cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Genetic Association Analysis under Complex Survey Sampling: The Hispanic Community Health Study/Study of Latinos
Creators: name: Kalsbeek, William D.
name: Heiss, Gerardo
name: Zeng, Donglin
name: Lin, Dan-Yu
name: Gonzalez, Franklyn
name: Fernández-Rhodes, Lindsay
name: Tao, Ran
name: Graff, Mariaelisa
name: Koch, Gary G.
name: North, Kari E.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2014

description: The cohort design allows investigators to explore the genetic basis of a variety of diseases and traits in a single study while avoiding major weaknesses of the case-control design. Most cohort studies employ multistage cluster sampling with unequal probabilities to conveniently select participants with desired characteristics, and participants from different clusters might be genetically related. Analysis that ignores the complex sampling design can yield biased estimation of the genetic association and inflation of the type I error. Herein, we develop weighted estimators that reflect unequal selection probabilities and differential nonresponse rates, and we derive variance estimators that properly account for the sampling design and the potential relatedness of participants in different sampling units. We compare, both analytically and numerically, the performance of the proposed weighted estimators with unweighted estimators that disregard the sampling design. We demonstrate the usefulness of the proposed methods through analysis of MetaboChip data in the Hispanic Community Health Study/Study of Latinos, which is the largest health study of the Hispanic/Latino population in the United States aimed at identifying risk factors for various diseases and determining the role of genes and environment in the occurrence of diseases. We provide guidelines on the use of weighted and unweighted estimators, as well as the relevant software.
"fnt2007midp_cv21_I790693.tab.gz" of "Measurement of the Inclusive Jet Cross Section at the Fermilab Tevatron p-pbar Collider Using a Cone-Based Jet Algorithm"
Creators: name: CDF Collaboration
Publisher: name: HEPData
Year: 2008

description: Link to fastNLO v2.1 table (converted from v1.4 format)
description: Fermilab-Tevatron. Measurement of the inclusive jet cross section in PBAR-P collisions at a centre of mass energy of 1.96 TeV. The data sample has an integrated luminosity of 1.13 fb-1 and a cone-based midpoint jet clustering algorithmis used. The numerical values here are those from the Erratum.
Dynamics of non-Markovian exclusion processes
Creators: name: Khoromskaia, Diana
name: Harris, Rosemary J.
name: Grosskinsky, Stefan
Publisher: name: arXiv
Year: 2014
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: Driven diffusive systems are often used as simple discrete models of collective transport phenomena in physics, biology or social sciences. Restricting attention to one-dimensional geometries, the asymmetric simple exclusion process (ASEP) plays a paradigmatic role to describe noise-activated driven motion of entities subject to an excluded volume interaction and many variants have been studied in recent years. While in the standard ASEP the noise is Poissonian and the process is therefore Markovian, in many applications the statistics of the activating noise has non-standard distribution with possible memory effects resulting from internal degrees of freedom or external sources. This leads to temporal correlations and can significantly affect the shape of the current-density relation as has been studied recently for a number of scenarios. In this paper we report a general framework to derive the fundamental diagram of ASEPs driven by non-Poissonian noise by using effectively only two simple quantities, viz., the mean residual lifetime of the jump distribution and a suitably defined temporal correlation length. We corroborate our results by detailed numerical studies for various noise statistics under periodic boundary conditions and discuss how our approach can be applied to more general driven diffusive systems.
description: 13 pages, 5 figures
Joint optimization of well placement and control for nonconventional well types
Creators: name: Humphries, Thomas D.
name: Haynes, Ronald D.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Optimization and Control (math.OC)
subject: FOS: Mathematics

description: Optimal well placement and optimal well control are two important areas of study in oilfield development. Although the two problems differ in several respects, both are important considerations in optimizing total oilfield production, and so recent work in the field has considered the problem of addressing both problems jointly. Two general approaches to addressing the joint problem are a simultaneous approach, where all parameters are optimized at the same time, or a sequential approach, where a distinction between placement and control parameters is maintained by separating the optimization problem into two (or more) stages, some of which consider only a subset of the total number of variables. This latter approach divides the problem into smaller ones which are easier to solve, but may not explore search space as fully as a simultaneous approach. In this paper we combine a stochastic global algorithm (Particle Swarm Optimization) and a local search (Mesh Adaptive Direct Search) to compare several simultaneous and sequential approaches to the joint placement and control problem. In particular, we study how increasing the complexity of well models (requiring more variables to describe the well's location and path) affects the respective performances of the two approaches. The results of several experiments with synthetic reservoir models suggest that the sequential approaches are better able to deal with increasingly complex well parameterizations than the simultaneous approaches.
Implementation of the essential use concept within REACH
Creators: name: Figuiere, Romain
name: Borchert, Flora
name: Wang, Zhanyun
name: Ågerstrand, Marlene
name: Cousins, Ian
Publisher: name: Zenodo
Year: 2023

description: Poster presented at the ZeroPM workshop: Achieving Zero Pollution of Persistent and Mobile Substances:
 Prevention through Chemical Alternatives, Policy Action and Market Transition
Simulation Studies for Electromagnetic Design of INO ICAL Magnet and its Response to Muons
Creators: name: Behera, S. P.
name: Bhatia, M. S.
name: Datar, V. M.
name: Mohanty, A. K.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Instrumentation and Detectors (physics.ins-det)
subject: FOS: Physical sciences

