cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Episodic modulations in supernova radio light curves from luminous blue variable supernova progenitor models
Creators: name: Moriya, Takashi J.
name: Groh, Jose H.
name: Meynet, Georges
Publisher: name: arXiv
Year: 2013
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: Ideally, one would like to know which type of core-collapse SNe is produced by different progenitors and the channels of stellar evolution leading to these progenitors. These links have to be very well known to use the observed frequency of different types of SN events for probing the star formation rate and massive star evolution in different types of galaxies. We investigate the link between LBV as SN progenitors and the appearance of episodic radio light curve modulations of the SN event. We use the 20Msun and 25Msun models with rotation at solar metallicity, part of an extended grid of stellar models computed by the Geneva team. At their pre-SN stage, these two models have recently been shown to have spectra similar to those of LBV stars and possibly explode as Type IIb SNe. Based on the wind properties before the explosion, we derive the density structure of their circumstellar medium. This structure is used as input for computing the SN radio light curve. We find that the 20Msun model shows radio light curves with episodic luminosity modulations, similar to those observed in some Type IIb SNe. This occurs because the evolution of the 20Msun model terminates in a region of the HR diagram where radiative stellar winds present strong density variations, caused by the bistability limit. The 25Msun model, ending its evolution in a zone of the HR diagram where no change of the mass-loss rates is expected, presents no such modulations in its radio SN light curve. Our results reinforce the link between SN progenitors and LBV stars. We also confirm the existence of a physical mechanism for a single star to have episodic radio light curve modulations. In the case of the 25Msun progenitors, we do not obtain modulations in the radio light curve, but our models may miss some outbursting behavior in the late stages of massive stars.
description: 5 pages, 3 figures, accepted by Astronomy & Astrophysics Letters
Extracellular water characterizes sex-specific differences in Autism Spectrum Disorder
Creators: name: Newman, Benjamin T.
name: Jacokes, Zachary
name: Van Horn, John D.
Publisher: name: F1000 Research Limited
Year: 2022

description: Autism spectrum disorder (ASD) is a complex, multifaceted disorder with a significant sex bias in both diagnosis rate and behavioral symptom profile. Previous studies have found structural differences in neuronal white matter (WM) with ASD being associated with lower FA and higher diffusivity. Studies on sex differences have suggested that ASD males and females may lack sex-specific differences seen in typically developing individuals. This study aims to characterize sex-specific differences in ASD using advanced models of brain microstructure including a metric of extracellular water.
The UCSC Xena platform for public and private cancer genomics data visualization and interpretation
Creators: name: Goldman, Mary
name: Craft, Brian
name: Zhu, Jing
name: Haussler, David
Publisher: name: F1000 Research Limited
Year: 2022

description: UCSC Xena (http://xena.ucsc.edu/) is a web-based visual integration and exploration tool for multi-omic data and associated clinical and phenotypic annotations. Researchers can easily view and explore public data, their own private data, or both using the Xena Browser. Private data are kept on the researcher's computer and are never uploaded to our public servers. We support Mac, Windows, and Linux.

 Questions Xena can help you answer:
 * Is overexpression of this gene associated with lower/higher survival?
 * What genes are differentially expressed between these two groups of samples?
 * What is the relationship between mutation, copy number, expression, etc for this gene?

 Xena showcases seminal cancer genomics datasets from TCGA, the Pan-Cancer Atlas, GDC, PCAWG, ICGC, and more; a total of more than 1500 datasets across 50 cancer types. We support virtually any type of functional genomics data: SNPs, INDELs, copy number variation, gene expression, ATAC-seq, DNA methylation, exon-, transcript-, miRNA-, lncRNA-expression and structural variants. We also support clinical data such as phenotype information, subtype classifications and biomarkers. All of our data is available for download via python or R APIs, or using our URL links.

 Our signature Visual Spreadsheet view shows multiple data types side-by-side enabling discovery of correlations across and within genes and genomic regions. We also have dynamic Kaplan-Meier survival analysis, powerful filtering and subgrouping, differential gene expression analysis, charts, statistical analyses, genomic signatures, and the ability to generate URLs to live views. We link out to the UCSC Genome Browser as well as MuPIT/CRAVAT and TumorMap.

 New features include:
 * Genome-wide differential gene expression analysis
 * Select samples directly from the screen for filtering and creating subgroups
 * Violin plots on any numerical data
 * Loading of Microsoft Excel files

 Our beta prototype site for visualizing single-cell data delivers million-cell-scale multi-omics data for interactive visualization in a web browser. Contact us for access to our beta prototype site.

