cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
New York City House Mice (Mus musculus) as Potential Reservoirs for Pathogenic Bacteria and Antimicrobial Resistance Determinants
Creators: name: Williams, Simon Hedley
name: Che, Xiaoyu
name: Paulick, Ashley
name: Guo, Cheng
name: Lee, Bohyun
name: Muller, Dorothy R.
name: Uhlemann, Anne-Catrin
name: Lowy, Franklin D.
name: Corrigan, Robert M.
name: Lipkin, W. Ian
Publisher: name: Columbia University
Year: 2018
Subjects: subject: Mice
subject: Environmental health
subject: Pathogenic bacteria
subject: Microbiology
subject: FOS: Biological sciences

description: House mice (Mus musculus) thrive in large urban centers worldwide. Nonetheless, little is known about the role that they may play in contributing to environmental contamination with potentially pathogenic bacteria. Here, we describe the fecal microbiome of house mice with emphasis on detection of pathogenic bacteria and antimicrobial resistance genes by molecular methods. Four hundred sixteen mice were collected from predominantly residential buildings in seven sites across New York City over a period of 13 months. 16S rRNA sequencing identified Bacteroidetes as dominant and revealed high levels of Proteobacteria. A targeted PCR screen of 11 bacteria, as indicated by 16S rRNA analyses, found that mice are carriers of several gastrointestinal disease-causing agents, including Shigella, Salmonella, Clostridium difficile, and diarrheagenic Escherichia coli. Furthermore, genes mediating antimicrobial resistance to fluoroquinolones (qnrB) and β-lactam drugs (blaSHV and blaACT/MIR) were widely distributed. Culture and molecular strain typing of C. difficile revealed that mice harbor ribotypes associated with human disease, and screening of kidney samples demonstrated genetic evidence of pathogenic Leptospira species. In concert, these findings support the need for further research into the role of house mice as potential reservoirs for human pathogens and antimicrobial resistance in the built environment.
title: How fish surveys provide a 'backbone' for jellyfish research
Creators: name: Bastian, Thomas
name: Lilley, Martin K. S.
name: Stokes, David
name: Beggs, Steven E.
name: Lynam, Christopher P.
name: Hays, Graeme C.
name: Davenport, John
name: Doyle, Thomas K.
Publisher: name: ASC 2010 - Theme session R
Year: 2024
Subjects: Ecosystem observation, processes and dynamics

description: No abstracts are to be cited without prior reference to the author.Jellyfish populations are apparently increasing in response to environmental changes (e.g. climate change, eutrophication, overfishing). These increases may ultimately affect commercially important fish stocks. To address this issue it is critical to understand broad-scale distribution and abundance of jellyfish. However, owing to financial and logistical constraints, dedicated jellyfish surveys are rare and alternatives must be found. Here we demonstrate how collaboration with fishery scientists has allowed us to scale-up our jellyfish research from small-scale targeted surveys to effective shelf- and basin-wide studies. Jellyfish bycatch data from the Irish Ground Fish Survey (Irish Marine Institute) have provided new insights into the distribution of the jellyfish Pelagia noctiluca, over a widespread area (>160 000 km2) around Ireland and the UK, where the species has had major impacts on the aquaculture industry. In the northern half of the Irish Sea, we were able to assess basin-wide jellyfish distribution and abundance by using bycatch records from the Methot-Isaacs–Kidd (MIK) Survey for pelagic juvenile gadoids, carried out by AFBI (Agri-Food and Biosciences Institute), Northern Ireland. Such datasets are extremely useful to investigate possible trends in interannual variations of jellyfish abundance, as has successfully been done in few other places in the world. We therefore encourage further development of collaborations between academic marine biologists and fishery scientists in the field, in order to gather enough information to address the current concern about the role of jellyfish in marine ecosystems and their potential impacts on human activities in an effective, robust manner.
Phase coherence in quasicondensate experiments: an ab initio analysis via the stochastic Gross-Pitaevskii equation
Creators: name: Gallucci, D.
name: Cockburn, S. P.
name: Proukakis, N. P.
Publisher: name: arXiv
Year: 2012
Subjects: subject: Quantum Gases (cond-mat.quant-gas)
subject: FOS: Physical sciences

description: We perform an ab initio analysis of the temperature dependence of the phase coherence length of finite temperature, quasi-one-dimensional Bose gases measured in the experiments of Richard et al. (Phys. Rev. Lett. 91, 010405 (2003)) and Hugbart et al. (Eur. Phys. J. D 35, 155-163 (2005)), finding very good agreement across the entire observed temperature range ($0.8
description: Amended manuscript with improved agreement to experiment, following some additional clarifications by Mathilde Hugbart and Fabrice Gerbier and useful comments by the reviewer; accepted for publication in Physical Review A
Viral Diversity of House Mice in New York City
Creators: name: Williams, Simon Hedley
name: Che, Xiaoyu
name: Garcia, Joel A.
name: Klena, John D.
name: Lee, Bohyun
name: Muller, Dorothy R.
name: Ulrich, Werner
name: Corrigan, Robert M.
name: Nichol, Stuart T.
name: Jain, Komal
name: Lipkin, W. Ian
Publisher: name: Columbia University
Year: 2018
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Microbial ecology
subject: Mice
subject: Viruses

