bluuebunny/crossref_metadata_2025_split huggingface dataset:
Correlation between haptically perceived quality characteristics and
measured technical parameters for leather surfaces
Authors: Falk Björn , Neumann Annika , Simon Falk , Stoll Andrea , Schmitt Robert 
Published: February 2014

Abstract
Rapidly changing market conditions and intense competition force companies
to secure their market position through constant customer-focused
innovation. To achieve the highest possible overlap between customer
requirements and product characteristics, customers' subjective opinions
have to be taken into account. For customers it is difficult to accurately
describe their exact requirements regarding the products they want. In this
paper a methodology is presented, that is able to measure and implement
exact requirements of human judgment and correlate them with technical
parameters.
gitter: A Robust and Accurate Method for Quantification of Colony Sizes From Plate Images
Authors: Wagih Omar , Parts Leopold 
Published: February 2014

Abstract
Colony-based screens that quantify the fitness of clonal populations on solid agar plates are perhaps the most important source of genome-scale functional information in microorganisms. The images of ordered arrays of mutants produced by such experiments can be difficult to process because of laboratory-specific plate features, morphed colonies, plate edges, noise, and other artifacts. Most of the tools developed to address this problem are optimized to handle a single setup and do not work out of the box in other settings. We present gitter, an image analysis tool for robust and accurate processing of images from colony-based screens. gitter works by first finding the grid of colonies from a preprocessed image and then locating the bounds of each colony separately. We show that gitter produces comparable colony sizes to other tools in simple cases but outperforms them by being able to handle a wider variety of screens and more accurately quantify colony sizes from difficult images. gitter is freely available as an R package from http://cran.r-project.org/web/packages/gitter under the LGPL. Tutorials and demos can be found at http://omarwagih.github.io/gitter
Biparental Resequencing Coupled With SNP Genotyping of a Segregating Population Offers Insights Into the Landscape of Recombination and Fixed Genomic Regions in Elite Soybean
Authors: Li Ying-hui , Liu Yu-lin , Reif Jochen C , Liu Zhang-xiong , Liu Bo , Mette Michael F , Chang Ru-zhen , Qiu Li-juan 
Published: February 2014

Abstract
Identification of genes underlying agronomic traits is dependent on the segregation of quantitative trait loci (QTL). A popular hypothesis is that elite lines are becoming increasingly similar to each other, resulting in large genomic regions with fixed genes. Here, we resequenced two parental modern elite soybean lines [ZhongHuang13 (ZH) and ZhongPin03-5373 (ZP)] and discovered 794,876 SNPs with reference to the published Williams82 genome. SNPs were distributed unevenly across the chromosomes, with 87.1% of SNPs clustering in 4.9% of the soybean reference genome. Most of the regions with a high density of SNP polymorphisms were located in the chromosome arms. Moreover, seven large regions that were highly similar between parental lines were identified. A GoldenGate SNP genotyping array was designed using 384 SNPs and the 254 recombinant inbred lines (F8) derived from the cross of ZP × ZH were genotyped. We constructed a genetic linkage map using a total of 485 molecular markers, including 313 SNPs from the array, 167 simple sequence repeats (SSRs), 4 expressed sequence tag–derived SSRs, and 1 insertion/deletion marker. The total length of the genetic map was 2594.34 cM, with an average marker spacing of 5.58 cM. Comparing physical and genetic distances, we found 20 hotspot and 14 coldspot regions of recombination. Our results suggest that the technology of resequencing of parental lines coupled with high-throughput SNP genotyping could efficiently bridge the genotyping gap and provide deep insights into the landscape of recombination and fixed genomic regions in biparental segregating populations of soybean with implications for fine mapping of QTL.
MicroRNA Regulation of Bovine Monocyte Inflammatory and Metabolic Networks in anIn VivoInfection Model
Authors: Lawless Nathan , Reinhardt Timothy A , Bryan Kenneth , Baker Mike , Pesch Bruce , Zimmerman Duane , Zuelke Kurt , Sonstegard Tad , O’Farrelly Cliona , Lippolis John D , Lynn David J 
Published: February 2014