 If you use us please cite our publication in Nature Biotechnology: https://www.nature.com/articles/s41587-020-0546-8
A Novel approach for Hybrid Database
Creators: name: Tiwari, Rajesh Kumar
Publisher: name: arXiv
Year: 2013
Subjects: subject: Databases (cs.DB)
subject: Cryptography and Security (cs.CR)
subject: Multimedia (cs.MM)
subject: FOS: Computer and information sciences

description: In the current world of economic crises, the cost control is one of the chief concerns for all types of industries, especially for the small venders. The small vendors are suppose to minimize their budget on Information Technology by reducing the initial investment in hardware and costly database servers like ORACLE, SQL Server, SYBASE, etc. for the purpose of data processing and storing. In other divisions, the electronic devices manufacturing companies want to increase the demand and reduce the manufacturing cost by introducing the low cost technologies. The new small devices like ipods, iphones, palm top etc. are now-a-days used as data computation and storing tools. For both the cases mentioned above, instead of going for the costly database servers which additionally requires extra hardware as well as the extra expenses in training and handling, the flat file may be considered as a candidate due to its easy handling nature, fast accessing, and of course free of cost. But the main hurdle is the security aspects which are not up to the optimum level. In this paper, we propose a methodology that combines all the merit of the flat file and with the help of a novel steganographic technique we can maintain the utmost security fence. The new proposed methodology will undoubtedly be highly beneficial for small vendors as well as for the above said electronic devices manufacturer
An evaluation of a meta-dimensional approach to combine multimodal omics and phenotypic data to identify subgroups of patients associated with morning cancer-related fatigue severity
Creators: name: Le, Caroline
name: Miaskowski, Christine
name: Roy, Ritu
name: Olshen, Adam
name: Kober, Kord M
Publisher: name: F1000 Research Limited
Year: 2022

description: Cancer-related fatigue (CRF) is the most common symptom associated with cancer and its treatments. CRF has a negative impact on patients’ ability to tolerate treatments and on their quality of life (QOL). One of the major knowledge gaps for CRF is a lack of knowledge of its underlying mechanisms. Increased knowledge of CRF mechanisms could identify potential therapeutic targets. CRF is a complex phenotype, which is the result of environmental (e.g., demographic, clinical, social) and molecular factors. By integrating data from multiple sources, we will have increased power to identify and better interpret the omics-phenotype relationships relative to an analysis that uses only a single source of omics data. The similarity network fusion (SNF) method uses networks of samples across different datatypes as a basis for integration. The fused network can identify groups of patients that have shared and complementary information across the data types. The purpose of this study was to create a fused network using multimodal data types and (1) evaluate this network for joint data profiles (JDPs) of patients, (2) evaluate the JDPs for an association with morning CRF, and (3) evaluate the patient characteristics associated with JDPs.

 The analysis evaluated transcriptomic, epigenomic, and phenotypic (i.e., age, income, performance, comorbidity burden) data for 299 oncology patients receiving chemotherapy (CTX). Patients with similar joint data profiles in the fused similarity network were identified using spectral clustering (k={2, 3, 4, 5}). Across the analyses, the phenotype network had the largest contribution to the unified network. JDPs differ in mean levels of morning fatigue for values of k > 3 (k=3, F=17.52, p-value=6.57x10-8; k=4, F=16.71, p-value=4.95x10-10; k=5, F=13.86, p-value=2.42x10-10). This approach demonstrated potential to identify clinically informative groups of patients through the fusion of different data types. These profiles are useful to identify high risk patients and novel therapeutic targets.
Delaunay Surfaces
Creators: name: Bendito, Enrique
name: Bowick, Mark J.
name: Medina, Agustin
Publisher: name: arXiv
Year: 2013
Subjects: subject: Differential Geometry (math.DG)
subject: Soft Condensed Matter (cond-mat.soft)
subject: FOS: Mathematics
subject: FOS: Physical sciences
subject: 53A05

description: We derive parametrizations of the Delaunay constant mean curvature surfaces of revolution that follow directly from parametrizations of the conics that generate these surfaces via the corresponding roulette. This uniform treatment exploits the natural geometry of the conic (parabolic, elliptic or hyperbolic) and leads to simple expressions for the mean and Gaussian curvatures of the surfaces as well as the construction of new surfaces.
description: 16 pages, 11 figures
Single cell-level analysis of responses to cancer immunotherapy using a syngeneic murine model of lung cancer
Creators: name: Subin Cho
name: Lee, Gyu Jin
name: Jaesang Kim
name: Sanghyuk Lee
Publisher: name: F1000 Research Limited
Year: 2022