description: The microbiome of wild Mus musculus (house mouse), a globally distributed invasive pest that resides in close contact with humans in urban centers, is largely unexplored. Here, we report analysis of the fecal virome of house mice in residential buildings in New York City, NY. Mice were collected at seven sites in Manhattan, Queens, Brooklyn, and the Bronx over a period of 1 year. Unbiased high-throughput sequencing of feces revealed 36 viruses from 18 families and 21 genera, including at least 6 novel viruses and 3 novel genera. A representative screen of 15 viruses by PCR confirmed the presence of 13 of these viruses in liver. We identified an uneven distribution of diversity, with several viruses being associated with specific locations. Higher mouse weight was associated with an increase in the number of viruses detected per mouse, after adjusting for site, sex, and length. We found neither genetic footprints to known human viral pathogens nor antibodies to lymphocytic choriomeningitis virus.
title: Communication networks in ecosystem-based fisheries management: Multi-disciplinary sector knowledge management in the Chesapeake Bay
Creators: name: Hartley, Troy W.
Publisher: name: ASC 2010 - Theme session R
Year: 2024
Subjects: Ecosystem observation, processes and dynamics

description: No abstracts are to be cited without prior reference to the author.Starting in 2008, over 80 state and federal agency partners and research institutions, with funding from the US Environmental Protection Agency and support from the US National Marine Fisheries Services, developed a new operational approach for ecosystem-based fishery management (EBFM) in the Chesapeake Bay. The EBFM project will lead to the adoption of fishery management plans (FMPs) that consider the interconnections between five key species in the Chesapeake Bay (striped bass, menhaden, American shad, blue crab, and oyster), their physical and living environments, and the human influences on the species and environments. This approach had engaged Bay managers, scientists, fishing industry, and other stakeholders in developing ecosystem-based FMPs through species teams that are developing background synthesis of the biological understanding for each species, and issues briefs on the major ecosystem interconnections and needs. Next, four Quantitative Ecosystem Teams (QETs) are developing performance measures related to habitat suitability, stock assessment, socio-economics, and foodweb issues, respectively, clarifying interdependences and opportunities for extending management actions into the watershed (i.e. crossing federal–state–local government scales). This paper presents a communication network analysis (CNA) of the EBFM pilot and its participants. CNAs employ survey instruments to construct communication maps among individuals involved in the EBFM pilot QETs. Network analysis software (InFlow) is used to measure the network structure (e.g. density, path lengths) and function (e.g. the centrality measures—beweenness, closeness) that manages two-way communication, information flow, and knowledge sharing among participants. Findings have ramifications for designing multidisciplinary, multistakeholder fishery management programmes.
title: CB-110
Creators: name: Pérez-Torrado, Francisco J.
name: Fernandez-Turiel, J. L.
Publisher: name: DIGITAL.CSIC
Year: 2025
Subjects: subject: Sediment
subject: Tephra
subject: Sedimentary>Volcaniclastic
subject: Tephrochronology
subject: Protect, restore and promote sustainable use of terrestrial ecosystems, sustainably manage forests, combat desertification, and halt and reverse land degradation and halt biodiversity loss

description: Collection method=manual; Geological unit= Volcán Tres Cruces fall deposit
Λ as the Cosmic Eigenvalue: Emergent Time, Vacuum Energy Regulation, and the Oscillatory Structure of Spacetime
Creators: name: Yaren, Chris
Publisher: name: Zenodo
Year: 2025

description: We propose a novel framework in which the cosmological constant Λ functions not as a fixed parameter but as a fundamental eigenvalue governing the oscillatory structure of spacetime. Λ defines the causal horizon, regulates the quantum mode spectrum, controls entropy accumulation, and sets the emergent tempo of time through cumulative phase evolution. This approach reframes the cosmological constant problem by naturally limiting vacuum energy mode sums and harmonizing quantum field theory with curved spacetime. We explore observational consequences of a dynamic or emergent Λ, including horizon-scale freezing, entropy bounds, and measurable redshift evolution. Connections to string theory, loop quantum gravity, and symmetry principles are discussed.
Supergraphs and the cubic Leigh-Strassler model
Creators: name: Minahan, Joseph A.
Publisher: name: arXiv
Year: 2011
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We discuss supergraphs and their relation to "chiral functions" in N=4 Super Yang-Mills. Based on the magnon dispersion relation and an explicit three-loop result of Sieg's we make an all loop conjecture for the rational contributions of certain classes of supergraphs. We then apply superspace techniques to the "cubic" branch of Leigh-Strassler N=1 superconformal theories. We show that there are order 2^L/L single trace operators of length L which have zero anomalous dimensions to all loop order in the planar limit. We then compute the anomalous dimensions for another class of single trace operators we call one-pair states. Using the conjecture we can find a simple expression for the rational part of the anomalous dimension which we argue is valid at least up to and including five-loop order. Based on an explicit computation we can compute the anomalous dimension for these operators to four loops.
description: 22 pages; v2: Conjecture modified to apply only for the rational part of the chiral functions. Typos fixed. Minor modifications
title: Habitat suitability modeling for sardine in a highly diverse ecosystem: the Mediterranean Sea
Creators: name: Ferra, Pilar Tugores
name: Marianna, Giannoulaki
name: Iglesias, Magdalena
name: Bonnano, Angelo
name: Tičina, Vjekoslav
name: Konstantinos, Tsagarakis
name: Athanassios, Machias
name: Patti, Bernando
name: Iole, Leonori
name: De Felice, Andrea
name: Campanella, Fabio
name: Díaz, Nuria
name: Giraldez, Ana
name: Vasilis, Valavanis
name: Papaconstantinou, Costas
Publisher: name: ASC 2010 - Theme session R
Year: 2024
Subjects: Ecosystem observation, processes and dynamics

