bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Supreme Court’s Use of Foreign Law in Constitutional Rights Cases
Authors: Simon Stephen A. 
Published: August 2013

AbstractA trio of Supreme Court decisions between 2002 and 2005 intensified debate over judicial reliance on foreign law. The literature has been dominated by arguments over the desirability of foreign law citations in the abstract, without sufficient attention to how the Court actually has used foreign law. To ground the normative debate, this article presents analysis of a newly created database containing cases from the Court’s earliest period to the present day in which the lead opinions relied on foreign law in deciding constitutional rights cases. The article uses this analysis to (1) make sense of why the recent trio of decisions was so controversial, even though the practice of citing foreign law was not new, and (2) show why many of the justifications offered by scholars for judicial reliance on foreign law bear no relation to how the Court has employed foreign law in practice.
ASPeak: an abundance sensitive peak detection algorithm for RIP-Seq
Authors: Kucukural Alper , Özadam Hakan , Singh Guramrit , Moore Melissa J. , Cenik Can 
Published: August 2013

Abstract
Summary: Unlike DNA, RNA abundances can vary over several orders of magnitude. Thus, identification of RNA–protein binding sites from high-throughput sequencing data presents unique challenges. Although peak identification in ChIP-Seq data has been extensively explored, there are few bioinformatics tools tailored for peak calling on analogous datasets for RNA-binding proteins. Here we describe ASPeak (abundance sensitive peak detection algorithm), an implementation of an algorithm that we previously applied to detect peaks in exon junction complex RNA immunoprecipitation in tandem experiments. Our peak detection algorithm yields stringent and robust target sets enabling sensitive motif finding and downstream functional analyses.
Availability: ASPeak is implemented in Perl as a complete pipeline that takes bedGraph files as input. ASPeak implementation is freely available at https://sourceforge.net/projects/as-peak under the GNU General Public License. ASPeak can be run on a personal computer, yet is designed to be easily parallelizable. ASPeak can also run on high performance computing clusters providing efficient speedup. The documentation and user manual can be obtained from http://master.dl.sourceforge.net/project/as-peak/manual.pdf.
Contact: alper.kucukural@umassmed.edu or ccenik@stanford.edu
PARSEC: PAtteRn SEarch and Contextualization
Authors: Allot Alexis , Anno Yannick-Noël , Poidevin Laetitia , Ripp Raymond , Poch Olivier , Lecompte Odile 
Published: August 2013

Abstract
Summary: We present PARSEC (PAtteRn Search and Contextualization), a new open source platform for guided discovery, allowing localization and biological characterization of short genomic sites in entire eukaryotic genomes. PARSEC can search for a sequence or a degenerated pattern. The retrieved set of genomic sites can be characterized in terms of (i) conservation in model organisms, (ii) genomic context (proximity to genes) and (iii) function of neighboring genes. These modules allow the user to explore, visualize, filter and extract biological knowledge from a set of short genomic regions such as transcription factor binding sites.
Availability: Web site implemented in Java, JavaScript and C++, with all major browsers supported. Freely available at lbgi.fr/parsec. Source code is freely available at sourceforge.net/projects/genomicparsec.
Contact: odile.lecompte@unistra.fr
Supplementary information: Supplementary data are available at Bioinformatics online.
Effects of Heat Treatments on the Milling, Physicochemical, and Cooking Properties of Two Long‐Grain Rice Cultivars During Storage
Authors: Lee Youngbum , Mauromoustakos Andronikos , Wang Ya‐Jane 
Published: August 2013