description: Immunotherapy is currently the most promising treatment modality for various types of cancers. It has been demonstrated that targeting immune checkpoint with PD-1 or CTLA-4 blockade can lead to longterm survival or complete remission from cancers. However, immunotherapy is limited in efficacy as only a minority of patients benefit from such therapies. Clearly, closer scrutiny of responses from various cells found in tumor tissues during immunotherapy would greatly enhance our understanding of the interactions within the tumor microenvironment and possibly point to novel targets. Here, we report a longitudinal study using a Lewis lung carcinoma syngeneic mouse model and anti-PD-1 antibody treatment. Specifically, we performed single-cell RNAseq using tumor tissues isolated from multiple time points and attempted to reconstruct potentially significant cellular interactions in response to the immunotherapy. Interestingly, natural killer cells in particular showed activation by anti-PD-1 antibody treatment and expressed elevated levels of Xcl-1 which has been implicated in recruiting conventional dendritic cells (cDCs). We present results from gene expression analysis suggesting enhanced antigen-presenting by cDCs and strategies for demonstrating the functionalities of altered cellular responses to immunotherapy.
Gravitational origin of the weak interaction's chirality
Creators: name: Alexander, Stephon
name: Marciano, Antonino
name: Smolin, Lee
Publisher: name: arXiv
Year: 2012
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: We present a new unification of the electro-weak and gravitational interactions based on the joining the weak SU(2) gauge fields with the left handed part of the space-time connection, into a single gauge field valued in the complexification of the local Lorentz group. Hence, the weak interactions emerge as the right handed chiral half of the space-time connection, which explains the chirality of the weak interaction. This is possible, because, as shown by Plebanski, Ashtekar, and others, the other chiral half of the space-time connection is enough to code the dynamics of the gravitational degrees of freedom. This unification is achieved within an extension of the Plebanski action previously proposed by one of us. The theory has two phases. A parity symmetric phase yields, as shown by Speziale, a bi-metric theory with eight degrees of freedom: the massless graviton, a massive spin two field and a scalar ghost. Because of the latter this phase is unstable. Parity is broken in a stable phase where the eight degrees of freedom arrange themselves as the massless graviton coupled to an SU(2) triplet of chirally coupled Yang-Mills fields. It is also shown that under this breaking a Dirac fermion expresses itself as a chiral neutrino paired with a scalar field with the quantum numbers of the Higgs.
description: 21 pages
The impact of physical activity on cardiovascular mortality in the general population
Creators: name: Takahashi, Tetsuya
name: Watanabe, Tetsu
name: Tamura, Harutoshi
name: Nishiyama, Satoshi
name: Takahashi, Hiroki
name: Arimoto, Takanori
name: Shishido, Tetsuro
name: Ichikawa, Kazunobu
name: Inoue, Sumito
name: Konta, Tsuneo
name: Ueno, Yoshiyuki
name: Kato, Takeo
name: Kayama, Takamasa
name: Watanabe, Masafumi
Publisher: name: IfADo - Leibniz Research Centre for Working Environment and Human Factors, Dortmund
Year: 2021
Subjects: physical activity
cardiovascular mortality
general population

description: The beneficial effect of moderate physical activity (PA) on morbidity and mortality has been observed in the general population. However, the ideal intensity of PA for improving cardiovascular longevity in Japanese general population is uncertain. The aim of this study was to investigate the relationship between the PA and cardiovascular mortality in the general population. This longitudinal cohort study included 1,826 apparently healthy subjects who participated in a community-based health checkup. There were 31 cardiovascular deaths during 10-year follow-up. Subjects were divided into 4 groups based on the quartiles of PA (low, mild, moderate and high). Kaplan-Meier analysis and multivariate Cox proportional hazard analysis demonstrated that the most favorable cardiovascular prognosis was observed in subjects with moderate PA followed by those with mild PA. High PA as well as low PA were associated with higher cardiovascular mortality compared with mild and moderate PA. Noteworthy, in subjects with high PA, Cox hazard analysis revealed that previous cardiovascular disease, smoking, brain natriuretic peptide levels, and Framingham risk score were associated with cardiovascular mortality. The results suggest a U-shaped association between cardiovascular mortality and PA. Mild to moderate PA was associated with favorable cardiovascular outcomes in the Japanese general population. High PA might be associated with poor cardiovascular outcomes in subjects with a history of heart disease and high coronary risk factors.
description: EXCLI Journal; 20:Doc1294; ISSN 1611-2156
Raw data related to article "A multiparameter liquid biopsy-based approach allows longitudinal tracking of cutaneous melanoma dynamics and early resistance to treatment"
Creators: name: Scaini, Maria Chiara
name: Poggiana, Cristina
name: CATONI, CRISTINA
Publisher: name: Zenodo
Year: 2023

