bluuebunny/crossref_metadata_2025_split huggingface dataset:
Disaster Metrics: Evaluation of de Boer's Disaster Severity Scale (DSS) Applied to Earthquakes
Authors: Bayram Jamil D. , Zuabi Shawki , McCord Caitlin M. , Sherak Raphael A.G. , Hsu Edberdt B. , Kelen Gabor D. 
Published: December 2014

AbstractIntroductionQuantitative measurement of the medical severity following multiple-casualty events (MCEs) is an important goal in disaster medicine. In 1990, de Boer proposed a 13-point, 7-parameter scale called the Disaster Severity Scale (DSS). Parameters include cause, duration, radius, number of casualties, nature of injuries, rescue time, and effect on surrounding community.HypothesisThis study aimed to examine the reliability and dimensionality (number of salient themes) of de Boer's DSS scale through its application to 144 discrete earthquake events.MethodsA search for earthquake events was conducted via National Oceanic and Atmospheric Administration (NOAA) and US Geological Survey (USGS) databases. Two experts in the field of disaster medicine independently reviewed and assigned scores for parameters that had no data readily available (nature of injuries, rescue time, and effect on surrounding community), and differences were reconciled via consensus. Principle Component Analysis was performed using SPSS Statistics for Windows Version 22.0 (IBM Corp; Armonk, New York USA) to evaluate the reliability and dimensionality of the DSS.ResultsA total of 144 individual earthquakes from 2003 through 2013 were identified and scored. Of 13 points possible, the mean score was 6.04, the mode = 5, minimum = 4, maximum = 11, and standard deviation = 2.23. Three parameters in the DSS had zero variance (ie, the parameter received the same score in all 144 earthquakes). Because of the zero contribution to variance, these three parameters (cause, duration, and radius) were removed to run the statistical analysis. Cronbach's alpha score, a coefficient of internal consistency, for the remaining four parameters was found to be robust at 0.89. Principle Component Analysis showed uni-dimensional characteristics with only one component having an eigenvalue greater than one at 3.17. The 4-parameter DSS, however, suffered from restriction of scoring range on both parameter and scale levels.ConclusionJan de Boer's DSS in its 7-parameter format fails to hold statistically in a dataset of 144 earthquakes subjected to analysis. A modified 4-parameter scale was found to quantitatively assess medical severity more directly, but remains flawed due to range restriction on both individual parameter and scale levels. Further research is needed in the field of disaster metrics to develop a scale that is reliable in its complete set of parameters, capable of better fine discrimination, and uni-dimensional in measurement of the medical severity of MCEs.BayramJD, ZuabiS, McCordCM, SherakRAG, HsuEB, KelenGD. Disaster metrics: evaluation of de Boer's Disaster Severity Scale (DSS) applied to earthquakes. Prehosp Disaster Med. 2015;30(1):1-6.
‘It’s just so much waste.’ A qualitative investigation of food waste in a universal free School Breakfast Program
Authors: Blondin Stacy A , Djang Holly Carmichael , Metayer Nesly , Anzman-Frasca Stephanie , Economos Christina D 
Published: December 2014

AbstractObjectiveTo understand stakeholders’ perspectives on food waste in a universal free School Breakfast Program implementing a Breakfast in the Classroom model.DesignSemi-structured focus groups and interviews were conducted with school district stakeholders. Inductive methods were used to code resulting transcripts, from which themes were identified. The analysis provides a thematic analysis of stakeholders’ perspectives on food waste in the School Breakfast Program.SettingTen elementary schools in a large urban school district implementing a universal free Breakfast in the Classroom model of the US national School Breakfast Program.SubjectsElementary-school students (n85), parents (n86), teachers (n44), cafeteria managers (n10) and school principals (n10).ResultsStakeholders perceived food waste as a problem and expressed concern regarding the amount of food wasted. Explanations reported for food waste included food-related (palatability and accessibility), child-related (taste preferences and satiation) and programme-related (duration, food service policies, and coordination) factors. Milk and fruit were perceived as foods particularly susceptible to waste. Several food waste mitigation strategies were identified by participants: saving food for later, actively encouraging children’s consumption, assisting children with foods during mealtime, increasing staff support, serving smaller portion sizes, and composting and donating uneaten food.ConclusionsStakeholders recognized food waste as a problem, reported myriad contributing factors, and have considered and employed multiple and diverse mitigation strategies. Changes to the menu and/or implementation logistics, as well as efforts to use leftover food productively, may be possible strategies of reducing waste and improving the School Breakfast Program’s economic, environmental and nutritional impact.
RACISM, GROUP POSITION, AND ATTITUDES ABOUT IMMIGRATION AMONG BLACKS AND WHITES1
Authors: Hutchings Vincent L. , Wong Cara 
Published: December 2014

