cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Inference in high dimensional regression
Creators: name: Rakshit, Prabrisha
Publisher: name: No Publisher Supplied
Year: 2023

description: This thesis proposes a novel statistical inference framework for high-dimensional generalized linear models (GLMs). The first project focuses on labeling patients in electronic health records as case or control using high-dimensional sparse logistic regression models. A lack of valid statistical inference methods for the case probability poses a major hurdle. To address this, the project proposes a novel bias-corrected estimator for the case probability and establishes its asymptotic normality. The second project considers high-dimensional sparse Poisson regression models and proposes bias-corrected estimators for linear and quadratic transformations of the high-dimensional regression vector. We apply the devised methodology to the high-dimensional mediation analysis, with a particular application of testing the interaction between the treatment variable and high-dimensional mediators. The third project presents the R package SIHR on statistical inferences in high-dimensional generalized linear models for continuous and binary outcomes. The package includes confidence interval construction and hypothesis testing for linear and quadratic functionals and demonstrates practical applications in both numerical examples and real data settings.
Pion vector and scalar form factors with dynamical overlap quarks
Creators: name: JLQCD
name: collaborations, TWQCD
name: :
name: Kaneko, T.
name: Aoki, S.
name: Chiu, T. W.
name: Fukaya, H.
name: Hashimoto, S.
name: Hsieh, T. H.
name: Matsufuru, H.
name: Noaki, J.
name: Onogi, T.
name: Shintani, E.
name: Yamada, N.
Publisher: name: arXiv
Year: 2008
Subjects: subject: High Energy Physics - Lattice (hep-lat)
subject: FOS: Physical sciences

description: We calculate the pion vector and scalar form factors in two-flavor QCD. Gauge configurations are generated with dynamical overlap quarks on a 16^3 x 32 lattice at a lattice spacing of 0.12 fm with sea quark masses down to a sixth of the physical strange quark mass. Contributions of disconnected diagrams to the scalar form factor is calculated employing the all-to-all quark propagators. We present a detailed comparison of the vector and scalar radii with chiral perturbation theory to two loops.
description: 7 pages; Talk presented at the XXVI International Symposium on Lattice Field Theory, July 14 - 19 2008, Williamsburg, Virginia, USA; v2: a reference added
Excised black hole spacetimes: quasi-local horizon formalism applied to the Kerr example
Creators: name: Vasset, Nicolas
name: Novak, Jérôme
name: Jaramillo, José Luis
Publisher: name: arXiv
Year: 2009
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: We present a numerical work aiming at the computation of excised initial data for black hole spacetimes in full general relativity, using Dirac gauge in the context of a constrained formalism for the Einstein equations. Introducing the isolated horizon formalism for black hole excision, we especially solve the non-conformally flat part of the equations, and assess the boundary condition problem for this part. In the stationary single black hole case, we present and justify a no-boundary treatment on the black hole horizon. We compare the data obtained with the well-known analytic Kerr solution in Kerr-Schild coordinates, and assess the widely used conformally flat approximation for simulating axisymmetric black hole spacetimes. Our method shows good concordance on physical and geometrical issues, with the particular application of the isolated horizon multipolar analysis to confirm that the solution obtained is indeed the Kerr spacetime. Finally, we discuss a previous suggestion in the literature for the boundary conditions for the conformal geometry on the horizon.
description: 15 pages, 5 figures. Part IV significantly expanded, and additional appendix included. Version coherent with the published paper
The underlying mechanisms related to social connectedness derived from Facebook
Creators: name: Wade, A
Publisher: name: University Of Tasmania
Year: 2023

