cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Gene × dietary pattern interactions in obesity: analysis of up to 68 317 adults of European ancestry
Creators: name: Rissanen, Harri
name: Perälä, Mia-Maria
name: Mikkilä, Vera
name: Ngwa, Julius S.
name: Manichaikul, Ani
name: Siscovick, David S.
name: North, Kari E.
name: Sonestedt, Emily
name: Liu, Yongmei
name: Nuotio, Marja-Liisa
name: Kristiansson, Kati
name: Bandinelli, Stefania
name: Voortman, Trudy
name: Qi, Qibin
name: Rukh, Gull
name: Booij, Lisanne
name: Houston, Denise K.
name: Hu, Frank B.
name: Follis, Jack L.
name: Smith, Caren E.
name: Ahmad, Shafqat
name: Harald, Kennet
name: Mckeown, Nicola M.
name: Johansson, Ingegerd
name: Kanoni, Stavroula
name: Nettleton, Jennifer A.
name: Lahti, Jari
name: Rich, Stephen
name: Wojczynski, Mary K.
name: Tanaka, Toshiko
name: Ganna, Andrea
name: Lemaitre, Rozenn N.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: Obesity is highly heritable. Genetic variants showing robust associations with obesity traits have been identified through genome-wide association studies. We investigated whether a composite score representing healthy diet modifies associations of these variants with obesity traits. Totally, 32 body mass index (BMI)- and 14 waist–hip ratio (WHR)-associated single nucleotide polymorphisms were genotyped, and genetic risk scores (GRS) were calculated in 18 cohorts of European ancestry (n = 68 317). Diet score was calculated based on self-reported intakes of whole grains, fish, fruits, vegetables, nuts/seeds (favorable) and red/processed meats, sweets, sugar-sweetened beverages and fried potatoes (unfavorable). Multivariable adjusted, linear regression within each cohort followed by inverse variance-weighted, fixed-effects meta-analysis was used to characterize: (a) associations of each GRS with BMI and BMI-adjusted WHR and (b) diet score modification of genetic associations with BMI and BMI-adjusted WHR. Nominally significant interactions (P = 0.006–0.04) were observed between the diet score and WHR-GRS (but not BMI-GRS), two WHR loci (GRB14 rs10195252; LYPLAL1 rs4846567) and two BMI loci (LRRN6C rs10968576; MTIF3 rs4771122), for the respective BMI-adjusted WHR or BMI outcomes. Although the magnitudes of these select interactions were small, our data indicated that associations between genetic predisposition and obesity traits were stronger with a healthier diet. Our findings generate interesting hypotheses; however, experimental and functional studies are needed to determine their clinical relevance.
Bayesian Inference for a 1-Factor Copula Model
Creators: name: Tan, Ban Kheng
name: Panagiotelis, Anastasios
name: Athanasopoulos, George
Publisher: name: Monash University
Year: 2022
Subjects: Econometric and statistical methods
Econometrics not elsewhere classified

description: We develop efficient Bayesian inference for the 1-factor copula model with two significant contributions over classical inference.
Interaction effect on adiabatic pump of charge and spin in quantum dot
Creators: name: Nakajima, Satoshi
name: Taguchi, Masahiko
name: Kubo, Toshihiro
name: Tokura, Yasuhiro
Publisher: name: arXiv
Year: 2015
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: We investigate the pumped charge and spin at zero-bias by adiabatic modulation of two control parameters using the full counting statistics with quantum master equation approach. First we study higher order effects of the pumping frequency in general Markov systems and show the equivalence between our approach and the real-time diagrammatic approach. An adiabatic modulation of the control parameters induces the Berry-Sinitsyn-Nemenman (BSN) phase. We show that the origin of the BSN phase is a non-adiabatic effect. The adiabatically pumped charge (spin) is given by a summation of (i) a time integral of the instantaneous steady charge (spin) current and (ii) a geometric surface integral of the BSN curvature, which results from the BSN phase. In quantum dots (QDs) weakly coupled to two leads, we show that (i) is usually dominant if the thermodynamic parameters are modulated although it is zero if the thermodynamic parameters are fixed to zero-bias. To observe the spin effects, we consider collinear magnetic fields, which relate to spins through the Zeeman effect, with different amplitudes applying to the QDs and the leads. For interacting one level QD, we calculate analytically the pumped charge and spin by modulating the magnetic fields and the coupling strengths to the leads in the weak and strong interacting limits. We show that the difference between these two limits appears through the averages of the numbers of the electron with up and down spin in the QD. For the quantum pump by the modulation of the magnetic fields of the QD and one lead, the energy-dependences of linewidth functions, which are usually neglected, are essential.
description: 18 pages, 3 figures, corrected typos
Nonparametric kernel estimation of the impact of tax policy on the demand for private health insurance in Australia
Creators: name: Gong, Xiaodong
name: Gao, Jiti
Publisher: name: Monash University
Year: 2022
Subjects: Econometric and statistical methods
Econometrics not elsewhere classified