description: The iron calorimeter (ICAL) detector at the India-based Neutrino Observatory (INO) will be used to measure neutrino mass hierarchy. The magnet in the ICAL detector will be used to distinguish the {μ^-} and {μ^+} events induced by {ν_μ} and {\bar{ν_μ}}, respectively. Due to the importance of the magnet in ICAL, an electromagnetic simulation has been carried out to study the B-field distribution in iron using various designs. The simulation shows better uniformity in the portion of the iron layer between the coils, which is bounded by regions which have lesser field strength as we move to the periphery of the iron layer. The ICAL magnet was configured to have a tiling structure that gave the minimum reluctance path while keeping a reasonably uniform field pattern.This translates into less Ampere-turns needed for generation of the required magnetic field. At low Ampere-turns, a larger fractional area with \vert B \vert \ge 1 Tesla (T) can be obtained by using a soft magnetic material. A study of the effect of the magnetic field on muon trajectories has been carried out using GEANT4. For muons up to 20 GeV, the energy resolution improves as the magnetic field increases from 1.1T to 1.8T. The charge identification efficiency for muons was found to be more than 90\% except for large zenith angles.
description: 9 pages, 14 figures
Genome-wide Association Study Identifies Five Susceptibility Loci for Follicular Lymphoma outside the HLA Region
Creators: name: Birmann, Brenda M.
name: Berndt, Sonja I.
name: Yeager, Meredith
name: Salles, Gilles
name: Kricker, Anne
name: Morton, Lindsay M.
name: Slager, Susan L.
name: Becker, Nikolaus
name: Link, Brian K.
name: Hjalgrim, Henrik
name: Wang, Zhaoming
name: Vijai, Joseph
name: de Sanjose, Silvia
name: Melbye, Mads
name: Foo, Jia-Nee
name: Severi, Gianluca
name: Teras, Lauren R.
name: Bracci, Paige M.
name: Ghesquières, Hervé
name: Linet, Martha S.
name: Gu, Jian
name: Tinker, Lesley F.
name: Skibola, Christine F.
name: Wang, Sophia S.
name: Vermeulen, Roel C.H.
name: Lan, Qing
name: Vajdic, Claire M.
name: Smith, Alex
name: Lightfoot, Tracy
name: Conde, Lucia
name: de Bakker, Paul I.W.
name: Holly, Elizabeth A.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2014

description: Genome-wide association studies (GWASs) of follicular lymphoma (FL) have previously identified human leukocyte antigen (HLA) gene variants. To identify additional FL susceptibility loci, we conducted a large-scale two-stage GWAS in 4,523 case subjects and 13,344 control subjects of European ancestry. Five non-HLA loci were associated with FL risk: 11q23.3 (rs4938573, p = 5.79 × 10−20) near CXCR5; 11q24.3 (rs4937362, p = 6.76 × 10−11) near ETS1; 3q28 (rs6444305, p = 1.10 × 10−10) in LPP; 18q21.33 (rs17749561, p = 8.28 × 10−10) near BCL2; and 8q24.21 (rs13254990, p = 1.06 × 10−8) near PVT1. In an analysis of the HLA region, we identified four linked HLA-DRβ1 multiallelic amino acids at positions 11, 13, 28, and 30 that were associated with FL risk (pomnibus = 4.20 × 10−67 to 2.67 × 10−70). Additional independent signals included rs17203612 in HLA class II (odds ratio [ORper-allele] = 1.44; p = 4.59 × 10−16) and rs3130437 in HLA class I (ORper-allele = 1.23; p = 8.23 × 10−9). Our findings further expand the number of loci associated with FL and provide evidence that multiple common variants outside the HLA region make a significant contribution to FL risk.
Genome-wide Scan of 29,141 African Americans Finds No Evidence of Directional Selection since Admixture
Creators: name: Deming, Sandra L.
name: Casey, Graham
name: Murphy, Adam
name: Press, Michael F.
name: Bock, Cathryn H.
name: Aldrich, Melinda C.
name: McNeill, Lorna H.
name: Bernstein, Leslie
name: Tandon, Arti
name: Caporaso, Neil
name: De Jager, Phillip L.
name: Bhatia, Gaurav
name: Ambrosone, Christine B.
name: Larkin, Emma
name: Amos, Christopher
name: Blot, William J.
name: Ingles, Sue A.
name: Bandera, Elisa V.
name: Harris, Curtis C.
name: Isaacs, William
name: Rodriguez-Gil, Jorge L.
name: Millikan, Robert C.
name: Diver, W. Ryan
name: Patterson, Nick
name: Berndt, Sonja I.
name: Kittles, Rick A.
name: Gapstur, Susan M.
name: Neslund-Dudas, Christine
name: Henderson, Brian E.
name: Gillanders, Elizabeth M.
name: Nyante, Sarah
name: John, Esther M.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2014