description: No abstracts are to be cited without prior reference to the author.Information integrated from different parts of the Mediterranean was used in order to model the spatial and temporal variability of the distribution grounds of sardine. Acoustic data recorded with a 38-kHz split-beam echosounder from the Aegean Sea (eastern Mediterranean), the Adriatic Sea (central Mediterranean), the Sicily Channel (central Mediterranean), and the Spanish waters (western Mediterranean) were analysed along with satellite environmental and bathymetry data to model the spatial distribution of sardine during summer, autumn, and early winter. Similarly, egg distribution data from the Spanish waters were used to model the potential spawning habitat of sardine during early winter. Satellite data were used as proxies to infer spatial variations of environmental factors and assess possible ecological relationships. Generalized additive models (GAMs) have been applied in a presence/absence approach. Model results were evaluated based on the estimation of receiver operating characteristic (ROC) plots. The environmental factors that were considered to affect sardine habitat during the different periods of year were identified and discussed. The selected model was used subsequently to identify those regions within the entire Mediterranean basin having higher probability of supporting sardine’s presence. Habitat suitability maps were produced for each year, period, and study area as well as for the entire Mediterranean basin, indicating suitable habitats for sardines. The temporal stability of these areas was also examined. The usefulness of such habitat suitability maps in environmental research and fishery management in a highly diverse environment like the Mediterranean is discussed.
Nearly flat band with Chern number C=2 on the dice lattice
Creators: name: Wang, Fa
name: Ran, Ying
Publisher: name: arXiv
Year: 2011
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: We point out the possibility of nearly flat band with Chern number C=2 on the dice lattice in a simple nearest-neighbor tightbinding model. This lattice can be naturally formed by three adjacent $(111)$ layers of cubic lattice, which may be realized in certain thin films or artificial heterostructures, such as SrTiO$_3$/SrIrO$_3$/SrTiO$_3$ trilayer heterostructure grown along $(111)$ direction. The flatness of two bands is protected by the bipartite nature of the lattice. Including the Rashba spin-orbit coupling on nearest-neighbor bonds separate the flat bands with others but maintains their flatness. Repulsive interaction will drive spontaneous ferromagnetism on the Kramer pair of flat bands and split them into two nearly flat bands with Chern number $C=\pm 2$. We thus propose that this may be a route to quantum anomalous Hall effect and further conjecture that partial filling of the C=2 band may realize exotic fractional quantum Hall effects.
description: updated references, 5 pages, 4 figures, RevTex4
Massive Gravity on de Sitter and Unique Candidate for Partially Massless Gravity
Creators: name: de Rham, Claudia
name: Renaux-Petel, Sebastien
Publisher: name: arXiv
Year: 2012
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: We derive the decoupling limit of Massive Gravity on de Sitter in an arbitrary number of space-time dimensions d. By embedding d-dimensional de Sitter into d+1-dimensional Minkowski, we extract the physical helicity-1 and helicity-0 polarizations of the graviton. The resulting decoupling theory is similar to that obtained around Minkowski. We take great care at exploring the partially massless limit and define the unique fully non-linear candidate theory that is free of the helicity-0 mode in the decoupling limit, and which therefore propagates only four degrees of freedom in four dimensions. In the latter situation, we show that a new Vainshtein mechanism is at work in the limit m^2\to 2 H^2 which decouples the helicity-0 mode when the parameters are different from that of partially massless gravity. As a result, there is no discontinuity between massive gravity and its partially massless limit, just in the same way as there is no discontinuity in the massless limit of massive gravity. The usual bounds on the graviton mass could therefore equivalently well be interpreted as bounds on m^2-2H^2. When dealing with the exact partially massless parameters, on the other hand, the symmetry at m^2=2H^2 imposes a specific constraint on matter. As a result the helicity-0 mode decouples without even the need of any Vainshtein mechanism.
description: 30 pages. Some clarifications and references added. New subsection 'Symmetry and Counting in the Full Theory' added. New appendix 'St\"uckelberg fields in the Na\"ive approach' added. Matches version published in JCAP
INFLUENCE OF NON-STEROID ANTI-INFLAMMATORY DRUGS ON THE HEMOSTASIS SYSTEM IN PATIENTS WITH RHEUMATOID ARTHRITIS
Creators: name: SIBIRKINA M.V.
Publisher: name: Zenodo
Year: 2023
Subjects: Rheumatoid Arthritis, Coronary Heart Disease, Non-Steroidal Anti-Inflammatory Drugs, Platelet Aggregation.

