Assessing the reproducibility of discriminant function analyses.

Data are the foundation of empirical research, yet all too often the datasets underlying published papers are unavailable, incorrect, or poorly curated. This is a serious issue, because future researchers are then unable to validate published results or reuse data to explore new ideas and hypotheses. Even if data files are securely stored and accessible, they must also be accompanied by accurate labels and identifiers. To assess how often problems with metadata or data curation affect the reproducibility of published results, we attempted to reproduce Discriminant Function Analyses (DFAs) from the field of organismal biology. DFA is a commonly used statistical analysis that has changed little since its inception almost eight decades ago, and therefore provides an opportunity to test reproducibility among datasets of varying ages. Out of 100 papers we initially surveyed, fourteen were excluded because they did not present the common types of quantitative result from their DFA or gave insufficient details of their DFA. Of the remaining 86 datasets, there were 15 cases for which we were unable to confidently relate the dataset we received to the one used in the published analysis. The reasons ranged from incomprehensible or absent variable labels, the DFA being performed on an unspecified subset of the data, or the dataset we received being incomplete. We focused on reproducing three common summary statistics from DFAs: the percent variance explained, the percentage correctly assigned and the largest discriminant function coefficient. The reproducibility of the first two was fairly high (20 of 26, and 44 of 60 datasets, respectively), whereas our success rate with the discriminant function coefficients was lower (15 of 26 datasets). When considering all three summary statistics, we were able to completely reproduce 46 (65%) of 71 datasets. While our results show that a majority of studies are reproducible, they highlight the fact that many studies still are not the carefully curated research that the scientific community and public expects

Journal Staff

The aluminum–zinc-vacancy (Al Zn −V Zn ) complex is identified as one of the dominant defects in Al-containing n -type ZnO after electron irradiation at room temperature with energies above 0.8 MeV. The complex is energetically favorable over the isolated V Zn , binding more than 90% of the stable V Zn ’s generated by the irradiation. It acts as a deep acceptor with the (0/− ) energy level located at approximately 1 eV above the valence band. Such a complex is concluded to be a defect of crucial and general importance that limits the n -type doping efficiency by complex formation with donors, thereby literally removing the donors, as well as by charge compensation

Hydrogen induced optically-active defects in silicon photonic nanocavities

This work was supported by Era-NET NanoSci LECSIN project coordinated by F. Priolo, by the Italian Ministry of University and Research, FIRB contract No. RBAP06L4S5 and by the EPSRC UKSp project. Partial financial support by the Norwegian Research Council is also acknowledged.We demonstrate intense room temperature photoluminescence (PL) from optically active hydrogen- related defects incorporated into crystalline silicon. Hydrogen was incorporated into the device layer of a silicon on insulator (SOI) wafer by two methods: hydrogen plasma treatment and ion implantation. The room temperature PL spectra show two broad PL bands centered at 1300 and 1500 nm wavelengths: the first one relates to implanted defects while the other band mainly relates to the plasma treatment. Structural characterization reveals the presence of nanometric platelets and bubbles and we attribute different features of the emission spectrum to the presence of these different kind of defects. The emission is further enhanced by introducing defects into photonic crystal (PhC) nanocavities. Transmission electron microscopy analyses revealed that the isotropicity of plasma treatment causes the formation of a higher defects density around the whole cavity compared to the ion implantation technique, while ion implantation creates a lower density of defects embedded in the Si layer, resulting in a higher PL enhancement. These results further increase the understanding of the nature of optically active hydrogen defects and their relation with the observed photoluminescence, which will ultimately lead to the development of intense and tunable crystalline silicon light sources at room temperature.Publisher PDFPeer reviewe

Acceptor-like deep level defects in ion-implanted ZnO

N-type ZnO samples have been implanted with MeV Zn⁺ ions at room temperature to doses between 1×10⁸ and 2×10¹⁰cm⁻², and the defect evolution has been studied by capacitance-voltage and deep level transient spectroscopy measurements. The results show a dose dependent compensation by acceptor-like defects along the implantation depth profile, and at least four ion-induced deep-level defects arise, where two levels with energy positions of 1.06 and 1.2 eV below the conduction band increase linearly with ion dose and are attributed to intrinsic defects. Moreover, a re-distribution of defects as a function of depth is observed already at temperatures below 400 K.This work was supported by the Norwegian Research Council through the Frienergi program and the Australian Research Council through the Discovery projects program