AbstractBovine mastitis is an inflammation-driven disease of the bovine mammary gland that costs the global dairy industry several billion dollars per year. Because disease susceptibility is a multifactorial complex phenotype, an integrative biology approach is required to dissect the molecular networks involved. Here, we report such an approach using next-generation sequencing combined with advanced network and pathway biology methods to simultaneously profile mRNA and miRNA expression at multiple time points (0, 12, 24, 36 and 48 hr) in milk and blood FACS-isolated CD14+ monocytes from animals infected in vivo with Streptococcus uberis. More than 3700 differentially expressed (DE) genes were identified in milk-isolated monocytes (MIMs), a key immune cell recruited to the site of infection during mastitis. Upregulated genes were significantly enriched for inflammatory pathways, whereas downregulated genes were enriched for nonglycolytic metabolic pathways. Monocyte transcriptional changes in the blood, however, were more subtle but highlighted the impact of this infection systemically. Genes upregulated in blood-isolated monocytes (BIMs) showed a significant association with interferon and chemokine signaling. Furthermore, 26 miRNAs were DE in MIMs and three were DE in BIMs. Pathway analysis revealed that predicted targets of downregulated miRNAs were highly enriched for roles in innate immunity (FDR &lt; 3.4E−8), particularly TLR signaling, whereas upregulated miRNAs preferentially targeted genes involved in metabolism. We conclude that during S. uberis infection miRNAs are key amplifiers of monocyte inflammatory response networks and repressors of several metabolic pathways.
Template Switching During Break-Induced Replication Is Promoted by the Mph1 Helicase in Saccharomyces cerevisiae
Authors: Štafa Anamarija , Donnianni Roberto A , Timashev Leonid A , Lam Alicia F , Symington Lorraine S 
Published: February 2014

Abstract
Chromosomal double-strand breaks (DSBs) that have only one end with homology to a donor duplex undergo repair by strand invasion followed by replication to the chromosome terminus (break-induced replication, BIR). Using a transformation-based assay system, it was previously shown that BIR could occur by several rounds of strand invasion, DNA synthesis, and dissociation. Here we describe a modification of the transformation-based assay to facilitate detection of switching between donor templates during BIR by genetic selection in diploid yeast. In addition to the expected recovery of template switch products, we found a high frequency of recombination between chromosome homologs during BIR, suggesting transfer of the DSB from the transforming linear DNA to the donor chromosome, initiating secondary recombination events. The frequency of BIR increased in the mph1Δ mutant, but the percentage of template switch events was significantly decreased, revealing an important role for Mph1 in promoting BIR-associated template switching. In addition, we show that the Mus81, Rad1, and Yen1 structure-selective nucleases act redundantly to facilitate BIR.
Preparation of Porous B-type Carbonate Apatite with Different Carbonate Contents for an Artificial Bone Substitute
Authors: Tanaka Toshimitsu , Yoshioka Tomohiko , Ikoma Toshiyuki , Tanaka Junzo 
Published: February 2014

ABSTRACTB-type carbonate apatite (B-CAp) powders were prepared by a wet method using Ca(OH)2 suspension and H3PO4 solution including NaHCO3 as a carbonate source, and porous B-CAp ceramics with two different amounts of carbonate contents were fabricated by sintering freeze-dried mixtures of the powders and gelatin composite. The porous B-CAp ceramics prepared had three-dimensionally interconnected pores. The sinterability of B-CAp ceramics was dependent on the chemical composition, especially sodium content and vacancy of OH site, and the carbonate contents did not directly influence the dissolution rate of porous B-CAp ceramics.
Metal-Semiconductor-Insulator-Metal Structure Field-Effect Transistors Based on Zinc Oxides and Doped Ferroelectric Thin Films
Authors: Jia Ze , Xu Jianlong , Wu Xiao , Zhang Mingming , Zhang Naiwen , Liu Jizhi , Liu Zhiwei , Liou Juin J. 
Published: February 2014

