Miracle-dz/UniFAR-FTUs huggingface dataset:
Tropical Pacific and Atlantic Climate Variability in CCSM3

Abstract Simulations of the El Nino–Southern Oscillation (ENSO) phenomenon and tropical Atlantic climate variability in the newest version of the Community Climate System Model [version 3 (CCSM3)] are examined in comparison with observations and previous versions of the model. The analyses are based upon multicentury control integrations of CCSM3 at two different horizontal resolutions (T42 and T85) under present-day CO2 concentrations. Complementary uncoupled integrations with the atmosphere and ocean component models forced by observed time-varying boundary conditions allow an assessment of the impact of air–sea coupling upon the simulated characteristics of ENSO and tropical Atlantic variability. The amplitude and zonal extent of equatorial Pacific sea surface temperature variability associated with ENSO is well simulated in CCSM3 at both resolutions and represents an improvement relative to previous versions of the model. However, the period of ENSO remains too short (2–2.5 yr in CCSM3 compared to 2.5.
A nested mixture model for protein identification using mass spectrometry

Mass spectrometry provides a high-throughput way to identify proteins in biological samples. In a typical experiment, proteins in a sample are first broken into their constituent peptides. The resulting mixture of peptides is then subjected to mass spectrometry, which generates thousands of spectra, each characteristic of its generating peptide. Here we consider the problem of inferring, from these spectra, which proteins and peptides are present in the sample. We develop a statistical approach to the problem, based on a nested mixture model. In contrast to commonly used two-stage approaches, this model provides a one-stage solution that simultaneously identifies which proteins are present, and which peptides are correctly identified. In this way our model incorporates the evidence feedback between proteins and their constituent peptides. Using simulated data and a yeast data set, we compare and contrast our method with existing widely used approaches (Peptide-Prophet/ProteinProphet) and with a recently published new approach, HSM. For peptide identification, our single-stage approach yields consistently more accurate results. For protein identification the methods have similar accuracy in most settings, although we exhibit some scenarios in which the existing methods perform poorly.
Combustion Behind Shock Waves

Laminar hydrocarbon flames, which have adiabatic flame speeds on the order of a meter per second, are conventionally described by a leading convective-diffusive zone followed by an energyreleasing reactive-diffusive region. On the other hand, combustion induced by a strong shock wave is typically modeled as a convective-reactive balance with negligible diffusion, which may be called a convective explosion or fast flame. The transition between these two modes of combustion is an important issue in flame acceleration and transition from deflagration to detonation. In this study, we examine the range of pre-mixed combustion modes possible behind shock waves through numerical solutions of the one-dimensional, steady reactive Navier-Stokes equations with a detailed chemical reaction mechanism for stoichiometric methane-air mixtures. Shock Mach numbers ranging between one and the Chapman-Jouguet (CJ) value, a maximum of about five for typical fuel-air mixtures, are considered. The mixture examined in this study is stoichiometric methane-air. Two issues are considered in depth; one is the transition from diffusion-controlled to diffusionless combustion when the combustion wave speed is specified; the other is the question of the existence of a well-defined adiabatic flame speed behind a strong shock wave.
What predicts anti‐Roma prejudice? Qualitative and quantitative analysis of everyday sentiments about the Roma

Institute of Psychology, ELTE E€ otv€ os Lor and University Institute of Cognitive Neuroscience and Psychology, Research Center for Natural Sciences, Hungarian Academy of Sciences Department of Brain and Cognitive Science, Massachusetts Institute of Technology Department of Psychological and Brain Sciences, University of Massachusetts Amherst Doctoral School of Psychology, ELTE E€ otv€ os Lor and University
Improving influenza virological surveillance in Europe: strain-based reporting of antigenic and genetic characterisation data, 11 European countries, influenza season 2013/14

Influenza antigenic and genetic characterisation data are crucial for influenza vaccine composition decision making. Previously, aggregate data were reported to the European Centre for Disease Prevention and Control by European Union/European Economic Area (EU/EEA) countries. A system for collecting case-specific influenza antigenic and genetic characterisation data was established for the 2013/14 influenza season. In a pilot study, 11 EU/EEA countries reported through the new mechanism. We demonstrated feasibility of reporting strain-based antigenic and genetic data and ca 10% of influenza virus-positive specimens were selected for further characterisation. Proportions of characterised virus (sub)types were similar to influenza virus circulation levels. The main genetic clades were represented by A/StPetersburg/27/2011(H1N1)pdm09 and A/Texas/50/2012(H3N2). A(H1N1)pdm09 viruses were more prevalent in age groups (by years) < 1 (65%; p = 0.0111), 20–39 (50%; p = 0.0046) and 40–64 (55%; p = 0.00001) while A(H3N2) viruses were most prevalent in those ≥ 65 years (62%*; p = 0.0012). Hospitalised patients in the age groups 6–19 years (67%; p = 0.0494) and ≥ 65 years (52%; p = 0.0005) were more frequently infected by A/Texas/50/2012 A(H3N2)-like viruses compared with hospitalised cases in other age groups. Strain-based reporting enabled deeper understanding of influenza virus circulation among hospitalised patients and substantially improved the reporting of virus characterisation data. Therefore, strain-based reporting of readily available data is recommended to all reporting countries within the EU/EEA.
Accumulation of unintegrated circular viral DNA in monocytes and growth‐arrested T cells following infection with HIV‐1