ABSTRACTDuring storage, the milling, physicochemical properties, and eating quality of rice change, which is generally termed “aging.” Aged rice is preferred by processors because of better processing characteristics, and therefore there are attempts to develop accelerated aging processes. In this study, the effects of various heat treatments and their influences on the milling, physicochemical, and cooking properties of two long‐grain rice cultivars during storage were investigated with a randomized complete block design with an 8 × 5 × 2 full‐factorial treatment design. Two long‐grain rice cultivars, Wells and XP723, were treated with eight different heat treatments, including two levels of UV irradiation, two levels of autoclaving, three levels of convection oven heating, and one control, and then stored for 180 days at room temperature. The heat treatments significantly influenced all properties, including head rice yield (HRY), surface lipid content, peak gelatinization temperature, pasting properties, and cooked rice texture. All properties except HRY exhibited a significant two‐way interaction of cultivar and heat treatment. The severe autoclaving treatment resulted in rice of significantly different protein compositions when compared with the control. Storage impacted all properties except HRY and peak gelatinization temperature. Autoclaving (particularly severe autoclaving) produced samples with more distinct characteristics for most properties. Cooked rice hardness and stickiness exhibited not only significant main effects but also significant two‐ and three‐factor interactions.
Reduction of Hepatitis A Virus on FRhK‐4 Cells Treated with Korean Red Ginseng Extract and Ginsenosides
Authors: Lee Min Hwa , Lee Bog‐Hieu , Lee Sanghyun , Choi Changsun 
Published: August 2013

AbstractRed ginseng has a variety of bioactive functions and is widely used as an oriental medicinal herb and food ingredient. The aim of this study was to investigate the antiviral effect of red ginseng extract and ginsenosides against hepatitis A virus (HAV). To examine the antiviral effect against HAV, 0 to 10 μg/mL of red ginseng and purified ginsenoside Rb1 and Rg1 were pre‐treated or co‐treated on FRhK‐4 cells. The HAV titer decreased significantly in all groups pretreated with red ginseng or purified ginsenosides. The reduction of HAV was significant in FRhK‐4 cells pre‐treated only with red ginseng. Our results showed that red ginseng and ginsenoside Rg1 and Rb1 could decrease HAV titers.
Unifying fossils and phylogenies for comparative analyses of diversification and trait evolution
Authors: Slater Graham J. , Harmon Luke J. 
Published: August 2013

Summary

The aim of macroevolutionary research is to understand pattern and process in phenotypic evolution and lineage diversification at and above the species level. Historically, this kind of research has been tackled separately by palaeontologists, using the fossil record, and by evolutionary biologists, using phylogenetic comparative methods.

Although both approaches have strengths, researchers gain most power to understand macroevolution when data from living and fossil species are analysed together in a phylogenetic framework. This merger sets up a series of challenges – for many fossil clades, well‐resolved phylogenies based on morphological data are not available, while placing fossils into phylogenies of extant taxa and determining their branching times is equally challenging. Once methods for building such trees are available, modelling phenotypic and lineage diversification using combined data presents its own set of challenges.

The five papers in this Special Feature tackle a disparate range of topics in macroevolutionary research, from time calibration of trees to modelling phenotypic evolution. All are united, however, in implementing novel phylogenetic approaches to understand macroevolutionary pattern and process in or using the fossil record. This Special Feature highlights the benefits that may be reaped by integrating data from living and extinct species and, we hope, will spur further integrative work by empiricists and theoreticians from both sides of the macroevolutionary divide.
Eosinophil peroxidase in sputum represents a unique biomarker of airway eosinophilia
Authors: Nair P. , Ochkur S. I. , Protheroe C. , Radford K. , Efthimiadis A. , Lee N. A. , Lee J. J. 
Published: August 2013

AbstractBackgroundSputum eosinophilia has been shown to be a predictor of response to anti‐eosinophil therapies in patients with airway diseases. However, quantitative cell counts and differentials of sputum are labor intensive. The objective of this study was to validate a novel ELISA‐based assay of eosinophil peroxidase (EPX) in sputum as a rapid and reliable marker of airway eosinophils.MethodsThe utility of EPX‐based ELISA as an eosinophil‐specific assay was achieved through comparisons with sputum eosinophil differential counts in freshly prepared and archived patient samples from a variety of clinical settings.ResultsEPX levels in sputum correlated with eosinophil percentage (rs = 0.84) in asthma patients with varying degrees of airway eosinophilia. Significantly, unlike assays of other eosinophil granule proteins (e.g., ECP and EDN), which often detect the presence of these proteins even in asthma patients with neutrophilic bronchitis, EPX‐based ELISA levels are not increased in this subset of asthma patients or in COPD patients lacking evidence of an airway eosinophilia. Moreover, sputum EPX was a surrogate marker of airway eosinophilia in other patient studies (e.g., allergen inhalation and treatment trials the anti‐(IL‐5) therapeutic Mepolizumab™). Finally, EPX levels in cytocentrifuged prepared sputum supernatants correlated with those from rapidly prepared noncentrifuged filtrates of sputum (rs = 0.94).Conclusion and clinical implicationEPX‐based ELISA is a valid, reliable, repeatable, and specific surrogate marker of eosinophils and/or eosinophil degranulation in the sputum of respiratory patients. The novel EPX assay is a valid and reproducible eosinophil‐specific assay that can potentially be developed into a point‐of‐care assessment of eosinophil activity in airway secretions.
On Christianity and ethics: Rupture as ethical practice in Ghanaian Pentecostalism
Authors: DASWANI GIRISH 
Published: August 2013

