cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Shared air: Examining the contribution of mold from home crawl spaces to home interiors
Creators: name: Stiegel, M.
name: Galeano, M.A. Overstreet
name: Miranda, Marie Lynn
name: Thomann, W.R.
Publisher: name: University of Notre Dame
Year: 2023

description: This project was designed to assess allergens and asthma triggers in the indoor homeenvironment. Because the Southeast has been the subject of relatively little research on indoor environmental health issues, despite having a climate very favorable to the growth andpersistence of molds, dust mites, and cockroaches, the project focused on six counties in NorthCarolina. It included field sampling in homes to measure levels of allergen and asthma triggers.The project then integrated the results of the sampling into a Geographic Information System(GIS) to develop models that associated risk factors with the presence of allergens and asthmatriggers in the home environment. Concurrently, CEHI worked with community partners,government agencies, and other interest groups to educate the public about homeenvironmental health risks and disseminate project findings. In order to help local communitiesstrengthen their own capacity to operate sustainable, preventive programs that addresshousing-based hazards, residents and community organizations and institutions needed goodinformation about the risks and contributing factors specific to their locale. The projectuncovered key insights regarding respiratory health threats in the home environment, which canin turn be used to tailor and prioritize intervention programs.
Practical considerations for ageing of drinking water membranes
Creators: name: Robinson, Shona Jacquelyn
Publisher: name: University of British Columbia
Year: 2018

description: This dissertation advances our understanding of practical considerations for ageing of membranes used in drinking water treatment. Fouling and cleaning of membranes are well understood, but knowledge of long-term changes (i.e. ageing) have not been fully explored. To date, changes in physical and chemical characteristics, and changes in membrane performance, have been attributed to ageing. The three major sections in this dissertation were structured around membrane performance. Firstly, the existing literature was comprehensively reviewed. Important membrane performance factors were identified via this review: resistance, fouling rate, cleaning rate, and susceptibility to breach. How chemical and physical characteristics impact these performance factors was also systematically assessed. Almost all of the reviewed research involved bench-scale ageing of membranes, with scant attention to full-scale ageing, and even less on how bench-scale ageing can be useful in understanding full-scale ageing. This recognition led to the two further research projects. Secondly, we investigated changes in performance factors and chemical characteristics for PVDF membranes aged in 8 full-scale water treatment plants (14 treatment trains ranging from new to 10 years of age). Membranes were harvested by plant operators regularly and analyzed in a standardized laboratory setting. Membranes exhibited stable behaviour until about 5 years of operation; after this time, performance factors and chemical characteristics began to change significantly. Clean membrane resistance and fouling rate increased for aged membranes. The mechanical properties of aged membranes deteriorated, suggesting that their susceptibility to breach was heightened. These performance changes correlated with the removal of hydrophilic additives from the membranes. The final research project sought to link performance changes observed at bench-scale with performance changes observed in the full-scale study. Two bench-scale ageing techniques were used to probe changes in performance and characteristics: soaking membranes in NaOCl cleaning agent, and cycling them with foulant and cleaning agent. The changes in membrane chemistry were similar for bench-scale and full-scale ageing, but performance differed. By comparing the two bench-scale techniques with the full-scale ageing findings, it was established that irreversible foulants are critical components of full-scale ageing, and the involvement of these can be approximated to some extent by cycling membranes.
Herschel PACS Spectroscopic Diagnostics of Local ULIRGs: Conditions and Kinematics in Mrk 231
Creators: name: Fischer, Jacqueline
name: Sturm, Eckhard
name: González-Alfonso, Eduardo
name: Graciá-Carpio, Javier
name: Hailey-Dunsheath, Steve
name: Poglitsch, Albrecht
name: Contursi, Alessandra
name: Lutz, Dieter
name: Genzel, Reinhard
name: Sternberg, Amiel
name: Verma, Aprajita
name: Tacconi, Linda
Publisher: name: arXiv
Year: 2010
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: In this first paper on the results of our Herschel PACS survey of local Ultraluminous Infrared Galaxies (ULIRGs), as part of our SHINING survey of local galaxies, we present far-infrared spectroscopy of Mrk 231, the most luminous of the local ULIRGs, and a type 1 broad absorption line AGN. For the first time in a ULIRG, all observed far-infrared fine-structure lines in the PACS range were detected and all were found to be deficient relative to the far infrared luminosity by 1 - 2 orders of magnitude compared with lower luminosity galaxies. The deficits are similar to those for the mid-infrared lines, with the most deficient lines showing high ionization potentials. Aged starbursts may account for part of the deficits, but partial covering of the highest excitation AGN powered regions may explain the remaining line deficits. A massive molecular outflow, discovered in OH and 18OH, showing outflow velocities out to at least 1400 km/sec, is a unique signature of the clearing out of the molecular disk that formed by dissipative collapse during the merger. The outflow is characterized by extremely high ratios of 18O / 16O suggestive of interstellar medium processing by advanced starbursts.
description: Accepted for publication in the Astronomy and Astrophysics Herschel Special Issue, 5 pages, 4 figures
Sensitivity Analysis for Unmeasured Confounding in Meta-Analyses
Creators: name: B. Mathur, Maya
name: J. VanderWeele, Tyler
Publisher: name: Taylor & Francis
Year: 2019
Subjects: subject: Medicine
subject: Biotechnology
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Science Policy
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Random-effects meta-analyses of observational studies can produce biased estimates if the synthesized studies are subject to unmeasured confounding. We propose sensitivity analyses quantifying the extent to which unmeasured confounding of specified magnitude could reduce to below a certain threshold the proportion of true effect sizes that are scientifically meaningful. We also develop converse methods to estimate the strength of confounding capable of reducing the proportion of scientifically meaningful true effects to below a chosen threshold. These methods apply when a “bias factor” is assumed to be normally distributed across studies or is assessed across a range of fixed values. Our estimators are derived using recently proposed sharp bounds on confounding bias within a single study that do not make assumptions regarding the unmeasured confounders themselves or the functional form of their relationships with the exposure and outcome of interest. We provide an R package, EValue, and a free website that compute point estimates and inference and produce plots for conducting such sensitivity analyses. These methods facilitate principled use of random-effects meta-analyses of observational studies to assess the strength of causal evidence for a hypothesis. Supplementary materials for this article are available online.
Variational Inference for Stochastic Block Models From Sampled Data
Creators: name: Tabouy, Timothée
name: Barbillon, Pierre
name: Chiquet, Julien
Publisher: name: Taylor & Francis
Year: 2019
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Biotechnology
subject: Evolutionary Biology
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Cancer
subject: 111714 Mental Health
subject: FOS: Health sciences
subject: Plant Biology