Cytocidal retrovirus infection is characterized by rapid accumulation of unintegrated viral DNA forms. These are thought to be generated by multiple rounds of reinfection and have been suggested to play a central role in cytopathogenesis. Here we have reviewed the work done in this area with HIV‐1, mostly using acutely and chronically infected T cell and monocytic cell lines and in some cases T cells blocked at S phase of the cell cycle by aphidicolin treatment. To these studies, we have compared our findings with HIV‐1 infected primary peripheral blood monocyte‐derived macrophages and untreated and growth‐arrested MT‐2 cells, two biologically disparate cell populations. Using 1‐ and 2‐long terminal repeat (LTR) circular forms as indicators of unintegrated viral DNA, we found similar rapid accumulation in both untreated and growth‐arrested MT‐2 cells. In contrast, we found much lower levels in monocyte/macrophages. Our findings suggest that accumulation of unintegrated viral DNA does not require virus production and reinfection in growth‐arrested T cells. The significantly lower levels found in monocyte/macrophages may reflect superinfection resistance, allowing the maintenance of a persistent infection. J. Leukoc. Biol. 56: 289–293; 1994.
The development of noun-modifying constructions in child Mandarin

This thesis is protected by copyright, with all rights reserved. By reading and using the thesis, the reader understands and agrees to the following terms: 1. The reader will abide by the rules and legal ordinances governing copyright regarding the use of the thesis. 2. The reader will use the thesis for the purpose of research or private study only and not for distribution or further reproduction or any other purpose. 3. The reader agrees to indemnify and hold the University harmless from and against any loss, damage, cost, liability or expenses arising from copyright infringement or unauthorized usage.
A laminopathic mutation disrupting lamin filament assembly causes disease-like phenotypes in Caenorhabditis elegans

Mutations in human LMNA cause Emery-Dreifuss muscular dystrophy; however, a mechanistic link between the effect of mutations on lamin filament assembly and disease phenotype has not been established. Here we show that changes in lamin filament structure translate into disease phenotypes in Caenorhabditis elegans by altering the character of the nuclear lamina.
Optimizing multicast content delivery over novel mobile networks

The rapid growth in mobile traffic leads to the current evolution trend of mobile networks towards a flat architecture. However, the centralized mobility management protocols (e.g. MIPv6, PMIPv6) are not optimized for the flat architecture due to their limitations e.g. complex tunnel management, scalability issue, etc. Hence, a novel mobility management has been proposed for the flat architecture, called distributed mobility management (DMM). IP multicast, an effective mechanism for traffic delivery, can be enabled in DMM by deploying MLD Proxy function at mobile access routers (MARs) with the upstream interface being configured to the multicast infrastructure (before mobility) or to the tunnel towards the mobile node’s mobility anchor (after mobility) (namely tunnel-based approach). In case of mobility, the utilization of the tunnel may result in the tunnel convergence problem when the multiple instances of the same multicast traffic converges to a MAR due to the multiple tunnels established with several mobility anchors (leading to the redundant traffic at the MARs). Compared to PMIPv6, the tunnel convergence problem may become much more severe, especially in highly mobile regime. In this paper, we propose some mechanisms to greatly reduce the amount of redundant traffic at the MARs with a minor increase of service disruption time compared to the tunnel-based approach. Keywords-Future Internet; IP multicast; multicast mobility; tunnel convergence problem; handover delay; Distributed Mobility Management.
ICML9 | CRICS7 - Salvador, Bahia - Brazil,

The hypothesis of a Neotropical origin of the Leishmania/Endotrypanum clade is reviewed. The position of the L. (Sauroleishmania) external to the subgenus L. (Leishmania) is not consistent with the Neotropical origin of the latter subgenus. It is suggested that this may be a consequence of a faster evolutionary rate in the L. (Sauroleishmania). The implications for the classsification of the phlebotomine sandflies of the hypothesis for a Neotropical origin of the Leishmania is also considered. The classification of Galati (1995) is proposed to be most consistent with the hypothesis of a Neotropical origin of the Leishmania, whilst classifications which place the New and Old World species in separate taxa are inconsistent with this hypothesis.
On the implementation of open boundary conditions for a general circulation model: The three-dimensional case