description: As a concept embedded in belonging, the beneficial outcomes associated with social connectedness are well demonstrated in previous research. The current research investigated whether social connectedness is derived from specific features within Facebook. Participants (N = 354) were Facebook users over the age of 18, who completed an online survey assessing Facebook feature social connectedness, and psychological wellbeing (e.g. depression, anxiety, and life satisfaction). Exploratory factor analysis (Maximum Likelihood with Direct Oblimin rotation) revealed seven distinct yet related factors, including face-to-face social connectedness, liking-derived connectedness, wall posting-derived connectedness, and Messenger-derived connectedness. Results of subsequent bivariate correlational analysis revealed that social connectedness derived from liking, Messenger, and to a lesser extent wall posts, was modestly but significantly associated with psychological wellbeing. The results have various theoretical and practical implications. Despite the cross-sectional design preventing causal inferences to be drawn, the current study contributes to our understanding of how belongingness needs can be met on Facebook via specific features, and the psychological experiences associated with this sense of connectedness. Future research implementing a longitudinal design is needed in order to determine causation, assisting researchers to make more conclusive interpretations about potential practical applications of the findings in clinical settings
Additional file 1 of Associations of genetic risk, BMI trajectories, and the risk of non-small cell lung cancer: a population-based cohort study
Creators: name: You, Dongfang
name: Wang, Danhua
name: Wu, Yaqian
name: Chen, Xin
name: Shao, Fang
name: Wei, Yongyue
name: Zhang, Ruyang
name: Lange, Theis
name: Ma, Hongxia
name: Xu, Hongyang
name: Hu, Zhibin
name: Christiani, David C.
name: Shen, Hongbing
name: Chen, Feng
name: Zhao, Yang
Publisher: name: figshare
Year: 2022
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 1: Appendix S1. Supplementary methods. Table S1. Characteristics of the study subjects for GWAS. Table S2. Summary of the 19 GWAS-identified SNPs associated with lung cancer. Table S3. Association between age-specific BMI and NSCLC risk. Table S4. Sensitivity analysis for the association between BMI trajectory and NSCLC risk. Table S5. Association of sPRSGWAS and wPRSGWAS with NSCLC risk. Table S6. Interaction analysis between age-specific BMI and the sPRSGWAS. Table S7. Interaction analysis between age-specific BMI and the wPRSGWAS. Table S8. Summary of four independent SNPs identified by GWIA. Table S9. Sensitivity analyses for the interaction between BMI trajectory and rs79297227, rs2336652, rs16018 and rs79297227. Table S10. Single-nucleotide polymorphisms used as instrumental variables in the multivariable Mendelian randomization analyses of BMI trajectory. Table S11. Sensitivity analysis of the relationship between BMI trajectory and lung cancer using one-sample Mendelian randomization. Table S12. Interaction analysis between age-specific BMI/BMI trajectories and the sPRSGWIA. Table S13. Interaction analysis between age-specific BMI/BMI trajectories and the wPRSGWIA. Figure S1. Stratification analysis for age-specific BMI and BMI trajectory on NSCLC risk by sex. Figure S2. Stratification analysis for age-specific BMI and BMI trajectory on NSCLC risk by smoking status. Figure S3. Stratification analysis for age-specific BMI and BMI trajectory on NSCLC risk by histological type. Figure S4. Association of multivariate-adjusted NSCLC risk with BMI trajectories according to PRSGWIA categories. Figure S5. Circle Manhattan Plot for interaction analysis between SNPs and BMI trajectory in regard to NSCLC risk. Figure S6. Analysis of the four loci and related gene expression in lung tissue.
title: Scoundrels in the C-Suite: How Should the Board Respond When a CEO’s Bad Behavior Makes the News?
Creators: name: Larcker, David F.
name: Tayan, Brian
Publisher: name: Corporate Governance Research Initiative
Year: 2016

description: The board of directors has a responsibility to investigate credible allegations that management has engaged in activity that is not in the interest of the company or its shareholders. In the case of illegal activity, the appropriate response is likely to be very clear. Less obvious are the actions directors should take when the CEO engages in behavior that is questionable but not illegal — such as making controversial public statements, having relations with an employee or contractor, or developing a reputation for overbearing or verbally abusive behavior. In this Closer Look, we examine the actions that boards take in response to CEO “bad behavior.” We ask: When are allegations serious enough or credible enough to merit boardroom attention? How can the board assess the impact of CEO misconduct on the organization broadly? Should the board be proactive in employing information gathering tools to detect early signs of CEO or employee misconduct?
Z' Boson Mixings with Z-γand Charge Assignments
Creators: name: Zhang, Ying
name: Wang, Qing
Publisher: name: arXiv
Year: 2009
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: Based on the general description for Z'-Z-γmixing as derived from the electroweak chiral Lagrangian, we characterize and classify the various new physics models involving the Z' boson that have appeared in the literature into five classes: 1. Models with minimal Z'-Z mass mixing; 2. Models with minimal Z'-Z kinetic mixing; 3. Models with general Z'-Z mixing; 4. Models with Z'-γkinetic and Z'-Z mixing; and 5. Models with Stueckelberg-type mixing. The corresponding mixing matrices are explicitly evaluated for each of these classes. We constrain and classify the Z' boson charges with respect to quark-leptons by anomaly cancellation conditions.
description: 17 pages
Deception detection using a task switching paradigm : an event-related potential study
Creators: name: Williams, SA
Publisher: name: University Of Tasmania
Year: 2023

description: Existing methods of lie detection have insufficient accuracy or applicability in forensic settings. The present study aimed to determine whether behavioural and electrophysiological markers of task switching occur when individuals switch between lying and truth telling, as these markers could be used to develop a new method of lie detection, using a modified task switching paradigm. Sixteen participants (five male, aged 18-34) completed a sincerity switching paradigm in which they switched and repeated lying and telling the truth about whether objects were on a previously memorised list. They also completed a comparable traditional task switching paradigm, in which they switched and repeated making environmental and directional judgements about similar objects. In both paradigms, significant switch costs were observed, and a significant ERP negativity occurred at similar latencies in the 500-600 ms post-target interval, on switch relative to repeat trials in a mixed block. The results suggest switching between lying and truth telling does involve task switching processes, and it may be possible to develop a lie detector based on behavioural and electrophysiological markers of sincerity switching. More research is needed to define the conditions under which these markers occur, and to develop a paradigm appropriate for use in forensic settings.
Additional file 3 of SRSF1 regulates primordial follicle formation and number determination during meiotic prophase I
Creators: name: Sun, Longjie
name: Lv, Zheng
name: Chen, Xuexue
name: Wang, Chaofan
name: Lv, Pengbo
name: Yan, Lu
name: Tian, Shuang
name: Xie, Xiaomei
name: Yao, Xiaohong
name: Liu, Jingjing
name: Wang, Zhao
name: Luo, Haoshu
name: Cui, Sheng
name: Liu, Jiali
Publisher: name: figshare
Year: 2023
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 3: Table 2. AS events were analysed in cKO and Ctrl ovaries.
Neutrinos and Future Concordance Cosmologies
Creators: name: Adshead, Peter
name: Easther, Richard
Publisher: name: arXiv
Year: 2008
Subjects: subject: Astrophysics (astro-ph)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We review the free parameters in the concordance cosmology, and those which might be added to this set as the quality of astrophysical data improves. Most concordance parameters encode information about otherwise unexplored aspects of high energy physics, up to the GUT scale via the "inflationary sector," and possibly even the Planck scale in the case of dark energy. We explain how neutrino properties may be constrained by future astrophysical measurements. Conversely, future neutrino physics experiments which directly measure these parameters will remove uncertainty from fits to astrophysical data, and improve our ability to determine the global properties of our universe.
description: Proceedings of paper given at Neutrino 2008 meeting (by RE)
Seeing the forest for the trees : ontological security and experiences of Tasmanian forests
Creators: name: Banham, Rebecca
Publisher: name: University Of Tasmania
Year: 2023

