Second-generation p-values: improved rigor, reproducibility, & transparency in statistical analyses

Verifying that a statistically significant result is scientifically meaningful is not only good scientific practice, it is a natural way to control the Type I error rate. Here we introduce a novel extension of the p-value - a second-generation p-value - that formally accounts for scientific relevance and leverages this natural Type I Error control. The approach relies on a pre-specified interval null hypothesis that represents the collection of effect sizes that are scientifically uninteresting or are practically null. The second-generation p-value is the proportion of data-supported hypotheses that are also null hypotheses. As such, second-generation p-values indicate when the data are compatible with null hypotheses, or with alternative hypotheses, or when the data are inconclusive. Moreover, second-generation p-values provide a proper scientific adjustment for multiple comparisons and reduce false discovery rates. This is an advance for environments rich in data, where traditional p-value adjustments are needlessly punitive. Second-generation p-values promote transparency, rigor and reproducibility of scientific results by a priori specifying which candidate hypotheses are practically meaningful and by providing a more reliable statistical summary of when the data are compatible with alternative or null hypotheses.Comment: 29 pages, 29 page Supplemen

Spatial Distributions of Tropical Cyclone Tornadoes by Intensity and Size Characteristics

Tropical cyclones that make landfall often spawn tornadoes. Previous studies have shown that these tornadoes are not uniformly distributed in the United States or in the tropical cyclone environment. They show that tornadoes tend to occur relatively close to the coastline and that they tend to cluster to the east-of-center in the tropical cyclone environment, particularly in the northeast and east-of-center quadrants. This study contributes to these studies by analyzing the spatial distributions of tropical cyclone tornadoes by intensity, path length, path width, and the damage potential index. The analyses confirm that most tornadoes occur relatively close to the coastline, but show that stronger tornadoes with larger paths are disproportionately common farther inland. They also confirm that the highest amount of activity is located within the northeast and east-of-center quadrants and show that the most potentially damaging tornadoes cluster in a sub region near the intersection of these two quadrants

Scalable Noise Estimation with Random Unitary Operators

We describe a scalable stochastic method for the experimental measurement of generalized fidelities characterizing the accuracy of the implementation of a coherent quantum transformation. The method is based on the motion reversal of random unitary operators. In the simplest case our method enables direct estimation of the average gate fidelity. The more general fidelities are characterized by a universal exponential rate of fidelity loss. In all cases the measurable fidelity decrease is directly related to the strength of the noise affecting the implementation -- quantified by the trace of the superoperator describing the non--unitary dynamics. While the scalability of our stochastic protocol makes it most relevant in large Hilbert spaces (when quantum process tomography is infeasible), our method should be immediately useful for evaluating the degree of control that is achievable in any prototype quantum processing device. By varying over different experimental arrangements and error-correction strategies additional information about the noise can be determined.Comment: 8 pages; v2: published version (typos corrected; reference added

High-Dose Carmustine, Etoposide, and Cyclophosphamide Followed by Allogeneic Hematopoietic Cell Transplantation for Non-Hodgkin Lymphoma