description: Abstract
The greatest medical, social and economic burden on society is primarily associated with rheumatoid arthritis (RA). The desire to improve the quality of life of RA patients sometimes justifies lifelong prescription of non-steroid anti-inflammatory drugs (NSAIDs). However, NSAIDs have a number of undesirable reactions, among which, in the last decade, complications from the cardiovascular system (CVS) have been given the greatest importance. Monitoring of the side effects of NSAIDs used in everyday practice is an urgent problem in modern medicine. This problem is especially relevant in rheumatic diseases, in which the systemic inflammatory process is associated with an increased risk of vascular accidents.
Comparison of methods to assess onset of breast development in the LEGACY Girls Study: methodological considerations for studies of breast cancer
Creators: name: Houghton, Lauren C.
name: Knight, Julia A.
name: De Souza, Mary J.
name: Goldberg, Mandy
name: White, Melissa L.
name: O’Toole, Karen
name: Chung, Wendy K.
name: Bradbury, Angela R.
name: Daly, Mary B.
name: Andrulis, Irene L.
name: John, Esther M.
name: Buys, Saundra S.
name: Terry, Mary Beth
Publisher: name: Columbia University
Year: 2018
Subjects: Breast--Growth
Breast--Cancer
Breast--Cancer--Risk factors
Puberty

description: Background
                Younger age at onset of breast development, which has been declining in recent decades, is associated with increased breast cancer risk independent of age at menarche. Given the need to study the drivers of these trends, it is essential to validate methods to assess breast onset that can be used in large-scale studies when direct clinical assessment of breast onset is not feasible.

                Methods
                Breast development is usually measured by Tanner stages (TSs), assessed either by physical examination or by mother’s report using a picture-based Sexual Maturation Scale (SMS). As an alternative, a mother-reported Pubertal Development Scale (PDS) without pictures has been used in some studies. We compared agreement of SMS and PDS with each other (n = 1022) and the accuracy of PDS with clinical TS as a gold standard for the subset of girls with this measure (n = 282) using the LEGACY cohort. We further compared prediction of breast onset using ROC curves and tested whether adding urinary estrone 1-glucuronide (E1G) improved the AUC.

                Results
                The agreement of PDS with SMS was high (kappa = 0.80). The sensitivity of PDS vs clinical TS was 86.6%. The AUCs for PDS alone and SMS alone were 0.88 and 0.79, respectively. Including E1G concentrations improved the AUC for both methods (0.91 and 0.86 for PDS and SMS, respectively).

                Conclusions
                The PDS without pictures is a highly accurate, sensitive, and specific method for assessing breast onset, especially in settings where clinical TS is not feasible. In addition, it is comparable to SMS methods with pictures and thus easier to implement in large-scale studies, particularly phone-based interviews where pictures may not be available. Urinary E1G can improve accuracy over than PDS or SMS alone.
Complete intracranial response to talimogene laherparepvec (T-Vec), pembrolizumab and whole brain radiotherapy in a patient with melanoma brain metastases refractory to dual checkpoint-inhibition
Creators: name: Blake, Zoë
name: Marks, Douglas K.
name: Gartrell, Robyn D.
name: Hart, Thomas
name: Horton, Patti
name: Cheng, Simon K.
name: Taback, Bret
name: Horst, Basil
name: Saenger, Yvonne M.
Publisher: name: Columbia University
Year: 2018
Subjects: Cancer--Immunotherapy
Melanoma--Treatment
Metastasis
Cancer--Treatment--Research

description: Background
                Immunotherapy, in particular checkpoint blockade, has changed the clinical landscape of metastatic melanoma. Nonetheless, the majority of patients will either be primary refractory or progress over follow up. Management of patients progressing on first-line immunotherapy remains challenging. Expanded treatment options with combination immunotherapy has demonstrated efficacy in patients previously unresponsive to single agent or alternative combination therapy.

                Case presentation
                We describe the case of a patient with diffusely metastatic melanoma, including brain metastases, who, despite being treated with stereotactic radiosurgery and dual CTLA-4/PD-1 blockade (ipilimumab/nivolumab), developed systemic disease progression and innumerable brain metastases. This patient achieved a complete CNS response and partial systemic response with standard whole brain radiation therapy (WBRT) combined with Talimogene laherparepvec (T-Vec) and pembrolizumab.

                Conclusion
                Patients who do not respond to one immunotherapy combination may respond during treatment with an alternate combination, even in the presence of multiple brain metastases. Biomarkers are needed to assist clinicians in evidence based clinical decision making after progression on first line immunotherapy to determine whether response can be achieved with second line immunotherapy.
title: Identifying the potential habitat of anchovy Engraulis encrasicolus at different life stages in the Mediterranean Sea
Creators: name: Marianna, Giannoulaki
name: Iglesias, Magdalena
name: Ferra, Pilar Tugores
name: Bonnano, Angelo
name: Quinci, Enza
name: De Felice, Andrea
name: Gramolini, Roberto
name: Liorzou, Bernand
name: Tičina, Vjekoslav
name: Pyrounaki, Maria Myrto
name: Konstantinos, Tsagarakis
name: Athanassios, Machias
name: Somarakis, Stylianos
name: Schismenou, Eudoxia
name: Basilone, Walter
name: Iole, Leonori
name: Patti, Bernando
name: Miguel, Joan
name: Oñate, Dolores
name: Roos, David
name: Bigot, Jean Louis
name: Vasilis, Valavanis
Publisher: name: ASC 2010 - Theme session R
Year: 2024
Subjects: Ecosystem observation, processes and dynamics

