bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation-as-a-Service for the Computational Sciences
Authors: Hopfgartner Frank , Hanbury Allan , Müller Henning , Eggel Ivan , Balog Krisztian , Brodt Torben , Cormack Gordon V. , Lin Jimmy , Kalpathy-Cramer Jayashree , Kando Noriko , Kato Makoto P. , Krithara Anastasia , Gollub Tim , Potthast Martin , Viegas Evelyne , Mercer Simon 
Published: October 2018

Evaluation in empirical computer science is essential to show progress and assess technologies developed. Several research domains such as information retrieval have long relied on systematic evaluation to measure progress: here, the Cranfield paradigm of creating shared test collections, defining search tasks, and collecting ground truth for these tasks has persisted up until now. In recent years, however, several new challenges have emerged that do not fit this paradigm very well: extremely large data sets, confidential data sets as found in the medical domain, and rapidly changing data sets as often encountered in industry. Crowdsourcing has also changed the way in which industry approaches problem-solving with companies now organizing challenges and handing out monetary awards to incentivize people to work on their challenges, particularly in the field of machine learning.
This article is based on discussions at a workshop on Evaluation-as-a-Service (EaaS). EaaS is the paradigm of not providing data sets to participants and have them work on the data locally, but keeping the data central and allowing access via Application Programming Interfaces (API), Virtual Machines (VM), or other possibilities to ship executables. The objectives of this article are to summarize and compare the current approaches and consolidate the experiences of these approaches to outline the next steps of EaaS, particularly toward sustainable research infrastructures.
The article summarizes several existing approaches to EaaS and analyzes their usage scenarios and also the advantages and disadvantages. The many factors influencing EaaS are summarized, and the environment in terms of motivations for the various stakeholders, from funding agencies to challenge organizers, researchers and participants, to industry interested in supplying real-world problems for which they require solutions.
EaaS solves many problems of the current research environment, where data sets are often not accessible to many researchers. Executables of published tools are equally often not available making the reproducibility of results impossible. EaaS, however, creates reusable/citable data sets as well as available executables. Many challenges remain, but such a framework for research can also foster more collaboration between researchers, potentially increasing the speed of obtaining research results.
Cells Lacking the RB1 Tumor Suppressor Gene Are Hyperdependent on Aurora B Kinase for Survival
Authors: Oser Matthew G. , Fonseca Raquel , Chakraborty Abhishek A. , Brough Rachel , Spektor Alexander , Jennings Rebecca B. , Flaifel Abdallah , Novak Jesse S. , Gulati Aditi , Buss Elizabeth , Younger Scott T. , McBrayer Samuel K. , Cowley Glenn S. , Bonal Dennis M. , Nguyen Quang-De , Brulle-Soumare Laura , Taylor Paula , Cairo Stefano , Ryan Colm J. , Pease Elizabeth J. , Maratea Kim , Travers Jon , Root David E. , Signoretti Sabina , Pellman David , Ashton Susan , Lord Christopher J. , Barry Simon T. , Kaelin William G. 
Published: October 2018

Abstract

Small cell lung cancer (SCLC) accounts for 15% of lung cancers and is almost always linked to inactivating RB1 and TP53 mutations. SCLC frequently responds, albeit briefly, to chemotherapy. The canonical function of the RB1 gene product RB1 is to repress the E2F transcription factor family. RB1 also plays both E2F-dependent and E2F-independent mitotic roles. We performed a synthetic lethal CRISPR/Cas9 screen in an RB1−/− SCLC cell line that conditionally expresses RB1 to identify dependencies that are caused by RB1 loss and discovered that RB1−/− SCLC cell lines are hyperdependent on multiple proteins linked to chromosomal segregation, including Aurora B kinase. Moreover, we show that an Aurora B kinase inhibitor is efficacious in multiple preclinical SCLC models at concentrations that are well tolerated in mice. These results suggest that RB1 loss is a predictive biomarker for sensitivity to Aurora B kinase inhibitors in SCLC and perhaps other RB1−/− cancers.

