bluuebunny/crossref_metadata_2025_split huggingface dataset:
Kidney-specific transposon-mediated gene transfer in vivo
Authors: Woodard Lauren E. , Cheng Jizhong , Welch Richard C. , Williams Felisha M. , Luo Wentian , Gewin Leslie S. , Wilson Matthew H. 
Published: March 2017

AbstractMethods enabling kidney-specific gene transfer in adult mice are needed to develop new therapies for kidney disease. We attempted kidney-specific gene transfer following hydrodynamic tail vein injection using the kidney-specific podocin and gamma-glutamyl transferase promoters, but found expression primarily in the liver. In order to achieve kidney-specific transgene expression, we tested direct hydrodynamic injection of a DNA solution into the renal pelvis and found that luciferase expression was strong in the kidney and absent from extra-renal tissues. We observed heterogeneous, low-level transfection of the collecting duct, proximal tubule, distal tubule, interstitial cells, and rarely glomerular cells following injection. To assess renal injury, we performed the renal pelvis injections on uninephrectomised mice and found that their blood urea nitrogen was elevated at two days post-transfer but resolved within two weeks. Although luciferase expression quickly decreased following renal pelvis injection, the use of the piggyBac transposon system improved long-term expression. Immunosuppression with cyclophosphamide stabilised luciferase expression, suggesting immune clearance of the transfected cells occurs in immunocompetent animals. Injection of a transposon expressing erythropoietin raised the haematocrit, indicating that the developed injection technique can elicit a biologic effect in vivo. Hydrodynamic renal pelvis injection enables transposon mediated-kidney specific gene transfer in adult mice.
Identification and comparative profiling of miRNAs in herbaceous peony (Paeonia lactiflora Pall.) with red/yellow bicoloured flowers
Authors: Zhao Daqiu , Wei Mengran , Shi Min , Hao Zhaojun , Tao Jun 
Published: March 2017

AbstractHerbaceous peony (Paeonia lactiflora Pall.) is popular worldwide because of its gorgeous flower colour, and the yellow flower is the rarest. However, its mechanism of yellow formation is still unexplored from the post-translational level. In this study, the anatomy of the petal, cell sap pH and metal elements were investigated in bicoloured flower cultivar ‘Jinhui’ with red outer-petal and yellow inner-petal, and the yellow formation was influenced by the anatomy of petal, while not by the cell sap pH and metal elements. Subsequently, microRNAs sequencing (miRNA-seq) was used to identify small RNAs (sRNAs). A total of 4,172,810 and 3,565,152 specific unique sRNAs were obtained, 207 and 204 conserved miRNAs and 38 and 42 novel miRNAs were identified from red outer-petal and yellow inner-petal, respectively, which were confirmed by subcloning. Among these miRNAs, 163 conserved and 28 novel miRNAs were differentially expressed in two wheel of petals. And 5 differentially expressed miRNAs and their corresponding target genes related to yellow formation were screened, and their dynamic expression patterns confirmed that the yellow formation might be under the regulation of miR156e-3p-targeted squamosa promoter binding protein-like gene (SPL1). These results improve the understanding of miRNA regulation of the yellow formation in P. lactiflora.
A facile template route to periodic mesoporous organosilicas nanospheres with tubular structure by using compressed CO2
Authors: Huang Xin , Li Wei , Wang Meijin , Tan Xiuniang , Wang Qian , Wang Cheng , Zhang Mengnan , Yuan Jing 
Published: March 2017

AbstractPeriodic mesoporous organosilicas (PMOs) nanospheres with tubular structure were prepared with compressed CO2using cationic and anionic mixed surfactant (CTAB/SDS) and triblock copolymer Pluronic P123 as bi-templates. TEM, N2adsorption-desorption, solid NMR, and FTIR were employed to characterize the obtained materials. Compressed CO2severed as acidic reagent to promote the hydrolysis of organosilicas, and could tune the morphology and structure of the obtained PMOs nanomaterials simple by adjusting the CO2pressure during the synthesis process. Rhodamine B (RB) and Ibuprofen (IBU), as the model dye and drug, were loaded into the prepared nanomaterials to reveal its adsorption and desorption ability. Furthermore, different molars of the surfactant (CTAB/SDS) and organosilane precursor (BTEB) were investigated to show the effect of the surfactant concentration on the morphology and structure of the PMOs prepared with compressed CO2, and some different structures were obtained. A possible mechanism for the synthesis of PMOs with tubular structure using compressed CO2was proposed based on the experimental results.
Validating judgments of perspective embedding
Authors: Whalen D. H. , Zunshine Lisa , Ender Evelyne , Kelbert Eugenia , Tougaw Jason , Barsky Robert F. , Steiner Peter , Holquist Michael 
Published: March 2017