description: This article deals with nonobserved dyads during the sampling of a network and consecutive issues in the inference of the stochastic block model (SBM). We review sampling designs and recover missing at random (MAR) and not missing at random (NMAR) conditions for the SBM. We introduce variants of the variational EM algorithm for inferring the SBM under various sampling designs (MAR and NMAR) all available as an R package. Model selection criteria based on integrated classification likelihood are derived for selecting both the number of blocks and the sampling design. We investigate the accuracy and the range of applicability of these algorithms with simulations. We explore two real-world networks from ethnology (seed circulation network) and biology (protein–protein interaction network), where the interpretations considerably depend on the sampling designs considered. Supplementary materials for this article are available online.
Improved Time-Domain Accuracy Standards for Model Gravitational Waveforms
Creators: name: Lindblom, Lee
name: Baker, John G.
name: Owen, Benjamin J.
Publisher: name: arXiv
Year: 2010
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: Model gravitational waveforms must be accurate enough to be useful for detection of signals and measurement of their parameters, so appropriate accuracy standards are needed. Yet these standards should not be unnecessarily restrictive, making them impractical for the numerical and analytical modelers to meet. The work of Lindblom, Owen, and Brown [Phys. Rev. D 78, 124020 (2008)] is extended by deriving new waveform accuracy standards which are significantly less restrictive while still ensuring the quality needed for gravitational-wave data analysis. These new standards are formulated as bounds on certain norms of the time-domain waveform errors, which makes it possible to enforce them in situations where frequency-domain errors may be difficult or impossible to estimate reliably. These standards are less restrictive by about a factor of 20 than the previously published time-domain standards for detection, and up to a factor of 60 for measurement. These new standards should therefore be much easier to use effectively.
description: 10 pages, 5 figures
Ball Covariance: A Generic Measure of Dependence in Banach Space
Creators: name: Pan, Wenliang
name: Wang, Xueqin
name: Zhang, Heping
name: Zhu, Hongtu
name: Zhu, Jin
Publisher: name: Taylor & Francis
Year: 2019
Subjects: subject: Biochemistry
subject: Space Science
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics

description: Technological advances in science and engineering have led to the routine collection of large and complex data objects, where the dependence structure among those objects is often of great interest. Those complex objects (e.g, different brain subcortical structures) often reside in some Banach spaces, and hence their relationship cannot be well characterized by most of the existing measures of dependence such as correlation coefficients developed in Hilbert spaces. To overcome the limitations of the existing measures, we propose Ball Covariance as a generic measure of dependence between two random objects in two possibly different Banach spaces. Our Ball Covariance possesses the following attractive properties: (i) It is nonparametric and model-free, which make the proposed measure robust to model mis-specification; (ii) It is nonnegative and equal to zero if and only if two random objects in two separable Banach spaces are independent; (iii) Empirical Ball Covariance is easy to compute and can be used as a test statistic of independence. We present both theoretical and numerical results to reveal the potential power of the Ball Covariance in detecting dependence. Also importantly, we analyze two real datasets to demonstrate the usefulness of Ball Covariance in the complex dependence detection.
Real-Time Dynamics and Conical Intersections
Creators: name: Casida, Mark Earl
name: Natarajan, Bhaarathi
name: Deutsch, Thierry
Publisher: name: arXiv
Year: 2011
Subjects: subject: Other Condensed Matter (cond-mat.other)
subject: FOS: Physical sciences

