bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inference for Case-Control Studies With Incident and Prevalent cases
Authors: Maziarz Marlena , Liu Yukun , Qin Jing , Pfeiffer Ruth M. 
Published: January 2019

Abstract
We propose and study a fully efficient method to estimate associations of an exposure with disease incidence when both, incident cases and prevalent cases, i.e., individuals who were diagnosed with the disease at some prior time point and are alive at the time of sampling, are included in a case-control study. We extend the exponential tilting model for the relationship between exposure and case status to accommodate two case groups, and correct for the survival bias in the prevalent cases through a tilting term that depends on the parametric distribution of the backward time, i.e., the time from disease diagnosis to study enrollment. We construct an empirical likelihood that also incorporates the observed backward times for prevalent cases, obtain efficient estimates of odds ratio parameters that relate exposure to disease incidence and propose a likelihood ratio test for model parameters that has a standard chi-squared distribution. We quantify the changes in efficiency of association parameters when incident cases are supplemented with, or replaced by, prevalent cases in simulations. We illustrate our methods by estimating associations of single nucleotide polymorphisms (SNPs) with breast cancer incidence in a sample of controls, incident and prevalent cases from the U.S. Radiologic Technologists Health Study.
Model Confidence Bounds for Variable Selection
Authors: Li Yang , Luo Yuetian , Ferrari Davide , Hu Xiaonan , Qin Yichen 
Published: January 2019

AbstractIn this article, we introduce the concept of model confidence bounds (MCB) for variable selection in the context of nested models. Similarly to the endpoints in the familiar confidence interval for parameter estimation, the MCB identifies two nested models (upper and lower confidence bound models) containing the true model at a given level of confidence. Instead of trusting a single selected model obtained from a given model selection method, the MCB proposes a group of nested models as candidates and the MCB's width and composition enable the practitioner to assess the overall model selection uncertainty. A new graphical tool—the model uncertainty curve (MUC)—is introduced to visualize the variability of model selection and to compare different model selection procedures. The MCB methodology is implemented by a fast bootstrap algorithm that is shown to yield the correct asymptotic coverage under rather general conditions. Our Monte Carlo simulations and real data examples confirm the validity and illustrate the advantages of the proposed method.
Justice reactions to deviant ingroup members: Ingroup identity threat motivates utilitarian punishments
Authors: Fousiani Kyriaki , Yzerbyt Vincent , Kteily Nour‐Sami , Demoulin Stéphanie 
Published: January 2019

To maintain a positive overall view of their group, people judge likeable ingroup members more favourably and deviant ingroup members more harshly than comparable outgroup members. Research suggests that such derogation of deviant ingroup members aims to restore the image of the group by symbolically excluding so‐called ‘black sheeps’. We hypothesized that information about a harm‐doer's group membership influences observers’ justice‐seeking reactions. Motives for punishment vary based on whether the goal is to punish past harm‐doing (i.e., retributive motives), help harm‐doers recognize the harm inflicted and reintegrate into society (i.e., restorative motives), or control harm‐doer's future behaviour through incapacitating practices and exclusion from society (i.e., utilitarian motives). We hypothesized that immoral behaviours by ingroup rather than outgroup members jeopardize the group's reputation and therefore activate utilitarian (i.e., exclusion‐oriented) motives for punishment. Study 1 (N = 187) confirmed that people displayed more utilitarian motives and less restorative motives when sanctioning an ingroup as opposed to an outgroup harm‐doer. Study 2 (N = 122) manipulated typicality to the ingroup. Participants displayed stronger utilitarian (i.e., exclusion‐oriented) punishment motives when the harm‐doer was presented as a typical ingroup rather than an outgroup member. Study 3 (N = 292) replicated the findings of Studies 1 and 2 and further showed that people displayed stronger utilitarian punishments against an ingroup offender through the experience of increased identity threat. Contrary to our expectations, observers’ ingroup identification did not moderate the effect of group membership or typicality to the ingroup on justice reactions. Yet, ingroup identification influenced both experienced identity threat (i.e., mediator) and utilitarian motives for punishment with high identifiers experiencing higher threat and displaying stronger utilitarian punishment motive. We discuss the results in terms of people's concern for the protection of their group identity.
A Survey of Information Visualization Books
Authors: Rees D. , Laramee R. S. 
Published: January 2019