description: The extent of recent selection in admixed populations is currently an unresolved question. We scanned the genomes of 29,141 African Americans and failed to find any genome-wide-significant deviations in local ancestry, indicating no evidence of selection influencing ancestry after admixture. A recent analysis of data from 1,890 African Americans reported that there was evidence of selection in African Americans after their ancestors left Africa, both before and after admixture. Selection after admixture was reported on the basis of deviations in local ancestry, and selection before admixture was reported on the basis of allele-frequency differences between African Americans and African populations. The local-ancestry deviations reported by the previous study did not replicate in our very large sample, and we show that such deviations were expected purely by chance, given the number of hypotheses tested. We further show that the previous study’s conclusion of selection in African Americans before admixture is also subject to doubt. This is because the FST statistics they used were inflated and because true signals of unusual allele-frequency differences between African Americans and African populations would be best explained by selection that occurred in Africa prior to migration to the Americas.
Partitioning Heritability of Regulatory and Cell-Type-Specific Variants across 11 Common Diseases
Creators: name: Daly, Mark
name: Sullivan, Patrick F.
name: Zang, Chongzhi
name: Collier, David A.
name: Huang, Hailiang
name: Stahl, Eli
name: Farh, Kai-How
name: Finucane, Hilary
name: Corvin, Aiden
name: Ripke, Stephan
name: Lee, S. Hong
name: Gusev, Alexander
name: Price, Alkes L.
name: Ripke, Stephan
name: Kähler, Anna K.
name: Neale, Benjamin M.
name: Bulik-Sullivan, Brendan
name: Walters, James T.R.
name: Wray, Naomi R.
name: Holmans, Peter A.
name: Xu, Han
name: Neale, Benjamin M.
name: Pers, Tune H.
name: Hultman, Christina M.
name: Trynka, Gosia
name: McCarroll, Steven A.
name: Purcell, Shaun M.
name: Raychaudhuri, Soumya
name: Lee, Phil
name: Pasaniuc, Bogdan
name: Bulik-Sullivan, Brendan
name: Vilhjálmsson, Bjarni J.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2014

description: Regulatory and coding variants are known to be enriched with associations identified by genome-wide association studies (GWASs) of complex disease, but their contributions to trait heritability are currently unknown. We applied variance-component methods to imputed genotype data for 11 common diseases to partition the heritability explained by genotyped SNPs (hg2) across functional categories (while accounting for shared variance due to linkage disequilibrium). Extensive simulations showed that in contrast to current estimates from GWAS summary statistics, the variance-component approach partitions heritability accurately under a wide range of complex-disease architectures. Across the 11 diseases DNaseI hypersensitivity sites (DHSs) from 217 cell types spanned 16% of imputed SNPs (and 24% of genotyped SNPs) but explained an average of 79% (SE = 8%) of hg2 from imputed SNPs (5.1× enrichment; p = 3.7 × 10−17) and 38% (SE = 4%) of hg2 from genotyped SNPs (1.6× enrichment, p = 1.0 × 10−4). Further enrichment was observed at enhancer DHSs and cell-type-specific DHSs. In contrast, coding variants, which span 1% of the genome, explained <10% of hg2 despite having the highest enrichment. We replicated these findings but found no significant contribution from rare coding variants in independent schizophrenia cohorts genotyped on GWAS and exome chips. Our results highlight the value of analyzing components of heritability to unravel the functional architecture of common disease.
An XMM-Newton View of the Radio Galaxy 3C 411
Creators: name: Bostrom, Allison
name: Reynolds, Christopher S.
name: Tombesi, Francesco
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: We present the first high signal-to-noise XMM-Newton observations of the broad-line radio galaxy 3C 411. After fitting various spectral models, an absorbed double power-law continuum and a blurred relativistic disk reflection model (kdblur) are found to be equally plausible descriptions of the data. While the softer power-law component ($Γ$=2.11) of the double power-law model is entirely consistent with that found in Seyfert galaxies (and hence likely originates from a disk corona), the additional power law component is very hard ($Γ$=1.05); amongst the AGN zoo, only flat-spectrum radio quasars have such hard spectra. Together with the very flat radio-spectrum displayed by this source, we suggest that it should instead be classified as a FSRQ. This leads to potential discrepancies regarding the jet inclination angle, with the radio morphology suggesting a large jet inclination but the FSRQ classification suggesting small inclinations. The kdblur model predicts an inner disk radius of at most 20 r$_g$ and relativistic reflection.
Classical and quantum spreading of a charge pulse
Creators: name: Gaury, Benoit
name: Weston, Joseph
name: Groth, Christoph
name: Waintal, Xavier
Publisher: name: arXiv
Year: 2014
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: With the technical progress of radio-frequency setups, high frequency quantum transport experiments have moved from theory to the lab. So far the standard theoretical approach used to treat such problems numerically--known as Keldysh or NEGF (Non Equilibrium Green's Functions) formalism--has not been very successful mainly because of a prohibitive computational cost. We propose a reformulation of the non-equilibrium Green's function technique in terms of the electronic wave functions of the system in an energy-time representation. The numerical algorithm we obtain scales now linearly with the simulated time and the volume of the system, and makes simulation of systems with 10^5 - 10^6 atoms/sites feasible. We illustrate our method with the propagation and spreading of a charge pulse in the quantum Hall regime. We identify a classical and a quantum regime for the spreading, depending on the number of particles contained in the pulse. This numerical experiment is the condensed matter analogue to the spreading of a Gaussian wavepacket discussed in quantum mechanics textbooks.
description: 4 pages, 5 figures; to be published in IEEE Xplore, in Proceedings to IEEE 17th International Workshop on Computational Electronics 2014, June 3 - 6, 2014, Paris, France. Correction of typographic mistakes and update of ref. 11
Stacking the Invisibles: A Guided Search for Low-Luminosity Milky Way Satellites
Creators: name: Sesar, B.
name: Banholzer, S. R.
name: Cohen, J. G.
name: Martin, N. F.
name: Grillmair, C. J.
name: Levitan, D.
name: Laher, R. R.
name: Ofek, E. O.
name: Surace, J. A.
name: Kulkarni, S. R.
name: Prince, T. A.
name: Rix, H. -W.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: Almost every known low-luminosity Milky Way dwarf spheroidal (dSph) satellite galaxy contains at least one RR Lyrae star. Assuming that a fraction of distant (60 < d_{helio} < 100 kpc) Galactic halo RR Lyrae stars are members of yet to be discovered low-luminosity dSph galaxies, we perform a {\em guided} search for these low-luminosity dSph galaxies. In order to detect the presence of dSph galaxies, we combine stars selected from more than 123 sightlines centered on RR Lyrae stars identified by the Palomar Transient Factory. We find that this method is sensitive enough to detect the presence of Segue 1-like galaxies (M_V= -1.5^{+0.6}_{-0.8}, r_h=30 pc) even if only ~20 sightlines were occupied by such dSph galaxies. Yet, when our method is applied to the SDSS DR10 imaging catalog, no signal is detected. An application of our method to sightlines occupied by pairs of close (<200 pc) horizontal branch stars, also did not yield a detection. Thus, we place upper limits on the number of low-luminosity dSph galaxies with half-light radii from 30 pc to 120 pc, and in the probed volume of the halo. Stronger constraints on the luminosity function may be obtained by applying our method to sightlines centered on RR Lyrae stars selected from the Pan-STARRS1 survey, and eventually, from LSST. In the Appendix, we present spectroscopic observations of an RRab star in the Boötes 3 dSph and a light curve of an RRab star near the Boötes 2 dSph.
description: emulateapj format, 10 pages, accepted to ApJ
Matrix Model Cosmology in Two Space-time Dimensions
Creators: name: Stern, A.
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: We examine solutions to the classical IKKT matrix model equations in three space-time dimensions. Closed, open and static two-dimensional universes naturally emerge from such models in the commutative limit. We show that tachyonic modes are a generic feature of these cosmological solutions.
description: 16 pages
Return of Genomic Results to Research Participants: The Floor, the Ceiling, and the Choices In Between
Creators: name: Amendola, Laura M.
name: Jarvik, Gail P.
name: Garrison, Nanibaa’ A.
name: Burke, Wylie
name: Berg, Jonathan S.
name: Connolly, John
name: Evans, James P.
name: Keating, Brendan
name: Rehm, Heidi L.
name: Gray, Stacy W.
name: Harley, John
name: Salama, Joseph
name: Van Driest, Sara L.
name: Clayton, Ellen W.
name: Sanderson, Saskia
name: Fullerton, Stephanie M.
name: Namjou, Bahram
name: Sharp, Richard R.
name: McCarty, Cathy
name: Chung, Wendy
name: Gallego, Carlos J.
name: Wolf, Wendy A.
name: Myers, Melanie
name: Lehmann, Lisa Soleymani
name: Williams, Marc S.
name: Wolf, Susan M.
name: Kullo, Iftikhar J.
name: Evans, Barbara J.
name: Prows, Cynthia A.
name: Brothers, Kyle
name: Holm, Ingrid A.
name: Vinks, Sander
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2014