ABSTRACTDifferent ferroelectric thin films and their related Metal-Semiconductor-Insulator-Metal (MSIM) structures include zinc oxide (ZnO) are studied, which can be utilized in back-gated ferroelectric field-effect transistors (FETs). The most ideal zinc oxide (ZnO) thin film prepared by sol-gel method are obtained under the pyrolysis temperature of 400°C and the annealing temperature of 600°C. The asymmetric or symmetric current-voltage characteristics of the heterostructures with ZnO are exhibited depending on different ferroelectric materials in them. The curves of drain current versus gate voltage for MSIM-structure FETs are investigated, in which obvious counterclockwise loops and a drain current switching ratio up to two orders of magnitude ate observed due to the modulation effect of remnant polarization on the channel resistance. The results also indicate the positive influences of impurity atom substitution in bismuth ferrite thin film for the MSIM-structure FETs.
VLS Growth of Position-controlled InP Nanowires and Formation of Radial Heterostructures on Mask-patterned InP Substrates
Authors: Kawaguchi Kenichi , Sudo Hisao , Matsuda Manabu , Ekawa Mitsuru , Yamamoto Tsuyoshi , Arakawa Yasuhiko 
Published: February 2014

ABSTRACTPosition-controlled InP nanowires (NWs) with separations of 10-100 μm were grown by the vapor-liquid-solid (VLS) method using Au-deposited SiO2-mask-patterned InP substrates. Excess indium species diffused from the large mask region formed plural tilted NW-like structures from single openings in addition to the vertical VLS NWs formed by Au catalyst. The introduction of HCl gas during the NW growth was found to efficiently suppress the tilted NW-like structures. Vertical InP NWs without anomalous growth were successfully formed by controlling the HCl flow rate. Moreover, single InP/InAsP/InP quantum wells (QWs) with wurtzite crystal phase structure were epitaxially grown on the sidewall of the position-controlled InP NWs, and two-dimensional arrayed patterns of photoluminescence (PL) coming from the radial QWs were clearly observed in the 1.3-μm wavelength region at room temperature.
Inflammation and cancer: The role of the human neutrophil
Authors: Anderson Ronald , Tintinger Gregory R. , Feldman Charles 
Published: February 2014

Chronic inflammation of both infective and non-infective origin has been implicated in the aetiology of
approximately 30% of all human epithelial malignancies. The primary carcinogens are reactive oxygen species
(ROS) derived from activated, infiltrating cells of the innate immune system, especially neutrophils, which
inflict oxidative damage on the DNA of bystander epithelial cells. The consequence is gene modifications which
initiate cellular transformation. The process of tumourigenesis is exacerbated by the sustained generation of
pro-proliferative ROS, as well as by the release of neutrophil-derived cytokines and proteases, all of which
contribute to tumour promotion and progression. It is now well recognised that, in addition to inflammation
causing cancer, many cancers per se induce an inflammatory response, with a high magnitude of neutrophil
influx being indicative of a poor prognosis. In this setting, CXC chemokines produced by tumours not only
promote neutrophil influx and hyperreactivity, but also cause autocrine activation of the proliferation of the
chemokine-producing tumour cells. These various mechanisms of inflammation-mediated tumourigenesis
are the primary focus of this review, together with a consideration of neutrophil-targeted anti-inflammatory
strategies with potential as adjunctive cancer therapy.
Insulin Resistance Modulates Iron-Related Proteins in Adipose Tissue
Authors: Moreno-Navarrete José María , Novelle Marta G. , Catalán Victoria , Ortega Francisco , Moreno Maria , Gomez-Ambrosi Javier , Xifra Gemma , Serrano Marta , Guerra Ester , Ricart Wifredo , Frühbeck Gema , Diéguez Carlos , Fernández-Real José Manuel 
Published: February 2014

OBJECTIVE
Circulating markers of iron overload are associated with insulin resistance. Less is known about the impact of iron overload on adipose tissue (AT). We hypothesized that gene expression markers of iron metabolism in AT could be associated with insulin action.

RESEARCH DESIGN AND METHODS
The AT expression of ferroportin (SLC40A1), transferrin (TF), TF receptor (TFRC), ferritin (FT) heavy polypeptide 1 (FTH1), and FT light polypeptide (FTL) was analyzed cross-sectionally in three independent cohorts and also after weight loss–induced changes in insulin sensitivity (clamp M value) in an independent fourth cohort.