ABSTRACTRupture, a common principle of the Pentecostal Christian faith, can also give rise to ethical disputes among believers. The study of such disputes provides insight into the ways ethical practice shapes the institutional continuities and the personal inconsistencies of a Christian life. All believers learn what Pentecostal rupture is, but they have different opinions about how it is achieved, and, once born again, they differ on what constitutes good or right religious observance. I suggest that approaching rupture as ethical practice allows for a better understanding of the religious subject's response to an incommensurability of values and practices internal to Pentecostalism.
The photographer's body: Populism, polarization, and the uses of victimhood in Venezuela
Authors: SAMET ROBERT 
Published: August 2013

ABSTRACTPolitical antagonism between supporters and opponents of former president Hugo Chávez has been a defining feature of daily life in Caracas for more than a decade. Despite their different political orientations, the antagonistic poles of “chavismo” and “the opposition” share striking similarities, starting at the level of political practice. I argue that Venezuela's political polarization reflects the shared logic of populism. Through the story of Jorge Tortoza—a photojournalist killed during the failed 2002 coup d’état against President Chávez—I describe how the chavista–opposition divide is produced and policed through performances of victimhood, performances that are essential to populist mobilization in Venezuela.
The poetics of village space when villages are new: Settlement form as history making in Papua, Indonesia
Authors: STASCH RUPERT 
Published: August 2013

ABSTRACTResettlement of dispersed populations into centralized villages has been a watershed cultural change across many world regions, often occurring under pressure from states, world religions, and markets. Recent village formation processes among Korowai of Papua, Indonesia, have been caused by such pressures but have also been heavily structured by Korowai understandings of geography. This article takes Korowai villages as a case study in the semiotics of space. The power of villages to be the pivot of historical transformation flows from this spatial form's “poetic density,” meaning its ladenness with a multiplicity of social principles, structures of feeling, and models of extralocal geopolitical articulation. Additionally, Korowai strongly orient to space as a field of heterogeneity. Their expectation that different spaces are charged with otherness of order has shaped their village‐forming actions and their intense focus on villages in thinking about contemporary history at large.
Predicting quality of life 5 years after medical discharge for traumatic spinal cord injury
Authors: Erosa Norma A. , Berry Jack W. , Elliott Timothy R. , Underhill Andrea T. , Fine Philip R. 
Published: August 2013

ObjectivesThis study tested an a priori contextual model of the mediating effects of participation on the predictive relationships of functional impairment, family satisfaction, and pain to quality of life (QoL) following traumatic spinal cord injury (SCI).DesignA longitudinal design was used to study 144 persons following discharge for traumatic SCI. Predictor variables included functional impairment and family satisfaction (at 12 months post‐discharge) and the presence of pain (at 24 months), and mediating variables were two indicators of participation (assessed 48 months post‐discharge). Life satisfaction and self‐rated health status at 60 months post‐discharge were the outcome variables.MethodsA path model tested hypothesized prospective effects of functional impairment, family satisfaction and pain on participation and the subsequent effects of participation on the QoL variables.ResultsGreater functional impairment and pain were predictive of less participation, and participation significantly predicted both indicators of QoL. The two participation variables mediated the relationship of functional impairment and pain to life satisfaction over time. Family satisfaction had an indirect effect on QoL through its association with social integration.ConclusionsParticipation appears to mediate the prospective influence of functional impairment, family satisfaction, and pain on QoL in the years following SCI. These findings provide insight into factors that can predict QoL post‐SCI and support the use of contextual models to understand the temporal influence of disability and psychological variables on participation and subsequent QoL.Statement of contribution

What is already known on this subject?