description: No abstracts are to be cited without prior reference to the author.Information integrated from different parts of the Mediterranean was used to model the spatial and temporal variability of the distribution grounds of anchovy at different life stages. Acoustic data recorded with a 38-kHz split-beam echosounder from the Aegean Sea (eastern Mediterranean), the Adriatic Sea and the Sicily Channel (central Mediterranean), the Spanish waters and the Gulf of Lions (western Mediterranean) were analysed along with satellite environmental and bathymetry data to model the spatial distribution of adult and juvenile anchovy during summer, autumn, and winter. Similarly, egg distribution data from summer surveys were used to model the potential spawning habitat of anchovy. Satellite data were used as proxies to infer spatial variations of environmental factors and assess possible ecological relationships. Generalized additive models (GAMs) were applied in a presence/absence approach. Model results were evaluated based on the estimation of receiver operating characteristic (ROC) plots. The environmental factors considered to affect anchovy during the different periods of year were identified and discussed. The selected model was subsequently used to identify those regions within the entire Mediterranean basin with higher probability of supporting suitable anchovy habitats. Potential habitat maps were produced for each year, period, and study area as well as for the entire Mediterranean basin indicating suitable areas for anchovy’s presence. The temporal stability of these areas was examined. The usefulness of such habitat suitability maps concerning the different life stages of a species in environmental research and fishery management is discussed.
Microscopic sub-barrier fusion calculations for the neutron star crust
Creators: name: Umar, A. S.
name: Uberacker, V. E.
name: Horowitz, C. J.
Publisher: name: arXiv
Year: 2012
Subjects: subject: Nuclear Theory (nucl-th)
subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: Fusion of very neutron rich nuclei may be important to determine the composition and heating of the crust of accreting neutron stars. Fusion cross sections are calculated using time-dependent Hartree-Fock theory coupled with density-constrained Hartree-Fock calculations to deduce an effective potential. Systems studied include 16O+16O, 16O+24O, 24O+24O, 12C+16O, and 12C+24O. We find remarkable agreement with experimental cross sections for the fusion of stable nuclei. Our simulations use the SLy4 Skyrme force that has been previously fit to the properties of stable nuclei, and no parameters have been fit to fusion data. We compare our results to the simple São Paulo static barrier penetration model. For the asymmetric systems 12C+24O or 16O+24O we predict an order of magnitude larger cross section than those predicted by the São Paulo model. This is likely due to the transfer of neutrons from the very neutron rich nucleus to the stable nucleus and dynamical rearrangements of the nuclear densities during the collision process. These effects are not included in potential models. This enhancement of fusion cross sections, for very neutron rich nuclei, can be tested in the laboratory with radioactive beams.
description: 9 pages, 11 figures, corrected small errors in Figs 10, 11, Phys. Rev. C in press
Measurement of the Z/gamma* + b-jet cross section in pp collisions at 7 TeV
Creators: name: CMS Collaboration
Publisher: name: arXiv
Year: 2012
Subjects: subject: High Energy Physics - Experiment (hep-ex)
subject: FOS: Physical sciences

description: The production of b jets in association with a Z/gamma* boson is studied using proton-proton collisions delivered by the LHC at a centre-of-mass energy of 7 TeV and recorded by the CMS detector. The inclusive cross section for Z/gamma* + b-jet production is measured in a sample corresponding to an integrated luminosity of 2.2 inverse femtobarns. The Z/gamma* + b-jet cross section with Z/gamma* to ll (where ll = ee or mu mu) for events with the invariant mass 60 < M(ll) < 120 GeV, at least one b jet at the hadron level with pT > 25 GeV and abs(eta) < 2.1, and a separation between the leptons and the jets of Delta R > 0.5 is found to be 5.84 +/- 0.08 (stat.) +/- 0.72 (syst.) +(0.25)/-(0.55) (theory) pb. The kinematic properties of the events are also studied and found to be in agreement with the predictions made by the MadGraph event generator with the parton shower and the hadronisation performed by PYTHIA.
description: Submitted to the Journal of High Energy Physics
The First Law of Binary Black Hole Mechanics in General Relativity and Post-Newtonian Theory
Creators: name: Tiec, Alexandre Le
name: Blanchet, Luc
name: Whiting, Bernard F.
Publisher: name: arXiv
Year: 2011
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: First laws of black hole mechanics, or thermodynamics, come in a variety of different forms. In this paper, from a purely post-Newtonian (PN) analysis, we obtain a first law for binary systems of point masses moving along an exactly circular orbit. Our calculation is valid through 3PN order and includes, in addition, the contributions of logarithmic terms at 4PN and 5PN orders. This first law of binary point-particle mechanics is then derived from first principles in general relativity, and analogies are drawn with the single and binary black hole cases. Some consequences of the first law are explored for PN spacetimes. As one such consequence, a simple relation between the PN binding energy of the binary system and Detweiler's redshift observable is established. Through it, we are able to determine with high precision the numerical values of some previously unknown high order PN coefficients in the circular-orbit binding energy. Finally, we propose new gauge invariant notions for the energy and angular momentum of a particle in a binary system.
description: 43 pages, 3 figures; matches the published version
title: A change in Fisheries Science to focus on the outcome rather than the output
Creators: name: Rossiter, Tom
Publisher: name: ASC 2010 - Theme session R
Year: 2024
Subjects: Ecosystem observation, processes and dynamics