Abstract
Previous work (Whalen, Zunshine, & Holquist, 2012) has shown that perspective embedding ("she thought I left" embedding her perspective on "I left") affects reading times for short vignettes. With increasing levels of embedment 1–5, reading times rose almost linearly. Level 0 was as slow as 3–4. Embedment level was determined by the authors, but validation by others is desirable. In Experiment 1, we trained 12 literature students to make embedment judgments. Their judgments correlated highly with ours (.94 on average) and agreed exactly in the majority of cases (74.5%); almost all were within one (94.2%). In Experiment 2, judgments of the first three paragraphs of "To Kill a Mockingbird" (Lee, 1960) yielded a lower level of agreement; literature uses subtle means for introducing perspective embedment, and individuals differ about including them. Assessment of perspective embedding, and exploration of sources of disagreements, provide new tools for analyzing literature.
Emotional effects of poetic phonology, word positioning and dominant stress peaks in poetry reading
Authors: Kraxenberger Maria , Menninghaus Winfried 
Published: March 2017

Abstract
This study tested the hypothesis that features of linguistically non-mandatory phonological recurrence (rhyme, alliteration,
assonance, and consonance), parameters of word positioning (position within a line and line position) and dominant stress peaks
are related to readers’ identification of distinctively joyful and sad words in poetry. To this end, forty-eight participants read
eight German poems, completed an underlining task, and filled out a brief questionnaire. Results show that these target features
are clearly of importance for readers’ perception of pronounced levels of joy and sadness. Words featuring alliteration, assonance
or consonance were significantly more often underlined as distinctively joyful than were words that lack these features. Our study
shows also that words that feature a dominant stress peak and are placed in more advanced positions within the poems were more
likely to be identified as emotional (distinctively joyful and sad) when compared to words in earlier and unstressed
positions.
Characterization of a PA14 domain-containing galactofuranose-specific β-d-galactofuranosidase from Streptomyces sp.
Authors: Matsunaga Emiko , Higuchi Yujiro , Mori Kazuki , Yairo Nao , Toyota Saki , Oka Takuji , Tashiro Kosuke , Takegawa Kaoru 
Published: March 2017

Abstract
As a constituent of polysaccharides and glycoconjugates, β-d-galactofuranose (Galf) exists in several pathogenic microorganisms. Although we recently identified a β-d-galactofuranosidase (Galf-ase) gene, ORF1110, in the Streptomyces strain JHA19, very little is known about the Galf-ase gene. Here, we characterized a strain, named JHA26, in the culture supernatant of which exhibited Galf-ase activity for 4-nitrophenyl β-d-galactofuranoside (pNP-β-d-Galf) as a substrate. Draft genome sequencing of the JHA26 strain revealed a putative gene, termed ORF0643, that encodes Galf-ase containing a PA14 domain, which is thought to function in substrate recognition. The recombinant protein expressed in Escherichia coli showed the Galf-specific Galf-ase activity and also released galactose residue of the polysaccharide galactomannan prepared from Aspergillus fumigatus, suggesting that this enzyme is an exo-type Galf-ase. BLAST searches using the amino acid sequences of ORF0643 and ORF1110 Galf-ases revealed two types of Galf-ases in Actinobacteria, suggesting that Galf-specific Galf-ases may exhibit discrete substrate specificities.
Pseudomonas aeruginosa cytochrome c551 denaturation by five systematic urea derivatives that differ in the alkyl chain length
Authors: Kobayashi Shinya , Fujii Sotaro , Koga Aya , Wakai Satoshi , Matubayasi Nobuyuki , Sambongi Yoshihiro 
Published: March 2017