description: This book chapter is a general introduction to photo-dynamics. An outlined structure to the theoretical studies on classical/quantum/mixed dynamics were described from the literature point of view. Such methods get constrained for the practical applications due to parametrizations/computational cost. As an alternate TDDFT-based dynamics studies are promising. we have shown that the TDDFT calculations could be as accurate as high quality monte-carlo calculations and the reliability of the TDDFT calculations for locating the conical intersection through the simple ring-opening reaction of oxirane. Pros and cons of TDDFT for photo-dynamics calculations have been presented for the development of this fast evolving field.
description: 26 pages, 7 figures, book chapter for the second edition of the book entitled " Time-Dependent-Density-Functional-Theory" by TDDFT experts from Springer
From Fixed-X to Random-X Regression: Bias-Variance Decompositions, Covariance Penalties, and Prediction Error Estimation
Creators: name: Rosset, Saharon
name: Tibshirani, Ryan J.
Publisher: name: Taylor & Francis
Year: 2019
Subjects: subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Cancer
subject: Plant Biology

description: In statistical prediction, classical approaches for model selection and model evaluation based on covariance penalties are still widely used. Most of the literature on this topic is based on what we call the “Fixed-X” assumption, where covariate values are assumed to be nonrandom. By contrast, it is often more reasonable to take a “Random-X” view, where the covariate values are independently drawn for both training and prediction. To study the applicability of covariance penalties in this setting, we propose a decomposition of Random-X prediction error in which the randomness in the covariates contributes to both the bias and variance components. This decomposition is general, but we concentrate on the fundamental case of ordinary least-squares (OLS) regression. We prove that in this setting the move from Fixed-X to Random-X prediction results in an increase in both bias and variance. When the covariates are normally distributed and the linear model is unbiased, all terms in this decomposition are explicitly computable, which yields an extension of Mallows’ Cp that we call RCp. RCp also holds asymptotically for certain classes of nonnormal covariates. When the noise variance is unknown, plugging in the usual unbiased estimate leads to an approach that we call RCp ^, which is closely related to Sp, and generalized cross-validation (GCV). For excess bias, we propose an estimate based on the “shortcut-formula” for ordinary cross-validation (OCV), resulting in an approach we call RCp+. Theoretical arguments and numerical simulations suggest that RCp+ is typically superior to OCV, though the difference is small. We further examine the Random-X error of other popular estimators. The surprising result we get for ridge regression is that, in the heavily regularized regime, Random-X variance is smaller than Fixed-X variance, which can lead to smaller overall Random-X error. Supplementary materials for this article are available online.
Debiased Inference on Treatment Effect in a High Dimensional Model
Creators: name: Wang, Jingshen
name: He, Xuming
name: Xu, Gongjun
Publisher: name: Taylor & Francis
Year: 2019
Subjects: subject: Ecology
subject: FOS: Biological sciences
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Cancer
subject: Inorganic Chemistry
subject: FOS: Chemical sciences

description: This article concerns the potential bias in statistical inference on treatment effects when a large number of covariates are present in a linear or partially linear model. While the estimation bias in an under-fitted model is well understood, we address a lesser known bias that arises from an over-fitted model. The over-fitting bias can be eliminated through data splitting at the cost of statistical efficiency, and we show that smoothing over random data splits can be pursued to mitigate the efficiency loss. We also discuss some of the existing methods for debiased inference and provide insights into their intrinsic bias-variance trade-off, which leads to an improvement in bias controls. Under appropriate conditions we show that the proposed estimators for the treatment effects are asymptotically normal and their variances can be well estimated. We discuss the pros and cons of various methods both theoretically and empirically, and show that the proposed methods are valuable options in post-selection inference.
Investigating the Effects of Juvenile Stress on Contextual Fear and Unconditioned Anxiety Related Behavior in Mice Selectively Bred for High and Low Alcohol Preference
Creators: name: Mukadam, Arbaaz Azim
Publisher: name: Purdue University Graduate School
Year: 2023
Subjects: classificationCode: 520201
subject: Behavioural genetics
classificationCode: 520202
subject: Behavioural neuroscience