description: This thesis explores Tasmanians' experiences of forests. Tasmania has been socially and environmentally shaped by decades of conflict popularly and provocatively termed the 'forestry wars'. In this context, I examine the link between human-forest engagements and 'ontological security' ‚Äö- a sense of familiarity and trust in the world and the self. In critiquing and remodelling Giddens' conceptualisation of ontological security, I argue that forests do important emotional and existential 'work' for people. For most participants, the state's forests symbolised ontological and emotional aspects of ontological security. Environmental sociology literature often adopts macro-level, realist, and/or quantitative frameworks which privilege themes of self-interest, rationality, or 'quantifiable' experiences of the nonhuman environment. The existing literature regarding Tasmanians' experiences with/in forests is dominated by political, discursive, and historical perspectives which heavily emphasise the construction of environmental conflict. Sociological approaches to this Tasmanian case study are absent. In contrast to these bodies of literature, I explore human-forest engagements through under-examined themes of vulnerability, ontology, emotion, and relationship. I conducted semi-structured interviews with 27 Tasmanians across the state. Eleven participants also contributed materials that they felt represented Tasmanian forests, including photographs, lyrics, and written pieces. Almost all participants were critical and distrustful of Tasmanian forestry politics, management, and practices, expressed concerns about local and global environmental issues, and associated forest experiences with processes of wellbeing, immersion, self-identity, and ontology. Yet participants also expressed ambivalent attitudes about Tasmania's forestry industry. These key findings indicate that Tasmanians' engagements with/in forests are complex, emotionally significant, and are bound up in experiences of identity, ontology, and vulnerability. These data illustrate Tasmanian forests as symbolic of six key aspects of ontological security: material constancy; routine and ritual; escape and refuge; self-narrative; the nonhuman; and the future. Through these operationalised points, I argue that participants' understandings and experiences of Tasmanian forests reflect the construction and experience of ontological security. This thesis contributes a unique micro-sociological approach to understanding human-forest engagements in Tasmania, and in doing so, undermines the polarising and alienating rhetoric of 'Tasmania's forestry wars'. This research also contributes a reworked model of ontological security, demonstrating the utility of the concept for qualitative research in environmental sociology.
The effect of manganese oxide scavenging on the distribution and sedimentation of molybdenum in saanich inlet, british columbia
Creators: name: Berrang, Peter Gottfired
Publisher: name: University of British Columbia
Year: 2011

description: This study investigated the process by which molybdenum was removed from sea water in Saanich Inlet, an anoxic fjord, whose basin sediments are enriched in molybdenum. Water samples were collected in the inlet from July 1971 to April 1972 at about two month intervals and were analyzed for pH, salinity, temperature, dissolved and suspended molybdenum, suspended manganese and iron, and dissolved oxygen and hydrogen sulphide. A new technique for the determination of dissolved and suspended molybdenum was developed. The data showed a negative correlation between dissolved molybdenum and suspended manganese, and a positive correlation between suspended molybdenum and suspended manganese. This suggested that molybdenum was being scavenged from sea water by suspended manganese oxides. The distribution of molybdenum in the basin surface sediments was qualitatively correlated to the distribution of suspended molybdenum in the overlying basin water. During about September to December, the molybdenum profile was described by a two layer system. In the top 75 m layer the molybdenum followed the salinity profile. Below 75 m the distribution was described by a one dimensional mathematical model. The yearly deposition of molybdenum in the basin sediments was calculated from the estimated sediment deposition rate. This value was not inconsistent with that calculated from the rate molybdenum is scavenged by manganese oxides from the basin water.
Exact solutions for shells collapsing towards a pre-existing black hole
Creators: name: Liu, Yuan
name: Zhang, Shuang Nan
Publisher: name: arXiv
Year: 2009
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: The gravitational collapse of a star is an important issue both for general relativity and astrophysics, which is related to the well known "frozen star" paradox. This paradox has been discussed intensively and seems to have been solved in the comoving-like coordinates. However, to a real astrophysical observer within a finite time, this problem should be discussed in the point of view of the distant rest-observer, which is the main purpose of this paper. Following the seminal work of Oppenheimer and Snyder (1939), we present the exact solution for one or two dust shells collapsing towards a pre-existing black hole. We find that the metric of the inner region of the shell is time-dependent and the clock inside the shell becomes slower as the shell collapses towards the pre-existing black hole. This means the inner region of the shell is influenced by the property of the shell, which is contrary to the result in Newtonian theory. It does not contradict the Birkhoff's theorem, since in our case we cannot arbitrarily select the clock inside the shell in order to ensure the continuity of the metric. This result in principle may be tested experimentally if a beam of light travels across the shell, which will take a longer time than without the shell. It can be considered as the generalized Shapiro effect, because this effect is due to the mass outside, but not inside as the case of the standard Shapiro effect. We also found that in real astrophysical settings matter can indeed cross a black hole's horizon according to the clock of an external observer and will not accumulate around the event horizon of a black hole, i.e., no "frozen star" is formed for an external observer as matter falls towards a black hole. (abridged)
description: 18 pages, 6 figures. Accepted for publication in Physics Letters B
The inward turn : reading masochism in Latin literature
Creators: name: Donnelly, EJ
Publisher: name: University Of Tasmania
Year: 2023