description: This paper is motivated by our attempt to answer an empirical question: how is private health insurance take-up in
Gene-based meta-analysis of genome-wide association studies implicates new loci involved in obesity
Creators: name: Pawitan, Yudi
name: Justice, Anne E.
name: Loos, Ruth J.F.
name: Kahali, Bratati
name: Locke, Adam E.
name: Siemelink, Marten A.
name: Speliotes, Elizabeth K.
name: Van Der Laan, Sander W.
name: Hägg, Sara
name: Ganna, Andrea
name: Berndt, Sonja I.
name: Pers, Tune H.
name: North, Kari E.
name: Ingelsson, Erik
name: Strachan, David P.
name: Esko, Tonu
name: Pasterkamp, Gerard
name: Hirschhorn, Joel N.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: To date, genome-wide association studies (GWASs) have identified >100 loci with single variants associated with body mass index (BMI). This approach may miss loci with high allelic heterogeneity; therefore, the aim of the present study was to use gene-based meta-analysis to identify regions with high allelic heterogeneity to discover additional obesity susceptibility loci. We included GWAS data from 123 865 individuals of European descent from 46 cohorts in Stage 1 and Metabochip data from additional 103 046 individuals from 43 cohorts in Stage 2, all within the Genetic Investigation of ANthropometric Traits (GIANT) consortium. Each cohort was tested for association between ∼2.4 million (Stage 1) or ∼200 000 (Stage 2) imputed or genotyped single variants and BMI, and summary statistics were subsequently meta-analyzed in 17 941 genes. We used the ‘VErsatile Gene-based Association Study’ (VEGAS) approach to assign variants to genes and to calculate gene-based P-values based on simulations. The VEGAS method was applied to each cohort separately before a gene-based meta-analysis was performed. In Stage 1, two known (FTO and TMEM18) and six novel (PEX2, MTFR2, SSFA2, IARS2, CEP295 and TXNDC12) loci were associated with BMI (P < 2.8 × 10−6 for 17 941 gene tests). We confirmed all loci, and six of them were gene-wide significant in Stage 2 alone. We provide biological support for the loci by pathway, expression and methylation analyses. Our results indicate that gene-based meta-analysis of GWAS provides a useful strategy to find loci of interest that were not identified in standard single-marker analyses due to high allelic heterogeneity.
On the geometry of mixed states and the Fisher information tensor
Creators: name: Contreras, Ivan
name: Ercolessi, Elisa
name: Schiavina, Michele
Publisher: name: arXiv
Year: 2015
Subjects: subject: Mathematical Physics (math-ph)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences
subject: 81S99

description: In this paper, we will review the co-adjoint orbit formulation of finite dimensional quantum mechanics, and in this framework, we will interpret the notion of quantum Fisher information index (and metric). Following previous work of part of the authors, who introduced the definition of Fisher information tensor, we will show how its antisymmetric part is the pullback of the natural Kostant-Kirillov-Souriau symplectic form along some natural diffeomorphism. In order to do this, we will need to understand the symmetric logarithmic derivative as a proper 1-form, settling the issues about its very definition and explicit computation. Moreover, the fibration of co-adjoint orbits, seen as spaces of mixed states, is also discussed.
description: 27 pages; Accepted Manuscript
Genetic determinants of telomere length and risk of common cancers: a Mendelian randomization study
Creators: name: Kraft, Peter
name: Kote-Jarai, Zsofia
name: Bickeböller, Heike
name: Lindström, Sara
name: Monteiro, Alvaro N.A.
name: Zhang, Chenan
name: Eeles, Rosalind A.
name: Berndt, Sonja I.
name: Wiklund, Fredrik
name: Haiman, Christopher A.
name: Hung, Rayjean J.
name: Houlston, Richard S.
name: Brennan, Paul
name: Heinrich, Joachim
name: Gong, Jian
name: Risch, Angela
name: Doherty, Jennifer A.
name: Andrulis, Irene L.
name: Mckay, James D.
name: Timofeeva, Maria N.
name: Grönberg, Henrik
name: Burgess, Stephen
name: Henderson, Brian E.
name: Chanock, Stephen J.
name: Landi, Maria Teresa
name: Chenevix-Trench, Georgia
name: Sellers, Thomas A.
name: Wang, Yufei
name: Muir, Ken
name: Schumacher, Fredrick
name: Amos, Christopher I.
name: Amin Al Olama, Ali
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: Epidemiological studies have reported inconsistent associations between telomere length (TL) and risk for various cancers. These inconsistencies are likely attributable, in part, to biases that arise due to post-diagnostic and post-treatment TL measurement. To avoid such biases, we used a Mendelian randomization approach and estimated associations between nine TL-associated SNPs and risk for five common cancer types (breast, lung, colorectal, ovarian and prostate cancer, including subtypes) using data on 51 725 cases and 62 035 controls. We then used an inverse-variance weighted average of the SNP-specific associations to estimate the association between a genetic score representing long TL and cancer risk. The long TL genetic score was significantly associated with increased risk of lung adenocarcinoma (P = 6.3 × 10−15), even after exclusion of a SNP residing in a known lung cancer susceptibility region (TERT-CLPTM1L) P = 6.6 × 10−6). Under Mendelian randomization assumptions, the association estimate [odds ratio (OR) = 2.78] is interpreted as the OR for lung adenocarcinoma corresponding to a 1000 bp increase in TL. The weighted TL SNP score was not associated with other cancer types or subtypes. Our finding that genetic determinants of long TL increase lung adenocarcinoma risk avoids issues with reverse causality and residual confounding that arise in observational studies of TL and disease risk. Under Mendelian randomization assumptions, our finding suggests that longer TL increases lung adenocarcinoma risk. However, caution regarding this causal interpretation is warranted in light of the potential issue of pleiotropy, and a more general interpretation is that SNPs influencing telomere biology are also implicated in lung adenocarcinoma risk.
Entropic Ricci curvature bounds for discrete interacting systems
Creators: name: Fathi, Max
name: Maas, Jan
Publisher: name: arXiv
Year: 2015
Subjects: subject: Probability (math.PR)
subject: Functional Analysis (math.FA)
subject: FOS: Mathematics