AbstractAllogeneic hematopoietic cell transplantation (HCT) has been shown to be curative in a group of patients with aggressive non-Hodgkin lymphoma (NHL). A previous study has demonstrated equivalent outcomes with a conditioning regimen based on total body irradiation and another not based on total body irradiation with preparative therapy using cyclophosphamide, carmustine, and etoposide (CBV) in autologous HCT. We investigated the safety and efficacy of using CBV in an allogeneic setting. Patients were required to have relapsed or be at high risk for subsequent relapse of NHL. All patients had a fully HLA-matched sibling donor. Patients received carmustine (15 mg/kg), etoposide (60 mg/kg), and cyclophosphamide (100 mg/kg) on days −6, −4, and −2, respectively, followed by allogeneic HCT. All patients were treated with cyclosporine and methylprednisolone as prophylaxis for graft-versus-host disease (GVHD). Thirty-one patients (median age, 46 years) who were felt to be inappropriate candidates for autologous transplantation were enrolled. Each subject had a median of 3 previous chemotherapy regimens. All patients engrafted. Fifteen of 31 patients are alive. Median follow-up time was 11.5 months (range, .4-126). There were 8 deaths due to relapse. Nonrelapse mortality (n = 8) included infection (n = 3), GVHD (n = 2), diffuse alveolar hemorrhage (n = 1), veno-occlusive disease in the setting of concurrent acute GVHD of the liver (n = 1), and leukoencephalopathy (n = 1). Probabilities of event-free survival and overall survival were, respectively, 44% (95% confidence interval, 26%-62%) and 51% (33%-69%) at 1 year and 44% (26%-62%) and 47% (29%-65%) at 5 years. Probability of relapse was 33% (15%-51%) at 1 year and 5 years. Probability of nonrelapse mortality was 31% (13%-49%) at 1 year and 5 years. Incidences were 29% for acute GVHD and 39% for chronic GVHD. None of the 12 patients who developed chronic GVHD has disease recurrence. Patients who had required >3 previous chemotherapy regimens before HCT had an increased probability of relapse. CBV is an effective preparative regimen for patients with aggressive NHL who undergo allogeneic HCT

Natural Orbitals and BEC in traps, a diffusion Monte Carlo analysis

We investigate the properties of hard core Bosons in harmonic traps over a wide range of densities. Bose-Einstein condensation is formulated using the one-body Density Matrix (OBDM) which is equally valid at low and high densities. The OBDM is calculated using diffusion Monte Carlo methods and it is diagonalized to obtain the "natural" single particle orbitals and their occupation, including the condensate fraction. At low Boson density, $na^3 < 10^{-5}$, where $n = N/V$ and $a$ is the hard core diameter, the condensate is localized at the center of the trap. As $na^3$ increases, the condensate moves to the edges of the trap. At high density it is localized at the edges of the trap. At $na^3 \leq 10^{-4}$ the Gross-Pitaevskii theory of the condensate describes the whole system within 1%. At $na^3 \approx 10^{-3}$ corrections are 3% to the GP energy but 30% to the Bogoliubov prediction of the condensate depletion. At $na^3 \gtrsim 10^{-2}$, mean field theory fails. At $na^3 \gtrsim 0.1$, the Bosons behave more like a liquid $^4$He droplet than a trapped Boson gas.Comment: 13 pages, 14 figures, submitted Phys. Rev.

System size and centrality dependence of the balance function in A+A collisions at sqrt[sNN]=17.2 GeV

Electric charge correlations were studied for p+p, C+C, Si+Si, and centrality selected Pb+Pb collisions at sqrt[sNN]=17.2 GeV with the NA49 large acceptance detector at the CERN SPS. In particular, long-range pseudorapidity correlations of oppositely charged particles were measured using the balance function method. The width of the balance function decreases with increasing system size and centrality of the reactions. This decrease could be related to an increasing delay of hadronization in central Pb+Pb collisions

Exploring drivers of litter decomposition in a greening Arctic: Results from a transplant experiment across a tree-line (Forthcoming)

Decomposition of plant litter is a key control over carbon (C) storage in the soil. The biochemistry of the litter being produced, the environment in which the decomposition is taking place, and the community composition and metabolism of the decomposer organisms exert a combined influence over decomposition rates. As deciduous shrubs and trees are expanding into tundra ecosystems as a result of regional climate warming, this change in vegetation represents a change in litter input to tundra soils and a change in the environment in which litter decomposes. To test the importance of litter biochemistry and environment in determining litter mass loss, we reciprocally transplanted litter between heath (Empetrum nigrum), shrub (Betula nana) and forest (Betula pubescens) at a sub-arctic tree-line in Sweden. As expansion of shrubs and trees promotes deeper snow, we also used a snow fence experiment in a tundra heath environment to understand the importance of snow depth, relative to other factors, in the decomposition of litter. Our results show that B. pubescens and B. nana leaf litter decomposed at faster rates than E. nigrum litter across all environments, while all litter species decomposed at faster rates in the forest and shrub environments than in the tundra heath. The effect of increased snow on decomposition was minimal, leading us to conclude that microbial activity over summer in the productive forest and shrub vegetation is driving increased mass loss compared to the heath. Using B. pubescens and E. nigrum litter, we demonstrate that degradation of carbohydrate-C is a significant driver of mass loss in the forest. This pathway was less prominent in the heath, which is consistent with observations that tundra soils typically have high concentrations of ‘labile’ C. This experiment suggests that further expansion of shrubs and trees may stimulate the loss of undecomposed carbohydrate-C in the tundra.REF Compliant by Deposit in Stirling's Repositor