description: Background: Melanoma heterogeneity is an obstacle in metastatic disease management. Although the advent of targeted therapy has significantly improved patient outcome, the occurrence of resistance makes monitoring of the tumor genetic landscape mandatory. Liquid biopsy could represent an important biomarker to track the evolution of the disease in real time. Thus, we aimed to correlate liquid biopsy dynamics with treatment response/progression by devising a multiplatform approach applied to longitudinal monitoring. We exploited Next Generation Sequencing and droplet digital PCR to analyze circulating tumor DNA genetic profile. The approach was applied to 17 stage IV melanoma patients treated with BRAF/MEK inhibitors, longitudinally tracked for up to 28 months.
Description: Data of hybridization capture-based target enrichment sequencing (SureSelect XT HS Target Enrichment System, Agilent Technologies) for 17 patients longitudinally followed for up to 28 months (median follow-up of 480 days, range: 77-853) for a total of 48 samples. Patients had a median age of 64 and there was equal representation of males and females (47% females). The following genes were sequenced on a NextSeq 550 instrument (Illumina) with a 300-cycle NextSeq 500/550 Mid Output v2 kit: ABL1, ADAMTS18, ARID2, ATM, BAP1, BRAF, CDK4, CDKN2A, CTNNB1, CYSLTR2, EGFR, EIF1AX, ERBB2, ERBB4, FBXW7, FGFR1, FGFR2, FGFR3, GNA11, GNAQ, GRIN2A, HOXD8, HRAS, IDH1, KDR, KIT, KRAS, MAP2K1, MAP2K2, MC1R, MET, MITF, MLH1, NF1, NRAS, PDGFRA, PIK3CA, PLCB4, PPP6C, PREX2, PTEN, PTPN11, RAC1, RB1, SF3B1, SRC, SRSF2, STK11, STK19, TERT, TP53, U2AF1 for SNP/INDEL analysis, and BRAF, CDC42, CDK4, ERBB2, FGFR1, FGFR3, NEDD9, NFAT5, PIK3CA, PPARG, PTK2, TUSC3 for CNV assessment.
Extended global symmetries for 4d N=1 SQCD theories
Creators: name: Gahramanov, Ilmar
name: Vartanov, Grigory
Publisher: name: arXiv
Year: 2013
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: In arXiv:0811.1909 Spiridonov and Vartanov, using the superconformal index technique, found that 4-dimensional N=1 SQCD theory with SU(2) gauge group and four flavors has 72 dual representations. Recently in arXiv:1209.1404 the authors showed that these dual theories, when coupled to 5d hypermultiplets with specific boundary conditions have an extended E_7 global symmetry. In this work we find that for a reduced theory with 3 flavors the explicit SU(6) global symmetry is enhanced to an E_6 symmetry in the presence of 5d hypermultiplets. We also show connections between indices of different theories in 3 and 4 dimensions.
description: 12 pages. V2: misprints corrected
Phase structure of hot dense QCD by a histogram method
Creators: name: Ejiri, Shinji
Publisher: name: arXiv
Year: 2013
Subjects: subject: High Energy Physics - Lattice (hep-lat)
subject: FOS: Physical sciences

description: We study the phase structure of QCD at high temperature and density by lattice QCD simulations adopting a histogram method. The quark mass dependence and the chemical potential dependence of the nature of phase transition are investigated focusing on the probability distribution function (histogram). The shape of the distribution function changes with the quark mass and chemical potential. Through the shape of the distribution, the critical surface which separates the first order transition and crossover regions in the heavy quark region is determined for the (2+1)-flavor case. Moreover, we determined the critical point at finite density for two-flavor QCD with an intermediate quark mass, using a Gaussian approximation of the complex phase distribution of the quark determinant. The chemical potential dependence of the critical quark mass is also evaluated in the situation where two light quarks and many massive quarks exist. We find that the first order transition region becomes wider with the chemical potential in the many-flavor QCD.
description: 16 pages, 20 figures, mini-review
In silico modelling optimization of antibiotic dosing to efficiently treat persistent biofilm infections
Creators: name: Blee, Johanna A
name: Gorochowski, Thomas
name: Hauert, Sabine
Publisher: name: F1000 Research Limited
Year: 2022

description: We developed individual-based in silico models to streamline the process of finding optimal treatment strategies and to effectively treat biofilm infections.
3D chromosome structure reconstruction using graph convolutional neural networks
Creators: name: Van Hovenga,
name: Jugal Kalita
name: Oluwatosin Oluwadare
Publisher: name: F1000 Research Limited
Year: 2022