AbstractInformation visualization is a rapidly evolving field with a growing volume of scientific literature and texts continually published. To keep abreast of the latest developments in the domain, survey papers and state‐of‐the‐art reviews provide valuable tools for managing the large quantity of scientific literature. Recently, a survey of survey papers was published to keep track of the quantity of refereed survey papers in information visualization conferences and journals. However, no such resources exist to inform readers of the large volume of books being published on the subject, leaving the possibility of valuable knowledge being overlooked. We present the first literature survey of information visualization books that addresses this challenge by surveying the large volume of books on the topic of information visualization and visual analytics. This unique survey addresses some special challenges associated with collections of books (as opposed to research papers) including searching, browsing and cost. This paper features a novel two‐level classification based on both books and chapter topics examined in each book, enabling the reader to quickly identify to what depth a topic of interest is covered within a particular book. Readers can use this survey to identify the most relevant book for their needs amongst a quickly expanding collection. In indexing the landscape of information visualization books, this survey provides a valuable resource to both experienced researchers and newcomers in the data visualization discipline.
Disentangling the Mechanisms of Symbolic Number Processing in Adults’ Mathematics and Arithmetic Achievement
Authors: Orrantia Josetxu , Muñez David , Matilla Laura , Sanchez Rosario , San Romualdo Sara , Verschaffel Lieven 
Published: January 2019

AbstractA growing body of research has shown that symbolic number processing relates to individual differences in mathematics. However, it remains unclear which mechanisms of symbolic number processing are crucial—accessing underlying magnitude representation of symbols (i.e., symbol‐magnitude associations), processing relative order of symbols (i.e., symbol‐symbol associations), or processing of symbols per se. To address this question, in this study adult participants performed a dots‐number word matching task—thought to be a measure of symbol‐magnitude associations (numerical magnitude processing)—a numeral‐ordering task that focuses on symbol‐symbol associations (numerical order processing), and a digit‐number word matching task targeting symbolic processing per se. Results showed that both numerical magnitude and order processing were uniquely related to arithmetic achievement, beyond the effects of domain‐general factors (intellectual ability, working memory, inhibitory control, and non‐numerical ordering). Importantly, results were different when a general measure of mathematics achievement was considered. Those mechanisms of symbolic number processing did not contribute to math achievement. Furthermore, a path analysis revealed that numerical magnitude and order processing might draw on a common mechanism. Each process explained a portion of the relation of the other with arithmetic (but not with a general measure of math achievement). These findings are consistent with the notion that adults’ arithmetic skills build upon symbol‐magnitude associations, and they highlight the effects that different math measures have in the study of numerical cognition.
Environmental filtering governs the spatial distribution of alien fishes in a large, human‐impacted Mediterranean river
Authors: Radinger Johannes , Alcaraz‐Hernández Juan Diego , García‐Berthou Emili 
Published: January 2019

AbstractAimTo analyse the occurrence and abundance of native versus alien fish species in relation to climate, land use, hydrologic alteration and habitat fragmentation in a heavily invaded and human‐impacted riverine ecosystem. To test whether co‐occurrence patterns of native versus alien species are structured by environmental filtering or biotic associations.LocationMediterranean, Iberian Peninsula, Ebro River catchment.MethodsWe modelled freshwater fish distributions and their association with environmental conditions using a hurdle model‐like approach involving boosted regression trees. Additionally, we applied a joint species distribution model to quantify the co‐occurrence of native versus alien fish species that can be attributed to shared environmental responses or potentially to biotic interactions.ResultsOur results point to environmental factors, rather than biotic associations, as major correlates of the increase of alien and the decline of native fishes in the Ebro River. We observed contrasting patterns of native versus alien species along the upstream‐downstream gradient. Alien species dominated in the lower reaches associated with warmer temperatures, higher shares of intensive land use and appeared facilitated by dams and river regulation. Native species richness was highest in the larger tributaries followed by a strong decline in the main stem which was related to the river network position and land use type. Fragmentation played a subordinate role in explaining fish richness and abundance patterns.Main conclusionsGiven the strong association with temperature, a further range expansion of alien fishes in the Ebro with future climate change may be expected. More local‐scale factors related to habitat degradation and hydrologic alteration will further exacerbate the invasion success of many alien fishes. Further multiple, independent species introductions might mask isolation and fragmentation effects of dams on the future spread and distribution of alien fish.
Population structure, genetic connectivity, and adaptation in the Olympia oyster (Ostrea lurida) along the west coast of North America
Authors: Silliman Katherine 
Published: January 2019