description: Juvenile stress (JS) is a known risk factor for the development of alcohol use disorder (AUD) and post-traumatic stress disorder (PTSD), both of which frequently occur together, suggesting common genetic influences on vulnerability toward these disorders. The present study investigated the impact of JS on contextual fear learning and extinction, as well as corticosterone (CORT) responses before and after JS, before and after contextual fear conditioning (CFC), and after fear extinction in male and female high-alcohol-preferring (HAP2) and low-alcohol-preferring (LAP2) mice. We also measured unconditioned anxiety-related behavior in the light-dark-transition test. No line differences were seen in fear acquisition, however, HAP2 mice showed faster fear extinction compared to LAP2 mice. No effects of JS were seen in HAP2 mice, whereas in LAP2 mice, JS reduced fear acquisition in males and facilitated fear extinction in females. Females showed greater fear relative to males, regardless of subgroup. Anxiety-related behavior, assessed by the light-dark transition test, did not correspond with fear-related behavior, as LAP2 females demonstrated more anxiolytic-like responses than LAP2 males, while HAP2 males demonstrated more anxiolytic-like responses than LAP2 males. There were no line differences in CORT during the juvenile stage; however, adult LAP2 mice showed greater CORT levels than HAP2 mice at baseline and after CFC and extinction testing. These findings provide new information regarding fear learning and extinction in these unique mouse lines that model mechanisms theorized to contribute to co-morbid AUD and PTSD.
Two Wide Planetary-Mass Companions to Solar-Type Stars in Upper Scorpius
Creators: name: Ireland, Michael J.
name: Kraus, Adam L.
name: Martinache, Frantz
name: Law, Nicholas M.
name: Hillenbrand, Lynne A.
Publisher: name: arXiv
Year: 2010
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: At wide separations, planetary-mass and brown dwarf companions to solar type stars occupy a curious region of parameters space not obviously linked to binary star formation or solar-system scale planet formation. These companions provide insight into the extreme case of companion formation (either binary or planetary), and due to their relative ease of observation when compared to close companions, they offer a useful template for our expectations of more typical planets. We present the results from an adaptive optics imaging survey for wide (50-500 AU) companions to solar type stars in Upper Scorpius. We report one new discovery of a ~14 M_J companion around GSC 06214-00210, and confirm that the candidate planetary mass companion 1RXS J160929.1-210524 detected by Lafreniere et al (2008) is in fact co-moving with its primary star. In our survey, these two detections correspond to ~4% of solar type stars having companions in the 6-20 M_J mass and 200-500 AU separation range. This figure is higher than would be expected if brown dwarfs and planetary mass companions were drawn from an extrapolation of the binary mass function. Finally, we discuss implications for the formation of these objects.
description: 11 Pages, 7 Figures, Accepted for ApJ
ПОВЫШЕНИЕ ЭКСПЛУАТАЦИОННЫХ ПОКАЗАТЕЛЕЙ ЛЕГКОВЫХ АВТОМОБИЛЕЙ НА СИНТЕТИЧЕСКОМ ГАЗОВОМ ТОПЛИВЕ
Creators: name: Бутаев, Азизжон
Publisher: name: Zenodo
Year: 2024

description: В данной тезисе сформированы задачи мониторинга особенностей повышения эксплуатационных показателей автомобилей, работающих на синтетическом газовом топливе.
RANK: Large-Scale Inference With Graphical Nonlinear Knockoffs
Creators: name: Fan, Yingying
name: Demirkaya, Emre
name: Li, Gaorong
name: Lv, Jinchi
Publisher: name: Taylor & Francis
Year: 2019
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: 69999 Biological Sciences not elsewhere classified
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics

description: Power and reproducibility are key to enabling refined scientific discoveries in contemporary big data applications with general high-dimensional nonlinear models. In this article, we provide theoretical foundations on the power and robustness for the model-X knockoffs procedure introduced recently in Candès, Fan, Janson and Lv in high-dimensional setting when the covariate distribution is characterized by Gaussian graphical model. We establish that under mild regularity conditions, the power of the oracle knockoffs procedure with known covariate distribution in high-dimensional linear models is asymptotically one as sample size goes to infinity. When moving away from the ideal case, we suggest the modified model-X knockoffs method called graphical nonlinear knockoffs (RANK) to accommodate the unknown covariate distribution. We provide theoretical justifications on the robustness of our modified procedure by showing that the false discovery rate (FDR) is asymptotically controlled at the target level and the power is asymptotically one with the estimated covariate distribution. To the best of our knowledge, this is the first formal theoretical result on the power for the knockoffs procedure. Simulation results demonstrate that compared to existing approaches, our method performs competitively in both FDR control and power. A real dataset is analyzed to further assess the performance of the suggested knockoffs procedure. Supplementary materials for this article are available online.
Dilute Fermi and Bose Gases
Creators: name: Sachdev, Subir
Publisher: name: arXiv
Year: 2011
Subjects: subject: Quantum Gases (cond-mat.quant-gas)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: I give a unified perspective on the properties of a variety of quantum liquids using the theory of quantum phase transitions. A central role is played by a zero density quantum critical point which is argued to control the properties of the dilute gas. An exact renormalization group analysis of such quantum critical points leads to a computation of the universal properties of the dilute Bose gas and the spinful Fermi gas near a Feshbach resonance.
description: 28 pages, 8 figures; adapted from Chapter 16 of Quantum Phase Transitions, Second Edition (see http://sachdev.physics.harvard.edu/qptweb/toc.html); contribution to Lecture Notes in Physics, "BCS-BEC crossover and the Unitary Fermi Gas" edited by W. Zwerger
Variational Inference for Stochastic Block Models from Sampled Data
Creators: name: Tabouy, Timothée
name: Barbillon, Pierre
name: Chiquet, Julien
Publisher: name: Taylor & Francis
Year: 2019
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Biotechnology
subject: Evolutionary Biology
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Plant Biology