This article discusses the results of an experimental survey on the performance of a select group of open boundary conditions (OBCs) for three- dimensional, primitive equation models. The focus is on passive conditions, where the model response at the open boundaries is dictated by the interior dynamics. The performance of the OBCs is tested in a series of numerical experiments conducted in a rotating channel which includes variable bottom topography and density stratification. The experiments are sele. cted to enhance nonlinear phenomena that comprises advection and the propagation of dispersive waves. The first two experiments study coastal upwelling with constant and time-varying wind forcing. The third experiment analyses the barotropic and baroclinic response of a coastal ocean due to the passage of a traveling storm. The open boundary condition with the best overall performance is the flow relaxation scheme on sea surface elevation and transport, a radiation condition for internal velocities, and a combined scheme of flow advection and relaxation for the temperature field. A modified gravity wave radiation scheme provides reasonable responses when combined with radiation conditions for internal velocities and an advection equation for temperature if the forcing is not changing direction rapidly at the open boundary. Schemes using the method of characteristics or traditional wave advection schemes fail when combined with radiation conditions for the baroclinic mode.
Erratum: On the structure of infrared singularities of gauge-theory amplitudes

A closed formula is obtained for the infrared singularities of dimensionally regularized, massless gauge-theory scattering amplitudes with an arbitrary number of legs and loops. It follows from an all-order conjecture for the anomalous-dimension matrix of n-jet operators in soft-collinear effective theory. We show that the form of this anomalous dimension is severely constrained by soft-collinear factorization, non-abelian exponentiation, and the behavior of amplitudes in collinear limits. Using a diagrammatic analysis, we demonstrate that these constraints imply that to three-loop order the anomalous dimension involves only two-parton correlations, with the possible exception of a single color structure multiplying a function of conformal cross ratios depending on the momenta of four external partons, which would have to vanish in all two-particle collinear limits. We suggest that such a function does not appear at three-loop order, and that the same is true in higher orders. Our formula predicts Casimir scaling of the cusp anomalous dimension to all orders in perturbation theory, and we explicitly check that the constraints exclude the appearance of higher Casimir invariants at four loops. Using known results for the quark and gluon form factors, we derive the three-loop coefficients of the 1/n pole terms (with n = 1,.,6) for an arbitrary n-parton scattering amplitude in massless QCD. This generalizes Catani's two-loop formula proposed in 1998.
INTRODUCTORY STATISTICS COURSE TERTIARY STUDENTS’ UNDERSTANDING OF P-VALUES

This study aimed to gain knowledge of students’ beliefs and difficulties in understanding p-values, and to use this knowledge to develop improved teaching programs. This study took place over four consecutive teaching semesters of a one-semester tertiary statistics unit. The study was cyclical, in that the results of each semester were used to inform the instructional design for the following semester. Over the semesters, the following instructional techniques were introduced: computer simulation, the introduction of hypothetical probabilistic reasoning using a familiar context, and the use of alternative representations. The students were also encouraged to write about their work. As the interventions progressed, a higher proportion of students successfully defined and used p-values in Null Hypothesis Testing procedures. First published May 2014 at Statistics Education Research Journal Archives
Extra families, Higgs spectrum, and oblique corrections

The standard model accommodates, but does not explain, three families of leptons and quarks, while various extensions suggest extra matter families. The oblique corrections from extra chiral families with relatively light (weak-scale) masses, M{sub f}{approx} , are analyzed and used to constrain the number of extra families and their spectrum. The analysis is motivated, in part, by recent N=2 supersymmetry constructions, but is performed in a model-independent way. It is shown that the correlations among the contributions to the three oblique parameters, rather than the contribution to a particular one, provide the most significant bound. Nevertheless, a single extra chiral family with a constrained spectrum is found to be consistent with precision data without requiring any other new physics source. Models with three additional families may also be accommodated but only by invoking additional new physics, most notably, a two-Higgs-doublet extension. The interplay between the spectra of the extra fermions and the Higgs boson(s) is analyzed in the case of either one or two Higgs doublets, and its implications are explored. In particular, the precision bound on the standard model-like Higgs boson mass is shown to be significantly relaxed in the presence of an extra relatively light chiral family.
The impact of a celebrity promotional campaign on the use of colon cancer screening: the Katie Couric effect.