Significance:
SCLC is rarely associated with actionable protooncogene mutations. We did a CRISPR/Cas9-based screen that showed that RB1−/− SCLC are hyperdependent on AURKB, likely because both genes control mitotic fidelity, and confirmed that Aurora B kinase inhibitors are efficacious against RB1−/− SCLC tumors in mice at nontoxic doses.
See related commentary by Dick and Li, p. 169.
This article is highlighted in the In This Issue feature, p. 151
Extratropical Cyclones: A Century of Research on Meteorology’s Centerpiece
Authors: Schultz David M. , Bosart Lance F. , Colle Brian A. , Davies Huw C. , Dearden Christopher , Keyser Daniel , Martius Olivia , Roebber Paul J. , Steenburgh W. James , Volkert Hans , Winters Andrew C. 
Published: October 2018

AbstractThe year 1919 was important in meteorology, not only because it was the year that the American Meteorological Society was founded, but also for two other reasons. One of the foundational papers in extratropical cyclone structure by Jakob Bjerknes was published in 1919, leading to what is now known as the Norwegian cyclone model. Also that year, a series of meetings was held that led to the formation of organizations that promoted the international collaboration and scientific exchange required for extratropical cyclone research, which by necessity involves spatial scales spanning national borders. This chapter describes the history of scientific inquiry into the structure, evolution, and dynamics of extratropical cyclones, their constituent fronts, and their attendant jet streams and storm tracks. We refer to these phenomena collectively as the centerpiece of meteorology because of their central role in fostering meteorological research during this century. This extremely productive period in extratropical cyclone research has been possible because of 1) the need to address practical challenges of poor forecasts that had large socioeconomic consequences, 2) the intermingling of theory, observations, and diagnosis (including dynamical modeling) to provide improved physical understanding and conceptual models, and 3) strong international cooperation. Conceptual frameworks for cyclones arise from a desire to classify and understand cyclones; they include the Norwegian cyclone model and its sister the Shapiro–Keyser cyclone model. The challenge of understanding the dynamics of cyclones led to such theoretical frameworks as quasigeostrophy, baroclinic instability, semigeostrophy, and frontogenesis. The challenge of predicting explosive extratropical cyclones in particular led to new theoretical developments such as potential-vorticity thinking and downstream development. Deeper appreciation of the limits of predictability has resulted from an evolution from determinism to chaos. Last, observational insights led to detailed cyclone and frontal structure, storm tracks, and rainbands.
Seasonal Forecasting of Onset of Summer Rains over South Africa
Authors: Ratnam J. V. , Doi Takeshi , Landman Willem A. , Behera Swadhin K. 
Published: October 2018

AbstractIn this study, we attempted to forecast the onset of summer rains over South Africa using seasonal precipitation forecasts generated by the Scale Interaction Experiment–Frontier Research Center for Global Change, version 2 (SINTEX-F2), seasonal forecasting system. The precipitation forecasts of the 12-member SINTEX-F2 system, initialized on 1 August and covering the period 1998–2015, were used for the study. The SINTEX-F2 forecast precipitation was also downscaled using dynamical and statistical techniques to improve the spatial and temporal representation of the forecasts. The Weather Research and Forecasting (WRF) Model with two cumulus parameterization schemes was used to dynamically downscale the SINTEX-F2 forecasts. The WRF and SINTEX-F2 precipitation forecasts were corrected for biases using a linear scaling method with a 31-day moving window. The results indicate the onset dates derived from the raw and bias-corrected model precipitation forecasts to have realistic spatial distribution over South Africa. However, the forecast onset dates have root-mean-square errors of more than 30 days over most parts of South Africa except over the northeastern province of Limpopo and over the Highveld region of Mpumalanga province, where the root-mean-square errors are about 10–15 days. The WRF Model with Kain–Fritsch cumulus scheme (bias-corrected SINTEX-F2) has better performance in forecasting the onset dates over Limpopo (the Highveld region) compared to other models, thereby indicating the forecast of onset dates over different regions of South Africa to be model dependent. The results of this study are important for improving the forecast of onset dates over South Africa.
ENSO-Related Global Ocean Heat Content Variations
Authors: Wu Quran , Zhang Xuebin , Church John A. , Hu Jianyu 
Published: October 2018