Life satisfaction and self‐rated health status are important aspects of quality of life following traumatic spinal cord injury.

Functional impairment has been inconsistently predictive of these variables over time.

Prospective research to date has not examined the mediating effects of participation in predicting quality of life.

What does this study add?

The results indicate that greater functional impairment and pain are prospectively predictive of lower participation.

Greater participation, in turn, is prospectively predictive of greater quality of life.

Participation appears to mediate the prospective influence of functional impairment, family satisfaction, and pain to quality of life.
Abiotic and Biotic Influences on Early‐Stage Survival in Two Shade‐Tolerant Tree Species in Brazil's Atlantic Forest
Authors: Jurinitz Cristiane F. , de Oliveira Alexandre A. , Bruna Emilio M. 
Published: August 2013

AbstractRegeneration dynamics in tropical forests are driven by many abiotic and biotic factors, including light availability, litter depth, and density‐dependent interactions with enemies. Whether ontogenetic stage also can play a critical role, however, is seldom considered. We address how early‐stage survival of two shade‐tolerant species is affected by canopy openness, litter depth, ontogenetic stage, and conspecific neighborhood in the understories of secondary forest fragments in the Brazilian Atlantic Forest. We monitored the survival of naturally occurring early‐stage individuals of one canopy and one understory tree species in six forest fragments for over 2 yr. We then compared how different abiotic and biotic variables, as well as the initial height of seedlings and the length of time interval, influenced variation in survival using generalized linear mixed‐effects models. Survival of the canopy species was negatively affected by light availability, while for the understory species increasing light availability either increased (for seedlings) or decreased (for saplings) survival. In addition, survival of both species at the seedling stage was positively related to litter depth. Finally, we found that conspecific neighbors were an important biotic factor reducing survival. Our results suggest different regeneration niches for these two tree species related to light availability. Moreover, we found that the effect of both abiotic factors depends on ontogenetic stage, a critical factor for understanding regeneration niches in the forest understory.
Public preferences for donor kidney allocation: a study in Iran
Authors: Asghari Fariba , Broumand Mohammadali , Heidari Akram 
Published: August 2013

AbstractIntroductionFair allocation of donor organs is essential to maintain public trust in a public healthcare system. A study of the public's views and opinions of this could clarify non‐medical prioritization criteria. We report our survey of public opinion of criteria for donor kidney allocation.MethodsThis was a cross‐sectional study using random digit dialing to phone interview 706 Tehran residents. Patient scenarios were presented to determine interviewee opinions on nine recipient criteria: probability for survival, previous transplant history, time on the waiting list, age, an individual's role in developing their kidney failure, gender, marital status, social status, and financial situation. Each scenario introduced two patients and interviewees then chose the better candidate for transplantation.ResultsMore than 50% of the participants chose length of waiting time, a patient's role in causing their disease, age, and survival time after transplantation as important allograft allocation criteria.ConclusionThis study disclosed other criteria in addition to the likelihood for successful transplantation—the patient's role in the development of their disease and patient age—which should be prioritization considerations.
TLR2,TLR3,TLR4 and CD14 gene polymorphisms associated with oral lichen planus risk
Authors: Stanimirovic Dragan , Zeljic Katarina , Jankovic Ljiljana , Magic Marko , Hadzi‐Mihajlovic Milos , Magic Zvonko 
Published: August 2013

