Replicability or reproducibility? On the replication crisis in computational neuroscience and sharing only relevant detail

Replicability and reproducibility of computational models has been somewhat understudied by “the replication movement.” In this paper, we draw on methodological studies into the replicability of psychological experiments and on the mechanistic account of explanation to analyze the functions of model replications and model reproductions in computational neuroscience. We contend that model replicability, or independent researchers' ability to obtain the same output using original code and data, and model reproducibility, or independent researchers' ability to recreate a model without original code, serve different functions and fail for different reasons. This means that measures designed to improve model replicability may not enhance (and, in some cases, may actually damage) model reproducibility. We claim that although both are undesirable, low model reproducibility poses more of a threat to long-term scientific progress than low model replicability. In our opinion, low model reproducibility stems mostly from authors' omitting to provide crucial information in scientific papers and we stress that sharing all computer code and data is not a solution. Reports of computational studies should remain selective and include all and only relevant bits of code

Fibrillar Elastomeric Micropatterns Create Tunable Adhesion Even to Rough Surfaces

Acknowledgements V.B., N.K.G., and E.A. contributed with conception and experimental design. V.B. performed the experiments. V.B., R.H., A.G., and R.M.M. carried out analysis and interpretation of data. V.B., R.H., A.G., and E.A. wrote the manuscript. V.B. and R.H. contributed equally to this work. V.B. acknowledges funding by SPP 1420 of the German Science Foundation DFG. E.A., N.K.G., and R.H. acknowledge funding from the European Research Council under the European Union/ERC Advanced Grant “Switch2Stick,” Agreement No. 340929.Peer reviewedPublisher PD

Watered Down Essences and Elusive Speech Communities: Two Objection Against Putnam's Twin Earth Argument

The paper presents two objections against Putnam’s Twin Earth argument, which was intended to secure semantic externalism. I first claim that Putnam’s reasoning rests on two assumptions and then try to show why these assumptions are contentious. The first objection is that, given what we know about science, it is unlikely that there are any natural-kind terms whose extension is codetermined by a small set of microstructures required by Putnam’s indexical account of extension determination. The second objection is that there may not be a plausible concept of a speech community whose adoption would classify Oscar and Twin Oscar as members of different speech communities and, at the same time, render Oscar and Twin Oscar as being in the same psychological state. I contend that Putnam’s argument fails because both objections are justified.Publikacja została sfinansowana ze środków Ministerstwa Nauki i Szkolnictwa Wyższego w ramach programu Narodowego Programu Rozwoju Humanistyki przyznanych na podstawie decyzji 0014/NPRH4/H3b/83/2016 - projekt „Przygotowanie i publikacja dwóch anglojęzycznych numerów monograficznych Internetowego Magazynu Filozoficznego HYBRIS” (3bH 15 0014 83)

Prewetting transition on a weakly disordered substrate : evidence for a creeping film dynamics

We present the first microscopic images of the prewetting transition of a liquid film on a solid surface. Pictures of the local coverage map of a helium film on a cesium metal surface are taken while the temperature is raised through the transition. The film edge is found to advance at constant temperature by successive avalanches in a creep motion with a macroscopic correlation length. The creep velocity varies strongly in a narrow temperature range. The retreat motion is obtained only at much lower temperature, conforming to the strong hysteresis observed for prewetting transition on a disordered surface. Prewetting transition on such disordered surfaces appears to give rise to dynamical phenomena similar to what is observed for domain wall motions in 2D magnets.Comment: 7 pages, 3 figures, to be published in Euro.Phys.Let

Addendum to "Nonlinear quantum evolution with maximal entropy production"

The author calls attention to previous work with related results, which has escaped scrutiny before the publication of the article "Nonlinear quantum evolution with maximal entropy production", Phys.Rev.A63, 022105 (2001).Comment: RevTex-latex2e, 2pgs., no figs.; brief report to appear in the May 2001 issue of Phys.Rev.

