bluuebunny/crossref_metadata_2025_split huggingface dataset:
Red, White, and Mormon: White Indians
Authors: Reeve W. Paul 
Published: January 2015

Abstract
This chapter considers the ways in which Mormons were derisively labeled “white Indians.” Outsiders continued to imagine Mormon-Indian conspiracies against white America. Especially during the Utah War and Mountain Meadows massacre, outsiders suggested that Mormons dressed like Indians to commit murder and mayhem, an accusation that predated the massacre by at least seven years. It also evaluates Mormon efforts to marry among the Indians and the way in which outsiders imagined that effort producing degraded offspring. Mormons were sometimes conflated with Native Americans as a perceived threat to American democracy. Some people suggested that the best solution to the Mormon problem was the Indian solution.
Black, White, and Mormon: Miscegenation
Authors: Reeve W. Paul 
Published: January 2015

Abstract
This chapter considers the ways in which outsiders imagined Mormonism as facilitating race mixing. Race, as something ascribed from the outside, is the focus here, especially as a lack of information invited many dubious depictions and racial characterizations of Mormons. Political cartoons imagined interracial polygamous families among Mormons and suggested that polygamy was darkening the white race and making it unfit for democracy. By the end of the century the “Mormon coon” emerged as a culture discourse to define a philandering black man. Mormonism in these depictions was associated with miscegenation and, as a result, was seen as a threat to American democracy.
Serum Uric Acid and Pulse Wave Velocity Among Healthy Adults: Baseline Data From the Brazilian Longitudinal Study of Adult Health (ELSA-Brasil)
Authors: Baena Cristina Pellegrino , Lotufo Paulo Andrade , Mill José Geraldo , Cunha Roberto de Sa , Benseñor Isabela J 
Published: January 2015

BACKGROUND
We aimed to evaluate a possible association between serum uric acid (SUA) levels and carotid-to-femoral pulse wave velocity (cf-PWV) among healthy participants of the ELSA-Brasil.

METHODS
We excluded subjects using antihypertensive medication, diuretics, allopurinol, binge drinkers, body mass index (BMI) &gt;35kg/m2, and those with history of cardiovascular diseases (CVD). In a cross-sectional and sex-specific analysis, linear regression models were built having cf-PWV as dependent variable and SUA as independent variable. Multiple adjustments were subsequently made for age, heart rate and blood pressure, BMI, and fasting glucose levels as covariates. Product interaction terms were built to test interaction between SUA and other covariates.

RESULTS
We analyzed 1,875 men and 1,713 women (mean ages, 48.9±8.4 and 50.2±8.7 years, respectively). SUA was linearly associated with cf-PWV in men (P = 0.01) and in women (P = 0.01). After full adjustment, the association remained significant for men (P = 0.01) and no longer significant for women (P = 0.10). Fully adjusted linear coefficients β (95% CI) were 0.06 (0.015; 0.112) and 0.04 (−0.01; 0.12) in men and women, respectively. Significant interaction between SUA and age (P = 0.02) fasting glucose (P &lt; 0.01) and BMI (P = 0.02) was found only for women.

CONCLUSION
In an apparently healthy population, SUA was significantly associated to cf-PWV in men but not in women.
MethylMix: an R package for identifying DNA methylation-driven genes
Authors: Gevaert Olivier 
Published: January 2015

Abstract
Summary: DNA methylation is an important mechanism regulating gene transcription, and its role in carcinogenesis has been extensively studied. Hyper and hypomethylation of genes is an alternative mechanism to deregulate gene expression in a wide range of diseases. At the same time, high-throughput DNA methylation assays have been developed generating vast amounts of genome wide DNA methylation measurements. Yet, few tools exist that can formally identify hypo and hypermethylated genes that are predictive of transcription and thus functionally relevant for a particular disease. To accommodate this lack of tools, we developed MethylMix, an algorithm implemented in R to identify disease specific hyper and hypomethylated genes. MethylMix is based on a beta mixture model to identify methylation states and compares them with the normal DNA methylation state. MethylMix introduces a novel metric, the ‘Differential Methylation value’ or DM-value defined as the difference of a methylation state with the normal methylation state. Finally, matched gene expression data are used to identify, besides differential, transcriptionally predictive methylation states by focusing on methylation changes that effect gene expression.
Availability and implementation: MethylMix was implemented as an R package and is available in bioconductor.
Contact: olivier.gevaert@stanford.edu
dslice: an R package for nonparametric testing of associations with application in QTL and gene set analysis
Authors: Ye Chao , Jiang Bo , Zhang Xuegong , Liu Jun S. 
Published: January 2015