description: Chromosome conformation capture (3C) is a method of measuring chromosome topology in terms of loci interaction. The Hi-C method is a derivative of 3C that allows for genome-wide quantification of chromosome interaction. From such interaction data, it is possible to infer the three-dimensional (3D) structure of the underlying chromosome. In this paper, we developed a novel method, HiC-GNN, for predicting the three-dimensional structures of chromosomes from Hi-C data. HiC-GNN is unique from other methods for chromosome structure prediction in that the models learned by HiC-GNN can be generalized to unseen data. To the authors’ knowledge, this generalizing capability is not present in any existing methods. HiC-GNN uses a node embedding algorithm and a graph neural network to predict the 3D coordinates of each genomic loci from the corresponding Hi-C contact data. Unlike other chromosome structure prediction methods, our method allows for the storage of pre-trained parameters which allows for prediction to occur on un-seen data. We show that these predictions on unseen data are accurate, thereby showing that our method is generalizable. We show that our method can generalize a single model across Hi-C resolutions, multiple restriction enzymes, and multiple cell populations while maintaining reconstruction accuracy across three Hi-C datasets. Our algorithm outperforms the state-of-the-art methods in accuracy of prediction and runtime and introduces a novel method for 3D structure prediction from Hi-C data. All our source codes and data are available at https://github.com/OluwadareLab/HiC-GNN , and is made available as a containerized application that can be run on any platform.
A Comparative Study of AGN Feedback Algorithms
Creators: name: Wurster, James
name: Thacker, Robert J.
Publisher: name: arXiv
Year: 2013
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: Modelling AGN feedback in numerical simulations is both technically and theoretically challenging, with numerous approaches having been published in the literature. We present a study of five distinct approaches to modelling AGN feedback within gravitohydrodynamic simulations of major mergers of Milky Way-sized galaxies. To constrain differences to only be between AGN feedback models, all simulations start from the same initial conditions and use the same star formation algorithm. Most AGN feedback algorithms have five key aspects: black hole accretion rate, energy feedback rate and method, particle accretion algorithm, black hole advection algorithm, and black hole merger algorithm. All models follow different accretion histories, with accretion rates that differ by up to three orders of magnitude at any given time. We consider models with either thermal or kinetic feedback, with the associated energy deposited locally around the black hole. Each feedback algorithm modifies the gas properties near the black hole to different extents. The particle accretion algorithms usually (but not always) maintain good agreement between the mass accreted by \dot{M} dt and the mass of gas particles removed from the simulation. The black hole advection algorithms dampen inappropriate dragging of the black holes by two-body interactions. Advecting the black hole a limited distance based upon local mass distributions has many desirably properties. The black holes merge when given criteria are met, and we find a range of merger times for different criteria. Using the M_{BH}-σrelation as a diagnostic of the remnants yields three models that lie within the one-sigma scatter of the observed relation and two that fall below it. The wide variation in accretion behaviours of the models reinforces the fact that there remains much to be learnt about the evolution of galactic nuclei. (abridged)
description: 24 pages, accepted to MNRAS
Measurement of the production cross section of jets in association with a Z boson in pp collisions at sqrt(s) = 7 TeV with the ATLAS detector
Creators: name: ATLAS Collaboration
Publisher: name: arXiv
Year: 2013
Subjects: subject: High Energy Physics - Experiment (hep-ex)
subject: FOS: Physical sciences

description: Measurements of the production of jets of particles in association with a Z boson in pp collisions at sqrt(s) = 7 TeV are presented, using data corresponding to an integrated luminosity of 4.6/fb collected by the ATLAS experiment at the Large Hadron Collider. Inclusive and differential jet cross sections in Z events, with Z decaying into electron or muon pairs, are measured for jets with transverse momentum pT > 30 GeV and rapidity |y| < 4.4. The results are compared to next-to-leading-order perturbative QCD calculations, and to predictions from different Monte Carlo generators based on leading-order and next-to-leading-order matrix elements supplemented by parton showers.
description: 35 pages plus author list (56 pages total), 17 figures, 4 tables, submitted to JHEP, All figures including auxiliary figures are available at https://atlas.web.cern.ch/Atlas/GROUPS/PHYSICS/PAPERS/STDM-2012-04/
The study of Immune microenvironment of Korean NSCLC patients
Creators: name: Seokbo Shim
name: Kwoneel Kim
Publisher: name: F1000 Research Limited
Year: 2022

description: According to the findings of a survey from Institute for Health Metrics and Evaluation (IHME), cancer is the second cause of death worldwide. In 2019, Lung & Bronchus cancer was estimated a second most common new cancer cases through both sex, and most death cancer cases in both males and females. About 80 percent to 85 percent of lung cancers are non-small cell lung cancer(NSCLC). Lung adenocarcinoma(LUAD) is the most common type of lung cancer seen in non-smokers, and smokers[3]. Therefore, understanding genetic and epigenetic interaction between genes are important to understand lung cancer. We conducted research on NSCLC and the immune landscape. Our co-researcher team divided the subtypes of the samples by using the NMF(Non-negative Matrix Factorization) clustering method using global protein, phospho and acetyl data. We attempted to explain this sample subtype with different methodologies for the gene or sample.
The landscape of neoantigen in Korean NSCLC patients
Creators: name: Jisoo Park
name: Kwoneel Kim
Publisher: name: F1000 Research Limited
Year: 2022

description: Lung cancer is one of the major worldwide health problems which accounts for 18% of global cancer-related deaths (Sung, Ferlay et al. 2021). About 80 percent to 85 percent of lung cancers are non-small cell lung cancer (NSCLC). Lung adenocarcinoma (LUAD) is the most common type of lung cancer seen in non-smokers, and smokers. Therefore, understanding genetic and epigenetic interaction between genes is important to understand lung cancer. We conducted research on NSCLC and the immune landscape. In this analysis, we profiled putative regulators in Korean NSCLC patients. Our co-researcher team divided the subtypes of the samples by using the Non-negative Matrix Factorization (NMF) clustering method using global protein, phosphor-proteome, and acetylproteome data. we hypothesized that neoantigens were favorably associated with survival in NSCLC patients.
 we analyze neoantigen counts and antigen processing and presentation machinery (APM) together, and this result was assumed to be different for each ‘multi-omics subtype’. We classified neoantigens into four subtypes. Then we performed regression analysis between neoantigen subtypes and overall survival time and found a high negative correlation with ‘validated novel neoantigen’ that one of the subtypes. Also, we found some validated novel neoantigens that are commonly expressed in patients, and these validated novel neoantigens act as a favorable factor for patient survival. Moreover, we performed a survival analysis validated novel neoantigen and APM together, and we found that the survival analysis result of combining these two factors has high explanatory power. Last, we see the pattern of multi-omics subtype in validated novel neoantigen and APM, we found that patterns of the immune system matched the survival patterns of patients with each multi-omics subtype.
Estimating treatment effect heterogeneity in randomized program evaluation
Creators: name: Imai, Kosuke
name: Ratkovic, Marc
Publisher: name: arXiv
Year: 2013
Subjects: subject: Applications (stat.AP)
subject: FOS: Computer and information sciences