description: No abstracts are to be cited without prior reference to the author.The world of marine science is rapidly changing. It seems that the more we learn, the more we appreciate the need to understand further, and today the demand for good marine science has never been greater. The customer base has shifted and dramatically. Historically, marine science has been targeted towards marine scientists; today the customer is society in its broadest sense and unfortunately all too often marine scientists have failed to communicate and deliver what the customer wants. This paper will look at three aspects of the issue. First, it will describe the customer base, focusing on fishers, and trace its development over the past two decades. Second, it addresses the question of “lack or underdevelopment” by scientists in terms of research and development (R&D) and links this to value for money (VFM). Finally, it presents a number of fishing and gear technology case studies, which have successfully addressed the challenge, and makes recommendations for the future.
"Distempers peculiar to negros" : colonial physicians, etiological investigations, and the racialization of medicine in the eighteenth-century British West Indies
Creators: name: Johnson, Hayley Rebecca
Publisher: name: University of British Columbia
Year: 2012

description: This thesis examines eighteenth-century colonial medical attitudes toward and discussions of human difference. By surveying five medical tracts written by physicians working in Britain’s West Indian colonies, it contributes greater understanding to contemporary notions of human variation. In addition, it also produces a counter-narrative to scholastic depictions of eighteenth-century British medicine, which argue that medical debates over human variation were dominated by theologically-based theories promoting the homogeneity of “man.” Intervening in this discussion, this paper posits that a number of contemporary colonial medical practitioners developed theories that were based not on theology or previous medical assumptions, but on empirical evidence. Through a series of clinical observations, these practitioners observed vast health disparities between their British and slave (“Negro”) patients; though the bodies of each group responded negatively to transplantation to the West Indies, Britons and Negros reportedly suffered distinctly from different forms of illness. In response to these observations, the highlighted physicians identified a set of diseases—including Yaws, the “Sleepy Distemper,” and the Guinea Worm—which they determined must be exclusive to Negros. Past historical scholarship claims that eighteenth-century physicians overwhelmingly agreed that humans varied as a result of climatic influence. Here, however, I contend that the medical practitioners studied in this paper concluded that variations in health, disease, and physiology were the result of innate, racially-determined bodily and mental characteristics. By positing that there were a number of exclusively “Negro” diseases, they simultaneously suggested that the bodies of Negros were racially pathological and that humanity was heterogeneous—two conclusions that historians of race argue were not reached until the works of nineteenth-century racial scientists. Throughout the following case studies, I argue that the racialization of medicine began as early as 1707 with the colonial writings of British physician Hans Sloane. While this initial racialization process did not overtly express any value judgements, it did suggest that Negros should be treated differently—if only in medical terms. It also directly contributed to and influenced racist medical declarations made about Africans and other minority groups throughout the two proceeding centuries.
Enabling multiplexed testing of pooled donor cells through whole-genome sequencing
Creators: name: Chan, Yingleong
name: Chan, Ying K.
name: Goodman, Daniel B.
name: Guo, Xiaoge
name: Chavez, Alejandro
name: Lim, Elaine T.
name: Church, George M.
Publisher: name: Columbia University
Year: 2018
Subjects: Single nucleotide polymorphisms
Genomes
Biology
Expectation-maximization algorithms

description: We describe a method that enables the multiplex screening of a pool of many different donor cell lines. Our method accurately predicts each donor proportion from the pool without requiring the use of unique DNA barcodes as markers of donor identity. Instead, we take advantage of common single nucleotide polymorphisms, whole-genome sequencing, and an algorithm to calculate the proportions from the sequencing data. By testing using simulated and real data, we showed that our method robustly predicts the individual proportions from a mixed-pool of numerous donors, thus enabling the multiplexed testing of diverse donor cells en masse.
              More information is available at
                  https://pgpresearch.med.harvard.edu/poolseq/
Mathematical models for immunodeficiency virus : post-treatment and memory activation
Creators: name: Herrera Reyes, Alejandra Donaji
Publisher: name: University of British Columbia
Year: 2012