description: We develop a new and systematic method for proving entropic Ricci curvature lower bounds for Markov chains on discrete sets. Using different methods, such bounds have recently been obtained in several examples (e.g., 1-dimensional birth and death chains, product chains, Bernoulli-Laplace models, and random transposition models). However, a general method to obtain discrete Ricci bounds had been lacking. Our method covers all of the examples above. In addition, we obtain new Ricci curvature bounds for zero-range processes on the complete graph. The method is inspired by recent work of Caputo, Dai Pra and Posta on discrete functional inequalities.
description: Published at http://dx.doi.org/10.1214/15-AAP1133 in the Annals of Applied Probability (http://www.imstat.org/aap/) by the Institute of Mathematical Statistics (http://www.imstat.org)
Estimation and inference in semiparametric quantile factor models
Creators: name: Ma, Shujie
name: Linton, Oliver
name: Gao, Jiti
Publisher: name: Monash University
Year: 2022
Subjects: Econometric and statistical methods
Econometrics not elsewhere classified

description: We propose an estimation methodology for a semiparametric quantile factor panel model. We provide tools for inference
Field co-inoculation of Bradyrhizobium sp. and Pseudomonas increases nutrients uptake of Vigna radiata L. from fertilized soil
Creators: name: Shah, Ghulam Abbas
name: Sadiq, Maqsood
name: Iqbal, Zahid
name: Shakoor, Noman
name: Shahid, Muhammad
name: Aulakh, Azhar Mehmood
name: Arthur, Kamusiime
name: Khan, Nadeem
name: Ismail, Iqbal M.I
name: Rashid, Muhammad Imtiaz
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Biotechnology
subject: Evolutionary Biology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Ecology
subject: Immunology
subject: FOS: Clinical medicine
subject: Developmental Biology
subject: Plant Biology
subject: Computational Biology

description: Nitrogen (N) and phosphorus (P) deficiency in soils limit plant growth. Consequently, chemical fertilizers are applied to fulfill crop nutrient demands. However, low nutrient utilization can make these fertilizers unprofitable for low-income smallholding farmers. Therefore, we studied the influence of Bradyrhizobium sp. and phosphate-solubilizing bacteria (Pseudomonas) on N and P utilization by mungbean crop from fertilized nutrient-deficient soil. We inoculated novel Bradyrhizobium sp. TAL-377 and Pseudomonas sp. 54RB strains alone or their combination with seeds of mungbean varieties (C-MUNG, NM-06, and NM-11). A basal dose of chemical fertilizers was applied at the rate of 60 kg N and 90 kg P ha−1 in the form of urea and single super phosphate in all plots before crop sowing. All inocula increased soil mineral N and P compared to control (P < 0.05). Co-inoculation increased mineral N by 30%, 18%, and 18% than Bradyrhizobium sp. alone and increase in P was 22, 29 and 43% than Pseudomonas sp. in C-MUNG, NM-06, and NM-11, respectively. This resulted in 35%, 45%, and 36% higher shoot N uptakes than Bradyrhizobium sp., and 46%, 84%, and 62% higher shoot P uptake than Pseudomonas sp. in the varieties. Similarly, root nodulation, mungbean grains, and biological yields were higher in co-inoculation treatments than single strain (p < .05). Hence, co-inoculation of Bradyrhizobium sp. and phosphorus solubilizing bacteria (Pseudomonas sp.) is a vital strategy to increase mungbean growth, yield, N and P utilization from chemical fertilizers applied in nutrient-deficient soils.
Effect of sewage sludge-derived amendments on the nutrient uptake by Chinese cabbage from Mediterranean soils
Creators: name: Černe, Marko
name: Palčić, Igor
name: Major, Nikola
name: Pasković, Igor
name: Perković, Josipa
name: Užila, Zoran
name: Filipović, Vilim
name: Romić, Marija
name: Ban, Smiljana Goreta
name: Heath, David John
name: Ban, Dean
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Pharmacology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: Plant Biology

description: The utilization of sewage sludge (SS) as a fertilizer for agricultural land is increasingly seen by many as the best option for recycling. This study investigates the effects of SS-derived compost (SSC) or biochar (SSB) amendments on N, P, K, Ca, Mg, Na, Fe, Mn and Mo uptake by Chinese cabbage (Brassica rapa L. subsp. pekinensis (Lour.) Hanelt) from terra rossa and rendzina soils. A two-factorial experiment was performed under greenhouse conditions whereby elemental concentrations (substrate, leachates and plants), edible tissue uptake (ETU), concentration ratios (CR) and soil characteristics were determined. The pH (7.03 to 7.32) and P content (286 to 421 mg/kg d.w.) in SSC- and SSB-amended soils increased, while EC (450 to 253 μS/cm) decreased. Phosphorous levels were higher in SSB-amended soils, although P leaching indicates a low environmental risk in both soils. In leaves, P (1.02 to 4.15 g/kg d.w.), K (12.8 to 21.8 g/kg d.w.), Mg (1.05 to 1.55 g/kg d.w.), Na (660 to 1350 mg/kg d.w.), and Mo (1.20 to 2.65 mg/kg d.w.) levels increased with amendment rate and were higher in SSC-amended soils. Nutrient bioavailability also increased with amendment rate, while cabbage biomass production increased proportionally to the dose. The P, K, and Mg levels were higher in leaves, while roots contained more Ca, Fe, and Mn. Despite amendment rates 10x the permitted dose of SS, they did not affect soil leachate, plant growth and biomass yield. Overall, adopting the cautionary principle is advised until the long-term effects are better understood.
Locality-aware parallel block-sparse matrix-matrix multiplication using the Chunks and Tasks programming model
Creators: name: Rubensson, Emanuel H.
name: Rudberg, Elias
Publisher: name: arXiv
Year: 2015
Subjects: subject: Distributed, Parallel, and Cluster Computing (cs.DC)
subject: FOS: Computer and information sciences
subject: D.1.3; F.1.2; G.1.0; G.4; G.1.3
subject: 68N19, 65F50