Abstract
Reversible denaturation of Pseudomonas aeruginosa cytochrome c551 (PAc551) could be followed using five systematic urea derivatives that differ in the alkyl chain length, i.e. urea, N-methylurea (MU), N-ethylurea (EU), N-propylurea (PU), and N-butylurea (BU). The BU concentration was the lowest required for the PAc551 denaturation, those of PU, EU, MU, and urea being gradually higher. Furthermore, the accessible surface area difference upon PAc551 denaturation caused by BU was found to be the highest, those by PU, EU, MU, and urea being gradually lower. These findings indicate that urea derivatives with longer alkyl chains are stronger denaturants. In this study, as many as five systematic urea derivatives could be applied for the reversible denaturation of a single protein, PAc551, for the first time, and the effects of the alkyl chain length on protein denaturation were systematically verified by means of thermodynamic parameters.
Physical activity, sedentary behaviour, and socioeconomic status among Finnish girls and boys aged 6–8 years
Authors: Lampinen Eeva‐Kaarina , Eloranta Aino‐Maija , Haapala Eero A. , Lindi Virpi , Väistö Juuso , Lintu Niina , Karjalainen Panu , Kukkonen‐Harjula Katriina , Laaksonen David , Lakka Timo A. 
Published: March 2017

AbstractWe studied differences in physical activity (PA), sedentary behaviour (SB), and the types of PA and SB between Finnish girls and boys and children from different socioeconomic backgrounds (SES). We assessed PA, SB, parental education, and household income using detailed questionnaires in a representative population sample of 486 children (238 girls, 248 boys) aged 6–8 years. Girls spent on average 1.7 h/day and boys 2.0 h/day in total PA (p = 0.002). Altogether 66% of girls and 54% of boys had less than 2 h of total PA per day (p = 0.012). Girls had lower levels of unsupervised PA (45 vs. 54 min/day, p = 0.001), supervised PA (1.5 vs. 1.9 h/week, p = 0.009), and PA during school recess (1.8 vs. 1.9 h/week, p = 0.032) than boys. Girls had higher levels of total SB (3.8 vs. 3.4 h/day, p = 0.015) but lower levels of screen‐based SB (1.5 vs. 1.9 h/day, p < 0.001) than boys. Lower parental education and household income were associated with lower levels of supervised PA in girls (p = 0.011 and p = 0.008, respectively) and in boys (p = 0.006 and p = 0.003, respectively). Lower parental education and household income were also related to higher levels of screen‐based SB in boys (p = 0.005 and p < 0.001, respectively) but not in girls. Girls have lower levels of total, unsupervised, and supervised PA, PA during recess, and screen‐based SB but higher levels of total SB than boys. Lower parental education and household income are associated with lower levels of supervised PA in both genders and higher levels of screen‐based SB in boys.
Developing an inventory of core lexical bundles in English research articles: a cross-disciplinary corpus-based study
Authors: Jalilifar Alireza , Ghoreishi Seyed Mohammad , Emam Roodband Seyed Abbas 
Published: March 2017

Abstract
Corpus linguistics has revealed that formulaic language forms an important part of written academic discourse. Recently, much research has focused on lexical bundles as a new category of formulaic language. The primary goal of the present study was to identify core lexical bundles in English research articles across different disciplines and to explore the functions they fulfil. The secondary goal was to determine the coverage of core bundles over lexical bundles from a corpus of research articles in applied linguistics. Using AntConc programme, the analysis started with the creation of three separate lists of lexical bundles from three corpora. Then, the common lexical bundles from these three lists were identified. In total, 661 core lexical bundles common across the three disciplines were identified. Functional analysis revealed the predominance of text-oriented bundles. In addition, core bundles covered 30.19% of the list of bundle types in the research articles. The functional utility of core bundles and their coverage in a domain-specific discipline reinforces the idea that lexical bundles can be transformed into useful learning and testing materials.
Effects of the 2013 SNAP Benefit Cut on Food Security
Authors: Katare Bhagyashree , Kim Jiyoon (June) 
Published: March 2017

AbstractEffects of the 2013 Supplemental Nutrition Assistance Program (SNAP) benefit cut on food security is examined by employing the annual Current Population Survey Food Security Supplement 2012–2014. Food security measured in December 2014 is compared with the corresponding statistics for December 2012 using difference‐in‐differences methods. Results confirm that reduced SNAP benefits significantly threatened the food security of SNAP households.
Enhanced methods to detect haplotypic effects on gene expression
Authors: Brown Robert , Kichaev Gleb , Mancuso Nicholas , Boocock James , Pasaniuc Bogdan 
Published: March 2017

Abstract

Motivation
Expression quantitative trait loci (eQTLs), genetic variants associated with gene expression levels, are identified in eQTL mapping studies. Such studies typically test for an association between single nucleotide polymorphisms (SNPs) and expression under an additive model, which ignores interaction and haplotypic effects. Mismatches between the model tested and the underlying genetic architecture can lead to a loss of association power. Here we introduce a new haplotype-based test for eQTL studies that looks for haplotypic effects on expression levels. Our test is motivated by compound heterozygous architectures, a common disease model for recessive monogenic disorders, where two different alleles can have the same effect on a gene’s function.