description: When evaluating the efficacy of social programs and medical treatments using randomized experiments, the estimated overall average causal effect alone is often of limited value and the researchers must investigate when the treatments do and do not work. Indeed, the estimation of treatment effect heterogeneity plays an essential role in (1) selecting the most effective treatment from a large number of available treatments, (2) ascertaining subpopulations for which a treatment is effective or harmful, (3) designing individualized optimal treatment regimes, (4) testing for the existence or lack of heterogeneous treatment effects, and (5) generalizing causal effect estimates obtained from an experimental sample to a target population. In this paper, we formulate the estimation of heterogeneous treatment effects as a variable selection problem. We propose a method that adapts the Support Vector Machine classifier by placing separate sparsity constraints over the pre-treatment parameters and causal heterogeneity parameters of interest. The proposed method is motivated by and applied to two well-known randomized evaluation studies in the social sciences. Our method selects the most effective voter mobilization strategies from a large number of alternative strategies, and it also identifies the characteristics of workers who greatly benefit from (or are negatively affected by) a job training program. In our simulation studies, we find that the proposed method often outperforms some commonly used alternatives.
description: Published in at http://dx.doi.org/10.1214/12-AOAS593 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org)
title: Evaluation of structural loading algorithm for ship-ice collisions during simulator training
Creators: name: Miller, Logan P.
Publisher: name: Memorial University of Newfoundland
Year: 2023

description: Simulator training is an attractive option for ice navigation training, as it lacks the financial and safety risk of real-world training. An important aspect of effective ship operation in ice is the ability of the operator to understand the capacity of their structure with regard to ice loads, but simulators lack advanced systems to help build on this experience. To this end, an algorithm was developed that can be used to provide simulator trainees with real-time feedback about structural loads from ship-ice collisions during simulator training. The methodology presented demonstrates how to determine a safe limit of collision energy for a given ship structure using non-linear finite element analysis. The calculation is then given for an example structure of Polar Class PC7. The algorithm is then implemented in a training simulator to calculate individual loads, and a user interface developed to communicate the magnitude of individual loads as compared to the pre-determined safe thresholds. An experimental campaign was designed to test the benefit of the system as a training tool. The campaign involved putting human participants through a series of ice navigation training scenarios, either with or without the benefit of the real-time feedback system. Eighteen participants, each novices without any seafaring experience, were recruited. Participants were assessed on a number of performance and safety metrics, such as time to complete the objective, average speed, and number of unsafe collisions. The results suggest that participants with real-time feedback were more comfortable with and were better able to judge ice-collisions during the training. The results also found that participants with access to real-time feedback were able to perform significantly faster in emergency scenarios, without greatly exceeding the capacity of their ship, as compared to participants who did not benefit from feedback.
Interband Quasiparticle Scattering in Superconducting LiFeAs Reconciles Photoemission and Tunneling Measurements
Creators: name: Hess, Christian
name: Sykora, Steffen
name: Hänke, Torben
name: Schlegel, Ronny
name: Baumann, Danny
name: Zabolotnyy, Volodymyr B.
name: Harnagea, Luminita
name: Wurmehl, Sabine
name: Brink, Jeroen van den
name: Büchner, Bernd
Publisher: name: arXiv
Year: 2012
Subjects: subject: Superconductivity (cond-mat.supr-con)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: Several angle resolved photoemission spectroscopy (ARPES) studies reveal a poorly nested Fermi surface of LiFeAs, far away from a spin density wave instability, and clear-cut superconducting gap anisotropies. On the other hand a very different, more nested Fermi surface and dissimilar gap anisotropies have been obtained from quasiparticle interference (QPI) data, which were interpreted as arising from intraband scattering within hole-like bands. Here we show that this ARPES-QPI paradox is completely resolved by interband scattering between the hole-like bands. The resolution follows from an excellent agreement between experimental quasiparticle scattering data and T-matrix QPI calculations (based on experimental band structure data), which allows disentangling interband and intraband scattering processes.
An empirical study to check the accuracy of approximating averages of ratios using ratios of averages
Creators: name: van Zyl, J. Martin
Publisher: name: arXiv
Year: 2013
Subjects: subject: Applications (stat.AP)
subject: Computation (stat.CO)
subject: FOS: Computer and information sciences