description: We present a method for parallel block-sparse matrix-matrix multiplication on distributed memory clusters. By using a quadtree matrix representation, data locality is exploited without prior information about the matrix sparsity pattern. A distributed quadtree matrix representation is straightforward to implement due to our recent development of the Chunks and Tasks programming model [Parallel Comput. 40, 328 (2014)]. The quadtree representation combined with the Chunks and Tasks model leads to favorable weak and strong scaling of the communication cost with the number of processes, as shown both theoretically and in numerical experiments. Matrices are represented by sparse quadtrees of chunk objects. The leaves in the hierarchy are block-sparse submatrices. Sparsity is dynamically detected by the matrix library and may occur at any level in the hierarchy and/or within the submatrix leaves. In case graphics processing units (GPUs) are available, both CPUs and GPUs are used for leaf-level multiplication work, thus making use of the full computing capacity of each node. The performance is evaluated for matrices with different sparsity structures, including examples from electronic structure calculations. Compared to methods that do not exploit data locality, our locality-aware approach reduces communication significantly, achieving essentially constant communication per node in weak scaling tests.
description: 35 pages, 14 figures
REDCap Data Lifecycle Management via Automated Billing
Creators: name: Chase, Philip
name: James-Woodley, Laurence
name: Chesney, Kyle
name: Stoffs, Taryn
name: Bentz, Michael
name: Kamma, Sai Pavan
name: Barnes, Christopher
Publisher: name: Zenodo
Year: 2024

description: To turn our REDCap system from a cost center into a revenue generator and address the proliferation of orphaned REDCap projects, the University of Florida’s CTS-IT charges a modest annual fee for each project. To do this we created REDCap Automated Billing. It generates revenue, reduces data privacy risks by incentivizing the deletion of abandoned projects, and improves the quality of research productivity metrics. This requires us to improve our investigator and project metadata, partner with fiscal staff, and automate novel data workflows.
Additional file 1 of Porcine versus bovine surfactant therapy for RDS in preterm neonates: pragmatic meta-analysis and review of physiopathological plausibility of the effects on extra-pulmonary outcomes
Creators: name: Foligno, Silvia
name: Luca, Daniele De
Publisher: name: figshare
Year: 2020
Subjects: subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Sociology
subject: FOS: Sociology
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Developmental Biology
subject: Science Policy

description: Additional file 1. Porcine versus bovine surfactant therapy for RDS in preterm neonates: pragmatic meta-analysis and review of physiopathological plausibility of the effects on non-respiratory outcomes.
REDCap Data Lifecycle Management via Automated Billing
Creators: name: Chase, Philip
name: James-Woodley, Laurence
name: Chesney, Kyle
name: Stoffs, Taryn
name: Bentz, Michael
name: Barnes, Christopher
Publisher: name: Zenodo
Year: 2024

description: To turn our REDCap system from a cost center into a revenue generator and address the proliferation of orphaned REDCap projects, the University of Florida’s CTS-IT charges a modest annual fee for each project. To do this we created REDCap Automated Billing. It generates revenue, reduces data privacy risks by incentivizing the deletion of abandoned projects, and improves the quality of research productivity metrics. This requires us to improve our investigator and project metadata, partner with fiscal staff, and automate novel data workflows.
Inference on a Semiparametric Model with Global Power Law and Local Nonparametric Trends
Creators: name: Gao, Jiti
name: Linton, Oliver
name: Peng, Bin
Publisher: name: Monash University
Year: 2022
Subjects: Econometric and statistical methods
Econometrics not elsewhere classified

description: This paper studies a model with both a parametric global trend and a nonparametric
MOESM1 of Porcine versus bovine surfactant therapy for RDS in preterm neonates: pragmatic meta-analysis and review of physiopathological plausibility of the effects on extra-pulmonary outcomes
Creators: name: Foligno, Silvia
name: Luca, Daniele
Publisher: name: figshare
Year: 2020
Subjects: subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Sociology
subject: FOS: Sociology
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Developmental Biology
subject: Science Policy

description: Additional file 1. Porcine versus bovine surfactant therapy for RDS in preterm neonates: pragmatic meta-analysis and review of physiopathological plausibility of the effects on non-respiratory outcomes.
title: Adressbuch der Stadt Zürich 1941
title: Adressbuch Zürich
titleType: AlternativeTitle
title: Adressbuch Stadt Zürich
titleType: AlternativeTitle
title: In vier Abteilungen auf Grund amtlicher Angaben nach Namen, Geschäftszweigen, Strassen und Behörden gegliedert
titleType: Subtitle
Creators: name: (:Unkn) Unknown
Publisher: name: Orell Füssli
Year: 1941
Subjects: subject: 330 Wirtschaft
subject: Zürich
subject: Adressbuch