Results
When the underlying true causal architecture for a simulated gene is a compound heterozygote, our method is better able to capture the signal than the marginal SNP method. When the underlying model is a single SNP, there is no difference in the power of our method relative to the marginal SNP method. We apply our method to empirical gene expression data measured in 373 European individuals from the GEUVADIS study and find 29 more eGenes (genes with at least one association) than the standard marginal SNP method. Furthermore, in 974 of the 3529 total eGenes, our haplotype-based method results in a stronger association signal than the standard marginal SNP method. This demonstrates our method both increases power over the standard method and provides evidence of haplotypic architectures regulating gene expression.

Availability and Implementation
http://bogdan.bioinformatics.ucla.edu/software/
The RNASeq-er API—a gateway to systematically updated analysis of public RNA-seq data
Authors: Petryszak Robert , Fonseca Nuno A , Füllgrabe Anja , Huerta Laura , Keays Maria , Tang Y Amy , Brazma Alvis 
Published: March 2017

Abstract

Motivation
The exponential growth of publicly available RNA-sequencing (RNA-Seq) data poses an increasing challenge to researchers wishing to discover, analyse and store such data, particularly those based in institutions with limited computational resources. EMBL-EBI is in an ideal position to address these challenges and to allow the scientific community easy access to not just raw, but also processed RNA-Seq data. We present a Web service to access the results of a systematically and continually updated standardized alignment as well as gene and exon expression quantification of all public bulk (and in the near future also single-cell) RNA-Seq runs in 264 species in European Nucleotide Archive, using Representational State Transfer.

Results
The RNASeq-er API (Application Programming Interface) enables ontology-powered search for and retrieval of CRAM, bigwig and bedGraph files, gene and exon expression quantification matrices (Fragments Per Kilobase Of Exon Per Million Fragments Mapped, Transcripts Per Million, raw counts) as well as sample attributes annotated with ontology terms. To date over 270 00 RNA-Seq runs in nearly 10 000 studies (1PB of raw FASTQ data) in 264 species in ENA have been processed and made available via the API.

Availability and Implementation
The RNASeq-er API can be accessed at http://www.ebi.ac.uk/fg/rnaseq/api. The commands used to analyse the data are available in supplementary materials and at https://github.com/nunofonseca/irap/wiki/iRAP-single-library.

Supplementary information
Supplementary data are available at Bioinformatics online.
GenoGAM: genome-wide generalized additive models for ChIP-Seq analysis
Authors: Stricker Georg , Engelhardt Alexander , Schulz Daniel , Schmid Matthias , Tresch Achim , Gagneur Julien 
Published: March 2017

AbstractMotivationChromatin immunoprecipitation followed by deep sequencing (ChIP-Seq) is a widely used approach to study protein–DNA interactions. Often, the quantities of interest are the differential occupancies relative to controls, between genetic backgrounds, treatments, or combinations thereof. Current methods for differential occupancy of ChIP-Seq data rely however on binning or sliding window techniques, for which the choice of the window and bin sizes are subjective.ResultsHere, we present GenoGAM (Genome-wide Generalized Additive Model), which brings the well-established and flexible generalized additive models framework to genomic applications using a data parallelism strategy. We model ChIP-Seq read count frequencies as products of smooth functions along chromosomes. Smoothing parameters are objectively estimated from the data by cross-validation, eliminating ad hoc binning and windowing needed by current approaches. GenoGAM provides base-level and region-level significance testing for full factorial designs. Application to a ChIP-Seq dataset in yeast showed increased sensitivity over existing differential occupancy methods while controlling for type I error rate. By analyzing a set of DNA methylation data and illustrating an extension to a peak caller, we further demonstrate the potential of GenoGAM as a generic statistical modeling tool for genome-wide assays.Availability and ImplementationSoftware is available from Bioconductor: https://www.bioconductor.org/packages/release/bioc/html/GenoGAM.html.Supplementary informationSupplementary information is available at Bioinformatics online.
Regulation of oxidized platelet lipidome: implications for coronary artery disease
Authors: Chatterjee Madhumita , Rath Dominik , Schlotterbeck Jörg , Rheinlaender Johannes , Walker-Allgaier Britta , Alnaggar Nada , Zdanyte Monika , Müller Iris , Borst Oliver , Geisler Tobias , Schäffer Tilman E. , Lämmerhofer Michael , Gawaz Meinrad 
Published: March 2017

Abstract

Aims
Hyperlipidaemia enhances susceptibility to thrombosis, while platelet oxidixed LDL (oxLDL) binding in acute coronary syndrome (ACS) correlates with activation status. This study explores the platelet lipidome in symptomatic coronary artery disease (CAD) patients and the functional consequences of the chemokine CXCL12 and its receptors CXCR-4/-7 on lipid uptake in platelets.