description: This paper deals with non-observed dyads during the sampling of a network and consecutive issues in the inference of the Stochastic Block Model (SBM). We review sampling designs and recover Missing At Random (MAR) and Not Missing At Random (NMAR) conditions for the SBM. We introduce variants of the variational EM algorithm for inferring the SBM under various sampling designs (MAR and NMAR) all available as an R package. Model selection criteria based on Integrated Classification Likelihood are derived for selecting both the number of blocks and the sampling design. We investigate the accuracy and the range of applicability of these algorithms with simulations. We explore two real-world networks from ethnology (seed circulation network) and biology (protein-protein interaction network), where the interpretations considerably depends on the sampling designs considered.
Pattern avoidance in partial permutations
Creators: name: Claesson, Anders
name: Jelinek, Vit
name: Jelinkova, Eva
name: Kitaev, Sergey
Publisher: name: arXiv
Year: 2010
Subjects: subject: Combinatorics (math.CO)
subject: FOS: Mathematics
subject: 05A15

description: Motivated by the concept of partial words, we introduce an analogous concept of partial permutations. A partial permutation of length n with k holes is a sequence of symbols $π= π_1π_2 ... π_n$ in which each of the symbols from the set {1,2,...,n-k} appears exactly once, while the remaining k symbols of $π$ are "holes". We introduce pattern-avoidance in partial permutations and prove that most of the previous results on Wilf equivalence of permutation patterns can be extended to partial permutations with an arbitrary number of holes. We also show that Baxter permutations of a given length k correspond to a Wilf-type equivalence class with respect to partial permutations with (k-2) holes. Lastly, we enumerate the partial permutations of length n with k holes avoiding a given pattern of length at most four, for each n >= k >= 1.
description: 34 pages, 17 figures. Submitted to the Electronic Journal of Combinatorics. An extended abstract will appear in proceedings of FPSAC 2010.
Transit timing variations in the HAT-P-13 planetary system
Creators: name: Pál, András
name: Sárneczky, Krisztián
name: Szabó, Gyula M.
name: Szing, Attila
name: Kiss, László L.
name: Mezö, György
name: Regály, Zsolt
Publisher: name: arXiv
Year: 2011
Subjects: subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: FOS: Physical sciences

description: In this Letter we present observations of recent HAT-P-13b transits. The combined analysis of published and newly obtained transit epochs shows evidence for significant transit timing variations since the last publicly available ephemerides. Variation of transit timings result in a sudden switch of transit times. The detected full range of TTV spans ~0.015 days, which is significantly more than the known TTV events exhibited by hot Jupiters. If we have detected a periodic process, its period should be at least ~3 years because there are no signs of variations in the previous observations. This argument makes unlikely that the measured TTV is due to perturbations by HAT-P-13c.
description: 5 pages, 2 figures, accepted for publication in MNRAS Letters (this version contains an additional measurement that has been acquired since the submission and acceptance of the paper, slightly polished since version 1). Measurements confirming our results are welcomed
Molecular interpretation of genome-wide association studies using multiomics analysis
Creators: name: Farhadi Hassan Kiadeh, Farnush
Publisher: name: University of British Columbia
Year: 2018