description: Anmerkung des Verlags: «Aus militärischen Gründen darf dem Adressbuch zurzeit kein Stadtplan beigegeben werden.»
Genome-wide admixture and association study of serum iron, ferritin, transferrin saturation and total iron binding capacity in African Americans
Creators: name: Lange, Leslie A.
name: Lange, Ethan M.
name: Li, Jin
name: Evans, Michele K.
name: Li, Yun
name: Willis, Monte S.
name: Zonderman, Alan B.
name: Nalls, Mike
name: Lu, Yurong
name: Wilson, James G.
name: Duan, Qing
name: Taylor, Herman A.
name: Singleton, Andrew B.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: Iron is an essential component of many important proteins and enzymes, including hemoglobin, which is responsible for carrying oxygen to the cells. African Americans (AAs) have a greater prevalence of iron deficiency compared with European Americans. We conducted genome-wide admixture-mapping and association studies for serum iron, serum ferritin, transferrin saturation (SAT) and total iron binding capacity (TIBC) in 2347 AAs participating in the Jackson Heart Study (JHS). Follow-up replication analyses for JHS iron-trait associated SNPs were conducted in 329 AA participants in the Healthy Aging in Neighborhoods of Diversity across the Life Span study (HANDLS). Higher estimated proportions of global African ancestry were significantly associated with lower levels of iron (P = 2.4 × 10−5), SAT (P = 0.0019) and TIBC (P = 0.042). We observed significant associations (P < 5 × 10−8) between serum TIBC levels and two independent SNPs around TF on chromosome 3, the first report of a genome-wide significant second independent signal in this region, and SNPs near two novel genes: HDGFL1 on chromosome 6 and MAF on chromosome 16. We also observed significant associations between ferritin levels and SNPs near GAB3 on chromosome X. We replicated our two independent associations at TF and our association at GAB3 in HANDLS. Our study provides evidence for both shared and unique genetic risk factors that are associated with iron-related measures in AAs. The top two variants in TF explain 11.2% of the total variation in TIBC levels in AAs after accounting for age, gender, body mass index and background ancestry.
Genome-wide association study of selenium concentrations
Creators: name: Morris, Steve
name: Xun, Pengcheng
name: Fornage, Myriam
name: Jordan, Joanne M.
name: Foy, Millennia
name: Hu, Frank B.
name: Chasman, Daniel I.
name: Rimm, Eric B.
name: Kraft, Peter
name: Cornelis, Marilyn C.
name: Gladyshev, Vadim N.
name: Mozaffarian, Dariush
name: He, Ka
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: Selenium (Se) is an essential trace element in human nutrition, but its role in certain health conditions, particularly among Se sufficient populations, is controversial. A genome-wide association study (GWAS) of blood Se concentrations previously identified a locus at 5q14 near BHMT. We performed a GW meta-analysis of toenail Se concentrations, which reflect a longer duration of exposure than blood Se concentrations, including 4162 European descendants from four US cohorts. Toenail Se was measured using neutron activation analysis. We identified a GW-significant locus at 5q14 (P < 1 × 10−16), the same locus identified in the published GWAS of blood Se based on independent cohorts. The lead single-nucleotide polymorphism (SNP) explained ∼1% of the variance in toenail Se concentrations. Using GW-summary statistics from both toenail and blood Se, we observed statistical evidence of polygenic overlap (P < 0.001) and meta-analysis of results from studies of either trait (n = 9639) yielded a second GW-significant locus at 21q22.3, harboring CBS (P < 4 × 10−8). Proteins encoded by genes at 5q14 and 21q22.3 function in homocysteine (Hcy) metabolism, and index SNPs for each have previously been associated with betaine and Hcy levels in GWAS. Our findings show evidence of a genetic link between Se and Hcy pathways, both involved in cardiometabolic disease.
Integrative pathway genomics of lung function and airflow obstruction
Creators: name: Lahousse, Lies
name: North, Kari E.
name: Wilson, James F.
name: Smith, Albert Vernon
name: Surakka, Ida
name: Wain, Louise V.
name: Vitart, Veronique
name: Morrison, Alanna C.
name: Gudnason, Vilmundur
name: Rawal, Rajesh
name: Alves, Alexessander C.
name: Obeidat, Ma'en
name: Huffman, Jennifer E.
name: Wilk, Jemma B.
name: Zhao, Jing Hua
name: Brody, Jennifer A.
name: Loth, Daan W.
name: Ramasamy, Adaikalavan
name: Hancock, Dana B.
name: Hofman, Albert
name: Tang, Wenbo
name: Evans, David M.
name: Deary, Ian J.
name: Strachan, David P.
name: Hui, Jennie
name: Soler Artigas, María
name: Gharib, Sina A.
name: Manichaikul, Ani
name: Birkland, Timothy P.
name: Imboden, Medea
name: Gläser, Sven
name: Boezen, H. Marike
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: Chronic respiratory disorders are important contributors to the global burden of disease. Genome-wide association studies (GWASs) of lung function measures have identified several trait-associated loci, but explain only a modest portion of the phenotypic variability. We postulated that integrating pathway-based methods with GWASs of pulmonary function and airflow obstruction would identify a broader repertoire of genes and processes influencing these traits. We performed two independent GWASs of lung function and applied gene set enrichment analysis to one of the studies and validated the results using the second GWAS. We identified 131 significantly enriched gene sets associated with lung function and clustered them into larger biological modules involved in diverse processes including development, immunity, cell signaling, proliferation and arachidonic acid. We found that enrichment of gene sets was not driven by GWAS-significant variants or loci, but instead by those with less stringent association P-values. Next, we applied pathway enrichment analysis to a meta-analyzed GWAS of airflow obstruction. We identified several biologic modules that functionally overlapped with those associated with pulmonary function. However, differences were also noted, including enrichment of extracellular matrix (ECM) processes specifically in the airflow obstruction study. Network analysis of the ECM module implicated a candidate gene, matrix metalloproteinase 10 (MMP10), as a putative disease target. We used a knockout mouse model to functionally validate MMP10's role in influencing lung's susceptibility to cigarette smoke-induced emphysema. By integrating pathway analysis with population-based genomics, we unraveled biologic processes underlying pulmonary function traits and identified a candidate gene for obstructive lung disease.
Intermediate filament protein accumulation in motor neurons derived from giant axonal neuropathy iPSCs rescued by restoration of gigaxonin
Creators: name: Chung, Wendy K.
name: Diaz, Alejandro Garcia
name: Greene, John Palmer
name: Henderson, Christopher E.
name: Van Coster, Rudy
name: Noggle, Scott A.
name: Samulski, Richard Jude
name: Johnson-Kerner, Bethany L.
name: Wichterle, Hynek
name: Maertens, Paul
name: Gray, Steven J.
name: Ahmad, Faizzan S.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: Giant axonal neuropathy (GAN) is a progressive neurodegenerative disease caused by autosomal recessive mutations in the GAN gene resulting in a loss of a ubiquitously expressed protein, gigaxonin. Gene replacement therapy is a promising strategy for treatment of the disease; however, the effectiveness and safety of gigaxonin reintroduction have not been tested in human GAN nerve cells. Here we report the derivation of induced pluripotent stem cells (iPSCs) from three GAN patients with different GAN mutations. Motor neurons differentiated from GAN iPSCs exhibit accumulation of neurofilament (NF-L) and peripherin (PRPH) protein and formation of PRPH aggregates, the key pathological phenotypes observed in patients. Introduction of gigaxonin either using a lentiviral vector or as a stable transgene resulted in normalization of NEFL and PRPH levels in GAN neurons and disappearance of PRPH aggregates. Importantly, overexpression of gigaxonin had no adverse effect on survival of GAN neurons, supporting the feasibility of gene replacement therapy. Our findings demonstrate that GAN iPSCs provide a novel model for studying human GAN neuropathologies and for the development and testing of new therapies in relevant cell types.
Large-scale behaviour of local and entanglement entropy of the free Fermi gas at any temperature
Creators: name: Leschke, Hajo
name: Sobolev, Alexander V.
name: Spitzer, Wolfgang
Publisher: name: arXiv
Year: 2015
Subjects: subject: Quantum Physics (quant-ph)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Mathematical Physics (math-ph)
subject: FOS: Physical sciences