BACKGROUND Public participation in many preventive health programs is suboptimal. While various interventions to increase participation have been studied, the impact of a celebrity spokesperson on cancer screening has not been rigorously examined. The objective of this study was to assess the impact of Katie Couric's March 2000 Today Show colorectal cancer awareness campaign on colonoscopy rates. METHODS A population-based observational study was conducted using 2 different data sources: (1) The Clinical Outcomes Research Initiative (CORI) database-a voluntary consortium of 400 endoscopists who performed 95 000 colonoscopies from July 1998 to December 2000; and (2) 44 000 adult members of a managed care organization. Using change point analyses and linear regression models, we compared colonoscopy utilization rates before and after Ms Couric's March 2000 television series. RESULTS The number of colonoscopies performed per CORI physician per month after Ms Couric's campaign increased significantly (15.0 per month before campaign; 18.1 after campaign; P<.001). After adjusting for temporal trends, a significantly higher postcampaign colonoscopy rate was sustained for 9 months. Analysis also demonstrated a trend toward an increase in the percentage of colonoscopies performed on women (43.4% before campaign; 47.4% after campaign; P =.054). Colonoscopy rates also increased significantly in the managed care organization after Ms Couric's campaign (1.3 per 1000 members per month before; 1.8 after; P<.001). CONCLUSIONS Katie Couric's televised colon cancer awareness campaign was temporally associated with an increase in colonoscopy use in 2 different data sets. These findings suggest that a celebrity spokesperson can have a substantial impact on public participation in preventive care programs.
Violent Relaxation Around a Massive Black Hole

I present galaxy models resulting from violent relaxation in the presence of a preexisting black hole. The models are computed by maximizing the entropy of the stellar dynamical system. I show that their properties are very similar to those of adiabatic growth models for a suitable choice of parameters. This suggests that observations of nuclear light profiles and kinematics alone may not be sufficient to discriminate between scenarios where a black hole grows adiabatically in the core of a galaxy and scenarios where the black hole formation precedes galaxy formation.
Supersymmetry and Cosmology

Cosmologynow providesunambiguous, quantitati ve evidencefor new particlephysics.I discusstheimplicationsof cosmologyfor supersymmetry andviceversa.Topicsinclude:motivationsfor supersymmetry; supersymmetrybreaking;darkenergy; freezeoutandWIMPs;neutralinodarkmatter; cosmologicallypreferredregionsof minimal super gravity; directandindirectdetectionof neutralinos;theDAMA andHEAT signals;inflation and reheating;gravitino darkmatter;Big Bangnucleosynthesis; andthecosmic microwave background.I concludewith speculationsabouttheprospects for a microscopicdescriptionof thedarkuniverse,stressingthenecessity of diverseexperimentson bothsidesof theparticlephysics/cosmologyinterface. Supportedin partby NationalScienceFoundationCAREERAwardPHY–0239817. c © 2004by JonathanL. Feng. SLAC Summer Institute, July 28 August 8, 2003, Stanford, California
Measurements of exclusive photoproduction processes at large values of t and u from 4 to 7.5 GeV

Exclusive photoproduction cross sections have been measured for the processes . gamma.p . -->. pi. /sup +/n, . gamma.p . -->. pi. /sup 0/p, . gamma.p . -->. pi. /sup -/. delta. /sup + +/, . gamma.p . -->. rho/sup 0/p, . gamma.p . -->. K/sup +/. lambda. , and . gamma.p . -->. K/sup +/. sigma. /sup 0/ at large t and u values at several energies for each process between 4 and 7.5 GeV. These measurements taken together with past data taken at small values of t and u provide complete angular distributions. The data show the usual small t and u peaks and a central region in which the cross section decreases approximately as s/sup -7/. The results are discussed within the context of parton or constituent models. (AIP)
Nemitin, a Novel Map8/Map1s Interacting Protein with Wd40 Repeats

In neurons, a highly regulated microtubule cytoskeleton is essential for many cellular functions. These include axonal transport, regional specialization and synaptic function. Given the critical roles of microtubule-associated proteins (MAPs) in maintaining and regulating microtubule stability and dynamics, we sought to understand how this regulation is achieved. Here, we identify a novel LisH/WD40 repeat protein, tentatively named nemitin (neuronal enriched MAP interacting protein), as a potential regulator of MAP8-associated microtubule function. Based on expression at both the mRNA and protein levels, nemitin is enriched in the nervous system. Its protein expression is detected as early as embryonic day 11 and continues through adulthood. Interestingly, when expressed in non-neuronal cells, nemitin displays a diffuse pattern with puncta, although at the ultrastructural level it localizes along the microtubule network in vivo in sciatic nerves. These results suggest that the association of nemitin to microtubules may require an intermediary protein. Indeed, co-expression of nemitin with microtubule-associated protein 8 (MAP8) results in nemitin losing its diffuse pattern, instead decorating microtubules uniformly along with MAP8. Together, these results imply that nemitin may play an important role in regulating the neuronal cytoskeleton through an interaction with MAP8.