Methods and results
Platelet–oxLDL detected by flow cytometry was enhanced (P = 0.04) in CAD patients, moderately correlated with platelet CXCR7 surface expression (ρ = 0.39; P &lt; 0.001), while inversely with CXCR4 (ρ = 0.35; P &lt; 0.001). Platelet–oxLDL was elevated (P = 0.01) in ACS patients with angiographic evidence of intracoronary thrombi. Ex vivo analysis of intracoronary thrombi sections revealed oxLDL deposition in platelet-enriched areas verified by immunofluorescence confocal microscopy. LDL–oxLDL uptake enhanced reactive oxygen species, mitochondrial superoxide generation, intraplatelet LDL to oxLDL conversion, and lipid peroxidation, counteracted by SOD2–mimetic MnTMPyP. Lipidomic analysis revealed enhanced intraplatelet-oxidized phospholipids, cholesteryl esters, sphingomyelin, ceramides, di- and triacylglycerols, acylcarnitines in CAD patients compared with age-matched controls as ascertained by liquid chromatography hyphenated to high-resolution mass spectrometry. LDL–oxLDL induced degranulation, αIIbβ3-integrin activation, apoptosis, thrombin generation estimated by calibrated automated thrombinoscopy, and shape change verified by live imaging using scanning ion conductance microscopy. Further, LDL–oxLDL enhanced thrombus formation ex vivo and in vivo in mice (ferric chloride-induced carotid artery injury). LDL–oxLDL enhanced platelet CXCL12 release, differentially regulated CXCR4–CXCR7 surface exposure, while CXCL12 prompted LDL–oxLDL uptake and synergistically augmented the LDL–oxLDL-induced pro-oxidative, thrombogenic impact on platelet function.

Conclusion
An altered platelet lipidome might be associated with thrombotic disposition in CAD, a mechanism potentially regulated by CXCL12–CXCR4–CXCR7 axis.
Intended Near-Total Removal of Koos Grade IV Vestibular Schwannomas: Reconsidering the Treatment Paradigm
Authors: Zumofen Daniel Walter , Guffi Tommaso , Epple Christian , Westermann Birgit , Krähenbühl Anna-Katharina , Zabka Susanne , Taub Ethan , Bodmer Daniel , Mariani Luigi 
Published: March 2017

Abstract

BACKGROUND
The goals of treating Koos grade IV vestibular schwannomas are to relieve brainstem compression, preserve or restore neurological function, and achieve long-term tumor control while minimizing tumor- and treatment-related morbidity.

OBJECTIVE
To propose a treatment paradigm involving the intentional near-total removal of Koos grade IV vestibular schwannomas, in which a small amount of residual tumor is not dissected off the cisternal portion of the facial nerve. Patients are then followed by a wait-and-scan approach. Any subsequent volumetric progression of the residual tumor is treated with radiosurgery.

METHODS
This is a case series of 44 consecutive unselected patients who underwent intended near-total resection of a Koos grade IV vestibular schwannoma through a retrosigmoid approach from January 2009 to December 2015. Pre- and postoperative volumetric analyses were performed on routine magnetic resonance imaging sequences (constructive interference in steady state and gadolinium-enhanced T1-weighted sequence).

RESULTS
The mean preoperative tumor volume was 10.9 cm3. The mean extent of resection was 89%. At the last clinical follow-up, facial nerve function was good [House and Brackmann (HB) I-II] in 89%, fair (HB III) in 9%, and poor (HB IV-VI) in 2% of the patients. At the last radiological follow-up, the residual tumor had become smaller or remained the same size in 84% of patients. Volumetric progression was negatively correlated with the original extent of resection and positively correlated with postoperative residual tumor volume (P = .01, P < .001, respectively).

CONCLUSION
Intended near-total removal results in excellent preservation of facial nerve function and has a low recurrence rate. Any progressive residual tumor may be treated by radiosurgery.