description: This thesis examines the masochistic persona in literature. Beginning with the Marquis de Sade's representation of masochism in Justine, it identifies three key tropes that make up the masochistic character: control, choice, and responsibility. These tropes are then applied to three classical texts: the Satyricon, the Lesbia poems of Catullus, and Seneca's Thyestes. The first section of this dissertation establishes the masochistic identities of these three characters: Encolpius is the masochistic victim of his own passive and submissive nature; Catullus' masochism manifests out of a distortion of his love for Lesbia; and Thyestes labours under masochistic delusion, as he is lured home to Argos by his desire for wealth. After establishing the masochistic identity of these three characters, the second section analyses the impact that masochists have upon narrative. Both Justine and Encolpius are first-person, intradiegetic narrators, and as such their masochism directly affects the narrative. They interpret and relay information in an unreliable way, which is coloured by their individual masochistic characteristics. Catullus' narrative is similarly biased as a result of his masochism. His perception of his relationship with Lesbia is that she holds all the power, and that he is powerless; the reader has no access to Lesbia's voice, or to any other information that may mediate Catullus' perspective. Finally, Thyestes' masochism means that his narrative ‚Äö- framed as it is in a mimetic, dramatic form ‚Äö- does not have the power to become unreliable, because his passivity and masochistic delusion make him an unpersuasive character. Ultimately, this thesis illustrates that masochistic characters have a pervasive impact on the development of a text's narrative: by their nature masochists vacillate, and so they effectively prolong narratives, move them laterally, and, by their self-reflexive victimisation bring about critical shifts in the narrative.
Spitzer-IRAC GLIMPSE of high mass protostellar objects II - SED modelling of a bonafide sample
Creators: name: Grave, J. M. C.
name: Kumar, M. S. N.
Publisher: name: arXiv
Year: 2009
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: We aim to estimate and analyse the physical properties of the infrared counterparts of HMPOs by comparing their spectral energy distributions (SED) with those predicted by radiative transfer accretion models of YSOs. The SED of 68 IRCs are extended beyond the GLIMPSE photometry to the possible limits, from the near-infrared to the millimetre wavelengths by using the 2MASS, GLIMPSE version 2.0 catalogs, MSX, IRAS and some single dish (and interferometric) (sub)mm data. An online SED fitting tool that uses 2D radiative transfer accretion models of YSOs is employed to fit the observed SED to obtain various physical parameters. The SED of IRCs were fitted by models of massive protostars with a range of masses between 5-42 Msun and ages between 10^3 and 10^6 years. The median mass and age are 10 Msun and 10^4 yrs. The envelopes are large with a mean size of ~ 0.2-0.3 pc and show a distribution that is very similar to the distribution of the sizes of 8 micron nebulae discussed in Paper I. The estimated envelope accretion rates are high with a mean value of 10^(-3) Msun/yr and show a power law dependence to mass with an exponent of 2, suggesting spherical accretion at those scales. Disks are found to exist in most of the sources with a mean mass of 10^(-1.4+-0.7) Msun. The observed infrared-millimetre SED of the infrared counterparts of HMPOs are successfully explained with an YSO accretion model. The modelled sources mostly represent proto-B stars although some of them could become O stars in future. We demonstrate that many of these results may represent a realistic picture of massive star formation, despite some of the results which may be an effect of the assumptions within the models.
description: 13 pages, 8 figures
title: Chairman and CEO: The Controversy Over Board Leadership Structure
Creators: name: Larcker, David F.
name: Tayan, Brian
Publisher: name: Corporate Governance Research Initiative
Year: 2016