description: As more research studies incorporate next-generation sequencing (including whole-genome or whole-exome sequencing), investigators and institutional review boards face difficult questions regarding which genomic results to return to research participants and how. An American College of Medical Genetics and Genomics 2013 policy paper suggesting that pathogenic mutations in 56 specified genes should be returned in the clinical setting has raised the question of whether comparable recommendations should be considered in research settings. The Clinical Sequencing Exploratory Research (CSER) Consortium and the Electronic Medical Records and Genomics (eMERGE) Network are multisite research programs that aim to develop practical strategies for addressing questions concerning the return of results in genomic research. CSER and eMERGE committees have identified areas of consensus regarding the return of genomic results to research participants. In most circumstances, if results meet an actionability threshold for return and the research participant has consented to return, genomic results, along with referral for appropriate clinical follow-up, should be offered to participants. However, participants have a right to decline the receipt of genomic results, even when doing so might be viewed as a threat to the participants’ health. Research investigators should be prepared to return research results and incidental findings discovered in the course of their research and meeting an actionability threshold, but they have no ethical obligation to actively search for such results. These positions are consistent with the recognition that clinical research is distinct from medical care in both its aims and its guiding moral principles.
ASHG/ACMG Report Points to Consider: Ethical, Legal and Psychosocial Implications of Genetic Testing in Children and Adolescents
Creators: name: Levy, Howard P.
name: Saal, Howard M.
name: Bombard, Yvonne
name: Berg, Jonathan S.
name: Berkman, Benjamin E.
name: Wilfond, Benjamin S.
name: McInerney, Joseph D.
name: Belmont, John W.
name: Botkin, Jeffrey R.
name: Spinner, Nancy B.
name: Holm, Ingrid A.
name: Ormond, Kelly E.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: In 1995, the American Society of Human Genetics (ASHG) and American College of Medical Genetics and Genomics (ACMG) jointly published a statement on genetic testing in children and adolescents. In the past 20 years, much has changed in the field of genetics, including the development of powerful new technologies, new data from genetic research on children and adolescents, and substantial clinical experience. This statement represents current opinion by the ASHG on the ethical, legal, and social issues concerning genetic testing in children. These recommendations are relevant to families, clinicians, and investigators. After a brief review of the 1995 statement and major changes in genetic technologies in recent years, this statement offers points to consider on a broad range of test technologies and their applications in clinical medicine and research. Recommendations are also made for record and communication issues in this domain and for professional education.
The role of social science in chemical substitution: The case of PFAS
Creators: name: Suffill, Ellise
name: Pahl, Sabine
name: White, Mat
Publisher: name: Zenodo
Year: 2023