RESULTS
In human AT, TF mRNA and protein levels were decreased with obesity and insulin resistance in the three cohorts and were positively associated with adipogenic mRNAs and insulin action. Otherwise, FTL mRNA and protein and SLC40A1 transcripts were positively associated with BMI and negatively linked to adipogenic genes and insulin action. Bariatric surgery–induced weight loss led to increased TF and decreased TFRC, FTH1, FTL, and SLC40A1 in subcutaneous AT in parallel to improved insulin action.

CONCLUSIONS
These results suggest that iron overload impacts on AT in association with insulin resistance.
Factors Associated with High-Frequency Cannabis Use and Driving among a Multi-site Sample of University Students in Ontario
Authors: Fischer Benedikt , Ivsins Andrew , Rehm Jürgen , Webster Cheryl , Rudzinski Katherine , Rodopoulos Jenny , Patra Jayadeep 
Published: February 2014

Cannabis use and driving (CUD) is a growing public health concern. This study’s main objective was to identify distinguishing characteristics associated with high-frequency CUD (HFCUD) activity (i.e., CUD > 12 times) in a multi-site sample of university students who had self-identified as having driven a car within 4 hours of cannabis use in the past year. Participants for the study (n = 248; age 18–28 years) were recruited by mass advertising at five universities in Ontario. Participants were screened for eligibility and assessed by an anonymous interview between April 2005 and March 2006. Bivariate analyses determined factors associated with HFCUD (i.e., > 12 times) vs. a low frequency of CUD (LFCUD); significant factors were subsequently entered into a discriminant function analysis model. HFCUD was associated with several variables, including frequent (i.e., at least weekly) cannabis use; daily driving; perception of own ability to drive not being impaired by cannabis use; and expectation of CUD in the next 12 months (all p < 0.0001). CUD among young drivers is an important health and safety risk requiring effective interventions. Given the strong association of HFCUD with frequent cannabis use, these phenomena need to be addressed conjointly. Furthermore, preventive interventions responsive to the specific socio-cultural contexts of possible CUD need to be developed and implemented.
Exit-Site Infection of Peritoneal Catheter is Reduced by the Use of Polyhexanide. Results of a Prospective Randomized Trial
Authors: Núñez-Moral M. , Sánchez-Álvarez E. , González-Díaz I. , Peláez-Requejo B. , Fernández-Viña A. , Quintana-Fernández A. , Rodríguez-Suárez C. 
Published: February 2014

Background One of the most common and severe complications affecting peritoneal dialysis (PD) patients is exit-site infection of the peritoneal catheter; it is therefore of vital importance to prevent it. This complication has a negative impact on the success of the technique. In spite of this, there are no clear guidelines concerning how to take care of the exit site. The objective of this study was to assess the efficacy of polyhexanide in preventing exit-site infection over a 12-month period. Methods We designed a single-center, prospective, open-labeled, randomized controlled clinical trial with parallel groups. Requirements for participation in the study included implantation of the peritoneal catheter at least six weeks before entering the study and no infectious complications requiring either hospital admission or antibiotic treatment for at least three months before entering into the study. Patients were randomized to be daily cured as follows: Group A: traditional care with saline serum and povidone-iodine; and Group B: polyhexanide solution. Exit sites were evaluated at baseline and every four to six weeks or if any event occurred, according to the Twardowski criteria. Results Of the 60 included patients, 46 completed the 12-month follow-up period. Six underwent transplantation, five died and three were transferred to hemodialysis (HD). The treatment was well tolerated, with no side effects nor abandonments due to such effects. Throughout the study period, six patients (20%) undergoing traditional care and only two (6,7%) receiving polyhexanide developed an exit-site infection ( p = 0.032). There were a total number of 12 infections; nine occurred in patients following the traditional approach and only three in patients treated with polyhexanide ( p = 0.037). The germs responsible for the infections were: S. aureus (six cases), Corynebacterium jeikeium (two cases) and P. aeruginosa (one case) in the saline serum and povidone-iodine group and P. aeruginosa (three cases) in the polyhexanide group. The mean rate of exit-site infection was 1 episode/36.6 patient-months for the traditional care group and 1 episode/102.7 patient-months for the polyhexanide group ( p = 0.017). Patients following the traditional treatment required fewer days to get infected than those using polyhexanide ( p = 0.033; log rank: 4.2). Conclusions These results show that using polyhexanide is efficient for the prevention of exit-site infections. Patients treated with this product suffer from fewer infections and need more time to become infected. Polyhexanide application is painless, no allergies have been described and it is well tolerated by patients. We therefore propose that it may be used routinely from now on for the care of healthy exit site.
Can Dialysis Patients be Accurately Identified using Healthcare Claims Data?
Authors: Taneja Charu , Berger Ariel , Inglese Gary W. , Lamerato Lois , Sloand James A. , Wolff Greg G. , Sheehan Michael , Oster Gerry 
Published: February 2014