description: The leading asymptotic large-scale behaviour of the spatially bipartite entanglement entropy (EE) of the free Fermi gas infinitely extended in multidimensional Euclidean space at zero absolute temperature, T=0, is by now well understood. Here, we present and discuss the first rigorous results for the corresponding EE of thermal equilibrium states at T>0. The leading large-scale term of this thermal EE turns out to be twice the first-order finite-size correction to the infinite-volume thermal entropy (density). Not surprisingly, this correction is just the thermal entropy on the interface of the bipartition. However, it is given by a rather complicated integral derived from a semiclassical trace formula for a certain operator on the underlying one-particle Hilbert space. But in the zero-temperature limit the leading large-scale term of the thermal EE considerably simplifies and displays a ln(1/T)-singularity which one may identify with the known logarithmic enhancement at T=0 of the so-called area-law scaling.
description: The paper has been slightly rewritten to improve its readability. In particular, we now restrict ourselves to von Neumann entropies. The title and the abstract have been changed. The references have been updated. 10 pages
Performance of a Quintuple-GEM Based RICH Detector Prototype
Creators: name: Blatnik, M.
name: Dehmelt, K.
name: Deshpande, A.
name: Dixit, D.
name: Feege, N.
name: Hemmick, T. K.
name: Lewis, B.
name: Purschke, M. L.
name: Roh, W.
name: Torales-Acosta, F.
name: Videbaek, T.
name: Zajac, S.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Instrumentation and Detectors (physics.ins-det)
subject: FOS: Physical sciences