Abstract
The modulation of the full-depth global integrated ocean heat content (GOHC) by El Niño–Southern Oscillation (ENSO) has been estimated in various studies. However, the quantitative results and the mechanisms at work remain uncertain. Here, a dynamically consistent ocean state estimate is utilized to study the large-scale integrated heat content variations during ENSO events for the global ocean. The full-depth GOHC exhibits a cooling tendency during the peak and decaying phases of El Niño, which is a result of the negative surface heat flux (SHF) anomaly in the tropics (30°S–30°N), partially offset by the positive SHF anomaly at higher latitudes. The tropical SHF anomaly acts as a lagged response to damp the convergence of oceanic heat transport, which redistributes heat from the extratropics and the subsurface layers (100–440 m) into the upper tropical oceans (0–100 m) during the onset and peak of El Niño. These results highlight the global nature of the oceanic heat redistribution during ENSO events, as well as how the redistribution process affects the full-depth GOHC. The meridional heat exchange across 30°S and 30°N is driven by ocean current anomalies, while multiple processes contribute to the vertical heat exchange across 100 m simultaneously. Heat advection due to unbalanced mass transport is distinguished from the mass balanced one, with significant contributions from the meridional and zonal overturning cells being identified for the latter in the vertical direction. Results presented here have implications for monitoring the planetary energy budget and evaluating ENSO’s global imprints on ocean heat content in different estimates.
Mixed Rossby–Gravity Wave–Wave Interactions
Authors: Eden Carsten , Chouksey Manita , Olbers Dirk 
Published: October 2018

AbstractMixed triad wave–wave interactions between Rossby and gravity waves are analytically derived using the kinetic equation for models of different complexity. Two examples are considered: initially vanishing linear gravity wave energy in the presence of a fully developed Rossby wave field and the reversed case of initially vanishing linear Rossby wave energy in the presence of a realistic gravity wave field. The kinetic equation in both cases is numerically evaluated, for which energy is conserved within numerical precision. The results are validated by a corresponding ensemble of numerical model simulations supporting the validity of the weak-interaction assumption necessary to derive the kinetic equation. Since they are generated by nonresonant interactions only, the energy transfers toward the respective linear wave mode with vanishing energy are small in both cases. The total generation of energy of the linear gravity wave mode in the first case scales to leading order as the square of the Rossby number in agreement with independent estimates from laboratory experiments, although a part of the linear gravity wave mode is slaved to the Rossby wave mode without wavelike temporal behavior.
Impact of Slant-Path Radiative Transfer in the Simulation and Assimilation of Satellite Radiances in Environment Canada’s Weather Forecast System
Authors: Shahabadi Maziar Bani , Aparicio Josep M. , Garand Louis 
Published: October 2018

Abstract
Slant satellite-viewing geometry is investigated for the simulation and assimilation of radiances in Environment Canada’s weather forecast system. The standard approach is to extract from a short-term forecast (trial field) a one-dimensional vertical profile, located at the ground footprint of the observation location, to compute the model equivalent of the observation. Since in general, the lines of sight are not vertical, the observation operator can be improved by interpolating the trial field to the slant path. The interpolation relies on the estimation of horizontal gradients of atmospheric variables, extracted at each altitude layer, and representative of a neighborhood of approximately 100 km. Using these slant profiles of the trial fields yields significant improvements in the simulation and assimilation of radiance observations. The impact of this modification in assimilation and forecasts is evaluated over two periods of two months. Both short-term and long-term effects are found, obtained not only from the more accurate interpolation of the trial fields, but also from a revision of the observation error suggested by the lower observation minus trial field difference statistics. The error standard deviation of the geopotential height shows, in the upper troposphere and lower stratosphere, in 12–48-h forecasts, up to 10% reduction in the zonal value at higher latitudes, and 1%–2% reduction in the global value. Given these improved statistics, a revision of the radiance error statistics was explored. Applying these revised statistics suggests that the impact of a slant operator extends into longer range.
Multiscale Characteristics of Different-Source Perturbations and Their Interactions for Convection-Permitting Ensemble Forecasting during SCMREX
Authors: Zhang Xubin 
Published: October 2018