AbstractPrevious research has shown that racial or ethnic prejudice is one of the most influential antecedents of opposition to more expansive immigration policies. In this paper, we explore whether a theoretical perspective derived from the group position model might represent an additional and complementary explanation for immigration attitudes. We also compare how well the prejudice and group position models explain immigration attitudes among both White and Black Americans. Most of the previous work in this literature focuses solely on Whites’ attitudes, and it remains unclear how well models designed with this group in mind might also apply to African Americans. We rely upon the 2004–2005 National Politics Study to explore the power of these models. In general, we find that measures derived from the group position model account for immigration attitudes even after controlling for various forms of out-group prejudice. The pattern of results also differs considerably across the two racial groups in our study.
HOW EXTERNAL RACIAL CLASSIFICATIONS SHAPE LATINO DATING CHOICES1
Authors: Feliciano Cynthia , Robnett Belinda 
Published: December 2014

AbstractUnderstanding how different dimensions of race relate to the lived experiences of Latinos may shed light on the assimilation trajectories of different segments of the Latino population. Existing research suggests that racial appearance influences Latinos’ socioeconomic outcomes due to discrimination. However, researchers have not examined how Latinos’ perceived race relates to their acceptance of other racial/ethnic groups, thus revealing their agency in the assimilation process and how it is shaped by existing racial structures. Using a sample of over 6000 profiles collected from an internet dating website, this study finds that considering others’ classifications of race in addition to self-identifications changes our understanding of Latinos’ acceptance of other racial/ethnic groups as dates. Latinos who appear White are most likely to exclude Blacks and include Whites as possible dates while the opposite is true for those classified as Black. Latinos perceivedasLatino fall somewhere in between those with a White versus Black racial phenotype in their acceptance of Blacks and Whites. These findings suggest that neither external classifications nor self-identifications of race alone can adequately assess the assimilation prospects of self-identified Latinos: those perceived as White may be assuming the position of Whites in the racial hierarchy, those perceived as Black may be assimilating into the bottom of the racial hierarchy along with African Americans, while those perceived as Latino may be maintaining an in-between status.
Lewis Sheiner ISoP/UCSF Lecturer Award: From Drug Use to Statistical Models and Vice Versa
Authors: Mentré F 
Published: December 2014

I was very honored to receive the University of California, San Francisco, and the International Society of Pharmacometrics Lewis Sheiner lecturer award in May 2013. In the present perspective, I outline the main points of my lecture at the American Conference of Pharmacometrics (slides in Supplementary Material 1). I first emphasize the scientific contributions of Lewis Sheiner as a quantitative pharmacologist toward the better use of drugs. I then focus on three statistical topics in pharmacometrics, describing Lewis Sheiner's impact and my own contributions and interactions with him.CPT Pharmacometrics Syst. Pharmacol. (2014) 3, e154; doi:10.1038/psp.2014.52; published online 29 December 2014
Energetic basis for the molecular-scale organization of bone
Authors: Tao Jinhui , Battle Keith C. , Pan Haihua , Salter E. Alan , Chien Yung-Ching , Wierzbicki Andrzej , De Yoreo James J. 
Published: December 2014