description: One of the most controversial issues in corporate governance is whether the CEO of a corporation should also serve as chairman of the board. In theory, an independent board chair improves the ability of the board to oversee management. However, an independent chairman is not unambiguously positive, and can lead to duplication of leadership, impair decision making, and create internal confusion — particularly when an effective dual chairman/CEO is already in place. In this Closer Look, we examine in detail the leadership structure of publicly traded corporations and the circumstances under which they are changed. We ask: What factors should the board consider in deciding whether to combine or separate board leadership? How can the board weigh the tradeoffs between stability of leadership, efficient decision making, and decreased oversight? What structure should be the default setting for a corporation? Why do activists advocate that corporations strictly separate the roles when there is little research support for this position?
title: “It’s more than just playing a sport”. A socio-cultural analysis of participation in netball across the lifespan
Creators: name: Pinchbeck, Jessica
Publisher: name: The Open University
Year: 2021

description: This thesis followed the journey of a small sample of women from one netball club located in the East of England to provide an insightful analysis into their childhood experiences of sport, exploring the extent to which this may have shaped their adult participation and the complexities of this connection. The study was conducted from an interpretivist perspective and used an ethnographic approach to examine how the women think and act in different situations, and how this develops over time as a result of previous experiences. These women and their experiences are not viewed in isolation but examined and studied in the wider context and alongside relationships in which their sports experiences have been socially constructed. Bourdieu’s (1984) theory of practice examines the extent to which social processes influence the behaviours, tastes, and judgements of individuals. This approach provides a valuable theoretical lens through which to view the sociocultural context of the women’s historical childhood experiences of sports participation alongside their current sports participation. Findings show support for the formation of a habitus towards sports participation developed throughout childhood which has endured into adulthood. The women’s habitus persists as a significant influence on their lives, demonstrated in the drive and passion to negotiate their netball participation, which can sometimes cause friction and tension in the women’s relationships. Subtle changes are evident in the behaviour and dispositions of the women as they enter different stages of their lives and also as their skill level in the sport increases. Habitus, developed throughout their childhood, influences the women’s tastes and socialises them into ways of behaving, however, their behaviour is also shaped and influenced by social structures. This study provides a unique connection of past and present to contribute to the knowledge and understanding of female sports participation.
On the Method to Infer an Atmosphere on a Tidally-Locked Super Earth Exoplanet and Upper limits to GJ 876d
Creators: name: Seager, S.
name: Deming, D.
Publisher: name: arXiv
Year: 2009
Subjects: subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: FOS: Physical sciences

description: We develop a method to infer or rule out the presence of an atmosphere on a tidally-locked hot super Earth. The question of atmosphere retention is a fundamental one, especially for planets orbiting M stars due to the star's long-duration active phase and corresponding potential for stellar-induced planetary atmospheric escape and erosion. Tidally-locked planets with no atmosphere are expected to show a Lambertian-like thermal phase curve, causing the combined light of the planet-star system to vary with planet orbital phase. We report Spitzer 8 micron IRAC observations of GJ 876 taken over 32 continuous hours and reaching a relative photometric precision of 3.9e-04 per point for 25.6 s time sampling. This translates to a 3 sigma limit of 5.13e-05 on a planet thermal phase curve amplitude. Despite the almost photon-noise limited data, we are unable to conclusively infer the presence of an atmosphere or rule one out on the non-transiting short-period super Earth GJ 876d. The limiting factor in our observations was the miniscule, monotonic photometric variation of the slightly active host M star, because the partial sine wave due to the planet has a component in common with the stellar linear trend. The proposed method is nevertheless very promising for transiting hot super Earths with the James Webb Space Telescope and is critical for establishing observational constraints for atmospheric escape.
description: Published in ApJ
Additional file 5 of SRSF1 regulates primordial follicle formation and number determination during meiotic prophase I
Creators: name: Sun, Longjie
name: Lv, Zheng
name: Chen, Xuexue
name: Wang, Chaofan
name: Lv, Pengbo
name: Yan, Lu
name: Tian, Shuang
name: Xie, Xiaomei
name: Yao, Xiaohong
name: Liu, Jingjing
name: Wang, Zhao
name: Luo, Haoshu
name: Cui, Sheng
name: Liu, Jiali
Publisher: name: figshare
Year: 2023
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 5: Fig. S3. Various genes were visually analysed using IGV.
Ultracold Atoms in 1D Optical Lattices: Mean Field, Quantum Field, Computation, and Soliton Formation
Creators: name: Mishmash, R. V.
name: Carr, L. D.
Publisher: name: arXiv
Year: 2008
Subjects: subject: Other Condensed Matter (cond-mat.other)
subject: Pattern Formation and Solitons (nlin.PS)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: In this work, we highlight the correspondence between two descriptions of a system of ultracold bosons in a one-dimensional optical lattice potential: (1) the discrete nonlinear Schrödinger equation, a discrete mean-field theory, and (2) the Bose-Hubbard Hamiltonian, a discrete quantum-field theory. The former is recovered from the latter in the limit of a product of local coherent states. Using a truncated form of these mean-field states as initial conditions, we build quantum analogs to the dark soliton solutions of the discrete nonlinear Schrödinger equation and investigate their dynamical properties in the Bose-Hubbard Hamiltonian. We also discuss specifics of the numerical methods employed for both our mean-field and quantum calculations, where in the latter case we use the time-evolving block decimation algorithm due to Vidal.
description: 14 pages, 2 figures; to appear in Journal of Mathematics and Computers in Simulation
Dataverse North Metadata Best Practices Guide v 3.0
Creators: name: Bascik, Teresa
name: Boisvert, Philippe
name: Cooper, Alexandra
name: Gagnon, Martine
name: Goodwin, Mark
name: Huck, John
name: Leahey, Amber
name: Stathis, Kelly
name: Steeleworthy, Michael
Publisher: name: Zenodo
Year: 2021
Subjects: Research data management
Dataverse
Metadata