description: Cerenkov technology is often the optimal choice for particle identification in high energy particle collision applications. Typically, the most challenging regime is at high pseudorapidity (forward) where particle identification must perform well at high high laboratory momenta. For the upcoming Electron Ion Collider (EIC), the physics goals require hadron ($π$, K, p) identification up to $\sim$~50 GeV/c. In this region Cerenkov Ring-Imaging is the most viable solution.\newline The speed of light in a radiator medium is inversely proportional to the refractive index. Hence, for PID reaching out to high momenta a small index of refraction is required. Unfortunately, the lowest indices of refraction also result in the lowest light yield ($\frac{dN_γ}{dx} \propto \sin^2{\left(θ_C \right)}$) driving up the radiator length and thereby the overall detector cost. In this paper we report on a successful test of a compact RICH detector (1 meter radiator) capable of delivering in excess of 10 photoelectrons per ring with a low index radiator gas ($CF_4$). The detector concept is a natural extension of the PHENIX HBD detector achieved by adding focusing capability at low wavelength and adequate gain for high efficiency detection of single-electron induced avalanches. Our results indicate that this technology is indeed a viable choice in the forward direction of the EIC. The setup and results are described within.
description: 10 pages, 15 figures
Loss of fibulin-4 disrupts collagen synthesis and maturation: implications for pathology resulting from EFEMP2 mutations
Creators: name: Urquhart, Greg
name: Tsunezumi, Jun
name: Ringuette, Léa-Jeanne
name: Papke, Christina L.
name: Terajima, Masahiko
name: Yanagisawa, Hiromi
name: Nagaoka, Hideaki
name: Yamauchi, Mitsuo
name: Yamashiro, Yoshito
name: Davis, Elaine C.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: Homozygous recessive mutations in either EFEMP2 (encoding fibulin-4) or FBLN5 (encoding fibulin-5), critical genes for elastogenesis, lead to autosomal recessive cutis laxa types 1B and 1A, respectively. Previously, fibulin-4 was shown to bind lysyl oxidase (LOX), an elastin/collagen cross-linking enzyme, in vitro. Consistently, reported defects in humans with EFEMP2 mutations are more severe and broad in range than those due to FBLN5 mutations and encompass both elastin-rich and collagen-rich tissues. However, the underlying disease mechanism in EFEMP2 mutations has not been fully addressed. Here, we show that fibulin-4 is important for the integrity of aortic collagen in addition to elastin. Smooth muscle-specific Efemp2 loss in mouse (termed SMKO) resulted in altered fibrillar collagen localization with larger, poorly organized fibrils. LOX activity was decreased in Efemp2-null cells, and collagen cross-linking was diminished in SMKO aortas; however, elastin cross-linking was unaffected and the level of mature LOX was maintained to that of wild-type aortas. Proteomic screening identified multiple proteins involved in procollagen processing and maturation as potential fibulin-4-binding partners. We showed that fibulin-4 binds procollagen C-endopeptidase enhancer 1 (Pcolce), which enhances proteolytic cleavage of the procollagen C-terminal propeptide during procollagen processing. Interestingly, however, procollagen cleavage was not affected by the presence or absence of fibulin-4 in vitro. Thus, our data indicate that fibulin-4 serves as a potential scaffolding protein during collagen maturation in the extracellular space. Analysis of collagen in other tissues affected by fibulin-4 loss should further increase our understanding of underlying pathologic mechanisms in patients with EFEMP2 mutations.
Hack's law in a drainage network model: A Brownian web approach
Creators: name: Roy, Rahul
name: Saha, Kumarjit
name: Sarkar, Anish
Publisher: name: arXiv
Year: 2015
Subjects: subject: Probability (math.PR)
subject: FOS: Mathematics

description: Hack [Studies of longitudinal stream profiles in Virginia and Maryland (1957). Report], while studying the drainage system in the Shenandoah valley and the adjacent mountains of Virginia, observed a power law relation $l\sim a^{0.6}$ between the length $l$ of a stream from its source to a divide and the area $a$ of the basin that collects the precipitation contributing to the stream as tributaries. We study the tributary structure of Howard's drainage network model of headward growth and branching studied by Gangopadhyay, Roy and Sarkar [Ann. Appl. Probab. 14 (2004) 1242-1266]. We show that the exponent of Hack's law is $2/3$ for Howard's model. Our study is based on a scaling of the process whereby the limit of the watershed area of a stream is area of a Brownian excursion process. To obtain this, we define a dual of the model and show that under diffusive scaling, both the original network and its dual converge jointly to the standard Brownian web and its dual.
description: Published at http://dx.doi.org/10.1214/15-AAP1134 in the Annals of Applied Probability (http://www.imstat.org/aap/) by the Institute of Mathematical Statistics (http://www.imstat.org)
Recent advances in understanding the genetic architecture of type 2 diabetes
Creators: name: Boehnke, Michael
name: Mohlke, Karen L.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: Genome-wide association (GWAS) and sequencing studies are providing new insights into the genetic basis of type 2 diabetes (T2D) and the inter-individual variation in glycemic traits, including levels of glucose, insulin, proinsulin and hemoglobin A1c (HbA1c). At the end of 2011, established loci (P < 5 × 10−8) totaled 55 for T2D and 32 for glycemic traits. Since then, most new loci have been detected by analyzing common [minor allele frequency (MAF)>0.05] variants in increasingly large sample sizes from populations around the world, and in trans-ancestry studies that successfully combine data from diverse populations. Most recently, advances in sequencing have led to the discovery of four loci for T2D or glycemic traits based on low-frequency (0.005 < MAF ≤ 0.05) variants, and additional low-frequency, potentially functional variants have been identified at GWAS loci. Established published loci now total ∼88 for T2D and 83 for one or more glycemic traits, and many additional loci likely remain to be discovered. Future studies will build on these successes by identifying additional loci and by determining the pathogenic effects of the underlying variants and genes.
Near-linear constructions of exact unitary 2-designs
Creators: name: Cleve, Richard
name: Leung, Debbie
name: Liu, Li
name: Wang, Chunhao
Publisher: name: arXiv
Year: 2015
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: A unitary 2-design can be viewed as a quantum analogue of a 2-universal hash function: it is indistinguishable from a truly random unitary by any procedure that queries it twice. We show that exact unitary 2-designs on n qubits can be implemented by quantum circuits consisting of ~O(n) elementary gates in logarithmic depth. This is essentially a quadratic improvement in size (and in width times depth) over all previous implementations that are exact or approximate (for sufficiently strong approximations).
description: 30 pages, 10 figures, presentation improved
Lagrangian transport through surfaces in volume-preserving flows
Creators: name: Karrasch, Daniel
Publisher: name: arXiv
Year: 2015
Subjects: subject: Chaotic Dynamics (nlin.CD)
subject: Classical Analysis and ODEs (math.CA)
subject: Dynamical Systems (math.DS)
subject: Exactly Solvable and Integrable Systems (nlin.SI)
subject: Fluid Dynamics (physics.flu-dyn)
subject: FOS: Physical sciences
subject: FOS: Mathematics
subject: 37N10, 37C60, 76A02