Significance
The remarkable mechanical properties of bone are determined by the organization and strength of binding at the mineral–collagen interface. Although the process through which collagen becomes mineralized has been extensively studied, little is known about the mechanisms or energetics that underlie the organization of this mineral–matrix composite. Combining molecular-scale imaging and analyses of collagen adsorption on four bone-related calcium phosphate phases, single-molecule force measurements and molecular simulations of collagen binding to hydroxyapatite, and electron microscopy analyses of bone and dentine, we determine the magnitude and chemistry of collagen–hydroxyapatite binding and show that calcium-deficient apatite is the only phase consistent with observed structural relationships.
ETS transcription factor ETV2 directly converts human fibroblasts into functional endothelial cells
Authors: Morita Rimpei , Suzuki Mayu , Kasahara Hidenori , Shimizu Nana , Shichita Takashi , Sekiya Takashi , Kimura Akihiro , Sasaki Ken-ichiro , Yasukawa Hideo , Yoshimura Akihiko 
Published: December 2014

Significance
Endothelial cells (ECs) form vasculature to provide vital elements, such as nutrients and oxygen, to tissues and organs in the body. Thus, creating ECs from nonvascular cells by transducing some transcription factors not only leads to the development of new strategies for patient-specific therapeutic angiogenesis, but also facilitates the maintenance of the solid organs that are regenerated from pluripotent stem cells. In this paper, we show that the single transcription factor ETV2, which is lentivirally transduced, induces expression of the multiple EC-specific molecules in coordination with endogenous FOXC2 in the fibroblasts, resulting in the conversion of primary human adult skin fibroblasts into functional ECs that form mature perfused vessels in vivo.
Hematopoietic IKBKE limits the chronicity of inflammasome priming and metaflammation
Authors: Patel Meghana N. , Bernard William G. , Milev Nikolay B. , Cawthorn William P. , Figg Nichola , Hart Dan , Prieur Xavier , Virtue Sam , Hegyi Krisztina , Bonnafous Stephanie , Bailly-Maitre Beatrice , Chu Yajing , Griffin Julian L. , Mallat Ziad , Considine Robert V. , Tran Albert , Gual Philippe , Takeuchi Osamu , Akira Shizuo , Vidal-Puig Antonio , Bennett Martin R. , Sethi Jaswinder K. 
Published: December 2014

Significance
Chronic low-grade inflammation plays a causative role in obesity-associated metabolic diseases. However, the mechanisms underlying chronicity of low-grade inflammation remain elusive. Herein, we identify inhibitor of κB kinase epsilon (IKBKE) as a new modulator of chronic inflammation in macrophages. We first show that IKBKE is clinically relevant in distinct tissues associated with metabolic diseases including obesity, nonalcoholic steatohepatitis, and atherosclerosis. In all cases, IKBKE expression predominates in macrophages and associates with chronic inflammation. In macrophages, IKBKE affects chronicity of inflammation by temporally limiting inflammasome priming. Both global IKBKE ablation and reconstitution with hematopoietic IKBKE reciprocally alters metaflammation in adipose tissue, liver, and the composition of advanced atherosclerotic plaques. These findings establish a nonpathogenic role for hematopoietic IKBKE in limiting inflammasome priming and metaflammation.
The QDREC web server: determining dose–response characteristics of complex macroparasites in phenotypic drug screens
Authors: Asarnow Daniel , Rojo-Arreola Liliana , Suzuki Brian M. , Caffrey Conor R. , Singh Rahul 
Published: December 2014

Abstract
Summary: Neglected tropical diseases (NTDs) caused by helminths constitute some of the most common infections of the world’s poorest people. The etiological agents are complex and recalcitrant to standard techniques of molecular biology. Drug screening against helminths has often been phenotypic and typically involves manual description of drug effect and efficacy. A key challenge is to develop automated, quantitative approaches to drug screening against helminth diseases. The quantal dose–response calculator (QDREC) constitutes a significant step in this direction. It can be used to automatically determine quantitative dose–response characteristics and half-maximal effective concentration (EC50) values using image-based readouts from phenotypic screens, thereby allowing rigorous comparisons of the efficacies of drug compounds. QDREC has been developed and validated in the context of drug screening for schistosomiasis, one of the most important NTDs. However, it is equally applicable to general phenotypic screening involving helminths and other complex parasites.
Availability and implementation: QDREC is publically available at: http://haddock4.sfsu.edu/qdrec2/. Source code and datasets are at: http://tintin.sfsu.edu/projects/phenotypicAssays.html.
Contact: rahul@sfsu.edu.
Supplementary information: Supplementary data are available at Bioinformatics online.
Knowledge-based modeling of peptides at protein interfaces: PiPreD
Authors: Oliva Baldo , Fernandez-Fuentes Narcis 
Published: December 2014