The aim of this study was to assess whether polymorphisms in toll‐like receptor (TLR) and cluster of differentiation 14 (CD14) genes are associated with oral lichen planus (OLP) risk and clinical course of the disease. The study group consisted of 101 patients with confirmed OLP and 104 healthy blood donors without systemic or oral mucosal diseases. Single nucleotide polymorphisms of TLR2 (rs3804099), TLR3 (rs3775291 and rs5743312), TLR4 (rs4986790 and rs4986791), and CD14 (rs2569190) genes were genotyped using real‐time PCR or PCR‐restriction fragment length polymorphism (PCR‐RFLP). The rs5743312 TLR3 gene polymorphism was associated with increased OLP risk in comparison with the wild type genotype (OR = 15.984, P = 0.011). No association with OLP risk was observed for the polymorphisms studied in TLR2, TLR4 and CD14 genes or for the rs3775291 polymorphism of the TLR3 gene. The polymorphisms of the TLR3 gene were in linkage disequilibrium (D′ = 1, r2 = 0.1). Identified haplotypes were not associated with the risk of OLP. The findings of the current study suggest that the TT genotype of the rs5743312 TLR3 gene polymorphism may play a significant role in the aetiology of OLP.
Performance of Ni‐based Anode‐Supported SOFCs with Doped Ceria Electrolyte at Low Temperatures Between 294 and 542°C
Authors: Suzuki Toshio , Liang Bo , Yamaguchi Toshiaki , Sumi Hirofumi , Hamamoto Koichi , Fujishiro Yoshinobu , Sammes Nigel M. 
Published: August 2013

The performance of a conventional anode‐supported microtubular SOFC using doped ceria as an electrolyte and Ni‐based cermet as an anode is evaluated at low operating temperature between 294 and 542°C. An open‐circuit voltage (OCV) of >0.9 V is obtained at all measured operating temperatures, and power generation is observed at temperatures as low as 294°C. The power density of the cell is 0.6 W/cm2 at 542°C operating temperature with 47% fuel utilization and is 5 mW/cm2 at 294°C operating temperature with an open‐circuit voltage of 0.95 V. According to impedance spectroscopy, a greater influence of gas flow rate, on the cell performance, is observed at higher operating temperature.
A(H1N1)pdm09 hemagglutinin D222G and D222N variants are frequently harbored by patients requiring extracorporeal membrane oxygenation and advanced respiratory assistance for severe A(H1N1)pdm09 infection
Authors: Ruggiero Tina , De Rosa Francesco , Cerutti Francesco , Pagani Nicole , Allice Tiziano , Stella Maria L. , Milia Maria G. , Calcagno Andrea , Burdino Elisa , Gregori Gabriella , Urbino Rosario , Di Perri Giovanni , Ranieri Marco V. , Ghisetti Valeria 
Published: August 2013

BackgroundIn patients with A(H1N1)pdm09 infection, severe lung involvement requiring admission to intensive care units (ICU) has been reported. Mutations at the hemagglutinin (HA) receptor binding site (RBS) have been associated with increased virulence and disease severity, representing a potential marker of critical illness.ObjectivesTo assess the contribution of HA‐RBS variability in critically ill patients, A(H1N1)pdm09 virus from adult patients with severe infection admitted to ICU for extracorporeal membrane oxygenation support (ECMO) during influenza season 2009–2011 in Piemonte (4·2 million inhabitants), northwestern Italy, was studied.Patients and methodsWe retrospectively analyzed HA‐RBS polymorphisms in ICU patients and compared with those from randomly selected inpatients with mild A(H1N1)pdm09 disease and outpatients with influenza from the local surveillance program.ResultsBy HA‐RBS direct sequencing of respiratory specimens, D222G and D222N viral variants were identified in a higher proportion in ICU patients (n = 8/24, 33·3%) than in patients with mild disease (n = 2/34, 6%) or in outpatients (n = 0/44) (Fisher's exact test P < 0·0001; OR 38·5; CI 95% 4·494–329·9). Eleven ICU patients died (42%), three of them carrying the D222G variant, which was associated with RBS mutation S183P in two. D222G and D222N mutants were identified in upper and lower respiratory samples.ConclusionsA(H1N1)pdm09 HA substitutions D222G and D222N were harbored in a significantly higher proportion by patients with acute respiratory distress for A(H1N1)pdm09 severe infection requiring ICU admission and ECMO. These data emphasize the importance of monitoring viral evolution for understanding virus–host adaptation aimed at the surveillance of strain circulation and the study of viral correlates of disease severity.