description: Advective transport of scalar quantities through surfaces is of fundamental importance in many scientific applications. From the Eulerian perspective of the surface it can be quantified by the well-known integral of the flux density. The recent development of highly accurate semi-Lagrangian methods for solving scalar conservation laws and of Lagrangian approaches to coherent structures in turbulent (geophysical) fluid flows necessitate a new approach to transport from the (Lagrangian) material perspective. We present a Lagrangian framework for calculating transport of conserved quantities through a given surface in $n$-dimensional, fully aperiodic, volume-preserving flows. Our approach does not involve any dynamical assumptions on the surface or its boundary.
description: 16 pages, 6 figures; v5: (almost) published version
Intraspecific differences in Androctunus crassicauda venom and envenomation symptoms
Creators: name: Safdarian, Mehdi
name: Vazirianzadeh, Babak
name: Ghorbani, Ahmad
name: Pashmforoosh, Narges
name: Baradaran, Masoumeh
Publisher: name: IfADo - Leibniz Research Centre for Working Environment and Human Factors, Dortmund
Year: 2022
Subjects: Androctunus crassicauda
intraspecific differences
envenomation symptoms
venom difference

description: Envenomation by Androctunus crassicauda is very frequent in Iran, especially in the south-west. This scorpion is one of the six scorpions whose venom is used to prepare anti-venom. Using HPLC, we discovered venom components of A. crassicauda varies from one specimen to another depending on geographical location, and this result is confirmed by those first found in various symptoms of A. crassicauda sting in envenomed persons from two separate geographical places (north and south of Khuzestan province). There was a significant relationship between symptoms and location of envenomation by A. crassicauda. Muscle spasm was more dominant in envenomed people from Northern cities, and venom chromatogram analysis showed the presence of at least six main sharp peaks in Northern A. crassicauda rather than Southern A. crassicauda. It shows intraspecific differences in venom of A. crassicauda that must be considered in treatment of stung people from different geographical locations as well as in the preparation of anti-venom.
description: EXCLI Journal; 21:Doc1222; ISSN 1611-2156
Solving the inverse Ising problem by mean-field methods in a clustered phase space with many states
Creators: name: Decelle, Aurélien
name: Ricci-Tersenghi, Federico
Publisher: name: arXiv
Year: 2015
Subjects: subject: Disordered Systems and Neural Networks (cond-mat.dis-nn)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: In this work we explain how to properly use mean-field methods to solve the inverse Ising problem when the phase space is clustered, that is many states are present. The clustering of the phase space can occur for many reasons, e.g. when a system undergoes a phase transition. Mean-field methods for the inverse Ising problem are typically used without taking into account the eventual clustered structure of the input configurations and may led to very bad inference (for instance in the low temperature phase of the Curie-Weiss model). In the present work we explain how to modify mean-field approaches when the phase space is clustered and we illustrate the effectiveness of the new method on different clustered structures (low temperature phases of Curie-Weiss and Hopfield models).
description: 6 pages, 5 figures
A prime ideal principle for two-sided ideals
Creators: name: Reyes, Manuel L.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Rings and Algebras (math.RA)
subject: Commutative Algebra (math.AC)
subject: FOS: Mathematics
subject: 16D25, 16N60 (Primary), 13A15, 16D20 (Secondary)

description: Many classical ring-theoretic results state that an ideal that is maximal with respect to satisfying a special property must be prime. We present a "Prime Ideal Principle" that gives a uniform method of proving such facts, generalizing the Prime Ideal Principle for commutative rings due to T.Y. Lam and the author. Old and new "maximal implies prime" results are presented, with results touching on annihilator ideals, polynomial identity rings, the Artin-Rees property, Dedekind-finite rings, principal ideals generated by normal elements, strongly noetherian algebras, and just infinite algebras.
description: 22 pages
Firedrake: automating the finite element method by composing abstractions
Creators: name: Rathgeber, Florian
name: Ham, David A.
name: Mitchell, Lawrence
name: Lange, Michael
name: Luporini, Fabio
name: McRae, Andrew T. T.
name: Bercea, Gheorghe-Teodor
name: Markall, Graham R.
name: Kelly, Paul H. J.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Mathematical Software (cs.MS)
subject: Numerical Analysis (math.NA)
subject: FOS: Computer and information sciences
subject: FOS: Mathematics
subject: G.1.8; G.4

description: Firedrake is a new tool for automating the numerical solution of partial differential equations. Firedrake adopts the domain-specific language for the finite element method of the FEniCS project, but with a pure Python runtime-only implementation centred on the composition of several existing and new abstractions for particular aspects of scientific computing. The result is a more complete separation of concerns which eases the incorporation of separate contributions from computer scientists, numerical analysts and application specialists. These contributions may add functionality, or improve performance. Firedrake benefits from automatically applying new optimisations. This includes factorising mixed function spaces, transforming and vectorising inner loops, and intrinsically supporting block matrix operations. Importantly, Firedrake presents a simple public API for escaping the UFL abstraction. This allows users to implement common operations that fall outside pure variational formulations, such as flux-limiters.
description: Minor revisions to v2