AbstractSummary : Many statistical problems in bioinformatics and genetics can be formulated as the testing of associations between a categorical variable and a continuous variable. A dynamic slicing method was proposed for non-parametric dependence testing, which has been demonstrated to have higher powers compared with traditional methods such as Kolmogorov–Smirnov test. We introduce an R package dslice to facilitate the use of dynamic slicing method in bioinformatic applications such as quantitative trait loci study and gene set enrichment analysis.Availability and implementation : dslice is implemented in Rcpp and available in the Comprehensive R Archive Network. The package is distributed under the GNU General Public License (version 2 or later).Contact : zhangxg@tsinghua.edu.cn or jliu@stat.harvard.edu .
Topology-function conservation in protein–protein interaction networks
Authors: Davis Darren , Yaveroğlu Ömer Nebil , Malod-Dognin Noël , Stojmirovic Aleksandar , Pržulj Nataša 
Published: January 2015

Abstract
Motivation: Proteins underlay the functioning of a cell and the wiring of proteins in protein–protein interaction network (PIN) relates to their biological functions. Proteins with similar wiring in the PIN (topology around them) have been shown to have similar functions. This property has been successfully exploited for predicting protein functions. Topological similarity is also used to guide network alignment algorithms that find similarly wired proteins between PINs of different species; these similarities are used to transfer annotation across PINs, e.g. from model organisms to human. To refine these functional predictions and annotation transfers, we need to gain insight into the variability of the topology-function relationships. For example, a function may be significantly associated with specific topologies, while another function may be weakly associated with several different topologies. Also, the topology-function relationships may differ between different species.
Results: To improve our understanding of topology-function relationships and of their conservation among species, we develop a statistical framework that is built upon canonical correlation analysis. Using the graphlet degrees to represent the wiring around proteins in PINs and gene ontology (GO) annotations to describe their functions, our framework: (i) characterizes statistically significant topology-function relationships in a given species, and (ii) uncovers the functions that have conserved topology in PINs of different species, which we term topologically orthologous functions. We apply our framework to PINs of yeast and human, identifying seven biological process and two cellular component GO terms to be topologically orthologous for the two organisms.
Availability and implementation: http://bio-nets.doc.ic.ac.uk/goCCA.zip
Contact: natasha@imperial.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
Isoniazid treatment to prevent TB in kidney and pancreas transplant recipients based on an interferon-γ-releasing assay: an exploratory randomized controlled trial
Authors: Kim Sung-Han , Lee Sang-Oh , Park In-Ah , Kim Sun-Mi , Park Su Jin , Yun Sung-Cheol , Jung Joo Hee , Shin Sung , Kim Young Hoon , Choi Sang-Ho , Kim Yang Soo , Woo Jun Hee , Park Su-Kil , Park Jung Sik , Han Duck Jong 
Published: January 2015

AbstractBackgroundWe performed a randomized trial of isoniazid treatment based on interferon-γ-releasing assay (IGRA) in kidney transplant (KT) recipients in an intermediate-TB-burden country.MethodsAll adult patients admitted to a KT institute between June 2010 and May 2013 were enrolled. The IGRA (T-SPOT.TB assay) was performed on all patients, and isoniazid treatment was given to those with clinical risk factors for latent TB infection (LTBI). Patients with positive IGRA who had no clinical risk factors for LTBI were randomly assigned to isoniazid treatment or a control group. The development of TB after KT was monitored between June 2010 and November 2013. The primary endpoint was the development of TB.ResultsOf the 784 patients who had no clinical risk factors for LTBI, 445 (57%) gave negative results in the IGRA, 76 (10%) indeterminate results and 263 (33%) positive results. Of the latter, 131 were allocated to isoniazid treatment and 132 to the control group. Three (2%) of the control group developed TB, whereas none of the isoniazid treatment group developed TB (rate difference 1.22 per 100 person-years, P = 0.09). Of the 521 patients with negative or indeterminate IGRA results, 4 [0.8%, 0.43 per 100 person-years (95% CI 0.12–1.09)] developed TB after KT.ConclusionsIGRA-based isoniazid treatment has a trend towards reducing TB development in KT recipients without clinical risk factors, but careful monitoring of TB development is needed in negative-IGRA KT recipients.
Performance of commonly used genotypic assays and comparison with phenotypic assays of HIV-1 coreceptor tropism in acutely HIV-1-infected patients
Authors: Ceresola Elisa Rita , Nozza Silvia , Sampaolo Michela , Pignataro Angela Rosa , Saita Diego , Ferrarese Roberto , Ripa Marco , Deng Wenjie , Mullins James I. , Boeri Enzo , Tambussi Giuseppe , Toniolo Antonio , Lazzarin Adriano , Clementi Massimo , Canducci Filippo 
Published: January 2015