description: Genome-wide association studies have found thousands of single-nucleotide polymorphisms associated with various human traits. Recently, a powerful statistical approach called MetaXcan has been proposed for interpreting genome-wide associations at the gene level. We extended MetaXcan to a multiomics application, using a brain cortex reference dataset that includes gene expression, DNA methylation, and histone acetylation data from approximately 400 individuals. Our approach, Multi-MetaXcan, consists of three steps. In the first step, we use regularized regression to build models that predict gene expression and variation in epigenomic modifications from single-nucleotide polymorphisms. We call these models genotype-based imputation models. In the second step, we apply these models to map genome-wide associations to gene-level and epigenomic-level associations. Finally, in the third step, our model summarizes all molecular-level associations at the gene level by building epigenome-based imputation models that predict gene expression levels from nearby epigenomic marks like CpG sites and transcriptionally active regions. In summary, Multi-MetaXcan identifies trait-associated genes whose expression levels are impacted by single-nucleotide polymorphisms and their influence on intermediate molecular traits such as DNA methylation and histone acetylation. We applied Multi-MetaXcan to a major depressive disorder genome-wide association study. As the result, we discovered 12 genes, 25 transcriptionally active regions, and 163 CpG sites associated with major depressive disorder corresponding to 74 genes in total. 26 of these genes fall within or close to previously identified major depressive disorder-associated genomic regions. Importantly, the inclusion of epigenomic data resulted in an additional 62 genes that were not identified by gene expression imputation model alone.
Single-charge rotating black holes in four-dimensional gauged supergravity
Creators: name: Chow, David D. K.
Publisher: name: arXiv
Year: 2010
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: We consider four-dimensional U(1)^4 gauged supergravity, and obtain asymptotically AdS_4, non-extremal, charged, rotating black holes with one non-zero U(1) charge. The thermodynamic quantities are computed. We obtain a generalization that includes a NUT parameter. The general solution has a discrete symmetry involving inversion of the rotation parameter, and has a string frame metric that admits a rank-2 Killing-Stackel tensor.
description: 9 pages
Spot-Based Generations for Meta-Fibonacci Sequences
Creators: name: Dalton, Barnaby
name: Rahman, Mustazee
name: Tanny, Stephen
Publisher: name: arXiv
Year: 2011
Subjects: subject: Combinatorics (math.CO)
subject: Number Theory (math.NT)
subject: FOS: Mathematics
subject: 11B37 (Primary) 39A99 (Secondary)

description: For many meta-Fibonacci sequences it is possible to identify a partition of the sequence into successive intervals (sometimes called blocks) with the property that the sequence behaves "similarly" in each block. This partition provides insights into the sequence properties. To date, for any given sequence, only ad hoc methods have been available to identify this partition. We apply a new concept - the spot-based generation sequence - to derive a general methodology for identifying this partition for a large class of meta-Fibonacci sequences. This class includes the Conolly and Conway sequences and many of their well-behaved variants, and even some highly chaotic sequences, such as Hofstadter's famous Q-sequence.
description: 11 pages, 4 figures
Closed timelike curves via post-selection: theory and experimental demonstration
Creators: name: Lloyd, Seth
name: Maccone, Lorenzo
name: Garcia-Patron, Raul
name: Giovannetti, Vittorio
name: Shikano, Yutaka
name: Pirandola, Stefano
name: Rozema, Lee A.
name: Darabi, Ardavan
name: Soudagar, Yasaman
name: Shalm, Lynden K.
name: Steinberg, Aephraim M.
Publisher: name: arXiv
Year: 2010
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Closed timelike curves (CTCs) are trajectories in spacetime that effectively travel backwards in time: a test particle following a CTC can in principle interact with its former self in the past. CTCs appear in many solutions of Einstein's field equations and any future quantum version of general relativity will have to reconcile them with the requirements of quantum mechanics and of quantum field theory. A widely accepted quantum theory of CTCs was proposed by Deutsch. Here we explore an alternative quantum formulation of CTCs and show that it is physically inequivalent to Deutsch's. Because it is based on combining quantum teleportation with post-selection, the predictions/retrodictions of our theory are experimentally testable: we report the results of an experiment demonstrating our theory's resolution of the well-known `grandfather paradox.
description: 5 pages, 4 figures
Availability of the Disgorgement of Profits Under the CISG
Creators: name: Baş-Süzel, Ece
name: Kurtulan-Güner, Gökçe
Publisher: name: Nordic Journal of Commercial Law
Year: 2020

description: The United Nations Convention on Contracts for the International Sale of Goods (CISG or the Convention) does not expressly state whether the remedy of disgorgement of profits can be awarded in cases of breach of contract. In this article, we argue that the disgorgement of profits is available both as a method for the calculation of damages under Art. 74 and as a remedy on its own when the remedy of compensatory damages fails to fulfill its functions. Therefore, we argue that the disgorgement of profits is in line with Art. 7(1) and Art. 7(2) of the Convention. However, the availability of the disgorgement of profits shall not be understood as undermining the primacy of compensatory damages and should be accepted only in exceptional cases, namely where second sales of non-substitutable goods and breaches of certain contractual stipulations make the calculation of loss impossible or impracticable.
description: Nordic Journal of Commercial Law, No. 2 (2020)
Spontaneous Lorentz Violation, Nambu-Goldstone Modes, and Massive Modes
Creators: name: Bluhm, Robert
Publisher: name: arXiv
Year: 2010
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: In any theory with spontaneous symmetry breaking, it is important to account for the massless Nambu-Goldstone and massive Higgs modes. In this short review, the fate of these modes is examined for the case of a bumblebee model, in which Lorentz symmetry is spontaneously broken.
description: 5 pages. Presented at the Fifth Meeting on CPT and Lorentz Symmetry, Bloomington, Indiana, June 28-July 2, 2010
From Fixed-X to Random-X Regression: Bias-Variance Decompositions, Covariance Penalties, and Prediction Error Estimation
Creators: name: Rosset, Saharon
name: J. Tibshirani, Ryan
Publisher: name: Taylor & Francis
Year: 2019
Subjects: subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Cancer
subject: Plant Biology