description: One of the most useful features of the Dataverse repository software is the large number of metadata fields it provides for describing research data. This guide is intended to support both the novice and experienced user in creating metadata for datasets in a Dataverse repository. It provides official definitions of metadata fields with clarifications and tips, distinguishes between required, recommended, and optional fields, and illustrates the use of fields with examples. This version of the guide has been updated to include coverage of all available metadata fields - citation, geospatial, social science and humanities, astronomy and astrophysics, life sciences, and journal metadata. The guide was created with permission from Harvard for the use of definitions and the Texas Digital Library for basic design. Ce guide est aussi disponible en français.
Ancestry inference from targeted NGS tests to enable precision medicine and improve racial/ethnic representation in clinical trials
Creators: name: De La Vega, Francisco M
name: Rhead, Brooke
name: Irvine, Sean
Publisher: name: F1000 Research Limited
Year: 2021

description: There are well-established racial and ethnic disparities in cancer incidence and outcomes, in part due to structural, socioeconomic, environmental, and behavioral factors. However, some of these differences can be attributed to biological factors, such as the frequency of cancer mutations that vary by ancestry. Further, race and ethnicity reporting in clinical trials occurs infrequently, and it is missing in up to 50% of patient medical records and genomic profiling tests. Representative participation in clinical trials would help minimize disparities in outcomes and enable the assessment of biological differences that may determine differential efficacy of drugs for oncology and other indications. Thus, the ascertainment of diversity in real-world genetic testing and clinical trial cohorts is needed. Rather than relying on self-reported race/ethnicity labels, ancestry can be inferred directly from sequencing data collected during tumor profiling and other tests. Ancestry is usually inferred from genome-wide data, either array or whole-genome sequencing (WGS), using unlinked random markers and clustering methods; but this approach is inappropriate for targeted next-generation sequencing (NGS) gene panels or even whole-exome sequencing (WES) data. Instead, we selected 654 ancestry informative markers (AIMs) overlapping the coding regions of 648 cancer genes targeted by the Tempus xT NGS assay. We implemented an ancestry inference algorithm using the selected AIMs to infer global ancestry proportions at the continental level (i.e., Africa, America, Europe, East Asia, and South Asia). We validated our methods by comparing our results with data from the 1,000 Genomes Project and local ancestry inference previously derived in the ICGC PCAWG project. We show that this method can infer ancestry and admixture proportions from targeted NGS testing data where race/ethnicity was missing, and report concordance with self-described labels where available. Our results suggest that inferred ancestry can facilitate research on ancestry correlates with cancer mutations and outcomes data.
Gauge Theories, Duality Relations and the Tensor Hierarchy
Creators: name: Bergshoeff, Eric A.
name: Hartong, Jelle
name: Hohm, Olaf
name: Huebscher, Mechthild
name: Ortin, Tomas
Publisher: name: arXiv
Year: 2009
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We compute the complete 3- and 4-dimensional tensor hierarchies, i.e. sets of p-form fields, with $1\le p\le D$, which realize an off-shell algebra of bosonic gauge transformations. We show how these tensor hierarchies can be put on-shell by introducing a set of duality relations, thereby introducing additional scalars and a metric tensor. These so-called duality hierarchies encode the equations of motion of the bosonic part of the most general gauged supergravity theories in those dimensions, including the (projected) scalar equations of motion. We construct gauge-invariant actions that include all the fields in the tensor hierarchies. We elucidate the relation between the gauge transformations of the p-form fields in the action and those of the same fields in the tensor hierarchy.
description: 48 pages, v2: number of clarifications, ref. added, to appear in JHEP
Additional file 1 of Fasciola gigantica excretory-secretory products (FgESPs) modulate the differentiation and immune functions of buffalo dendritic cells through a mechanism involving DNMT1 and TET1
Creators: name: Mei, Xuefang
name: Shi, Wei
name: Zhao, Wenping
name: Luo, Honglin
name: Zhang, Yaoyao
name: Wang, Yurui
name: Sheng, Zhaoan
name: Wang, Dongying
name: Zhu, Xing-Quan
name: Huang, Weiyi
Publisher: name: figshare
Year: 2020
Subjects: subject: Immunology
subject: FOS: Clinical medicine

description: Additional file 1: Table S1. List of primers used in the SYBR green-based qRT-PCR analysis.
UN CONTRIBUTO ALLO STUDIO DELL'ITALIANO DELLA COMUNICAZIONE EPISTOLARE NEL SEICENTO: LE LETTERE DI JAN BRUEGHEL IL VECCHIO A FEDERICO BORROMEO ED ERCOLE BIANCHI
Creators: name: ARGENZIANO, ROSA
Publisher: name: Universit� degli Studi di Milano
Year: 2016