Hydrodynamic object recognition using pressure sensing

Hydrodynamic sensing is instrumental to fish and some amphibians. It also represents, for underwater vehicles, an alternative way of sensing the fluid environment when visual and acoustic sensing are limited. To assess the effectiveness of hydrodynamic sensing and gain insight into its capabilities and limitations, we investigated the forward and inverse problem of detection and identification, using the hydrodynamic pressure in the neighbourhood, of a stationary obstacle described using a general shape representation. Based on conformal mapping and a general normalization procedure, our obstacle representation accounts for all specific features of progressive perceptual hydrodynamic imaging reported experimentally. Size, location and shape are encoded separately. The shape representation rests upon an asymptotic series which embodies the progressive character of hydrodynamic imaging through pressure sensing. A dynamic filtering method is used to invert noisy nonlinear pressure signals for the shape parameters. The results highlight the dependence of the sensitivity of hydrodynamic sensing not only on the relative distance to the disturbance but also its bearing

Mouse models for studying prostate cancer bone metastasis.

Once tumor cells metastasize to the bone, the prognosis for prostate cancer patients is generally very poor. The mechanisms involved in bone metastasis, however, remain elusive, because of lack of relevant animal models. In this manuscript, we describe step-by-step protocols for the xenograft mouse models that are currently used for studying prostate cancer bone metastasis. The different routes of tumor inoculation (intraosseous, intracardiac, intravenous and orthotopic) presented are useful for exploring the biology of bone metastasis

Are social organizational factors independently associated with a current bacterial sexually transmitted infection among urban adolescents and young adults?

This study explored the relationship between the social organization of neighborhoods including informal social control and social cohesion and a current bacterial sexually transmitted infection (STI) among adolescents and young adults in one U.S. urban setting. Data for the current study were collected from April 2004 to April 2007 in a cross-sectional household study. The target population included English-speaking, sexually-active persons between the ages of 15 and 24 years who resided in 486 neighborhoods. The study sample included 599 participants from 63 neighborhoods. A current bacterial STI was defined as diagnosis of a chlamydia and/or gonorrhea infection at the time of study participation. Participants reported on informal social control (i.e. scale comprised of 9 items) and social cohesion (i.e. scale comprised of 5 items) in their neighborhood. In a series of weighted multilevel logistic regression models stratified by gender, greater informal social control was significantly associated with a decreased odds of a current bacterial STI among females (AOR 0.53, 95% CI 0.34, 0.84) after controlling for individual social support and other factors. The association, while in a similar direction, was not significant for males (AOR 0.73, 95% CI 0.48, 1.12). Social cohesion was not significantly associated with a current bacterial STI among females (OR 0.85, 95% CI 0.61, 1.19) and separately, males (OR 0.98, 95% CI 0.67, 1.44). Greater individual social support was associated with an almost seven-fold increase in the odds of a bacterial STI among males (AOR 6.85, 95% CI 1.99, 23.53), a finding which is in contrast to our hypotheses. The findings suggest that neighborhood social organizational factors such as informal social control have an independent relationship with sexual health among U.S. urban youth. The causality of the relationship remains to be determined

Relevant baseline characteristics for describing patients with knee osteoarthritis: results from a Delphi survey

BACKGROUND: Inclusion/exclusion criteria and baseline characteristics are essential for assessing the applicability of trial results to a given patient and the comparability of study populations for meta-analyses. This Delphi survey aimed to generate a set of baseline characteristics for describing patients with knee osteoarthritis enrolled in clinical studies. METHODS: Survey participants comprised clinical experts (n = 23; mean age 54 y; from 4 continents) that had authored at least two randomized trials on knee osteoarthritis. First, given a prepared list of baseline patient characteristics, the experts were asked to add characteristics they considered important for assessing comparability of patient populations in different trials that evaluated the efficacy of non-surgical interventions for treating knee osteoarthritis. Next, they were asked to rate the importance of each characteristic, on a scale of 0 (not important) to 10 (highly important), according to three outcome categories: pain, function, and structure. RESULTS: Participants identified 121 baseline characteristics. A rating ≥7 points was assigned to 39 characteristics (e.g., age, depression, global knee pain, daily dose of pain killers, Kellgren-Lawrence grading); of these, 20 were related to pain, 15 to function, and 23 to structural outcomes. Global knee pain was the only baseline characteristic that fulfilled among experts the predefined consensus criteria. CONCLUSIONS: Experts identified a large number of characteristics for describing patients with knee osteoarthritis. Disagreement and uncertainty prevailed over the relevance of these characteristics. Our findings justified further efforts to define appropriate, broadly acceptable sets of baseline characteristics for describing patients with knee osteoarthritis