AbstractObjectivesAlthough founder viruses in primary HIV-1 infections (PHIs) typically use the CCR5 coreceptor (R5-tropic), 3%–19% of subjects also harbour CXCR4-using viruses (X4-tropic), making tropism determination before CCR5 antagonist usage mandatory. Genotypic methods can be used to accurately determine HIV-1 tropism in chronically infected patients.MethodsWe compared the results of genotypic methods [geno2pheno, PSSMx4r5 including a novel nucleotide-input version (ntPSSM) and distant segments (ds)Kernel] to predict coreceptor usage in a cohort of 67 PHIs. Specimens with discrepant results were phenotypically tested after cloning the V3 gene region into proviral backbones. Recombinant viruses were used to infect U87 indicator cell lines bearing CD4 and either CCR5 or CXCR4.ResultsGeno2pheno10%, PSSMx4r5 and (ds)Kernel gave identical predictions in 85% of cases. Geno2pheno10% predicted the presence of CXCR4 viruses in 18% of patients. Two patients were predicted to carry X4-tropic viruses by all algorithms and X4-tropic viruses were detected in at least one of the recombinant AD8 or NL4-3 backbone-based assays. Ten samples resulted in discordant predictions with at least one algorithm. Full concordance between tropism prediction by using population sequencing and phenotypic assays was observed only with ntPSSM. Geno2pheno prediction and the phenotypic assay gave the same results in a minority of ‘discordant’ patients.ConclusionsCompared with both PSSMx4r5 versions, (ds)Kernel and our phenotypic assay, geno2pheno10% overestimated the frequency of X4-tropic viruses (18% versus 3%). ntPSSM was able to detect one additional X4 virus compared with (ds)Kernel that was confirmed with the phenotypic assay.
Global Oct4 target gene analysis reveals novel downstream PTEN and TNC genes required for drug-resistance and metastasis in lung cancer
Authors: Tang Yen-An , Chen Chi-Hsin , Sun H. Sunny , Cheng Chun-Pei , Tseng Vincent S. , Hsu Han-Shui , Su Wu-Chou , Lai Wu-Wei , Wang Yi-Ching 
Published: January 2015

Abstract
Overexpression of Oct4, a stemness gene encoding a transcription factor, has been reported in several cancers. However, the mechanism by which Oct4 directs transcriptional program that leads to somatic cancer progression remains unclear. In this study, we provide mechanistic insight into Oct4-driven transcriptional network promoting drug-resistance and metastasis in lung cancer cell, animal and clinical studies. Through an integrative approach combining our Oct4 chromatin-immunoprecipitation sequencing and ENCODE datasets, we identified the genome-wide binding regions of Oct4 in lung cancer at promoter and enhancer of numerous genes involved in critical pathways which promote tumorigenesis. Notably, PTEN and TNC were previously undefined targets of Oct4. In addition, novel Oct4-binding motifs were found to overlap with DNA elements for Sp1 transcription factor. We provided evidence that Oct4 suppressed PTEN in an Sp1-dependent manner by recruitment of HDAC1/2, leading to activation of AKT signaling and drug-resistance. In contrast, Oct4 transactivated TNC independent of Sp1 and resulted in cancer metastasis. Clinically, lung cancer patients with Oct4 high, PTEN low and TNC high expression profile significantly correlated with poor disease-free survival. Our study reveals a critical Oct4-driven transcriptional program that promotes lung cancer progression, illustrating the therapeutic potential of targeting Oc4 transcriptionally regulated genes.
Metabolic Imaging Using Proton Magnetic Spectroscopy as a Predictor of Outcome After Surgery for Cervical Spondylotic Myelopathy
Authors: Holly Langston T. , Ellingson Benjamin M. , Salamon Noriko 
Published: January 2015

Study Design:
A single-center magnetic resonance spectroscopy (MRS) imaging and surgical outcome study involving 16 patients with cervical spondylotic myelopathy (CSM).