description: The present research is focused on a corpus consisting of 77 letters written by the Flemish painter Jan Brueghel the Elder and conserved at the Ambrosiana Library of Milan. The letters have been sent during a period starting from 1596 to 1624 to the Cardinal Federico Borromeo and to Ercole Bianchi, a notorious collector of Borromeo?s entourage. Cardinal Borromeo and Ercole Bianchi were both not only Brueghel?s friends, but also two of his most important customers; the painter realized for them many artworks, whose stories are testified by the letters at the Ambrosiana Library. Being fully written in Italian, these letters constitute a precious documentation of the linguistic relations between Flemands and Milan in the XVIIth century. Because of his self-educated competence with the Italian language, the painter decided to ask for the help of chosen secretaries in his correspondence with Borromeo and Bianchi. Among them, the most important was Peter Paul Rubens, polyglot and cultured artist, whose role was already acknowledged at the time of the first publication of the letters (by Giovanni Crivelli, 1868). In this work the identity of two other Brueghel?s occasional secretaries will be proposed for the first time, Philip Rubens (Peter?s brother) and Ferdinand Van den Eijnden, Brueghel?s brother-in law. Besides, a third hand (secretary X) documented throughout the correspondence remains unknown. The plurality of hands in Brueghel?s correspondence has allowed the disclosure of different levels of Italian owned by flemish non-professional writers: at the lowest level we can find Brueghel?s Italian, which is called by the painter himself mal schrito (bad written) because of its many mistakes and grammatical irregularities. Among all, the letters written by Peter Paul Rubens result the best written, mostly from a syntactic point of view. The last chapter consists of an artistic glossary collecting all the art related words found in the correspondence collected at the Ambrosiana Library being authored by Brueghel and other four Brueghel?s related Flemish painters, namely Brueghel?s son, Jan the Younger, Josse and Philip de Momper and Paul Bril, Brueghel?s collaborators and friends.
Necessary conditions on entanglement catalysts
Creators: name: Sanders, Yuval
name: Gour, Gilad
Publisher: name: arXiv
Year: 2009
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Given a pure state transformation $ψ\mapstoϕ$ restricted to entanglement-assisted local operations with classical communication, we determine a lower bound for the dimension of a catalyst allowing that transformation. Our bound is stated in terms of the generalised concurrence monotones (the usual concurrence of two qubits is one such monotone). We further provide tools for deriving further conditions upon catalysts of pure state transformations.
description: Brief Report, 4 pages, accepted in PRA
Comment on "Photon energy and carrier density dependence of spin dynamics in bulk CdTe crystal at room temperature"
Creators: name: Jiang, J. H.
name: Wu, M. W.
Publisher: name: arXiv
Year: 2009
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: We comment on the conclusion by Ma et al. [Appl. Phys. Lett. {\bf 94}, 241112 (2009)] that the Elliott-Yafet mechanism is more important than the D'yakonov-Perel' mechanism at high carrier density in intrinsic bulk CdTe at room temperature. We point out that the spin relaxation is solely from the D'yakonov-Perel' mechanism. The observed peak in the density dependence of spin relaxation time is exactly what we predicted in a recent work [Phys. Rev. B {\bf 79}, 125206 (2009)].
description: 2 pages
Reconstructing Quintom from Ricci Dark Energy
Creators: name: Feng, Chao-Jun
Publisher: name: arXiv
Year: 2008
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: The holographic dark energy with Ricci scalar as IR cutoff called Ricci dark energy(RDE) probes the nature of dark energy with respect to the holographic principle of quantum gravity theory. The scalar field dark energy models like quintom are often viewed as effective description of the underlying field theory of dark energy. In this letter, we assume RDE model as the underlying field theory to find how the generalized ghost condensate model(GGC) that can easily realize quintom behavior can be used to effectively describe it and reconstruct the function $h(ϕ)$ of the generalized ghost condensate model.
description: 16 pages, 6 figures, v2 published version
Multi-quasiparticle gamma-band structure in neutron-deficient Ce and Nd isotopes
Creators: name: Sheikh, J. A.
name: Bhat, G. H.
name: Palit, R.
name: Naik, Z.
name: Sun, Y.
Publisher: name: arXiv
Year: 2009
Subjects: subject: Nuclear Theory (nucl-th)
subject: Nuclear Experiment (nucl-ex)
subject: FOS: Physical sciences

description: The newly developed multi-quasiparticle triaxial projected shell-model approach is employed to study the high-spin band structures in neutron-deficient even-even Ce- and Nd-isotopes. It is observed that gamma-bands are built on each intrinsic configuration of the triaxial mean-field deformation. Due to the fact that a triaxial configuration is a superposition of several K-states, the projection from these states results in several low-lying bands originating from the same intrinsic configuration. This generalizes the well-known concept of the surface gamma-oscillation in deformed nuclei based on the ground-state to gamma-bands built on multi-quasiparticle configurations. This new feature provides an alternative explanation on the observation of two I=10 aligning states in 134Ce and both exhibiting a neutron character.
description: 15 pages, 9 figures, accepted by Nucl. Phys. A
Identification of a ¹Δ [delta] u - ¹Σ [sigma] ⁺g transition of CS₂ in the near ultraviolet
Creators: name: Malm, David Nelson
Publisher: name: University of British Columbia
Year: 2011