description: Poster presented at the ZeroPM workshop: Achieving Zero Pollution of Persistent and Mobile Substances:
 Prevention through Chemical Alternatives, Policy Action and Market Transition
Ethiopian Socio Economic Survey - Agriculture Post Harvest Questionnaire
Creators: name: Central Statistical Agency
Publisher: name: National Academic Digital Repository of Ethiopia
Year: 2022

description: Datasets For Ethiopian Socio Economic Survey Agriculture(post harvest wave 4) Questionnaire Section 1: Household Roster https://nadre.ethernet.edu.et/record/20575/files/sect1_ph_w4.csv?download=1 Section 10: Harvest Labour https://nadre.ethernet.edu.et/record/20575/files/sect10_ph_w4.csv?download=1 Section 11: Crop Desposition https://nadre.ethernet.edu.et/record/20575/files/sect11_ph_w4.csv?download=1 Section 9: Crop Harvest by Field https://nadre.ethernet.edu.et/record/20575/files/sect9_ph_w4.csv?download=1
Fast-SL: An efficient algorithm to identify synthetic lethal reaction sets in metabolic networks
Creators: name: Pratapa, Aditya
name: Balachandran, Shankar
name: Raman, Karthik
Publisher: name: arXiv
Year: 2014
Subjects: subject: Molecular Networks (q-bio.MN)
subject: FOS: Biological sciences

description: Synthetic lethal reaction/gene-sets are sets of reactions/genes where only the simultaneous removal of all reactions/genes in the set abolishes growth of an organism. In silico, synthetic lethal sets can be identified by simulating the effect of removal of gene sets from the reconstructed genome-scale metabolic network of an organism. Flux balance analysis (FBA), based on linear programming, has emerged as a powerful tool for the in silico analyses of metabolic networks. To identify all possible synthetic lethal reactions combinations, an exhaustive sampling of all possible combinations is computationally expensive. We surmount the computational complexity of exhaustive search by iteratively restricting the sample space of reaction combinations for search, resulting in a substantial reduction in the running time. We here propose an algorithm, Fast-SL, which provides an efficient way to analyse metabolic networks for higher order lethal reaction sets. Fast-SL offers a substantial speed-up through a massive reduction in the search space for synthetic lethals; in the case of E. coli, Fast-SL reduces the search space for synthetic lethal triplets by over 4000-fold. Fast-SL also compares favourably with SL Finder, an algorithm for identifying synthetic lethal sets, by Suthers et al (2009), which involves the solution of a bi-level Mixed Integer Linear Programming problem. We have implemented the Fast-SL algorithm in MATLAB, building upon COBRA toolbox v2.0.
title: Il “De unitate intellectus” di Tommaso d’Aquino e la “doppia verità”
Creators: name: Petagine , Antonio
Publisher: name: Roma Tre-Press
Year: 2010

description: Il De unitate intellectus di Tommaso d'Aquino si presta molteplici letture. L'opuscolo tommasiano può esser visto come una piccola storia della psicologia peripatetica, come un puntuale esercizio di esegesi di un testo filosofico (il De anima di Aristotele), o come una piccola summa di filosofia dell'uomo. Il testo è tutte queste cose, ma per meglio dire è "anche" tutte queste cose, perché il De unitate, nella sua finalità più immediata, è uno scritto polemico, diretto contro presunti e famigerati "averroisti", ossia maestri cristiani che insegnavano presso la Facoltà delle Arti dell'Università di Parigi, i quali sostenevano la tesi di un unico intelletto per tutta la specie umana.

description: B@belonline vol. 9 Scienza e sapienza nel Medioevo. Agostinismo e aristotelismo a confronto
D4.2 Environmental Assessment Platform for Buildings.
Creators: name: Rembrandt Koppelaar
name: Calvo, Alex
Publisher: name: Zenodo
Year: 2023

description: D4.2 - The environmental performance and circularity assessment for the built environment requires a holistic and whole life analysis approach. This task will deliver the environmental assessment capability component of the SPHERE platform, studying the whole service life of the building. Within the scope of the Task, the three pillars of circular economy platform, (1) Use of BIM in the digital twin, (2) Life Cycle Management, and (3) Continuous Assessment and Monitoring for Circularity, will be studied by the help of the digital twin approach. Outputs received from task 2.5 (performance, environmental and economics on ILCD) will be introduced enabling the circular economy’s SHPERE platform in the context of a vertically integrated life cycle design. These outputs are aimed to align the further modules integration in line with SPHERE’s ILCD approach. The task will deliver the report on the digital twin circularity methodology of Sphere and the integrated and interoperable assessment service module of the SPHERE platform.
From Kinks to Compactons
Creators: name: Bazeia, D.
name: Losano, L.
name: Marques, M. A.
name: Menezes, R.
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: This work deals with the presence of localized structures in relativistic systems described by a single real scalar field in two-dimensional spacetime. We concentrate on kinks and compactons in models with standard kinematics, and we develop a procedure that help us to smoothly go from kinks to compactons in the suggested scenario. We also show how the procedure works in the braneworld scenario, for flat brane in the five-dimensional spacetime with a single extra dimension of infinite extent. The brane unveils a hybrid profile when the kink becomes a compacton, behaving as a thick or thin brane, depending on the extra dimension being inside or outside a compact space.
description: 7 pages, 7 figures; new version, to appear in PLB
"Ich weiss, was ich kann." : Expertenbeurteilung zur Förderung von Selbstwirksamkeitserwartungen bei Jugendlichen mit gesundheitlicher Problematik in der Berufsberatung der Invalidenversicherung
Creators: name: Bürgi, Cornelia
Publisher: name: Zürcher Hochschule für Angewandte Wissenschaften
Year: 2016
Subjects: 158: Angewandte Psychologie
305: Soziale Gruppen
331: Arbeitsökonomie