Abstract
Motivation: Protein–protein interactions (PPIs) underpin virtually all cellular processes both in health and disease. Modulating the interaction between proteins by means of small (chemical) agents is therefore a promising route for future novel therapeutic interventions. In this context, peptides are gaining momentum as emerging agents for the modulation of PPIs.
Results: We reported a novel computational, structure and knowledge-based approach to model orthosteric peptides to target PPIs: PiPreD. PiPreD relies on a precompiled and bespoken library of structural motifs, iMotifs, extracted from protein complexes and a fast structural modeling algorithm driven by the location of native chemical groups on the interface of the protein target named anchor residues. PiPreD comprehensive and systematically samples the entire interface deriving peptide conformations best suited for the given region on the protein interface. PiPreD complements the existing technologies and provides new solutions for the disruption of selected interactions.
Availability and implementation: Database and accessory scripts and programs are available upon request to the authors or at http://www.bioinsilico.org/PIPRED.
Contact: narcis.fernandez@gmail.com
RRDistMaps: a UCSF Chimera tool for viewing and comparing protein distance maps
Authors: Chen Jonathan E. , Huang Conrad C. , Ferrin Thomas E. 
Published: December 2014

Abstract
Motivation: Contact maps are a convenient method for the structural biologists to identify structural features through two-dimensional simplification. Binary (yes/no) contact maps with a single cutoff distance can be generalized to show continuous distance ranges. We have developed a UCSF Chimera tool, RRDistMaps, to compute such generalized maps in order to analyze pairwise variations in intramolecular contacts. An interactive utility, RRDistMaps, visualizes conformational changes, both local (e.g. binding-site residues) and global (e.g. hinge motion), between unbound and bound proteins through distance patterns. Users can target residue pairs in RRDistMaps for further navigation in Chimera. The interface contains the unique features of identifying long-range residue motion and aligning sequences to simultaneously compare distance maps.
Availability and implementation: RRDistMaps was developed as part of UCSF Chimera release 1.10, which is freely available at http://rbvi.ucsf.edu/chimera/download.html, and operates on Linux, Windows, and Mac OS.
Contact: conrad@cgl.ucsf.edu
J-Circos: an interactive Circos plotter
Authors: An Jiyuan , Lai John , Sajjanhar Atul , Batra Jyotsna , Wang Chenwei , Nelson Colleen C 
Published: December 2014

Abstract
Summary: Circos plots are graphical outputs that display three dimensional chromosomal interactions and fusion transcripts. However, the Circos plot tool is not an interactive visualization tool, but rather a figure generator. For example, it does not enable data to be added dynamically nor does it provide information for specific data points interactively. Recently, an R-based Circos tool (RCircos) has been developed to integrate Circos to R, but similarly, Rcircos can only be used to generate plots. Thus, we have developed a Circos plot tool (J-Circos) that is an interactive visualization tool that can plot Circos figures, as well as being able to dynamically add data to the figure, and providing information for specific data points using mouse hover display and zoom in/out functions. J-Circos uses the Java computer language to enable, it to be used on most operating systems (Windows, MacOS, Linux). Users can input data into J-Circos using flat data formats, as well as from the Graphical user interface (GUI). J-Circos will enable biologists to better study more complex chromosomal interactions and fusion transcripts that are otherwise difficult to visualize from next-generation sequencing data.
Availability and implementation: J-circos and its manual are freely available at http://www.australianprostatecentre.org/research/software/jcircos
Contact: j.an@qut.edu.au
Supplementary information: Supplementary data are available at Bioinformatics online.
UProC: tools for ultra-fast protein domain classification
Authors: Meinicke Peter 
Published: December 2014