description: For a number of researchers a number of publications for each author is simulated using the zeta distribution and then for each publication a number of citations per publication simulated. Bootstrap confidence intervals indicate that the difference between the average of ratios and the ratio of averages are not significant, and there are no significant differences in the distributions in realistic problems when using the two-sample Kolmogorov-Smirnov test to compare distributions. It was found that the log-logistic distribution which is a general form for the ratio of two correlated Pareto random variables, give a good fit to the estimated ratios.
description: 3 tables, 3 figures
Dipole glass parameter behaviour for ferro-antiferroelectric solid mixtures
Creators: name: Korynevskii, M. A.
name: Solovyan, V. B.
Publisher: name: arXiv
Year: 2013
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: A new definition of a dipole glass parameter for ferro-antiferroelectric solid mixtures is suggested. It is constructed on the nearest neighbours pair correlation functions for interacting dipole momenta. The behaviour of the dipole glass parameter is calculated and discussed.
description: 8 pages, 3 figures
Simple groups and the number of countable models
Creators: name: Tanović, Predrag
Publisher: name: arXiv
Year: 2013
Subjects: subject: Logic (math.LO)
subject: FOS: Mathematics
subject: 03C45

description: Let $T$ be a complete, superstable theory with fewer than $2^{\aleph_{0}}$ countable models. Assuming that generic types of infinite, simple groups definable in $T^{eq}$ are sufficiently non-isolated we prove that $ω^ω$ is the strict upper bound for the Lascar rank of $T$.
description: Submitted to Achive for Mathematical Logic
The depletion of gas in high-redshift dwarf galaxies from an inhomogeneous reionization
Creators: name: Sobacchi, Emanuele
name: Mesinger, Andrei
Publisher: name: arXiv
Year: 2013
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: The reionization of the intergalactic medium (IGM) was likely inhomogeneous and extended. By heating the IGM and photo-evaporating gas from the outskirts of galaxies, this process can have a dramatic impact on the growth of structures. Using a suite of spherically-symmetric collapse simulations spanning a large parameter space, we study the impact of an ionizing ultraviolet background (UVB) on the condensation of baryons onto dark matter halos. We present an expression for the halo baryon fraction, which is an explicit function of: (i) halo mass; (ii) UVB intensity; (iii) redshift; (iv) redshift at which the halo was exposed to a UVB. We also present a corresponding expression for the characteristic or critical mass, defined as the halo mass which retains half of its baryons compared to the global value. Since our results are general and physically-motivated, they can be broadly applied to inhomogeneous reionization models.
description: 5 pages, 3 figures
The Mid-Infrared and Optical Decay of SN 2011fe
Creators: name: McClelland, Colin M.
name: Garnavich, Peter M.
name: Milne, Peter A.
name: Shappee, Benjamin J.
name: Pogge, Richard W.
Publisher: name: arXiv
Year: 2013
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: We measure the decay rate of the mid-IR luminosity from type Ia supernova 2011fe between six months and one year after explosion using Spitzer/IRAC observations. The fading in the 3.6 micron channel is 1.48+/-0.02 mag/100d, which is similar to that seen in blue optical bands. The supernova brightness fades at 0.78+/-0.02 mag/100d in the 4.5 micron channel which is close to that observed in the near-IR. We argue that the difference is a result of doubly ionized iron-peak elements dominating the bluer IRAC band while singly ionized species are controlling the longer wavelength channel. To test this, we use Large Binocular Telescope spectra taken during the same phases to show that doubly ionized emission lines do fade more slowly than their singly ionized cousins. We also find that [Co III] emission fades at more than twice the radioactive decay rate due to the combination of decreasing excitation in the nebula, recombination and cobalt decaying to iron. The nebular emission velocities of [Fe III] and [Co III] lines show a smaller blue-shift than emission from singly ionized atoms. The Si II velocity gradient near maximum light combined with our nebular velocity measurements suggest SN 2011fe was a typical member of the `low velocity gradient' class of type Ia. Analyzing IRAC photometry from other supernovae we find that mid-IR color of type Ia events is correlated with the early light curve width and can be used as an indicator of the radioactive nickel yield.
description: 11 pages, 6 figures, 3 tables
Simultaneous analysis of large INTEGRAL/SPI datasets: optimizing the computation of the solution and its variance using sparse matrix algorithms
Creators: name: Bouchet, L.
name: Amestoy, P.
name: Buttari, A.
name: Rouet, F. -H.
name: Chauvin, M.
Publisher: name: arXiv
Year: 2013
Subjects: subject: Instrumentation and Methods for Astrophysics (astro-ph.IM)
subject: FOS: Physical sciences