description: In dieser Arbeit wurde mittels Interviews mit ExpertInnen der Berufsberatung der Invalidenversicherung (BB-IV) Fragen zur Relevanz und persönlichem Einfluss auf eine Förderung von Selbstwirksamkeitserwartungen (SWE) bei Jugendlichen mit gesundheitlichen Einschränkungen geklärt. Es wurde auch analysiert, ob deren Beurteilung der beiden Faktoren in Zusammenhang mit ihrer selber eingeschätzten allgemeinen Selbstwirksamkeit steht. Es folgten zwei weitere Fragestellungen zur Wirksamkeit der einzelnen der vier Quellen von SWE nach Bandura (1997) sowie zu den bei der BB-IV angewendeten Interventionen zur Förderung von SWE. Die Interviews wurden mit sechs BerufsberaterInnen der Invalidenversicherung (IV) der SVA Aargau durchgeführt (davon vorab ein Pretestinterview). Diese ExpertInnen wurden über den Ablauf informiert, haben sich mit Hilfe einer Übersicht von Interventionsansätzen zur Förderung von SWE bei Jugendlichen in der BB-IV und zur sozialkognitiven Laufbahntheorie (Lent, Brown & Hackett, 1994; 2002) sowie dem Interviewleitfaden auf die Interviews vorbereitet. Die Mehrheit der ExpertInnen hat die Förderung von SWE bei Jugendlichen in der BB-IV als relevant beurteilt.
Gene Expression in Transformed Lymphocytes Reveals Variation in Endomembrane and HLA Pathways Modifying Cystic Fibrosis Pulmonary Phenotypes
Creators: name: Rommens, Johanna M.
name: Dang, Hong
name: Huang, Jinyan
name: Knowles, Michael R.
name: Sun, Wei
name: Zhou, Yi-Hui
name: Liang, Liming
name: Drumm, Mitchell L.
name: Gallins, Paul
name: Stonebraker, Jaclyn R.
name: Pace, Rhonda G.
name: Jones, Lisa C.
name: Guo, XueLiang
name: Wright, Fred A.
name: Strug, Lisa J.
name: Cutting, Garry R.
name: O’Neal, Wanda K.
name: Wolf, Whitney E.
name: Madar, Vered
name: Moffatt, Miriam F.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: Variation in cystic fibrosis (CF) phenotypes, including lung disease severity, age of onset of persistent Pseudomonas aeruginosa (P. aeruginosa) lung infection, and presence of meconium ileus (MI), has been partially explained by genome-wide association studies (GWASs). It is not expected that GWASs alone are sufficiently powered to uncover all heritable traits associated with CF phenotypic diversity. Therefore, we utilized gene expression association from lymphoblastoid cells lines from 754 p.Phe508del CF-affected homozygous individuals to identify genes and pathways. LPAR6, a G protein coupled receptor, associated with lung disease severity (false discovery rate q value = 0.0006). Additional pathway analyses, utilizing a stringent permutation-based approach, identified unique signals for all three phenotypes. Pathways associated with lung disease severity were annotated in three broad categories: (1) endomembrane function, containing p.Phe508del processing genes, providing evidence of the importance of p.Phe508del processing to explain lung phenotype variation; (2) HLA class I genes, extending previous GWAS findings in the HLA region; and (3) endoplasmic reticulum stress response genes. Expression pathways associated with lung disease were concordant for some endosome and HLA pathways, with pathways identified using GWAS associations from 1,978 CF-affected individuals. Pathways associated with age of onset of persistent P. aeruginosa infection were enriched for HLA class II genes, and those associated with MI were related to oxidative phosphorylation. Formal testing demonstrated that genes showing differential expression associated with lung disease severity were enriched for heritable genetic variation and expression quantitative traits. Gene expression provided a powerful tool to identify unrecognized heritable variation, complementing ongoing GWASs in this rare disease.
From Annotation to Modeling: Computational Horizons for Medieval Slavic Studies
Creators: name: Dombrowski, Quinn
Publisher: name: Stanford Digital Repository
Year: 2023
Subjects: subject: Handwritten text recognition
subject: Digitization
subject: Natural language processing
subject: Treebanks (Linguistics)
subject: Digital humanities

