Replicator degrees of freedom allow publication of misleading failures to replicate

In recent years, the field of psychology has begun to conduct replication tests on a large scale. Here, we show that “replicator degrees of freedom” make it far too easy to obtain and publish false-negative replication results, even while appearing to adhere to strict methodological standards. Specifically, using data from an ongoing debate, we show that commonly exercised flexibility at the experimental design and data analysis stages of replication testing can make it appear that a finding was not replicated when, in fact, it was. The debate that we focus on is representative, on key dimensions, of a large number of other replication tests in psychology that have been published in recent years, suggesting that the lessons of this analysis may be far reaching. The problems with current practice in replication science that we uncover here are particularly worrisome because they are not adequately addressed by the field’s standard remedies, including preregistration. Implications for how the field could develop more effective methodological standards for replication are discussed. © 2019 National Academy of Sciences. All rights reserved

REVIEWS REVIEWS REVIEWS Disturbance and the rising tide: the

low-island ecosystem

The Nature of Associated Absorption and the UV-X-ray Connection in 3C 288.1

We discuss new Hubble Space Telescope spectroscopy of the radio-loud quasar, 3C 288.1. The data cover ~590 A to ~1610 A in the quasar rest frame. They reveal a wealth of associated absorption lines (AALs) with no accompanying Lyman-limit absorption. The metallic AALs range in ionization from C III and N III to Ne VIII and Mg X. We use these data and photoionization models to derive the following properties of the AAL gas: 1) There are multiple ionization zones within the AAL region, spanning a factor of at least ~50 in ionization parameter. 2) The overall ionization is consistent with the ``warm'' X-ray continuum absorbers measured in Seyfert 1 nuclei and other QSOs. However, 3) the column densities implied by the AALs in 3C 288.1 are too low to produce significant bound-free absorption at any UV-X-ray wavelengths. Substantial X-ray absorption would require yet another zone, having a much higher ionization or a much lower velocity dispersion than the main AAL region. 4) The total hydrogen column density in the AAL gas is log N_H (cm-2)= 20.2. 5) The metallicity is roughly half solar. 6) The AALs have deconvolved widths of ~900 km/s and their centroids are consistent with no shift from the quasar systemic velocity (conservatively within +/-1000 km/s). 7) There are no direct indicators of the absorber's location in our data, but the high ionization and high metallicity both suggest a close physical relationship to the quasar/host galaxy environment. Finally, the UV continuum shape gives no indication of a ``blue bump'' at higher energies. There is a distinct break of unknown origin at ~1030 A, and the decline toward higher energies (with spectral index alpha = -1.73, for f_nu ~ nu^alpha) is even steeper than a single power-law interpolation from 1030 A to soft X-rays.Comment: 27 pages with figures and tables, in press with Ap

Complete Genome Sequence of Vibrio gazogenes ATCC 43942

Vibrio gazogenes ATCC 43942 has the potential to synthesize a plethora of metabolites which are of clinical and agricultural significance in response to environmental triggers. The complete genomic sequence of Vibrio gazogenes ATCC 43942 is reported herein, contributing to the knowledge base of strains in the Vibrio genus

Single hadron response measurement and calorimeter jet energy scale uncertainty with the ATLAS detector at the LHC

The uncertainty on the calorimeter energy response to jets of particles is derived for the ATLAS experiment at the Large Hadron Collider (LHC). First, the calorimeter response to single isolated charged hadrons is measured and compared to the Monte Carlo simulation using proton-proton collisions at centre-of-mass energies of sqrt(s) = 900 GeV and 7 TeV collected during 2009 and 2010. Then, using the decay of K_s and Lambda particles, the calorimeter response to specific types of particles (positively and negatively charged pions, protons, and anti-protons) is measured and compared to the Monte Carlo predictions. Finally, the jet energy scale uncertainty is determined by propagating the response uncertainty for single charged and neutral particles to jets. The response uncertainty is 2-5% for central isolated hadrons and 1-3% for the final calorimeter jet energy scale.Comment: 24 pages plus author list (36 pages total), 23 figures, 1 table, submitted to European Physical Journal

Parity-related molecular signatures and breast cancer subtypes by estrogen receptor status

INTRODUCTION: Relationships of parity with breast cancer risk are complex. Parity is associated with decreased risk of postmenopausal hormone receptor–positive breast tumors, but may increase risk for basal-like breast cancers and early-onset tumors. Characterizing parity-related gene expression patterns in normal breast and breast tumor tissues may improve understanding of the biological mechanisms underlying this complex pattern of risk. METHODS: We developed a parity signature by analyzing microRNA microarray data from 130 reduction mammoplasty (RM) patients (54 nulliparous and 76 parous). This parity signature, together with published parity signatures, was evaluated in gene expression data from 150 paired tumors and adjacent benign breast tissues from the Polish Breast Cancer Study, both overall and by tumor estrogen receptor (ER) status. RESULTS: We identified 251 genes significantly upregulated by parity status in RM patients (parous versus nulliparous; false discovery rate = 0.008), including genes in immune, inflammation and wound response pathways. This parity signature was significantly enriched in normal and tumor tissues of parous breast cancer patients, specifically in ER-positive tumors. CONCLUSIONS: Our data corroborate epidemiologic data, suggesting that the etiology and pathogenesis of breast cancers vary by ER status, which may have implications for developing prevention strategies for these tumors

Jaguar Densities across Human-Dominated Landscapes in Colombia: The Contribution of Unprotected Areas to Long Term Conservation

Large carnivores such as jaguars (Panthera onca) are species of conservation concern because they are suffering population declines and are keystone species in their ecosystems. Their large area requirements imply that unprotected and ever-increasing agricultural regions can be important habitats as they allow connectivity and dispersal among core protected areas. Yet information on jaguar densities across unprotected landscapes it is still scarce and crucially needed to assist management and range-wide conservation strategies. Our study provides the first jaguar density estimates of Colombia in agricultural regions which included cattle ranching, the main land use in the country, and oil palm cultivation, an increasing land use across the Neotropics. We used camera trapping across two agricultural landscapes located in the Magdalena River valley and in the Colombian llanos (47–53 stations respectively; >2000 trap nights at both sites) and classic and spatially explicit capture-recapture models with the sex of individuals as a covariate. Density estimates were 2.52±0.46–3.15±1.08 adults/100 km2 in the Magdalena valley, whereas 1.12±0.13–2.19±0.99 adults/100 km2 in the Colombian llanos, depending on analysis used. We suggest that jaguars are able to live across unprotected human-use areas and co-exist with agricultural landscapes including oil-palm plantations if natural areas and riparian habitats persist in the landscape and hunting of both jaguar and prey is limited. In the face of an expanding agriculture across the tropics we recommend land-use planning, adequate incentives, regulations, and good agricultural practices for range-wide jaguar connectivity and survival