AbstractThe multiscale characteristics of initial conditions (ICs), model physics (MO), and lateral boundary conditions (LBCs) perturbations, as well as their interactions, are investigated for an experimental convection-permitting ensemble prediction system used in southern China, with a focus on 32 12-h forecasts collected over a half-month period of the Southern China Monsoon Rainfall Experiment (SCMREX) in May 2014. Forecast perturbations differed from each other in terms of magnitude, evolution, and vertical distribution between components at different scales. The meso-β-scale MO perturbations show faster growth and saturation, as well as larger magnitude than the meso-α-scale ones, especially in the presence of moist convection. For IC perturbations, damping was present for nonprecipitation variables, while rapid growth and saturation occurred for precipitation. Adding LBCs perturbations to IC or MO perturbations caused linear impacts, which caused consistent, although small, perturbation increments. Nonlinear impacts of adding MO perturbations to IC perturbations were evident and were intrinsic to the predictability limits of IC and MO perturbations, which were closely related to moist dynamics. These nonlinear impacts had the most significant effects on meso-β-scale precipitation perturbations and can effectively improve precipitation prediction. These results highlight the importance of developing multiscale and multisource perturbation methods that reasonably include the interactions among different-scale perturbations from different sources, especially the nonlinear impacts of adding MO perturbations to IC perturbations.
Attitudes of Residents and Program Directors Towards Research in Otolaryngology Residency
Authors: Mansi Ahmed , Karam Wade N. , Chaaban Mohamad R. 
Published: October 2018

Objective: To determine attitudes of residents and program directors towards research during residency training. Study Design: Survey of current otolaryngology residents and program directors. Setting: Otolaryngology residency programs. Methods: An anonymous web-based survey ( www.surveymonkey.com ) was sent to 106 program directors (PDs) and 115 program coordinators. The program coordinators subsequently sent it to residents. Fisher exact tests and correlations were used to determine statistically significant differences. Results: Overall, 178 residents and 31 PDs responded to our surveys. All residents surveyed reported some research experience prior to residency. Residents who reported a previous first-author manuscript publication prior to residency were more likely than residents who had no previous first-author publication to report a first-author publication during residency (58.44% vs 27.27%, P < .0001); 33% of the residents reported academics as a desired future career setting after residency. The most significant barrier to research perceived by the residents was time constraint due to residency duties and personal commitments (93% and 74%, respectively). The second and third most common barriers to research were lack of statistical knowledge at 52% and lack of interest in research at 43.6%. Conclusions: Research is a required component of otolaryngology residency training. The most significant barrier in our survey was the lack of protected research time, followed by lack of biostatistical knowledge and interest. Program directors may need to implement structured research rotations tailored to individual residents’ research interests and integrate training in research methodology and biostatistics.
Reduced cortical thickness in subjects at clinical high risk for psychosis and clinical attributes
Authors: Kwak Yoo Bin , Kim Minah , Cho Kang Ik Kevin , Lee Junhee , Lee Tae Yong , Kwon Jun Soo 
Published: October 2018