description: Nowdays, HIV infection can be controlled by anti-retroviral drug therapy (ART). However, a persistent viral reservoir in treated patients prevents the eradication of HIV infection. H-iART is an innovator treatment that consists of regular ART and the drugs Maraviroc and Darunavir, and H-iART was enforced with Auranofin. The drug Maraviroc (MRV) was proved to be a good CCR5 inhibitor, which is a HIV correceptor. The drug Auranofin has been shown to accelerate the activation rate of latent cells and also alters the kinetics of viral rebound when drug treatment is interrupted. Recent studies on monkeys infected with SIV have shown a complete suppression of the viral load during H-iART with Auranofin treatment and a persistent suppression of it in the absence of ART. Motivated by the results of the experiments I present deterministic and stochastic models of HIV after treatment interruption. For H-iART treatment, the ODE models were used as a start point to create three different continuous time multi-type branching process. From equations for the probability generating function we use analytic solutions, numerical approximations, or numerical simulations to extract the probability of observable viral blips. We compare our results with the data of two rhesus macaques. We find that more than one latent cell needs to activate in order to observe the data blips, and that the net reproductive number of virus must be very close to one. Since this is unlikely, these results suggest that the viral dynamics must be more complex than our model allows for. For the ART+Auranofin treatment, I will present an ODE model of HIV population dynamics including drug treatment and the immune response to model the viral rebound at treatment interruption.
Fluctuations and Correlations of Conserved Charges in the $(2+1)$ Polyakov Quark Meson Model
Creators: name: Chatterjee, Sandeep
name: Mohan, Kirtimaan A.
Publisher: name: arXiv
Year: 2012
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Lattice (hep-lat)
subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: We consider the $(2+1)$ flavor Polyakov Quark Meson Model and study the fluctuations (correlations) of conserved charges upto sixth (fourth) order. Comparison is made with lattice data wherever available and overall good qualitative agreement is found, more so for the case of the normalised susceptibilities. The model predictions for the ratio of susceptibilities go to that of an ideal gas of hadrons as in Hadron Resonance Gas Model at low temperatures while at high temperature the values are close to that of an ideal gas of massless quarks. Our study provides a strong basis for the use of PQM as an effective model to understand the topology of the QCD phase diagram.
description: modified text, version accepted for publication in PRD
title: Data archaeology and rescue: recycling old information for new concerns
Creators: name: Hawkins, S. J.
name: Firth, L.
name: Genner, M. J.
name: Mieszkowska, N.
name: Jenkins, S. R.
name: Burrows, M. T.
Publisher: name: ASC 2010 - Theme session R
Year: 2024
Subjects: Ecosystem observation, processes and dynamics

description: No abstracts are to be cited without prior reference to the author.Long-term data are essential to disentangle climate driven changes from those caused by natural fluctuations coupled with regional and local scale impacts such as fishing, pollution, and habitat loss. We describe two case studies where data stretching back 50-100 years have been used to explore climate-driven change. Records of fish surveys dating back to before World War I were retrieved as written records from cellars, drawers, and cupboards at the Marine Biological Association of the United Kingdom (MBA), garages of long deceased members of staff, as well as from obsolete electronic media. These were then analysed to disentangle the interaction between fishing pressure and climate change on bottom fish assemblages. This work has contributed to the policy arena via IPCC 2007 as well as the UK Marine Climate Change Impact Programme (MCCIP). In parallel with this work, broad-scale and long-term records of intertidal species were collated building on pioneering surveys from the 1950s which provided a baseline from a previously warm period allowing comparison with recent patterns determined by re-surveys between 2002 and 2010. These have shown major shifts in biogeographic ranges during the recent period of rapid warming. This work has informed policy via MCCIP as well as providing contextual information for management of marine conservation areas. High-quality publications have resulted from both studies. They have also informed current debate on adaptation to climate change.
Epigenome-wide association study of total serum immunoglobulin E in children: a life course approach
Creators: name: Peng, Cheng
name: Cardenas, Andres
name: Rifas-Shiman, Sheryl L.
name: Hivert, Marie-France
name: Gold, Diane R.
name: Platts-Mills, Thomas A.
name: Lin, Xihong
name: Oken, Emily
name: Baccarelli, Andrea A.
name: Litonjua, Augusto A.
name: DeMeo, Dawn L.
Publisher: name: Columbia University
Year: 2018
Subjects: Immunoglobulin E
Epigenetics
Genomics
Environmental health

description: Background
                IgE-mediated sensitization may be epigenetically programmed in utero, but early childhood environment may further alter complex traits and disease phenotypes through epigenetic plasticity. However, the epigenomic footprint underpinning IgE-mediated type-I hypersensitivity has not been well-understood, especially under a longitudinal early-childhood life-course framework.

                Methods
                We used epigenome-wide DNA methylation (IlluminaHumanMethylation450 BeadChip) in cord blood and mid-childhood peripheral blood to investigate pre- and post-natal methylation marks associated with mid-childhood (age 6.7–10.2) total serum IgE levels in 217 mother-child pairs in Project Viva—a prospective longitudinal pre-birth cohort in eastern Massachusetts, USA. We identified methylation sites associated with IgE using covariate-adjusted robust linear regressions.

