 28 covariates. Interpretation of cluster weight status and glycemic control was based on mean BMIz and HbA1c, respectively. Results: The sample was 49.5% female and 55.5% non-Hispanic white (NHW); mean±SD age=17.6±4.5 years, T1D duration=7.8±1.9 years, BMIz=0.61±0.94, and HbA1c=76±21 mmol/mol (9.1±1.9)%. Six weight-glycemia clusters were identified, including four normal weight, one overweight, and one subgroup with obesity. No cluster had a mean HbA1c <58 mmol/mol (7.5%). Cluster 1 (34.0%) was normal weight with the lowest HbA1c and comprised 85% NHW participants with the highest socioeconomic position, insulin pump use, dietary quality, and physical activity. Subgroups with very poor glycemic control (ie, ≥108 mmol/mol (≥12.0%); cluster 4, 4.4%, and cluster 5, 7.5%) and obesity (cluster 6, 15.4%) had a lower proportion of NHW youth, lower socioeconomic position, and reported decreased pump use and poorer health behaviors (overall p<0.01). The overweight subgroup with very poor glycemic control (cluster 5) showed the highest lipids and blood pressure (p<0.01). Conclusions: There are distinct subgroups of youth and young adults with T1D that share weight-glycemia phenotypes. Subgroups may benefit from tailored interventions addressing differences in clinical care, health behaviors, and underlying health inequity. © Author(s) (or their employer(s)) 2020. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ

Realistic Equations of State for the Primeval Universe

Early universe equations of state including realistic interactions between constituents are built up. Under certain reasonable assumptions, these equations are able to generate an inflationary regime prior to the nucleosynthesis period. The resulting accelerated expansion is intense enough to solve the flatness and horizon problems. In the cases of curvature parameter \kappa equal to 0 or +1, the model is able to avoid the initial singularity and offers a natural explanation for why the universe is in expansion.Comment: 32 pages, 5 figures. Citations added in this version. Accepted EPJ

Identification of clinically relevant dysglycemia phenotypes based on continuous glucose monitoring data from youth with type 1 diabetes and elevated hemoglobin A1c

Background/Objective: To identify and characterize subgroups of adolescents with type 1 diabetes (T1D) and elevated hemoglobin A1c (HbA1c) who share patterns in their continuous glucose monitoring (CGM) data as “dysglycemia phenotypes.”. Methods: Data were analyzed from the Flexible Lifestyles Empowering Change randomized trial. Adolescents with T1D (13-16 years, duration >1 year) and HbA1c 8% to 13% (64-119 mmol/mol) wore blinded CGM at baseline for 7 days. Participants were clustered based on eight CGM metrics measuring hypoglycemia, hyperglycemia, and glycemic variability. Clusters were characterized by their baseline features and 18 months changes in HbA1c using adjusted mixed effects models. For comparison, participants were stratified by baseline HbA1c (≤/>9.0% [75 mmol/mol]). Results: The study sample included 234 adolescents (49.8% female, baseline age 14.8 ± 1.1 years, baseline T1D duration 6.4 ± 3.7 years, baseline HbA1c 9.6% ± 1.2%, [81 ± 13 mmol/mol]). Three Dysglycemia Clusters were identified with significant differences across all CGM metrics (P <.001). Dysglycemia Cluster 3 (n = 40, 17.1%) showed severe hypoglycemia and glycemic variability with moderate hyperglycemia and had a lower baseline HbA1c than Clusters 1 and 2 (P <.001). This cluster showed increases in HbA1c over 18 months (p-for-interaction = 0.006). No other baseline characteristics were associated with Dysglycemia Clusters. High HbA1c was associated with lower pump use, greater insulin doses, more frequent blood glucose monitoring, lower motivation, and lower adherence to diabetes self-management (all P <.05). Conclusions: There are subgroups of adolescents with T1D for which glycemic control is challenged by different aspects of dysglycemia. Enhanced understanding of demographic, behavioral, and clinical characteristics that contribute to CGM-derived dysglycemia phenotypes may reveal strategies to improve treatment

Non-vacuum Solutions of Bianchi Type VI_0 Universe in f(R) Gravity

In this paper, we solve the field equations in metric f(R) gravity for Bianchi type VI_0 spacetime and discuss evolution of the expanding universe. We find two types of non-vacuum solutions by taking isotropic and anisotropic fluids as the source of matter and dark energy. The physical behavior of these solutions is analyzed and compared in the future evolution with the help of some physical and geometrical parameters. It is concluded that in the presence of isotropic fluid, the model has singularity at $\tilde{t}=0$ and represents continuously expanding shearing universe currently entering into phantom phase. In anisotropic fluid, the model has no initial singularity and exhibits the uniform accelerating expansion. However, the spacetime does not achieve isotropy as $t\rightarrow\infty$ in both of these solutions.Comment: 20 pages, 5 figures, accepted for publication in Astrophys. Space Sc

Trust and normative control in multi-agent systems: an empirical study

Despite relevant insights from socio-economics, little research in multi-agent systems has addressed the interconnections between trust and normative notions such as contracts and sanctions. Focusing our attention on scenarios of betrayal, in this paper we combine the use of trust and sanctions in a negotiation process. We describe a scenario of dyadic relationships between truster agents, which make use of trust and/or sanctions, and trustees characterized by their ability and integrity, which may influence their attitude toward betrayal. Both agent behavior models are inspired in socio-economics literature. Through simulation, we show the virtues and shortcomings of exploiting trust, sanctions and a combination of both

Dietary intake and risk of non-severe hypoglycemia in adolescents with type 1 diabetes

Aims To determine the association between dietary intake and risk of non-severe hypoglycemia in adolescents with type 1 diabetes. Methods Type 1 adolescents from a randomized trial wore a blinded continuous glucose monitoring (CGM) system at baseline for one week in free-living conditions. Dietary intake was calculated as the average from two 24-h dietary recalls. Non-severe hypoglycemia was defined as having blood glucose < 70 mg/dL for ≥ 10 min but not requiring external assistance, categorized as daytime and nocturnal (11 PM–7AM). Data were analyzed using logistic regression models. Results Among 98 participants with 14,277 h of CGM data, 70 had daytime hypoglycemia, 66 had nocturnal hypoglycemia, 55 had both, and 17 had neither. Soluble fiber and protein intake were positively associated with both daytime and nocturnal hypoglycemia. Glycemic index, monounsaturated fat, and polyunsaturated fat were negatively associated with daytime hypoglycemia only. Adjusting for total daily insulin dose per kilogram eliminated all associations. Conclusions Dietary intake was differentially associated with daytime and nocturnal hypoglycemia. Over 80% of type 1 adolescents had hypoglycemia in a week, which may be attributed to the mismatch between optimal insulin dose needed for each meal and actually delivered insulin dose without considering quality of carbohydrate and nutrients beyond carbohydrate