description: This paper is a write-up of a keynote from El’Manuscript 2021, reflecting on the ways in which the field of computationally-supported medieval Slavic studies has and has not changed since the mid-2000’s. Looking towards developments in the broader fields of digital humanities and natural-language processing, it explores the ways that recent improvements in the tools at our disposal for mass digitization of manuscripts and text analysis at scale open up possibilities for working with manuscripts that have received very little attention. For these advancements to be feasible, however, scholars will need to prepare and share their digitized texts and annotations in ways that are not currently the norm, though a number of projects provide exemplary models of how these new conventions could be put into practice.
Spectroscopy of southern Galactic disk planetary nebulae. Notes on chemical composition and emission-line stars
Creators: name: Górny, S. K.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: We present low resolution spectroscopic observations for a sample of 53 planetary nebulae (PNe) located in the southern sky between Vela and Norma constellations and pertaining to the Galactic disk with expected Galactocentric distance range of 5 to 10 kpc. We derive nebular chemical composition and plasma parameters with the classical empirical method. For most of the observed objects, this has been done for the first time. The distributions of the chemical abundances of the observed disk sample are generally indistinguishable from Galactic bulge and inner-disk PNe populations. The exceptions are possible differences in the He/H distribution, as compared to bulge PNe and Ne/Ar, compared to inner-disk PNe sample. The derived O/H ratios for the observed disk PNe fit to the concept of flattening of the chemical gradient in the inner parts of the Milky Way. We use the spectra to search for emission-line central stars in the observed sample. We found 6 new emission-line central stars comprising examples of all known types: WEL, VL and [WR]. We confirm that these types represent three evolutionary unconnected forms of enhanced mass-loss in the central stars of PNe. We note on the problem of high ionisation PNe with nebular CIV emission that can mimic the presence of WEL central stars in 1D spectra.
description: 35 pages, 19 figures, 4 tables (Note: corrected error in measured flux of [O II] 7325 lines in Table B.1)
Leveraging Multi-ethnic Evidence for Mapping Complex Traits in Minority Populations: An Empirical Bayes Approach
Creators: name: Kooperberg, Charles
name: Li, Yun
name: Coram, Marc A.
name: Reiner, Alex P.
name: Duan, Qing
name: Chan, Kei Hang K.
name: Tang, Hua
name: Candille, Sophie I.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: Elucidating the genetic basis of complex traits and diseases in non-European populations is particularly challenging because US minority populations have been under-represented in genetic association studies. We developed an empirical Bayes approach named XPEB (cross-population empirical Bayes), designed to improve the power for mapping complex-trait-associated loci in a minority population by exploiting information from genome-wide association studies (GWASs) from another ethnic population. Taking as input summary statistics from two GWASs—a target GWAS from an ethnic minority population of primary interest and an auxiliary base GWAS (such as a larger GWAS in Europeans)—our XPEB approach reprioritizes SNPs in the target population to compute local false-discovery rates. We demonstrated, through simulations, that whenever the base GWAS harbors relevant information, XPEB gains efficiency. Moreover, XPEB has the ability to discard irrelevant auxiliary information, providing a safeguard against inflated false-discovery rates due to genetic heterogeneity between populations. Applied to a blood-lipids study in African Americans, XPEB more than quadrupled the discoveries from the conventional approach, which used a target GWAS alone, bringing the number of significant loci from 14 to 65. Thus, XPEB offers a flexible framework for mapping complex traits in minority populations.
Meta-analysis for Discovering Rare-Variant Associations: Statistical Methods and Software Programs
Creators: name: Lin, Dan-Yu
name: Tang, Zheng-Zheng
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: There is heightened interest in using next-generation sequencing technologies to identify rare variants that influence complex human diseases and traits. Meta-analysis is essential to this endeavor because large sample sizes are required for detecting associations with rare variants. In this article, we provide a comprehensive overview of statistical methods for meta-analysis of sequencing studies for discovering rare-variant associations. Specifically, we discuss the calculation of relevant summary statistics from participating studies, the construction of gene-level association tests, the choice of transformation for quantitative traits, the use of fixed-effects versus random-effects models, and the removal of shadow association signals through conditional analysis. We also show that meta-analysis based on properly calculated summary statistics is as powerful as joint analysis of individual-participant data. In addition, we demonstrate the performance of different meta-analysis methods by using both simulated and empirical data. We then compare four major software packages for meta-analysis of rare-variant associations—MASS, RAREMETAL, MetaSKAT, and seqMeta—in terms of the underlying statistical methodology, analysis pipeline, and software interface. Finally, we present PreMeta, a software interface that integrates the four meta-analysis packages and allows a consortium to combine otherwise incompatible summary statistics.
Integrability vs exact solvability in the quantum Rabi and Dicke models
Creators: name: Batchelor, Murray T.
name: Zhou, Huan-Qiang
Publisher: name: arXiv
Year: 2014
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: The Rabi model describes the simplest interaction between light and matter via a two-level quantum system interacting with a bosonic field. We demonstrate that the fully quantised version of the Rabi model is integrable in the Yang-Baxter sense at two parameter values. The model is argued to be not Yang-Baxter integrable in general. This is in contrast to the claim that the quantum Rabi model is integrable based on a phenomenological criterion of quantum integrability not presupposing the existence of a set of commuting operators. Similar Yang-Baxter integrable points are identified for the generalised Rabi model and the fully quantised Dicke model. The integrable points have particular implications for the level statistics of the Dicke model.
description: 5 pages, 1 figure, some points clarified, unified description of the Rabi and Dicke models, additional and updated references
Meta-analysis of Correlated Traits via Summary Statistics from GWASs with an Application in Hypertension
Creators: name: Liang, Jingjing
name: McKnight, Barbara
name: Rotimi, Charles
name: Nalls, Mike
name: Sun, Yan V.
name: Young, J. Hunter
name: Bottinger, Erwin
name: Liu, Kiang
name: Arnett, Donna K.
name: Zhu, Xiaofeng
name: Smith, Jennifer A.
name: Yanek, Lisa R.
name: Franceschini, Nora
name: Chakravati, Aravinda
name: Redline, Susan
name: Cooper, Richard S.
name: Edwards, Todd L.
name: Fox, Ervin
name: Tayo, Bamidele O.
name: Chen, Wei
name: Sale, Michele
name: Feng, Tao
name: Liu, Yongmei
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: Genome-wide association studies (GWASs) have identified many genetic variants underlying complex traits. Many detected genetic loci harbor variants that associate with multiple—even distinct—traits. Most current analysis approaches focus on single traits, even though the final results from multiple traits are evaluated together. Such approaches miss the opportunity to systemically integrate the phenome-wide data available for genetic association analysis. In this study, we propose a general approach that can integrate association evidence from summary statistics of multiple traits, either correlated, independent, continuous, or binary traits, which might come from the same or different studies. We allow for trait heterogeneity effects. Population structure and cryptic relatedness can also be controlled. Our simulations suggest that the proposed method has improved statistical power over single-trait analysis in most of the cases we studied. We applied our method to the Continental Origins and Genetic Epidemiology Network (COGENT) African ancestry samples for three blood pressure traits and identified four loci (CHIC2, HOXA-EVX1, IGFBP1/IGFBP3, and CDH17; p < 5.0 × 10−8) associated with hypertension-related traits that were missed by a single-trait analysis in the original report. Six additional loci with suggestive association evidence (p < 5.0 × 10−7) were also observed, including CACNA1D and WNT3. Our study strongly suggests that analyzing multiple phenotypes can improve statistical power and that such analysis can be executed with the summary statistics from GWASs. Our method also provides a way to study a cross phenotype (CP) association by using summary statistics from GWASs of multiple phenotypes.
D4.3 Documentation of human thermal model, including end-user instructions.
Creators: name: Porkka, Janne
name: Piira, Kalevi
name: Nykänen, Esa
Publisher: name: Zenodo
Year: 2023