description: The strongest features in the absorption spectrum of CS₂ in the region 2900Å to 3500Å are identified, from temperature studies, as a π → π* ¹Δu - ¹Σ⁺g transition, where the Renner-Teller effect has split the ¹Δu state into ¹B₂ and ¹A₂ component states of a bent molecule. Analysis of some of the least severely perturbed bands of the ¹B₂ - ¹Σ⁺g transitions (3300 - 2900Å) shows that they form a parallel-polarized progression in the bending vibration, to an upper state with r(C - S) = 1.54₄Å, < SĈS = 163°, and a barrier to linearity of ~ 1400 cm⁻¹. Two hitherto unrecognized progressions of 'hot' bands, a weak vibronic ∏ - ∏ and a stronger vibronic Δ - Δ progression in the region 3300Å to 3500Å, are assigned to the ¹A₂ - ¹Σ⁺g transiton. This is a new type of transition, which does not appear in cold absorption, but whose 'hot' bands can obtain an amount of intensity (proportional to K²) through Renner-Teller mixing.
Heidegger in the Arab context : Fathi Meskini
Creators: name: Sahi, MM
Publisher: name: University Of Tasmania
Year: 2023

description: During the last two decades of the twentieth century, Heidegger was re-introduced to the Arabic world; however, while, originally, he had been presented as just another existentialist philosopher, this re-introduction saw him viewed quite differently by contemporary Arabic thinkers. In this thesis, I examine the impact of Heidegger on one such thinker, Fathi Meskini. He argues that Heidegger is less important for his treatment of existential issues than for his critique of hermeneutic reason, which helps reveal the history of metaphysics. In my treatment of Meskini's appropriation of Heidegger into Arabic thinking, I first discuss the problem of the language of Being, and Meskini's attempt to deconstruct philosophical Islamic tradition, from the moment when Aristotle's thinking was indigenised in the Arabic context. This Islamic tradition thought about the problem of being and expressed it in its own language. It is this tradition that constituted the basis of all Arabic reason throughout the twentieth century. Since the meaning of Being is accessed through the hermeneutics of the human being, I then go on to consider the way Meskini uses Heidegger's hermeneutic distinction between what-questioning, and who-questioning as a means to critique what Meskini called 'identical reason'. This mode of reason is still dominant in the Arabic sphere, in the thinking of both modernists and traditionalists. Meskini raises the question of how who-questioning can establish the meaning of belongingness, beyond the conflict between the self and other so as to achieve what he calls the 'new enlightenment of the last Muslim'.
On the consistency between the observed amount of CP violation in the K- and Bd-systems within minimal flavor violation
Creators: name: Buras, Andrzej J.
name: Guadagnoli, Diego
Publisher: name: arXiv
Year: 2009
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We reappraise the question whether the Standard Model, and Minimal Flavor Violating (MFV) models at large, can simultaneously describe the observed CP violation in the K- and Bd-systems. We find that CP violation in the Bd-system, measured most precisely through (sin 2 beta)_{J/psi Ks}, implies |epsilon_K^{SM}| = 1.78(25) x 10^{-3} for the parameter epsilon_K, measuring indirect CP violation in the K-system, to be compared with the experimental value |epsilon_K^{exp}| = 2.23(1) x 10^{-3}. To bring this prediction to 1 sigma agreement with experiment, we explore then the simplest new-physics possibility not involving new phases, namely that of MFV scenarios with no new effective operators besides the Standard Model ones. We emphasize the crucial input and/or measurements to be improved in order to probe this case. In particular we point out that this tension could be removed in this framework, with interesting signatures, e.g. correlated suppression patterns for rare K decay branching ratios. On the other hand, MFV contributions from new operators appear, in the calculable case of the MSSM, to worsen the situation. We finally explore some well-motivated new-physics scenarios beyond MFV, like those involving generic new contributions in Z-penguins.
description: 10 pages, 3 figures. v2: typo corrected, references improved, small textual modifications. Version submitted to journal
Spiraling Solitons: a Continuum Model for Dynamical Phyllotaxis and Beyond
Creators: name: Nisoli, Cristiano
Publisher: name: arXiv
Year: 2009
Subjects: subject: Soft Condensed Matter (cond-mat.soft)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: A novel, protean, topological soliton has recently been shown to emerge in systems of repulsive particles in cylindrical geometries, whose statics is described by the number-theoretical objects of phyllotaxis. Here we present a minimal and local continuum model that can explain many of the features of the phyllotactic soliton, such as locked speed, screw shift, energy transport and, for Wigner crystal on a nanotube, charge transport. The treatment is general and should apply to other spiraling systems. Unlike e.g. Sine-Gornon-like systems, our solitons can exist between non-degenerate structure, imply a power flow through the system, dynamics of the domains it separates; we also predict pulses, both static and dynamic. Applications include charge transport in Wigner Crystals on nanotubes or A- to B-DNA transitions.
description: 8 Pages, 6 Figures, Phys Rev E in press