Abstract
Motivation: With rapidly increasing volumes of biological sequence data the functional analysis of new sequences in terms of similarities to known protein families challenges classical bioinformatics.
Results: The ultrafast protein classification (UProC) toolbox implements a novel algorithm (‘Mosaic Matching’) for large-scale sequence analysis. UProC is by three orders of magnitude faster than profile-based methods and in a metagenome simulation study achieved up to 80% higher sensitivity on unassembled 100 bp reads.
Availability and implementation: UProC is available as an open-source software at https://github.com/gobics/uproc. Precompiled databases (Pfam) are linked on the UProC homepage: http://uproc.gobics.de/.
Contact: peter@gobics.de.
Supplementary information: Supplementary data are available at Bioinformatics online.
Reduced herding of flounders by floating bridles: application in Gulf of Maine Northern shrimp trawls to reduce bycatch
Authors: He Pingguo , Rillahan Christopher , Balzano Vincent 
Published: December 2014

Abstract
We hypothesized that a floating trawl bridle that does not contact the seabed would reduce the herding of fish, especially bottom dwelling flounders, and thus reduce bycatch of these fish in shrimp trawls. We further hypothesized that, due to the non-herding nature of northern shrimp (Pandalus borealis), the use of an off-bottom floating bridle would not reduce shrimp catch. These hypotheses were tested in the field by comparing a trawl with regular bottom-tendering wire bridles and the same trawl with floating synthetic bridles in the Gulf of Maine northern shrimp fishery. As expected, no statistically significant differences in catch rates and size were found for the targeted northern shrimp (146.3 ± 10.58 kg h−1 control vs. 140.8 ± 9.35 kg h−1, p = 0.13). Total finfish bycatch was reduced by 14.9%, and the difference was statistically different (p = 0.01). The most important reduction was the catch of juvenile American plaice (Hippoglossoides platessoides) with a significant reduction of 20.0% (p = 0.01). For witch flounder (Glyptocephalus cynoglossus), a reduction of 19.3% was found, but it was not statistically significant (p = 0.14). The reduction of Acadian redfish (Sebastes fasciatus) (by 28.0%, p = 0.02) was also statistically different. Catch of targeted silver hake (Merluccius bilinearis) was reduced by 10.8%, but the difference was only marginally significant (p = 0.07). An analysis of length frequencies for the targeted shrimp and major bycatch species revealed no size-related selection between the gears with regular bridles and floating bridles. The reductions in flounder bycatch indicate reduced herding of benthic species when the bridles are kept off bottom. This easy modification may be readily adopted in the northern shrimp fisheries in the North Atlantic, and can also possibly be applied in other shrimp and prawn fisheries with further experimentation.
Mass-segregation trends in SDSS galaxy groups
Authors: Roberts Ian D. , Parker Laura C. , Joshi Gandhali D. , Evans Fraser A. 
Published: December 2014

Abstract
It has been shown that galaxy properties depend strongly on their host environment. In order to understand the relevant physical processes driving galaxy evolution it is important to study the observed properties of galaxies in different environments. Mass segregation in bound galaxy structures is an important indicator of evolutionary history and dynamical friction time-scales. Using group catalogues derived from the Sloan Digital Sky Survey Data Release 7 (SDSS DR7), we investigate mass-segregation trends in galaxy groups at low redshift. We investigate average galaxy stellar mass as a function of group-centric radius and find evidence for weak mass segregation in SDSS groups. The magnitude of the mass segregation depends on both galaxy stellar mass limits and group halo mass. We show that the inclusion of low-mass galaxies tends to strengthen mass-segregation trends, and that the strength of mass segregation tends to decrease with increasing group halo mass. We find the same trends if we use the fraction of massive galaxies as a function of group-centric radius as an alternative probe of mass segregation. The magnitude of mass segregation that we measure, particularly in high-mass haloes, indicates that dynamical friction is not acting efficiently.