Graphene-passivated nickel as an oxidation-resistant electrode for spintronics.

We report on graphene-passivated ferromagnetic electrodes (GPFE) for spin devices. GPFE are shown to act as spin-polarized oxidation-resistant electrodes. The direct coating of nickel with few layer graphene through a readily scalable chemical vapor deposition (CVD) process allows the preservation of an unoxidized nickel surface upon air exposure. Fabrication and measurement of complete reference tunneling spin valve structures demonstrate that the GPFE is maintained as a spin polarizer and also that the presence of the graphene coating leads to a specific sign reversal of the magneto-resistance. Hence, this work highlights a novel oxidation-resistant spin source which further unlocks low cost wet chemistry processes for spintronics devices.R.S.W. acknowledges funding from EPSRC (Doctoral training award). S.H. acknowledges funding from ERC Grant InsituNANO (Project Reference 279342). P.S. acknowledges the Institut Universitaire de France for junior fellowship support. This research was partially supported by the EU FP7 work programme under Grant GRAFOL (Project Reference 285275).This is the accepted manuscript. The final version is available from ACS at http://pubs.acs.org/doi/abs/10.1021/nn304424x

In situ observations of the atomistic mechanisms of Ni catalyzed low temperature graphene growth.

The key atomistic mechanisms of graphene formation on Ni for technologically relevant hydrocarbon exposures below 600 °C are directly revealed via complementary in situ scanning tunneling microscopy and X-ray photoelectron spectroscopy. For clean Ni(111) below 500 °C, two different surface carbide (Ni2C) conversion mechanisms are dominant which both yield epitaxial graphene, whereas above 500 °C, graphene predominantly grows directly on Ni(111) via replacement mechanisms leading to embedded epitaxial and/or rotated graphene domains. Upon cooling, additional carbon structures form exclusively underneath rotated graphene domains. The dominant graphene growth mechanism also critically depends on the near-surface carbon concentration and hence is intimately linked to the full history of the catalyst and all possible sources of contamination. The detailed XPS fingerprinting of these processes allows a direct link to high pressure XPS measurements of a wide range of growth conditions, including polycrystalline Ni catalysts and recipes commonly used in industrial reactors for graphene and carbon nanotube CVD. This enables an unambiguous and consistent interpretation of prior literature and an assessment of how the quality/structure of as-grown carbon nanostructures relates to the growth modes.L.L.P. acknowledges funding from Area di Ricerca Scientifica e Tecnologica of Trieste and from MIUR through Progetto Strategico NFFA. C.A. acknowledges support from CNR through the ESF FANAS project NOMCIS. C.A. and C.C. acknowledge financial support from MIUR (PRIN 2010-2011 nº 2010N3T9M4). S.B. acknowledges funding from ICTP TRIL program. S.H. acknowledges funding from ERC grant InsituNANO (n°279342). R.S.W. acknowledges funding from EPSRC (Doctoral training award), and the Nano Science & Technology Doctoral Training Centre Cambridge (NanoDTC). The help of C. Dri and F. Esch (design) and P. Bertoch and F. Salvador (manufacturing) in the realization of the high temperature STM sample holder is gratefully acknowledged. We acknowledge the Helmholtz-Zentrum-Berlin Electron storage ring BESSY II for provision of synchrotron radiation at the ISISS beamline and we thank the BESSY staff for continuous support of our experiments.This is the accepted manuscript. The final version is available from ACS at http://pubs.acs.org/doi/abs/10.1021/nn402927q