description: Nowadays, analyzing and reducing the ever larger astronomical datasets is becoming a crucial challenge, especially for long cumulated observation times. The INTEGRAL/SPI X-gamma-ray spectrometer is an instrument for which it is essential to process many exposures at the same time in order to increase the low signal-to-noise ratio of the weakest sources. In this context, the conventional methods for data reduction are inefficient and sometimes not feasible at all. Processing several years of data simultaneously requires computing not only the solution of a large system of equations, but also the associated uncertainties. We aim at reducing the computation time and the memory usage. Since the SPI transfer function is sparse, we have used some popular methods for the solution of large sparse linear systems; we briefly review these methods. We use the Multifrontal Massively Parallel Solver (MUMPS) to compute the solution of the system of equations. We also need to compute the variance of the solution, which amounts to computing selected entries of the inverse of the sparse matrix corresponding to our linear system. This can be achieved through one of the latest features of the MUMPS software that has been partly motivated by this work. In this paper we provide a brief presentation of this feature and evaluate its effectiveness on astrophysical problems requiring the processing of large datasets simultaneously, such as the study of the entire emission of the Galaxy. We used these algorithms to solve the large sparse systems arising from SPI data processing and to obtain both their solutions and the associated variances. In conclusion, thanks to these newly developed tools, processing large datasets arising from SPI is now feasible with both a reasonable execution time and a low memory usage.
description: 13 pages, 5 figures
Is GBT 1355+5439 a dark galaxy?
Creators: name: Oosterloo, T. A.
name: Heald, G. H.
name: de Blok, W. J. G.
Publisher: name: arXiv
Year: 2013
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: We present HI imaging of GBT 1355+5439 performed with the Westerbork Synthesis Radio Telescope. This is a dark HI object recently discovered close to the nearby galaxy M101. We find GBT 1355+5439 to be an HI cloud 5x3 arcmin in size. The total HI image and the kinematics show that the cloud consists of condensations that have small (~10 km/s) motions with respect to each other. The column densities of the HI are low; the observed peak value is 7.1x10^{19} cm^{-2}. The velocity field shows a mild velocity gradient over the body of GBT 1355+5439, possibly due to rotation, but it may also indicate large-scale radial motions. Although our data are limited in sensitivity, at all positions the HI velocity dispersion is higher than 5 km/s and no narrow, cold, HI component is seen. Because its distance is not known, we considered various possibilities for the nature of GBT 1355+5439. Both the scenarios that it is a tidal remnant near M101 and that it is a dark dwarf companion of M101 meet difficulties. Neither do the data fit the properties of known compact High-Velocity Clouds in the Galactic halo exactly, but we cannot entirely exclude this option and deeper observations are required. We also considered the possibility that GBT 1355+5439 is a gas-rich dark minihalo in the outer regions of the Local Group. Interestingly, it would then have similar properties as the clouds of a proposed Local Group population recently found in the ALFALFA survey. In this case, the HI mass of GBT 1355+5439 would be about a few times 10^5 Msol, its size about 1 kpc, and the dynamical mass M_dyn > 5x10^7 Msol. However, if GBT 1355+5439 is a dark Local Group object, the internal kinematics of the HI appears to be different from that of gas-dominated, almost dark galaxies of similar size.
description: Accepted for publication in A&A
Quantum corrections to short folded superstring in AdS_3 x S^3 x M^4
Creators: name: Beccaria, Matteo
name: Macorini, Guido
Publisher: name: arXiv
Year: 2012
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We consider integrable superstring theory on AdS_3 x S^3 x M^4 where M^4=T^4 or M^4=S^3 x S^1 with generic ratio of the radii of the two 3-spheres. We compute the one-loop energy of a short folded string spinning in AdS_3 and rotating in S^3. The computation is performed by world-sheet small spin perturbation theory as well as by quantizing the classical algebraic curve characterizing the finite-gap equations. The two methods give equal results up to regularization contributions that are under control. One important byproduct of the calculation is the part of the energy which is due to the dressing phase in the Bethe Ansatz. Remarkably, this contribution E_1^{dressing} turns out to be independent on the radii ratio. In the M^4=T^4 limit, we discuss how E_1^{dressing} relates to a recent proposal for the dressing phase tested in the su(2) sector. We point out some difficulties suggesting that quantization of the AdS_3 classical finite-gap equations could be subtler than the easier AdS_5 x S^5 case.
description: 37 pages, one reference added in v2
Fractionalization of minimal excitations in integer quantum Hall edge channels
Creators: name: Grenier, C.
name: Dubois, J.
name: Jullien, T.
name: Roulleau, P.
name: Glattli, D. C.
name: Degiovanni, P.
Publisher: name: arXiv
Year: 2013
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: A theoretical study of the single electron coherence properties of Lorentzian and rectangular pulses is presented. By combining bosonization and the Floquet scattering approach, the effect of interactions on a periodic source of voltage pulses is computed exactly. When such excitations are injected into one of the channels of a system of two copropagating quantum Hall edge channels, they fractionalize into pulses whose charge and shape reflects the properties of interactions. We show that the dependence of fractionalization induced electron/hole pair production in the pulses amplitude contains clear signatures of the fractionalization of the individual excitations. We propose an experimental setup combining a source of Lorentzian pulses and an Hanbury Brown and Twiss interferometer to measure interaction induced electron/hole pair production and more generally to reconstruct single electron coherence of these excitations before and after their fractionalization.
description: 18 pages, 10 figures, 1 table