Objectives: Although neuroanatomical abnormalities in subjects at clinical high risk for psychosis have been considered a putative biomarker of psychosis, relevance of cortical thickness alterations remains contested due to discrepant findings. Inconsistencies persist in Asian clinical high risk studies, despite their advantageous settings well-controlled for confounds. Attributes of cortical thickness alterations in clinical high risk subjects warrant further examination. Methods: We examined cortical thickness at the whole-brain level in 74 clinical high risk subjects and 34 demographically matched healthy controls recruited from Seoul Youth Clinic, South Korea. Clinical symptoms were assessed using the Scale of Prodromal Symptoms, and their associations with cortical thickness were explored using partial correlation analysis. Results: Compared to healthy control, clinical high risk exhibited significant cortical thinning in bilateral prefrontal cortex and inferior parietal lobule clusters. Reduced thickness in the left prefrontal cortex cluster was associated with more severe Scale of Prodromal Symptoms general symptoms scores and the right inferior parietal lobule cluster with Scale of Prodromal Symptoms disorganization symptoms. Conclusions: Thickness deficits found in the present clinical high risk sample demonstrated a degree of consistency with those reported in the previous Seoul Youth Clinic study. While inconsistencies reported between the present and previous Seoul Youth Clinic samples may reflect markedly decreased rate of converters, consistencies may be relevant to clinical attributes beyond transition, such as the prevalence of comorbidities. Particular recruitment strategies employed for sample selections should also be considered for findings in Asian clinical high risk samples. Our results suggest potential utility of cortical thickness alterations in clinical high risk subjects beyond the frame of transition.
Self-affirmation and defensive processing of graphic cigarette warning labels by African American smokers: A community-based study
Authors: Iles Irina A , Nan Xiaoli , Ma Zexin , Feldman Robert , Butler James , Wang Min Qi , Zhao Xiaoquan 
Published: October 2018

Objective: Promoting smoking cessation through effective health messaging among African American smokers is of great urgency as African Americans suffer disproportionally more from smoking-related diseases compared to White smokers. This research examines the potential impact of self-affirmation on reducing defensive processing of graphic cigarette warning labels among African American smokers. Method: We conducted an experimental study in which participants were instructed to self-affirm (or not) prior to viewing graphic cigarette warning labels. Results: We found that although self-affirmation had no main effect on defensive processing, it interacted with initial/preexisting attitudes towards smoking to influence defensive responses such as message derogation and perceived message manipulation. For participants with more positive initial attitudes towards smoking, self-affirmation led to reduced message derogation and perceived message manipulation. For these individuals, we also found an indirect effect of self-affirmation on intentions to quit smoking through perceived message manipulation. Self-affirmation had largely no effects on participants with less positive initial attitudes towards smoking. Conclusion: The theoretical and practical implications of these findings are discussed.
Does Depleting Self-Control Result in Poorer Vigilance Performance?
Authors: Satterfield Kelly , Harwood Amanda E. , Helton William S. , Shaw Tyler H. 
Published: October 2018

Objective: To investigate whether depleting self-control prior to vigilance results in a steeper vigilance decrement. Background: The resource-control theory of vigilance asserts that an inherent bias toward self-generated mind-wandering draws attentional resources away from the primary task. This study seeks to test whether depleting self-control, the potential mechanism of self-generated mind-wandering, results in poorer vigilance performance. Method: This study featured a between-subjects design where participants either completed a typing task that depleted self-control resources or a standard typing task that did not require self-control before performing a vigilance task. In the self-control depletion condition, participants typed a passage while omitting any “e” and “space” keys. In the standard typing task, participants typed the same passage without skipping any keys. Following both typing tasks, participants in both conditions completed an identical 12-min vigilance task. Results: Results demonstrated decreased accuracy and increased reaction times over time for both groups. Depleting self-control did not result in significant differences in accuracy, reaction time, nor a steeper vigilance decrement. Conclusion: These results provide evidence against resource-control theory and self-control as an explanation for vigilance, and provide further support for cognitive resource theory as the predominant explanation for vigilance impairments. Application: It is still unclear exactly what constitutes a “resource.” A better understanding of the nature of these resources can help researchers and practitioners identify how they can be replenished, which could enhance human performance in situations requiring vigilance such as baggage screening.