Background While health insurance claims data are often used to estimate the costs of renal replacement therapy in patients with end-stage renal disease (ESRD), the accuracy of methods used to identify patients receiving dialysis — especially peritoneal dialysis (PD) and hemodialysis (HD) — in these data is unknown. Methods The study population consisted of all persons aged 18 – 63 years in a large US integrated health plan with ESRD and dialysis-related billing codes (i.e., diagnosis, procedures) on healthcare encounters between January 1, 2005, and December 31, 2008. Using billing codes for all healthcare encounters within 30 days of each patient's first dialysis-related claim (“index encounter”), we attempted to designate each study subject as either a “PD patient” or “HD patient.” Using alternative windows of ± 30 days, ± 90 days, and ± 180 days around the index encounter, we reviewed patients’ medical records to determine the dialysis modality actually received. We calculated the positive predictive value (PPV) for each dialysis-related billing code, using information in patients’ medical records as the “gold standard.” Results We identified a total of 233 patients with evidence of ESRD and receipt of dialysis in healthcare claims data. Based on examination of billing codes, 43 and 173 study subjects were designated PD patients and HD patients, respectively (14 patients had evidence of PD and HD, and modality could not be ascertained for 31 patients). The PPV of codes used to identify PD patients was low based on a ± 30-day medical record review window (34.9%), and increased with use of ± 90-day and ± 180-day windows (both 67.4%). The PPV for codes used to identify HD patients was uniformly high — 86.7% based on ± 30-day review, 90.8% based on ± 90-day review, and 93.1% based on ± 180-day review. Conclusions While HD patients could be accurately identified using billing codes in healthcare claims data, case identification was much more problematic for patients receiving PD.
Socio-Economic Status and Peritonitis in Australian Non-Indigenous Peritoneal Dialysis Patients
Authors: Tang Wen , Grace Blair , McDonald Stephen P. , Hawley Carmel M. , Badve Sunil V. , Boudville Neil C. , Brown Fiona G. , Clayton Philip A. , Johnson David W. 
Published: February 2014

♦Background The aim of the present study was to investigate the relationship between socio-economic status (SES) and peritoneal dialysis (PD)-related peritonitis. ♦Methods Associations between area SES and peritonitis risk and outcomes were examined in all non-indigenous patients who received PD in Australia between 1 October 2003 and 31 December 2010 (peritonitis outcomes). SES was assessed by deciles of postcode-based Australian Socio-Economic Indexes for Areas (SEIFA), including Index of Relative Socio-economic Disadvantage (IRSD), Index of Relative Socio-economic Advantage and Disadvantage (IRSAD), Index of Economic Resources (IER) and Index of Education and Occupation (IEO). ♦Results 7,417 patients were included in the present study. Mixed-effects Poisson regression demonstrated that incident rate ratios for peritonitis were generally lower in the higher SEIFA-based deciles compared with the reference (decile 1), although the reductions were only statistically significant in some deciles (IRSAD deciles 2 and 4 – 9; IRSD deciles 4 – 6; IER deciles 4 and 6; IEO deciles 3 and 6). Mixed-effects logistic regression showed that lower probabilities of hospitalization were predicted by relatively higher SES, and lower probabilities of peritonitis-associated death were predicted by less SES disadvantage status and greater access to economic resources. No association was observed between SES and the risks of peritonitis cure, catheter removal and permanent hemodialysis (HD) transfer. ♦Conclusions In Australia, where there is universal free healthcare, higher SES was associated with lower risks of peritonitis-associated hospitalization and death, and a lower risk of peritonitis in some categories.