Bandgap narrowing in Mn doped GaAs probed by room-temperature photoluminescence

The electronic band structure of the (Ga,Mn)As system has been one of the most intriguing problems in solid state physics over the past two decades. Determination of the band structure evolution with increasing Mn concentration is a key issue to understand the origin of ferromagnetism. Here we present room temperature photoluminescence and ellipsometry measurements of Ga_{100%-x}Mn_{x}As alloy. The up-shift of the valence-band is proven by the red shift of the room temperature near band gap emission from the Ga_{100%-x}Mn_{x}As alloy with increasing Mn content. It is shown that even a doping by 0.02 at.% of Mn affects the valence-band edge and it merges with the impurity band for a Mn concentration as low as 0.6 at.%. Both X-ray diffraction pattern and high resolution cross-sectional TEM images confirmed full recrystallization of the implanted layer and GaMnAs alloy formation.Comment: 24 pages, 7 figures, accepted at Phys. Rev. B 201

Ab initio data-analytics study of carbon-dioxide activation on semiconductor oxide surfaces

The excessive emissions of carbon dioxide (CO2) into the atmosphere threaten to shift the CO2 cycle planet-wide and induce unpredictable climate changes. Using artificial intelligence (AI) trained on high-throughput first principles based data for a broad family of oxides, we develop a strategy for a rational design of catalytic materials for converting CO2 to fuels and other useful chemicals. We demonstrate that an electron transfer to the π-antibonding orbital of the adsorbed molecule and the associated bending of the initially linear molecule, previously proposed as the indicator of activation, are insufficient to account for the good catalytic performance of experimentally characterized oxide surfaces. Instead, our AI model identifies the common feature of these surfaces in the binding of a molecular O atom to a surface cation, which results in a strong elongation and therefore weakening of one molecular C-O bond. This finding suggests using the C-O bond elongation as an indicator of CO2 activation. Based on these findings, we propose a set of new promising oxide-based catalysts for CO2 conversion, and a recipe to find more

EMIC Waves in the Outer Magnetosphere: Observations of an Off-Equator Source Region.

Electromagnetic ion cyclotron (EMIC) waves at large L shells were observed away from the magnetic equator by the Magnetospheric MultiScale (MMS) mission nearly continuously for over four hours on 28 October 2015. During this event, the wave Poynting vector direction systematically changed from parallel to the magnetic field (toward the equator), to bidirectional, to antiparallel (away from the equator). These changes coincide with the shift in the location of the minimum in the magnetic field in the southern hemisphere from poleward to equatorward of MMS. The local plasma conditions measured with the EMIC waves also suggest that the outer magnetospheric region sampled during this event was generally unstable to EMIC wave growth. Together, these observations indicate that the bidirectionally propagating wave packets were not a result of reflection at high latitudes but that MMS passed through an off-equator EMIC wave source region associated with the local minimum in the magnetic field

Co-design and robots: A case study of a robot dog for aging people

© Springer International Publishing AG 2016. The day-to-day experiences of aging citizens differ significantly from young, technologically savvy engineers. Yet, well-meaning engineers continue to design technologies for aging citizens, informed by skewed stereotypes of aging without deep engagements from these users. This paper describes a co-design project based on the principles of Participatory Design that sought to provide aging people with the capacity to co-design technologies that suit their needs. The project combined the design intuitions of both participants and designers, on equal footing, to produce a companion robot in the form of a networked robotic dog. Besides evaluating a productive approach that empowers aging people in the process of co-designing and evaluating technologies for themselves, this paper presents a viable solution that is playful and meaningful to these elderly people; capable of enhancing their independence, social agency and well-being

Mandated data archiving greatly improves access to research data

The data underlying scientific papers should be accessible to researchers both now and in the future, but how best can we ensure that these data are available? Here we examine the effectiveness of four approaches to data archiving: no stated archiving policy, recommending (but not requiring) archiving, and two versions of mandating data deposition at acceptance. We control for differences between data types by trying to obtain data from papers that use a single, widespread population genetic analysis, STRUCTURE. At one extreme, we found that mandated data archiving policies that require the inclusion of a data availability statement in the manuscript improve the odds of finding the data online almost a thousand-fold compared to having no policy. However, archiving rates at journals with less stringent policies were only very slightly higher than those with no policy at all. At one extreme, we found that mandated data archiving policies that require the inclusion of a data availability statement in the manuscript improve the odds of finding the data online almost a thousand fold compared to having no policy. However, archiving rates at journals with less stringent policies were only very slightly higher than those with no policy at all. We also assessed the effectiveness of asking for data directly from authors and obtained over half of the requested datasets, albeit with about 8 days delay and some disagreement with authors. Given the long term benefits of data accessibility to the academic community, we believe that journal based mandatory data archiving policies and mandatory data availability statements should be more widely adopted