Objective:
In the present study, we assess the utility of MRS to quantify metabolic changes within the spinal cord and predict surgical outcome in CSM patients.

Summary of Background Data:
MRS is an advanced spinal imaging modality that can provide pertinent metabolic and biochemical information regarding spinal cord function. Previous studies have demonstrated significant abnormalities in specific cellular metabolite concentrations in CSM patients.

Methods:
Sixteen patients with CSM were evaluated. Single voxel MRS was performed in the cervical cord. N-acetyl-aspartate (NAA) and choline metabolite concentration ratios with respect to creatine were quantified, as well as the presence or absence of a lactate peak. The modified Japanese Orthopaedic Association (mJOA) scale was used as the functional assessment measure. Correlation of MRS metabolites with change in mJOA score was performed.

Results:
The mean follow-up time was 19 months. There was a statistically significant improvement between mean preoperative and postoperative mJOA score after surgery (P<0.0001). The NAA/Cr ratio demonstrated a significant relationship to the change in mJOA score after surgery (P=0.0479; R
2=0.2513). The Cho/NAA ratio demonstrated an even stronger correlation with the change in mJOA score after surgery (P=0.0065; R
2=0.4219). Neither the Cho/Cr ratio, nor the presence of a lactate peak or T2-weighted signal change was significantly correlated with change in mJOA score after surgery.

Conclusions:
MRS is a novel, noninvasive imaging modality that provides pertinent information regarding spinal cord cellular and metabolic function. In a cohort of operatively treated CSM patients, the NAA/Cr and Cho/NAA ratios were predictive of neurological outcome, as both were significantly associated with change in mJOA score after surgery.
Management of Ingested Foreign Bodies in Children
Authors: Kramer Robert E. , Lerner Diana G. , Lin Tom , Manfredi Michael , Shah Manoj , Stephen Thomas C. , Gibbons Troy E. , Pall Harpreet , Sahn Ben , McOmber Mark , Zacur George , Friedlander Joel , Quiros Antonio J. , Fishman Douglas S. , Mamula Petar 
Published: January 2015

ABSTRACTForeign body ingestions in children are some of the most challenging clinical scenarios facing pediatric gastroenterologists. Determining the indications and timing for intervention requires assessment of patient size, type of object ingested, location, clinical symptoms, time since ingestion, and myriad other factors. Often the easiest and least anxiety‐producing decision is the one to proceed to endoscopic removal, instead of observation alone. Because of variability in pediatric patient size, there are less firm guidelines available to determine which type of object will safely pass, as opposed to the clearer guidelines in the adult population. In addition, the imprecise nature of the histories often leaves the clinician to question the timing and nature of the ingestion. Furthermore, changes in the types of ingestions encountered, specifically button batteries and high‐powered magnet ingestions, create an even greater potential for severe morbidity and mortality among children. As a result, clinical guidelines regarding management of these ingestions in children remain varied and sporadic, with little in the way of prospective data to guide their development. An expert panel of pediatric endoscopists was convened and produced the present article that outlines practical clinical approaches to the pediatric patient with a variety of foreign body ingestions. This guideline is intended as an educational tool that may help inform pediatric endoscopists in managing foreign body ingestions in children. Medical decision making, however, remains a complex process requiring integration of clinical data beyond the scope of these guidelines. These guidelines should therefore not be considered to be a rule or to be establishing a legal standard of care. Caregivers may well choose a course of action outside of those represented in these guidelines because of specific patient circumstances. Furthermore, additional clinical studies may be necessary to clarify aspects based on expert opinion instead of published data. Thus, these guidelines may be revised as needed to account for new data, changes in clinical practice, or availability of new technology.
The Arabidopsis Transcription Factor BRASSINOSTEROID INSENSITIVE1-ETHYL METHANESULFONATE-SUPPRESSOR1 Is a Direct Substrate of MITOGEN-ACTIVATED PROTEIN KINASE6 and Regulates Immunity
Authors: Kang Sining , Yang Fan , Li Lin , Chen Huamin , Chen She , Zhang Jie 
Published: January 2015