                Results
                Nineteen methylation marks in cord blood were associated with IgE in mid-childhood (FDR
Rebuttal of Kowalenko's paper as concerns the irrationality of Euler's constant
Creators: name: Coffey, Mark W.
name: Sondow, Jonathan
Publisher: name: arXiv
Year: 2012
Subjects: subject: Number Theory (math.NT)
subject: FOS: Mathematics
subject: 11J72

description: We rebut Kowalenko's claims in 2010 that he proved the irrationality of Euler's constant, and that his rational series for it is new.
description: 3 pages including a referee's report; added Goldbach's theorem and a reference for it
Classical ladder operators, polynomial Poisson algebras and classification of superintegrable systems
Creators: name: Marquette, Ian
Publisher: name: arXiv
Year: 2011
Subjects: subject: Mathematical Physics (math-ph)
subject: Exactly Solvable and Integrable Systems (nlin.SI)
subject: FOS: Physical sciences

description: We recall results concerning one-dimensional classical and quantum systems with ladder operators. We obtain the most general one-dimensional classical systems respectively with a third and a fourth order ladder operators satisfying polynomial Heisenberg algebras. These systems are written in terms of the solutions of quartic and quintic equations. We use these results to present two new families of superintegrable systems and examples of trajectories that are deformed Lissajous's figures.
description: 18 pages
title: Fishers: the forgotten scientists
Creators: name: Hind, Edward
Publisher: name: ASC 2010 - Theme session R
Year: 2024
Subjects: Ecosystem observation, processes and dynamics

description: No abstracts are to be cited without prior reference to the author.Fisheries managers and scientists are currently attempting to improve the knowledge base for fisheries management through collation of multi-institutional and multidisciplinary research. Although these attempts at knowledge management are necessary for good practice in fishery science, they could be in vain. Building on previous research in North America, Europe, and the Indo-Pacific, research in Ireland shows that fishers feel omitted from knowledge management exercises connected to fishery management and as a result are sceptical of scientific knowledge communicated to them by fishery managers. This reduces fishers’ will to take fishery management policies based on science seriously and can compromise their compliance with fishery regulations and their cooperation with fishery managers. Novel interview techniques conducted on fishers based in Galway Bay show that fishers do indeed have unique knowledge that should be part of the knowledge base for fishery management. Far from being simply ecological, fishers’ knowledge gives detailed insights into the strategies of fishers. Analysis of these strategies by fishery managers could greatly inform fishery management policy. Inclusion of fishers’ knowledge would help to legitimise fishery management and science among fishers. This legitimization would increase the chance of fishery management policy being successful. However, despite recognition by some scientists that fishers’ knowledge could be used alongside traditional scientific knowledge to provide a basis for better fishery management policies, it is rarely used by fishery managers. The omission of a proposal to include stakeholder knowledge in recent proposed reforms to the European Union’s common fishery policy suggests that fishers will remain forgotten scientists.
The critical points of lattice trees and lattice animals in high dimensions
Creators: name: Mejía Miranda, Yuri
Publisher: name: University of British Columbia
Year: 2012

description: We study lattice trees and lattice animals in high dimensions. Lattice trees and animals are interesting combinatorial objects used to model branched polymers in polymer science. They are also of interest in combinatorics and in the study of critical phenomena in statistical physics. [Abstract portion beginning here modified and differs from the print copy]. Our study takes place in the nearest-neighbor and spread-out models on the d-dimensional integer lattice. On either graph, a lattice animal is a finite connected subgraph, and a lattice tree is an animal without cycles.   Let t_n and a_n be the number of lattice trees and animals with n bonds that contain the origin, respectively. Standard subadditivity arguments provide the existence of the  growth constants τ and α, which are the limit, as the dimension d goes to infinity,  of the n-th root of t_n and a_n, respectively.] We are interested in the critical points of these models, which are the reciprocals of the corresponding growth constants. We rigorously calculate the first three terms of a 1/d-expansion for the critical points of nearest-neighbor lattice trees and animals. The proof follows a recursive argument similar to the one used by Hara and Slade (1995), van der Hofstad and Slade (2006), to obtain analogous results for the critical points of self-avoiding walks and percolation.   To provide the leading terms in the expansions, we use a mean-field model, related to the Galton-Watson branching process with critical Poisson offspring distribution, and results obtained with the lace expansion. The leading terms are also calculated in the spread-out model. Then we develop expansions for the nearest-neighbor generating functions and, together with the lace expansion, obtain the first and second correction terms. Our result gives a rigorous proof for previous work on the subject [11],[21, 36]. Given the algorithmic nature of the proof, it can be extended, with sufficient labor, to compute higher degree terms. It may provide the starting point for proving the existence of an asymptotic expansion with rational coefficients, for the critical point of nearest-neighbor lattice trees.
Metalworking Ceramics
Creators: name: Bayley, Justine
Publisher: name: Archaeology Data Service
Year: 2023

description: Medieval Ceramics: Journal of the Medieval Ceramics Research Group, 16, 3-10
description: This paper outlines the range of ceramic finds, and their specific attributes, which provide evidence for the metallurgical processes that were carried out in medieval Britain. These are mainly crucibles and moulds associated with the working of copper alloys, gold and silver; evidence for lead, tin and pewter working is much rarer, while the only ceramics associated with iron-working are vitrified clay hearth linings. A typology of Late Saxon and medieval crucibles is presented, together with details of related forms such as cupels for the refining of precious metals, parting vessels and distillation vessels, and the technology of moulds. The potential of these finds for scientific analyses and further research is also summarised.