AbstractEffective management of threatened and exploited species requires an understanding of both the genetic connectivity among populations and local adaptation. The Olympia oyster (Ostrea lurida), patchily distributed from Baja California to the central coast of Canada, has a long history of population declines due to anthropogenic stressors. For such coastal marine species, population structure could follow a continuous isolation‐by‐distance model, contain regional blocks of genetic similarity separated by barriers to gene flow, or be consistent with a null model of no population structure. To distinguish between these hypotheses in O. lurida, 13,424 single nucleotide polymorphisms (SNPs) were used to characterize rangewide population structure, genetic connectivity, and adaptive divergence. Samples were collected across the species range on the west coast of North America, from southern California to Vancouver Island. A conservative approach for detecting putative loci under selection identified 235 SNPs across 129 GBS loci, which were functionally annotated and analyzed separately from the remaining neutral loci. While strong population structure was observed on a regional scale in both neutral and outlier markers, neutral markers had greater power to detect fine‐scale structure. Geographic regions of reduced gene flow aligned with known marine biogeographic barriers, such as Cape Mendocino, Monterey Bay, and the currents around Cape Flattery. The outlier loci identified as under putative selection included genes involved in developmental regulation, sensory information processing, energy metabolism, immune response, and muscle contraction. These loci are excellent candidates for future research and may provide targets for genetic monitoring programs. Beyond specific applications for restoration and management of the Olympia oyster, this study lends to the growing body of evidence for both population structure and adaptive differentiation across a range of marine species exhibiting the potential for panmixia. Computational notebooks are available to facilitate reproducibility and future open‐sourced research on the population structure of O. lurida.
Exploring the potential for rosacea therapeutics of siRNA dispersion in topical emulsions
Authors: Colombo Stefano , Harmankaya Necati , Water Jorrit J. , Bohr Adam 
Published: January 2019

AbstractRosacea is a prevalent skin condition dependent on the individual genetic profile. The current pharmacological management of this condition is mostly based on small molecule drugs predominately effective in ameliorating the inflammatory condition. Emerging molecular approaches could present an opportunity for managing rosacea conditions at transcriptomic level, and in the future allow personalized approaches. RNA medicines, such as small RNA interference (siRNA), could provide a flexible and applicable tool reaching this aim. However, the topical siRNA delivery by dermatological emulsions, commonly used in the daily management of rosacea, is still largely unexplored. Consequently, RNA interference application to rosacea was defined on molecular bases by genetic expression meta‐data analysis. Based on this, a siRNA directed against TLR2 was designed and validated in vitro on murine macrophages and fibroblasts. Next, siRNA was dispersed in the continuous phase of emulsions and was characterized for commonly used dermatologic bases. Finally, the potential delivery performance of the topical emulsions was tested in vivo on healthy Balb/c mice. It was found that the interaction of siRNA with combination of excipients, such as urea and glycerol, is likely to favour the siRNA delivery, inducing genetic silencing of TLR2. These findings provide a foundation for the future development of topical RNA‐based dispersions for topical molecular medicines, by emphasizing on the formulation and therapeutic‐based opportunities with dermatological treatments.
Environmental characteristics of spawning and nursery grounds of Japanese sardine and mackerels in the Kuroshio and Kuroshio Extension area
Authors: Sogawa Sayaka , Hidaka Kiyotaka , Kamimura Yasuhiro , Takahashi Masanori , Saito Hiroaki , Okazaki Yuji , Shimizu Yugo , Setou Takashi 
Published: January 2019

AbstractThe sustainable use of marine resources requires understanding the surrounding ecosystem and elucidating mechanisms of variation. However, we still lack a comprehensive understanding of environmental variation in the spawning and nursery grounds of important fisheries species Japanese sardine (Sardinops melanostictus) and mackerels (Scomber japonicus and Scomber australasicus) in the northwest Pacific. Here, we investigate detailed physical, chemical, and biological environment variations in the spawning and nursery grounds along the Kuroshio and Kuroshio Extension area from intensive investigation in spawning season (April) of 2013. We found similar water mass property and copepod community in the egg‐rich Kuroshio area and the larvae‐rich downstream Kuroshio Extension area, indicating environmental variability is small during transportation and development processes. The egg‐rich northern Izu Islands region showed high copepod abundance, although low nutrient and chlorophyll concentrations were observed. Eggs were scarce or absent in the second survey 10 days after abundant eggs were observed in the region, along with differences in water property and copepod community. This indicates that not only the location but also the specific water characteristic and copepod community are a determining factor for spawning. Indicator communities of copepod found in our study (indicator community of transportation process from spawning ground, of non‐spawning ground, and of reproductive area in the Kuroshio Extension area) would be a key factor for recruitment prediction.
Least concern to endangered: Applying climate change projections profoundly influences the extinction risk assessment for wild Arabica coffee
Authors: Moat Justin , Gole Tadesse W. , Davis Aaron P. 
Published: January 2019