Abstract
Pathogen-associated molecular patterns (PAMPs) are recognized by plant pattern recognition receptors to activate PAMP-triggered immunity (PTI). Mitogen-activated protein kinases (MAPKs), as well as other cytoplasmic kinases, integrate upstream immune signals and, in turn, dissect PTI signaling via different substrates to regulate defense responses. However, only a few direct substrates of these signaling kinases have been identified. Here, we show that PAMP perception enhances phosphorylation of BRASSINOSTEROID INSENSITIVE1-ETHYL METHANESULFONATE-SUPPRESSOR1 (BES1), a transcription factor involved in brassinosteroid (BR) signaling pathway, through pathogen-induced MAPKs in Arabidopsis (Arabidopsis thaliana). BES1 interacts with MITOGEN-ACTIVATED PROTEIN KINASE6 (MPK6) and is phosphorylated by MPK6. bes1 loss-of-function mutants display compromised resistance to bacterial pathogen Pseudomonas syringae pv tomato DC3000. BES1 S286A/S137A double mutation (BES1SSAA) impairs PAMP-induced phosphorylation and fails to restore bacterial resistance in bes1 mutant, indicating a positive role of BES1 phosphorylation in plant immunity. BES1 is phosphorylated by glycogen synthase kinase3 (GSK3)-like kinase BR-insensitive2 (BIN2), a negative regulator of BR signaling. BR perception inhibits BIN2 activity, allowing dephosphorylation of BES1 to regulate plant development. However, BES1SSAA does not affect BR-mediated plant growth, suggesting differential residue requirements for the modulation of BES1 phosphorylation in PTI and BR signaling. Our study identifies BES1 as a unique direct substrate of MPK6 in PTI signaling. This finding reveals MAPK-mediated BES1 phosphorylation as another BES1 modulation mechanism in plant cell signaling, in addition to GSK3-like kinase-mediated BES1 phosphorylation and F box protein-mediated BES1 degradation.
The correlation between corporate governance and market value: regime or signal?
Authors: Li Chang , Zheng Wei , Chang Philip , Li Shanmin 
Published: January 2015

Purpose– As literatures argue that managers’ personalities will affect both corporate governance structures and corporate performance, the correlation between them is a mixed result. The purpose of this paper is to separate different routes leading to the mixed correlation, and name the separated routes as regime effect and signal effect.Design/methodology/approach– By theoretical analysis, the authors list three routes leading to the correlation between corporate governance and corporate performance. Routes 1 and 2 show that governance can directly and indirectly change the performance; while route 3 shows that both the governance and performance are results of managers’ personalities, and the governance has no influence onto the performance, which means the correlation led by route 3 is fake. By design a new econometric methodology, this paper separates the mixed correlation between corporate governance and performance, and names the correlation led by routes 1 and 2 as the regime effect and the correlation led by route 3 as signal effect.Findings– By an empirical research on Chinese listed corporates, the authors find that the correlations between Chinese listed corporates’ market value and main corporate governance factors can be separated into regime effects and signal effects; and the authors also find that some factors (Share of Institutional Investors, Share of Real Controller and the Squared, Dummy of Identical CEO and Chairman, Ownership Concentration) only show regime effects, some factors (Separating Extent of Ownership and Controlling Right, Dummy of Provincial State-Owned Firms) only show signal effects, and some factors (Dummy of Republic State-Owned Firms, Scale of Board) show both. What’s more, the authors find out an interesting result that the state-owning has no negative regime effect on China SOEs’ performance but very significantly negative signal effect; in this paper, the authors suggest that this means the key negative factors of Chinese SOEs is not state-owning ownership structure but the managers’ corruption.Practical implications– As only the factors with regime effects can directly and indirectly affect corporates’ performance and the factors with signal effects show that there’re some managers’ personalities affecting both the governance and performance, the separation method in this paper can help shareholders knowing which governance factors will be helpful to improve the performance and which others will show managers’ hard-working or corruption intention.Originality/value– Separate the regime effect and the signal effect from the correlation between corporate governance and performance.