description: In statistical prediction, classical approaches for model selection and model evaluation based on covariance penalties are still widely used. Most of the literature on this topic is based on what we call the “Fixed-X” assumption, where covariate values are assumed to be nonrandom. By contrast, it is often more reasonable to take a “Random-X” view, where the covariate values are independently drawn for both training and prediction. To study the applicability of covariance penalties in this setting, we propose a decomposition of Random-X prediction error in which the randomness in the covariates contributes to both the bias and variance components. This decomposition is general, but we concentrate on the fundamental case of ordinary least-squares (OLS) regression. We prove that in this setting the move from Fixed-X to Random-X prediction results in an increase in both bias and variance. When the covariates are normally distributed and the linear model is unbiased, all terms in this decomposition are explicitly computable, which yields an extension of Mallows’ Cp that we call RCp. RCp also holds asymptotically for certain classes of nonnormal covariates. When the noise variance is unknown, plugging in the usual unbiased estimate leads to an approach that we call RCp ^, which is closely related to Sp, and generalized cross-validation (GCV). For excess bias, we propose an estimate based on the “shortcut-formula” for ordinary cross-validation (OCV), resulting in an approach we call RCp+. Theoretical arguments and numerical simulations suggest that RCp+ is typically superior to OCV, though the difference is small. We further examine the Random-X error of other popular estimators. The surprising result we get for ridge regression is that, in the heavily regularized regime, Random-X variance is smaller than Fixed-X variance, which can lead to smaller overall Random-X error. Supplementary materials for this article are available online.
32036: Oxford at Home and Race Roundtable
Creators: name: Project, Lockdown2020 and Beyond
Publisher: name: University of Oxford
Year: 2023
Subjects: classificationCode: 479999
subject: Other language, communication and culture not elsewhere classified

description: I've had an interesting time doing my Oxford degree at home, trying to recreate Oxford conditions in my household have been hilarious, my family just won't have it! The privileges of silence, the need for space, leaving books everywhere, it just doesn't work! Alongside managing my work I've also done this Race Roundtable (photo and link attached). It's been a chilling few weeks since the brutal murder of George Floyd, trying to manage my degree while being involved in anti-racist conversations and work have been exhausting but I do think we have some hope! And I really do think this pandemic will change our world in more ways than we think.Link: https://youtu.be/lxmRXH2cQj8 on Pembroke JCR Youtube
RANK: Large-Scale Inference with Graphical Nonlinear Knockoffs
Creators: name: Fan, Yingying
name: Demirkaya, Emre
name: Li, Gaorong
name: Lv, Jinchi
Publisher: name: Taylor & Francis
Year: 2018
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: 69999 Biological Sciences not elsewhere classified
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics

description: Power and reproducibility are key to enabling refined scientific discoveries in contemporary big data applications with general high-dimensional nonlinear models. In this paper, we provide theoretical foundations on the power and robustness for the model-X knockoffs procedure introduced recently in Candès, Fan, Janson and Lv (2018) in high-dimensional setting when the covariate distribution is characterized by Gaussian graphical model. We establish that under mild regularity conditions, the power of the oracle knockoffs procedure with known covariate distribution in high-dimensional linear models is asymptotically one as sample size goes to infinity. When moving away from the ideal case, we suggest the modified model-X knockoffs method called graphical nonlinear knockoffs (RANK) to accommodate the unknown covariate distribution. We provide theoretical justifications on the robustness of our modified procedure by showing that the false discovery rate (FDR) is asymptotically controlled at the target level and the power is asymptotically one with the estimated covariate distribution. To the best of our knowledge, this is the first formal theoretical result on the power for the knockoffs procedure. Simulation results demonstrate that compared to existing approaches, our method performs competitively in both FDR control and power. A real data set is analyzed to further assess the performance of the suggested knockoffs procedure.
Structural and biochemical insights into the cardiac and skeletal muscle excitation-contraction coupling machinery
Creators: name: Wong King Yuen, Siobhan Meagan
Publisher: name: University of British Columbia
Year: 2020