description: This deliverable introduces a new concept called Human Thermal Model (HTM) providing personalised indoor conditions suitable for various users. First, the theoretical background for HTM is explained. Then, we give a technical description on monitoring and controlling thermal conditions based on user input. Third, a user story and an example are given to help designer on considering optimal thermal conditions for various users. Fourth, we tell about integration of HTM to the SPHERE digital Twin through user stories and this work will be further developed in WP5. Fifth, we go briefly through testing of the HTM performed under WP6 Demonstration. Finally, we conclude to an overview telling designer to take into account that different individuals operating the space may have even 6oC difference in preferred optimal temperature.
Multiple Hepatic Regulatory Variants at the GALNT2 GWAS Locus Associated with High-Density Lipoprotein Cholesterol
Creators: name: Collins, Francis S.
name: Mohlke, Karen L.
name: Civelek, Mete
name: Wu, Ying
name: Fogarty, Marie P.
name: Marvelle, Amanda F.
name: Vadlamudi, Swarooparani
name: Kangas, Antti J.
name: Jackson, Anne U.
name: Boehnke, Michael
name: Buchkovich, Martin L.
name: Roman, Tamara S.
name: Gonzalez, Arlene J.
name: Gaulton, Kyle J.
name: Huyghe, Jeroen R.
name: Laakso, Markku
name: Fuchsberger, Christian
name: Lusis, Aldons J.
name: Sethupathy, Praveen
name: Kuusisto, Johanna
name: Ala-Korpela, Mika
name: Soininen, Pasi
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: Genome-wide association studies (GWASs) have identified more than 150 loci associated with blood lipid and cholesterol levels; however, the functional and molecular mechanisms for many associations are unknown. We examined the functional regulatory effects of candidate variants at the GALNT2 locus associated with high-density lipoprotein cholesterol (HDL-C). Fine-mapping and conditional analyses in the METSIM study identified a single locus harboring 25 noncoding variants (r2 > 0.7 with the lead GWAS variants) strongly associated with total cholesterol in medium-sized HDL (e.g., rs17315646, p = 3.5 × 10−12). We used luciferase reporter assays in HepG2 cells to test all 25 variants for allelic differences in regulatory enhancer activity. rs2281721 showed allelic differences in transcriptional activity (75-fold [T] versus 27-fold [C] more than the empty-vector control), as did a separate 780-bp segment containing rs4846913, rs2144300, and rs6143660 (49-fold [AT– haplotype] versus 16-fold [CC+ haplotype] more). Using electrophoretic mobility shift assays, we observed differential CEBPB binding to rs4846913, and we confirmed this binding in a native chromatin context by performing chromatin-immunoprecipitation (ChIP) assays in HepG2 and Huh-7 cell lines of differing genotypes. Additionally, sequence reads in HepG2 DNase-I-hypersensitivity and CEBPB ChIP-seq signals spanning rs4846913 showed significant allelic imbalance. Allelic-expression-imbalance assays performed with RNA from primary human hepatocyte samples and expression-quantitative-trait-locus (eQTL) data in human subcutaneous adipose tissue samples confirmed that alleles associated with increased HDL-C are associated with a modest increase in GALNT2 expression. Together, these data suggest that at least rs4846913 and rs2281721 play key roles in influencing GALNT2 expression at this HDL-C locus.