AbstractArabica coffee (Coffea arabica) is a key crop in many tropical countries and globally provides an export value of over US$13 billion per year. Wild Arabica coffee is of fundamental importance for the global coffee sector and of direct importance within Ethiopia, as a source of harvestable income and planting stock. Published studies show that climate change is projected to have a substantial negative influence on the current suitable growing areas for indigenous Arabica in Ethiopia and South Sudan. Here we use all available future projections for the species based on multiple general circulation models (GCMs), emission scenarios, and migration scenarios, to predict changes in Extent of Occurrence (EOO), Area of Occupancy (AOO), and population numbers for wild Arabica coffee. Under climate change our results show that population numbers could reduce by 50% or more (with a few models showing over 80%) by 2088. EOO and AOO are projected to decline by around 30% in many cases. Furthermore, present‐day models compared to the near future (2038), show a reduction for EOO of over 40% (with a few cases over 50%), although EOO should be treated with caution due to its sensitivity to outlying occurrences. When applying these metrics to extinction risk, we show that the determination of generation length is critical. When applying the International Union for Conservation of Nature's Red list of Threatened Species (IUCN Red List) criteria, even with a very conservative generation length of 21 years, wild Arabica coffee is assessed as Threatened with extinction (placed in the Endangered category) under a broad range of climate change projections, if no interventions are made. Importantly, if we do not include climate change in our assessment, Arabica coffee is assessed as Least Concern (not threatened) when applying the IUCN Red List criteria.
Peritumoral pseudocapsule status according to pathological characteristics from robot‐assisted laparoscopic partial nephrectomy for localized renal cell carcinoma
Authors: Takagi Toshio , Yoshida Kazuhiko , Kondo Tsunenori , Kobayashi Hirohito , Iizuka Junpei , Okumi Masayoshi , Ishida Hideki , Nagashima Yoji , Tanabe Kazunari 
Published: January 2019

ObjectiveTo investigate peritumoral pseudocapsule status in patients with renal cell carcinoma who underwent robot‐assisted laparoscopic partial nephrectomy, and to examine predictive factors associated with the absence of peritumoral pseudocapsule.MethodsA total of 367 patients with clinical T1 renal cell carcinoma who underwent robot‐assisted laparoscopic partial nephrectomy were divided into two groups according to peritumoral pseudocapsule status. The groups were compared in terms of patient and tumor characteristics. Multivariate logistic regression analysis was carried out to identify predictive factors for the absence of peritumoral pseudocapsule.ResultsOf the 367 tumors, 323 (88%) were surrounded by a peritumoral pseudocapsule. The mean tumor size was 30 mm, and 70% of the patients were male. Tumors with a peritumoral pseudocapsule had a larger diameter than those without (31 vs 26 mm; P = 0.0008). A peritumoral pseudocapsule was observed in 92% of the clear cell, in 89% of the papillary and in 86% of the clear cell papillary renal cell carcinoma cases compared with just 50% in the chromophobe renal cell carcinoma cases (P < 0.0001). Sex, age, Fuhrman grade and tumor complexity did not differ among patients. A multivariate analysis showed that smaller tumor size (≥34 vs <34 mm, odds ratio 3.31; P = 0.0023) and chromophobe renal cell carcinoma (vs other subtypes, odds ratio 12.5; P < 0.0001) predicted an absence of peritumoral pseudocapsule.ConclusionsSmall tumor size and chromophobe renal cell carcinoma were significant predictors of a lack of peritumoral pseudocapsule, suggesting that a positive surgical margin must be avoided for these tumors when an enucleation technique is used for robot‐assisted laparoscopic partial nephrectomy.
Hydration of calcium aluminates at 60°C – Development paths of C2AHx in dependence on the content of free water
Authors: Hueller Florian , Neubauer Juergen , Kaessner Stefan , Goetz‐Neunhoeffer Friedlinde 
Published: January 2019

AbstractThe influence of water loss during the hydration of calcium aluminates on the phase development is investigated at 60°C. This is relevant for applications in which calcium aluminate cement (CAC) based formulations are exposed to quick drying during hydration. The presented results provide new insights into the well‐known conversion processes occurring in CAC pastes. Using in situ XRD two different routes of the development of initially formed C2AH8 are determined: (a) transformation to C3AH6 + AH3 in the presence of sufficient free water and (b) dehydration to C2AH5 at a lack of free water. Moreover, the influence of precuring of the pastes at 23°C before heating to 60°C is investigated. The increasing loss of free water with increasing precuring time resulting from both, precipitation of hydrate phases and evaporation, causes incomplete hydration of CA or CA2 as well as dehydration of C2AH8 instead of conversion into C3AH6. Comparative investigations of sealed samples always revealed complete hydration of CA and CA2 as well as complete conversion of C2AH8.