description: Excitation-contraction (EC) coupling describes the process whereby the depolarizing action potential is transduced into a rapid increase of cytosolic calcium (Ca²⁺) that initiates muscle contraction. Proper execution of EC coupling relies on the coordinated communication between two calcium channels: plasma membrane-bound, L-type voltage-gated calcium channels (CaVs) and the intracellular Ryanodine Receptors (RyRs). CaVs respond to membrane depolarization by conveying an intracellular signal to the RyR. In skeletal muscle, CaV1.1 mechanically couples to the RyR; in cardiac tissue, extracellular Ca²⁺ entry via CaVs trigger RyR opening. The net effect of RyR activation is elevation of intracellular Ca²⁺ levels, activating the contractile machinery. In skeletal muscle, the nature of the physical CaV-RyR coupling has been an area of intense interest: do the channels directly interact or are auxiliary proteins required? Recently, a novel adaptor protein, STAC3, has been identified as playing a role in trafficking and maintaining components of the EC coupling machinery in a functional state. Indeed, STAC3-null mice and fish exhibit failure of skeletal muscle EC coupling. Chapter 2 presents x-ray crystallographic and isothermal titration calorimetry (ITC) data showing a direct interaction between STAC3 and CaV1.1. EC coupling assays reveal the importance of this interaction in EC coupling. The CaV1.1-STAC3 interaction is perturbed by the Native American Myopathy STAC3 mutation. L-type voltage-gated calcium channels fulfill dual roles as voltage-sensors for EC coupling and calcium ion conduits. In non-muscle cells, STAC3 facilitates CaV1.1’s functional membrane expression and alters the current properties of CaV1.2, suggesting a role of STAC proteins as a CaV regulator. Chapter 3 presents electrophysiology data illustrating the significant effect of STAC3 on modulating CaV1.2 currents. Detection of an interaction to Calmodulin (CaM), a well-known CaV regulator, suggests that STAC proteins may exert its effect on ion conduction via CaM. Genetic defects in the EC coupling machinery underlie numerous congenital myopathies and life-threatening cardiac arrhythmias. Chapter 4 explores the implications of disease-associated mutations within the cardiac Ryanodine Receptor (RyR2) using structural, spectroscopic, and thermal stability assays. An anion binding site within the N-terminal RyR2 region and maintenance of proper domain interfaces are key to RyR2 stability and normal functioning.
Mass Transfer in Binary Stars using SPH. II. Eccentric Binaries
Creators: name: Lajoie, Charles-Philippe
name: Sills, Alison
Publisher: name: arXiv
Year: 2010
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: Despite numerous efforts to better understand binary star evolution, some aspects of it remain poorly constrained. In particular, the evolution of eccentric binaries has remained elusive mainly because the Roche lobe formalism derived for circular binaries does not apply. Here, we report the results of our Smoothed Particle Hydrodynamics simulations of mass transfer in eccentric binaries using an alternate method in which we model only the outermost layers of the stars with appropriate boundary conditions. Using this technique, along with properly relaxed model stars, we characterize the mass transfer episodes of binaries with various orbital parameters. In particular, we show that these episodes can be described by Gaussians with a FWMH of ~0.12 P_orb and that the peak rates occur after periastron, at an orbital phase of ~0.58, independently of the eccentricity and mass of the stars. The accreted material is observed to form a rather sparse envelope around either or both stars. Although the fate of this envelope is not modeled in our simulations, we show that a constant fraction (~5%) of the material transferred is ejected from the systems. We discuss this result in terms of the non-conservative mass transfer scenario. We suggest our results could be incorporated in analytical and binary population synthesis studies to help better understand the evolution of eccentric binaries and the formation of exotic stellar populations.
description: 14 pages, 16 figures, 2 tables. Accepted for publication in The Astrophysical Journal
Active Region Moss: Basic physical parameters and their temporal variation
Creators: name: Tripathi, D.
name: Mason, H. E.
name: Del Zanna, G.
name: Young, P. R.
Publisher: name: arXiv
Year: 2010
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: We present a study of the physical plasma parameters such as electron temperature, electron density, column depth and filling factors in the moss regions and their variability over a short (an hour) and a long period (5 consecutive days) of time. Primarily, we have analyzed the spectroscopic observations recorded by the Extreme-ultraviolet Imaging Spectrometer (EIS) aboard Hinode. In addition we have used supplementary observations taken from TRACE and the X-Ray Telescope (XRT). We find that the moss emission is strongest in the Fe xii and Fe xiii lines. Based on analyses using line ratios and emission measure we found that the moss region has a characteristic temperature of log T = 6.2. The electron densities measured at different locations in the moss regions using Fe xii ratios are about 1-3\times1010 cm(-3) and about 2-4\times10^9 cm^(-3) using Fe xiii and Fe xiv. The electron density substantially increases (by a factor of about 3-4 or even more in some cases) when a background subtraction was performed. The density and temperature show very small variation over time. The filling factor of the moss plasma can vary between 0.1-1 and the path length along which the emission originates is from a few 100 to a few 1000 kms long. By combining the observations recorded by TRACE, EIS and XRT, we find that the moss regions correspond to the foot-points of both hot and warm loops.
description: 10 pages, 12 figures, Accepted for publication in Astronomy and Astrophysics